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Developer XD 2.0.4

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1. Figure 7 32 Creating a relational feature at the Customized Features dialog box Features and click Add The Customized Features dialog opens select the Rela tional tab 2 The Insert Text drop down box lets you add patterns for ruleset objects allowing you to assign more meaningful names to customized features which reflect the names of the classes and layers involved The following feature values are avail able class name image layer name thematic layer name variable value variable name level name feature value Insert a name for the relational feature to be created Select the target for the relational function the concerning area Choose the relational function to be applied in the drop down box Define the distance of the related image objects Depending on the related image objects the distance can be either horizontal expressed as a unit or vertical image object levels Select the feature for which to compute the relation Select a class group or no class to apply the relation 9 Click Apply to create the feature without leaving the dialog box or click OK to create it close the dialog box 10 After creation the new relational feature will be listed in the Feature View window under Class Related Features gt Customized NN BW on Relations between surrounding objects can exist either on the same level or on a level lower or higher in the image object hierarchy table 7 1 Relations be
2. 0 145 7 7 2 Arithmetic Customized Features o oeo sa roce ose 145 7 1 3 Relational Customized Features oaoa 146 7 1 4 Saving and Loading Customized Features 150 7 1 5 Finding Customized Features aoaaa 150 7 7 0 Defining Feature Groups lt 6 4 e sosa tei a e bab dee wt 150 RS Customized Algorithms sec a e a ee eR eS 151 7 8 1 Dependencies and Scope Consistency Rules 151 7 8 2 Handling of References to Local Items During Runtime 152 7 8 3 Domain Handling in Customized Algorithms 153 7 8 4 Creating a Customized Algorithm 153 7 8 5 Using Customized Algorithms 156 7 8 6 Modifying a Customized Algorithm 156 7 8 7 Executing a Customized Algorithm for Testing 157 7 8 8 Deleting a Customized Algorithm 157 7 8 9 Using a Customized Algorithm in Another Rule Set 157 Tr M ear iip aea ie Tes os ee he DE Maen aua hte e Ge aa nas 158 791 The Maps Concepi 84 6 a ee ee pae Ep e e 158 7 9 2 Adding a Map to a Project to Create Multi Project Maps 159 7 9 3 Copying a Map for Multi Scale Analysis 159 794 Editing Map Properties lt lt o o eces 5 28554 88 Bee eS 160 T99 Displaying Maps o eooc eie aoa a BAe Se SG See eS 160 7 9 6 Synchronizing Maps lt s s saro teria cheas oust 160 79 7 Saving and Deleting Maps 161 7 9 8 Working with Mu
3. 1087 02 1087 H1500367_0 S airs Figure 5 13 Folder structure in the Workspace window Supported Import Templates e You can use various import templates to import scenes Each import template is provided by a connector Connectors are available according to which edition of the Definiens Server you are using e Generic import templates are available for simple file structures of import data When using generic import templates make sure that the file format you want to import is supported e Import templates provided by connectors are used for loading the image data ac cording to the file structure that is determined by the image reader or camera pro ducing your image data Customized import templates can be created for more specialized file structures of import data A full list of supported and generic image formats is available in the accompanying volume Supported Connectors and Drivers 3 By default the connectors for predefined import are stored in the installation folder under bin drivers import If you want to use a different storage folder you can change this setting under Tools gt Options gt General 27 September 2012 User Guide Projects and Workspaces 77 Generic Import Templates Import Description File Formats File Based Windows Linux Template Connec tor Generic A scene may consist of All Yes Yes Yes one file per multiple image layers All scene image layers a
4. 59 4 5 5 Comparing Features Using the 2D Scatter Plot 59 4 5 6 Comparing Features Using the 2D Feature Space Plot 61 4 5 7 Using Metadata and Features 0 62 5 Projects and Workspaces 65 5 1 Creating a Simple Project o ee we ha ea ee ee 65 5 2 Creating a Project with Predefined Settings 66 3 2 1 Pile Formats oe eee ekaa rinst erioed hpa whe wd 66 52 2 The Create Project Dialog Box o coc c toc ae aa e 67 5 2 3 Editing Multidimensional Map Parameters 68 5 2 4 Assigning No Data Values oasa 69 5 2 5 Importing Image Layers of Different Scales 71 S28 Geocoding 5c heaved we ev Be eee SHS 71 5 2 7 Multisource DataFusion 22 72 5 3 Creating Saving and Loading Workspaces 73 5 3 1 Opening and Creating New Workspaces 74 5 3 2 Importing Scenes into a Workspace 75 5 3 3 Importing Images with Annotations 78 5 3 4 Configuring the Workspace Display 78 5 4 Managing Data in Plate View uaaa 79 5 4 1 Navigating Through a Plate 80 27 September 2012 User Guide CONTENTS j SA2 Selc nga Single Well c sisaan ow Baw we ee A 81 Sda Select Multiple Welle lt 5 ea dow bn we ee ee eo Se 81 S44 Define Plate Layout 03 26 eee ee ee eR iek 81 JAI Save Plate Layout pi a eye ee ae ee we ee Ee Se 82 34 6 Load Plate Layout s
5. Drage COject Iformetion Fesue Value ct urter 4 Figure 7 23 The number of the selected object here is 41 7 6 Tutorial Using Process Related Features for Advanced Local Processing One more powerful tool comes with local processing When a child process is executed the image objects in the image object domain know their parent process object PPO It can be very useful to directly compare properties of those image objects with the proper ties of the PPO A special group of features the process related features do exactly this job Process Tree Tryout PPO sienple use a 2 at Level 1 delete Basic Segmentation find Nucleus please switch to Outlines calculating the Maximum brightest value of the Nuclei Layer Layer 2 Ih unclassified at desktop bright manf Layer 2 highest brightest value in Layer BL unclassified with Mean Layer 2 bright at desktop _active catch the brightest object loop _active at desktop lt unclassified all Mean Layer 2 diff PPO 0 gt 50 Example for the usage of PPO 0 as _octive at desktop nudieus loop unclassified at desktop 200 shape 0 1 compct 0 9 Merge the objects using the information inside the Cel Layer Layer 3 find Background nucleus at desktop for all How to use PPO 1 aze loop cyto at desktop e golgi at desktop for af Show PPO 2 sw golg at desktop lt _active2 process Tree F
6. An essential feature of this functionality is to link the high resolution map seen by the user with the lower resolution map on which the analysis is performed When an active pixel is selected the process creates a region around it stored as a region variable This region defines a subset of the active map and it is on this subset map that the analysis is performed The Select Input Mode algorithm lets you set the mode for user input via a graphical user interface for most functions set the Input Mode parameter to normal The settings for such widgets can be defined in Widget Configuration The input is then configured to activate the rule set that selects the subset before taking the user back to the beginning 9 3 Exporting Data Results of Definiens analyses can be exported in several vector or raster formats In addition statistical information can be created or exported There are three mechanisms e Data export generated by a rule set e Data export triggered by an action e Data export initiated by Export menu commands based on a currently displayed map of an open project 9 3 1 Automated Data Export Data export triggered by rule sets is executed automatically Which items are exported is determined by export algorithms available in the Process Tree window For a detailed description of these export algorithms consult the Reference Book You can modify where and how the data is exported 9 3 2 Reporting Data on a S
7. Classification gt Class Hierarchy gt Edit Classes gt Delete Samples which deletes all samples from the currently selected class Classification gt Samples gt Delete Samples of Classes which opens the Delete Samples of Selected Classes dialog box Move the desired classes from the Available Classes to the Selected Classes list or vice versa and click OK e To delete all samples you have assigned select Classification gt Samples gt Delete All Samples Alternatively you can delete samples by using the Delete All Samples algorithm or the Delete Samples of Class algorithm 6 4 3 Training and Test Area Masks Existing samples can be stored in a file called a training and test area TTA mask which allows you to transfer them to other scenes User Guide 27 September 2012 112 Developer XD 2 0 4 To allow mapping samples to image objects you can define the degree of overlap that a sample image object must show to be considered within in the training area The TTA mask also contains information about classes for the map You can use these classes or add them to your existing class hierarchy Creating and Saving a TTA Mask Create TTA Mask from EA Figure 6 32 The Create TTA Mask from Samples dialog box 1 From the main menu select Classification gt Samples gt Create TTA Mask from Samples 2 In the dialog box select the image object level that contains the samples that you want to use for the TTA
8. To modify a widget just double click it or right click it and choose Edit on the context menu User Guide 27 September 2012 226 Developer XD 2 0 4 Widget Configuration Parameter Text Description Variable Figure 10 11 Widget Configuration dialog box 7 To delete a widget right click it and choose Delete from the context menu 10 1 10 Exporting Action Definition to File Export an action definition to file This can be used to extend action libraries of Architect XD users with new actions definitions 1 To export an action definition select an action in the Analysis Builder window and choose Library gt Export Action on the main menu 2 Select the path and click OK 27 September 2012 User Guide 11 Advanced Data Visualizations 11 1 Accuracy Assessment Accuracy assessment methods can produce statistical outputs to check the quality of the classification results Tables from statistical assessments can be saved as txt files while graphical results can be exported in raster format Accuracy Assessment SubcellularLevel Statistic type Classification Stabity Classes classes Background Save filename accuracy Save statistics Show statistics Chose Figure 11 1 Accuracy Assessment dialog box 1 Choose Tools gt Accuracy Assessment on the menu bar to open the Accuracy As sessment dialog box 2 A project can contain different classifications on different image object
9. this is called segmentation and creates undefined objects By definition these objects will be relatively crude but we can refine them later on with further rule sets It is preferable to create fairly large objects as smaller numbers are easier to work with Right click in the Process Tree window and select Append New from the right click menu The Edit Process dialog appears In the Name field enter Create objects and remove background Press OK TIP In the Edit Process box you have the choice to run a process imme diately by pressing Execute or to save it to the Process Tree window for later execution by pressing OK In the Process Tree window right click on this new rule and select Insert Child In the Algorithm drop down box select Multiresolution Segmentation In the Segmentation Set tings which now appear in the right hand side of the dialog box change Scale Parameter to 50 Press Execute The image now breaks up into large regions When you now click on parts of the image you ll see that because our initial images are very distinct the software has isolated the shapes fairly accurately It has also created several large objects out of the white background NOTE This action illustrates the parent child concept in Definiens Devel oper XD 2 0 4 It s possible to keep using Append New to add more and more rules but it s best to group related rules in a container a parent pro cess w
10. Geocodryg W Mediderencscnal Map Pas ameter Nunberofvices 23 Cale Sice dutarce 6 28932530084713 Sice stat fa 0375 Number of ames f1 Frame dotance fs Fiame stat Figure 5 5 Layer Properties dialog box e Change Slice parameters only to change the third dimension of a 3D map e Change Frame parameters only to change the time dimension of a time series map e Change Slice and Frame parameters to change the third and the time dimension of a 4D map Editable parameters are listed in table 5 1 on the next page Multidimensional Map Pa rameters Confirm with OK and return to the previous dialog box After the a with a new map has been created or saved the parameters of multidimensional maps cannot be changed any more 5 2 4 Assigning No Data Values No data values can be assigned to scenes with two dimensions only This allows you to set the value of pixels that are not to be analyzed Only no data value definitions can be applied to maps that have not yet been analyzed User Guide 27 September 2012 70 Developer XD 2 0 4 Table 5 1 Multidimensional Map Parameters Parameter Description Calc button Default Number of slices The number of Click the Calc button to 1 two dimensional images each calculate the rounded ratio of representing a slice of a height and width of the three dimensional scene internal map Slice distance Change the spatial distance no influence 1 between slices Slice start C
11. This option is especially important while working with multiple image view panes because only one image view pane is active at a time CSV Decimal separator for CSV file export Use period as decimal separator This setting does not apply to csv file export during automated image analysis Column delimiter for CSV file export Reports Use semicolon as column delimiter This setting does not apply to csv file export during automated image analysis Date format for reports DD MM YYYY or MM DD YYYY Select or edit the notation of dates used in reports exported by export actions User Guide 27 September 2012 250 Developer XD 2 0 4 Developer XD Default feature unit Change the default feature unit for newly created features that have a unit Pixels Use pixels as default feature unit Same as project unit Use the unit of the project It can be checked in the Modify Project dialog box Default new level name Change the default name for newly created image object levels Changes are only applied after restart Load extension algorithms No Deactivate algorithms created with the Definiens Developer XD 2 0 4 SDK Software Development Kit Yes Activate algorithms created with the Definiens Developer XD 2 0 4 SDK Keep rule set on closing project Process Editing Yes Keep current rule set when closing a project Helpful for developing on multiple projects
12. An action can contain workspace automation subroutines and produce subsets copies or tiles as a internal activity of an action Such actions can be executed as rule sets If several actions containing multiple workspace automation subroutines are assembled in one solution dax file each action is submitted for processing sequentially or else an action might search for tiles that do not yet exist because the preceding action is still being processed Information kept in parameter sets is transferred between the different stages of the workspace automation Different subroutines of different actions are able to access vari ables of parameter sets When creating actions you should use special Variables Opera tion algorithms to enable actions to automatically exchange parameter sets 10 1 5 Creating a New Action Library Before wrapping a rule set as an action definition you have to create a new action library 1 Choose Library gt New Action Library from the main menu The Create New Action Library dialog box opens 2 Select a Name and a Location for the new action library Click OK to create the new dlx file 3 The action library is loaded to the Analysis Builder window The Analysis Builder window changes its name to Edit Library Name of the Library As the editing mode is active you can immediately start editing the action library 10 1 6 Assembling and Editing an Action Library When assembling a new action library you wrap ru
13. Display all Algorithms always box is selected To customize the display uncheck this box and press the left facing arrow under Move All which will clear the list You can then select individual algorithms to move them to the Available Algorithms list or double click their headings to move whole groups 27 September 2012 User Guide Basic Rule Set Editing 39 Select Process Algorithms Process related operation Segmentation execute chid processes EE chessboard segnertation execute chad as senes R quadtree based segmentation i Bi conan spit segnertation then FE mulresolution segmentation else FE specta difference segnertation theow FA euti tiveshold segmentation catch BB contrast liter segmentation fi cel tule set options Advanced Classification Basic Classification OLX find domain extrema WE assign class 2X find local extrema Ki classification find enclosed by class Ki hierarchical classification find enclosed by image object Dik remove classification gt connector By assign class by slice overlap Prototyp Variables operation bme E update variable LAY compute statistical value i compose text update region update image object list F Display all algorithms always Cox Cancel Figure 4 3 The Select Process Algorithms Dialog Box 4 2 3 Loops amp Cycles Loops amp Cycles allows you to specify how many times you would like a process and its child processes to be repeated The process ru
14. Hamamatsu z Stack ndpi To visualize It is necessary to use Edit Aperio Annotation Links and Apply Aperio Anno tation Links for more information on these algorithms see the Reference Book 5 3 4 Configuring the Workspace Display Definiens Developer XD 2 0 4 offers several options for customizing the Workspace To select what information is displayed in columns right click in the pane see fig ure 5 14 to display the context menu 1 2 Expand All Menus will auto fit the columns to the width of the pane If this is selected the menu will subsequently display the Collapse All Menus option Selecting Insert Column or Modify Column displays the Modify Column dialog box figure 5 15 e In Type select the column you wish to display e In Name enter the text to appear in the heading e In Width select the width in pixels e In Alignment choose between left right and center e Press OK to confirm You can change the position of a column by dragging it with the mouse Select Delete Column to get rid of a column 27 September 2012 User Guide Projects and Workspaces 79 Expand all columns Insert column Modify column Delete column Modify views Figure 5 14 Context menu in Workspace information pane Modify column Eceo of image layer Bitdepth Figure 5 15 Modify Column Dialog Box 4 Modify Views launches the Edit Views dialog box figure 5 16 which lets you sa
15. No Remove current rule set from the Process Tree window when closing a project Ask Open a message box when closing Always do profiling Yes Always use time measurement of processes execution to control the process performance No Does not use time measurement of processes Action for double click on a process Edit Open the Edit Process dialog box Execute Execute the process immediately Switch to classification view after process execution Yes Show the classification result in the map view window after executing a process No Current map view does not change Switch off comments in process tree No Comments in process tree are active Yes No comments in process tree Ask before deleting current level Undo Yes Use Delete Level dialog box for deletion of image objects levels No Delete image objects levels without reconfirmation Recommended for advanced users only Enable undo for process editing operations Yes Enable undo function to go backward or forward in the operation s history No Disable undo to minimize memory usage 27 September 2012 User Guide Options 251 Min number of operation items available for undo priority Minimum number of operation items available for undo Additional items can be deleted if maximum memory is not exceeded as defined in Max amount of memory allowed for undo stack MB below Default is 5 Max amount of
16. Select a type of scaling mode used for displaying scale values and calculating rescaling operations Auto Automatic setting dependent on the image data Unit m pxl Resolution expressed in meters per pixel for example 40 m pxl Magnification Magnification factor used similar as in microscopy for example 40x Percent Relation of the scale to the source scene scale for example 40 Pixels Relation of pixels to the original scene pixels for example 1 20 pxl pxl Display scale bar Choose whether to display the scale bar in the map view by default Scale bar default position Choose where to display the scale bar by default Import magnification if undefined Select a magnification used for new scenes only in cases where the image data has no default magnification defined Default 20x Display selected object s distance in status bar Shows or hides distance values from the active mouse cursor position to the selected image object in the image view Because this calculation can reduce performance in certain situations it has been made optional Instant render update on slider Choose whether to update the rendering of the Transparency Slider instantly No The view is updated only after the slider control is released or after it has been inactive for one second Yes The view is updated instantly as the slider control is moved Use right mouse button for adjusting window leveling S
17. visible checkbox Window Leveling The Window Leveling dialog box figure 2 15 lets you control the parameters for manually adjusting image levels on screen Leveling sets the brightness of pixels that are displayed The Center value specifies the mid point of the equalization range the Width value sets the limits on either side of it figure 2 14 It is also possible to adjust these parameters using the mouse with the right hand mouse button held down moving the mouse horizontally adjusts the center of window leveling moving it vertically adjusts the width This function must be enabled in Tools gt Options The Predefined Values drop down box contains medical presets for use with Definiens Lung Expert 27 September 2012 User Guide Starting Developer 19 Manage Aliases for Layers Alias Laye Benovo o gt r val Alas Layer cel eerie 2 Layer 2 cell_example tf 2 Layer 3 cell_example tf 3 Layer_Cel_Stain ana assigned gt Layer_Marker1_Stain lt not assigned gt Layer_Marker2_Stain anot assigned gt Layer_Nucleus_Stain cnot assigqned gt Layer_Spot_Stain lt rat assigned gt Figure 2 13 Manage Aliases for Layers dialog box Center Center Center I I o gt t _ Width Width Width Figure 2 14 Window leveling On a black white gradient adjusting the center value defines the mid point of the gradient The width value specifies the limits on each side Window Leveling Center
18. 1 and assign it to a new class Square Isolating the Star There are criteria you could use to identify the star but as we re using the software to separate and classify squares circles and stars we can be pragmatic after defining background circles and squares the star is the only objects remaining So the only thing left to do is to classify anything unclassified as a star Simply set up a parent called Define and isolate stars select Assign Class select un classified in the Class Filter and give it the value Star in Use Class 3 1 4 The Complete Rule Set 22 35s Create objects and remove background FE 22 345 200 shape 0 1 compct 0 5 creating New Level bL lt 0 001s with Brightness gt 230 at New Level Background 0 015s Background at New Level merge region 0 125s Define and isolate circles PL 0 125s with Eliptic Fit gt 0 95 at New Level Circle 0 0945 Define and isolate squares BL 0 0945 wth Rectangular Fit 1 at New Level Square lt 0 001s Define and isolate stars PL lt 0 001s unclassified at New Level Star ujal gt Main Figure 3 2 Complete rule set list for shapes tutorial User Guide 27 September 2012 4 Basic Rule Set Editing 4 1 Creating and Editing Processes in the Process Tree Window Rule sets are built up from single processes which are displayed in the Process Tree and created using the Edit Process dialog box A single process can operate
19. 1 To open the Sample Selection Information window choose Classification gt Sam ples gt Sample Selection Information or View gt Sample Selection Information from the main menu 2 Names of classes are displayed in the Class column The Membership column shows the membership value of the Nearest Neighbor classifier for the selected image object 3 The Minimum Dist column displays the distance in feature space to the closest sample of the respective class 4 The Mean Dist column indicates the average distance to all samples of the corre sponding class 5 The Critical Samples column displays the number of samples within a critical dis tance to the selected class in the feature space 6 The Number of Samples column indicates the number of samples selected for the corresponding class The following highlight colors are used for a better visual overview e Gray Used for the selected class e Red Used if a selected sample is critically close to samples of other classes in the feature space e Green Used for all other classes that are not in a critical relation to the se lected class The critical sample membership value can be changed by right clicking inside the win dow Select Modify Critical Sample Membership Overlap from the context menu The default value is 0 7 which means all membership values higher than 0 7 are critical Modify Threshold Enter membership overlap value oe _ ows Figure 6 30 The Modify Threshold
20. Microsoft Office or an image processing program User Guide 27 September 2012 10 Rule Sets for Definiens Architect XD 10 1 Action Libraries An action is a predefined building block within an image analysis solution Configured actions can perform different tasks such as object detection classification or exporting re sults and sequences of actions represent a ready to use solution for accomplishing image analysis tasks An action library is a collection of action definitions which are essentially unconfigured actions action definitions enable users to specify actions and assemble solutions To make rule sets usable as unconfigured actions in action libraries they must be packaged and given a user interface In the Analysis Builder window you package pieces of rule sets each of them solving a specific part of a solution into action definitions Action definitions are grouped into libraries and define dependencies on actions Furthermore you can create different user interface components called widgets for an action library user to adjust action parame ters For testing the created action libraries with relevant data you can build analysis solutions in the Analysis Builder window 10 1 1 Creating User Parameters As the parameters of an action can be set by users of action libraries using products such as Architect XD you must place adjustable variables in a parameter set You should use unique names for variables and mu
21. Well Plate or Run for a cell screening device To add an item right click a folder and select Add Item The new folder is displayed in the tree view of the Workspace window You can edit the folder name To rename a folder right click it and choose Rename on the context menu 3 Move folders to rearrange them by drag and drop operations Ne Saving and Moving Workspaces Workspaces are saved automatically whenever they are changed If you create one or more copies of a workspace changes to any of these will result in an update of all copies irrespective of their location Moving a workspace is easy because you can move the complete workspace folder and continue working with the workspace in the new location If file connections related to the input data are lost the Locate Image dialog box opens where you can restore them this automatically updates all other input data files that are stored under the same input root folder If you have loaded input data from multiple input root folders you only have to relocate one file per input root folder to update all file connections We recommend that you do not move any output files that are stored by default within the workspace folder These are typically all dpr project files and by default all results files However if you do you can modify the path of the output root folder under which all output files are stored User Guide 27 September 2012 192 Developer XD 2 0 4 To modi
22. button is used to finish the creation of objects and allows you to edit or delete them Creating Polygon Objects To draw polygons set the selected thematic to Polygon Click in the map view to set vertices in the thematic polygon layer Right click and select Close Polygon to complete the shape This object can touch or cross any existing image object The following cursor actions are available e Click and hold the left mouse button as you drag the cursor across the map view to create a path with points e To create points at closer intervals drag the cursor more slowly or hold Ctrl while dragging e Release the mouse button to automatically close the polygon e Click along a path in the image to create points at each click To close the polygon double click or select Close Polygon in the context menu User Guide 27 September 2012 124 Developer XD 2 0 4 Figure 7 5 New thematic polygon object The polygon borders are independent of existing image object borders e To remove the last point before the polygon is complete select Delete Last Point in the context menu Creating Lines and Points When drawing lines click in the map view to set vertices in the thematic line layer Right click and choose Finish Line to stop drawing This object can touch or cross any existing image object Generate point objects on a thematic point layer in one of the following ways e Click in the thematic layer The point s co ordinates are displ
23. from a shapefile Thematic Layer 1 e Select the following feature Object Features gt Thematic Attributes gt Thematic Object Attribute gt Thematic Layer 1 e Set the threshold to for example gt 0 or Sample according to the content of your thematic attributes e For the parameter Use Class select the new class for assignment Converting Objects to samples e To mark the classified image objects as samples add another child process e Use the classified image objects to samples algorithm From the Image Object Domain list select New Level No further conditions are required e Execute the process 6 4 6 Selecting Samples with the Sample Brush The Sample Brush is an interactive tool that allows you to use your cursor like a brush creating samples as you sweep it across the map view Go to the Sample Editor toolbar View gt Toolbars gt Sample Editor and press the Select Sample button Right click on the image in map view and select Sample Brush Drag the cursor across the scene to select samples By default samples are not reselected if the image objects are already classified but existing samples are replaced if drag over them again These settings can be changed in the Sample Brush group of the Options dialog box To deselect samples press Shift as you drag User Guide 27 September 2012 116 Developer XD 2 0 4 Edit Process agoen pacarenent Fae rage tyt Doman New Lever l Posner al ctyect
24. gt Feature View This section lists a very brief overview of functions For more detailed information con sult the Reference Book 27 September 2012 User Guide Basic Rule Set Editing 53 Otyect issue Cutomaed Lae Var Men Bugares Laya 1 Lye 2 Max oat E Shandieed deviation Pastore e To rogbo Tongs T Toore E Hue Shanto hies D Shige oTo Vade Sy Howdy Clave Flelsted lashes Scene laue Pree Canton Metadata Fesise Vanade i Figure 4 14 Feature tree in the Feature View window Object Features Object features are calculated by evaluating image objects themselves as well as their embedding in the image object hierarchy They are grouped as follows e Customized features are user created Type features refer to an image object s position in space e Layer value features utilize information derived from the spectral properties of image objects e Geometry features evaluate an image object s shape e Position features refer to the position of an image object relative to a scene e Texture features allow texture values based on layers and shape Texture after Haralick is also available e Object Variables are local variables for individual image objects e Hierarchy features provide information about the embedding of an image object within the image object hierarchy e Thematic attribute features are used to describe an image object using information provided
25. is cleared If you want to stretch the smaller image layers to the scene size select the Enforce Fitting checkbox e Thematic layers can be inserted removed and edited in the same manner as image layers e If not done automatically you can load Metadata source files to make them avail able within the map 5 2 3 Editing Multidimensional Map Parameters When creating a new map you can check and edit parameters of multidimensional maps that represent 3D 4D or time series scenes Typically these parameters are taken au tomatically from the image data set and this display is for checking only However in 27 September 2012 User Guide Projects and Workspaces 69 special cases you may want to change the number the distance and the starting item of slices and frames The preconditions for amending these values are e The project includes at least two slices or frames e The new project has not yet been created or the new map has not yet been saved e For changing Slice parameters of 3D maps the height of the internal map has to be five times larger or more than the width e For changing Frame parameters of time series maps the width of the internal map has to be five times larger or more than the height To open the edit multidimensional map parameters create a new project or add a map to an existing one After preloading image layers press the Edit button The Layer Properties dialog box opens Layer Properties Poel pine
26. sciences position marks serve as geographic identifiers But geocoding is helpful for life User Guide 27 September 2012 72 Developer XD 2 0 4 sciences image analysis too Typical examples include working with subsets at multiple magnifications or with thematic layers for transferring image analysis results Typically available geocoding information is automatically detected if not you can en ter co ordinates manually Images without geocodes create automatically a virtual co ordinate system with a value of 0 0 at the upper left and a unit of 1 pixel For such images geocoding represents the pixel co ordinates instead of geographic co ordinates The software cannot reproject image layers or thematic layers Therefore all image layers must belong to the same co ordinate system in order to be read properly If the co ordinate system is supported geographic co ordinates from inserted files are detected automati cally If the information is not included in the image file but is nevertheless available you can edit it manually After importing a layer in the Create New Project or Modify Existing Project dialog boxes double click on a layer to open the Layer Properties dialog box figure 5 8 To edit geocoding information select the Geocoding check box You can edit the following e x co ordinate of the lower left corner of the image e y co ordinate of the lower left corner of the image e Pixel size defining the geometric resolut
27. slivers 27 September 2012 Display the setting for removal of slivers Default is No User Guide n 13 Aperio Spectrum Database Integration 13 1 Creating a Developer XD Workspace from the Aperio Spectrum Database You can launch Developer XD directly from the Aperio Spectrum Database if you follow these simple steps 1 Connect to the Aperio Spectrum Database 2 In your web browser select the Aperio Spectrum image files in the database that you wish to open in Developer XD by selecting the checkbox 3 Click Analyze select Definiens Developer XD Analysis and click the Analyze button 3 4 Open the created file with the Definiens Import Utility and specify the name and location of the workspace dpj file 5 Pressing Import will create the new workspace and projects and launch Developer XD Working with the open workspace requires an active database connection Database connections can be managed by going to File gt Connection Manager to display the Connections dialog box figure 13 1 Press New to configure a new connection or Edit to amend an existing one either step will display the Edit Connection dialog 1 Enter a name for the new connection 2 Choose Aperio Launch from Spectrum as template 3 Enter your login and password details 4 In the parameters field enter the IP addresses of the Aperio Webserver To connect to an Aperio Spectrum database you will be required to have Aperio Spectrum 11 1
28. 10 9 Add Action dialog box with sample actions The filter is set for the action subset you selected You can select a different filter or display all available actions The Found area displays only those actions that satisfy the filter setting criteria Depending on the action library each action is classified with a token for its subsection e g lt C gt for classifications lt D gt for detections lt E gt for export actions and lt ST gt for special tasks To search for a specific action enter the name or a part of the name in the Find Text box The Found area displays only those actions that contain the characters you entered Select the desired action and confirm with OK The new action is displayed as a bar in the Analysis Builder window You must now set the properties of the action 1 Go to the Analysis Builder window 2 In the upper sequencing pane select the action you want to customize 3 Configure the action in the lower properties pane by customizing various settings Settings For each solution you must define the general settings These settings associate your image data with the appropriate actions General settings include the pixel size and bit depth Alternatively you can load a calibration file that corresponds to the settings of your image reader camera or instrument With general settings you further set the content of the image layers It is necessary to open a workspace with the data you want to analyze and open
29. 3 To remove an action from your solution click the button with a minus sign on the right of the action bar 4 Icons inform you about the state of each action e A red error triangle indicates that you must specify this action before it can be processed or another action must be processed previously The green tick mark indicates that the action has been processed successfully Selecting an Action To select an action for the analysis solution of your data click on a plus sign in an Action Definition button in the Analysis Builder window The Add Action dialog box opens 27 September 2012 User Guide Rule Sets for Definiens Architect XD 221 Add Actions lt C gt Classify Cells in Populations by Brightness lt C gt Classify Cells in Populations by Size lt C gt Classify Nuclei in Populations by Brightness lt C gt Classify Nuclei in Populations by Sie lt C gt Flag Marked Nuclei 1 lt C gt Flag Marked Nuclei 2 lt D gt Cell Body Simulation lt D gt Detection of Cytoplasm Diffuse Stain lt D gt Detection of Cytoplasm Microtubule Stain lt D gt Detection of Nuclei OAPL Hoechst lt D gt Detection of Nuclei Oreq5 lt D gt Membrane Simulation lt D gt Spot Detection Advanced lt D gt Spot Detection Basic lt E gt Export Object Data lt E gt Export Population Data Description Please select an action and press the Add button in order to add the action to the Analysis Builder La e Figure
30. Classification Filter fa El T C unchsssi ied DO _tempCloss DO Background ge Cet DO Nucleus C Always use all classes Use Asay lt no atao v Figure 6 7 The Edit Classification Filter dialog box 6 2 Classification Algorithms 6 2 1 The Assign Class Algorithm The Assign Class algorithm is the most simple classification algorithm It uses a threshold condition to determine whether an image object belongs to a class or not This algorithm is used when a single threshold condition is sufficient 1 In the Edit Process dialog box select Assign Class from the Algorithm list 2 The Image Object Level domain is selected by default In the Parameter pane se lect the Threshold Condition you wish to use and define the operator and reference value 3 In the Class Filter select or create a class to which the algorithm applies 6 2 2 The Classification Algorithm The Classification algorithm uses class descriptions to classify image objects It evaluates the class description and determines whether an image object can be a member of a class Classes without a class description are assumed to have a membership value of one You can use this algorithm if you want to apply fuzzy logic to membership functions or if you have combined conditions in a class description Based on the calculated membership value information about the three best fitting classes is stored in the image object classification window therefore you can s
31. During the execution of a customized algorithm image objects can refer to local rule set items This might be the case if for example they get classified using a local class or if a local temporary image object level is created After execution the references have to be removed to preserve the consistency of the image object hierarchy The application offers two options to handle this cleanup process When Delete Local Results is enabled the software automatically deletes locally created image object levels removes all classifications using local classes and removes all local image object variables However this process takes some time since all image objects need to be scanned and potentially modified For customized algorithms that are called frequently or that do not create any references this additional checking may cause a significant runtime overhead If not necessary we therefore do not recommend enabling this option When Delete Local Results is disabled the application leaves local image object levels classifications using local classes and local image object variables unchanged Since these references are only accessible within the customized algorithm the state of the image object hierarchy might then no longer be valid When developing a customized algorithm you should therefore always add clean up code at the end of the procedure 27 September 2012 User Guide Advanced Rule Set Concepts 153 to ensure no local reference
32. Inpervioun General Waterboces 63722 175720 40M Geacelard Genel 6372312 0 000000 10342 12992381 inperio Genera 3757250 5103407 000000 3924471 W sterbedes 4 380284 12382331 Ruy 0 000000 C wdce amp epnd Ome Figure 6 26 The Class Separation Distance Matrix dialog box Using the Optimization Results You can automatically apply the results of your Feature Space Optimization efforts to the project 1 In the Feature Space Optimization Advanced Information dialog box click Apply to Classes to generate a nearest neighbor classifier using the current feature space for selected classes 2 Click Apply to Std NN to use the currently selected feature space for the Standard Nearest Neighbor classifier 3 Check the Classify Project checkbox to automatically classify the project when choosing Apply to Std NN or Apply to Classes 6 4 2 Working with the Sample Editor The Sample Editor window is the principal tool for inputting samples For a selected class it shows histograms of selected features of samples in the currently active map The same values can be displayed for all image objects at a certain level or all levels in the image object hierarchy You can use the Sample Editor window to compare the attributes or histograms of image objects and samples of different classes It is helpful to get an overview of the feature distribution of image objects or samples of specific classes The features of an image object can be compared to t
33. Select ID Column Dialog Box 7 2 2 Displaying a Thematic Layer To display a thematic layer select View gt View Settings from the main menu Right click the Layer row and select the layer you want to display from the context menu View Settings Scale Parameter Analysis Figure 7 2 View Settings window with selected thematic layer The thematic layer is displayed in the map view and each thematic object is displayed in a different random color To return to viewing your image data go back to the Layer row and select Image Data 7 2 3 The Thematic Layer Attribute Table The values of thematic objects are displayed in the Thematic Layer Attribute Table which is launched via Tools gt Thematic Layer Attribute Table To view the thematic attributes open the Manual Editing toolbar Choose Thematic Edit ing as the active editing mode and select a thematic layer from the Select Thematic Layer drop down list User Guide 27 September 2012 122 Developer XD 2 0 4 The attributes of the selected thematic layer are now displayed in the Thematic Layer At tribute Table They can be used as features in the same way as any other feature provided by Definiens Thematic Layer Attribute Tabie Figure 7 3 Thematic Layer Attribute Table window The table supports integers strings and doubles The column type is set automatically according to the attribute and table column widths can be up to 255 characters Class name and class
34. Variables for classes image object levels features image layers thematic layers maps and regions enable you to write rule sets in a more abstract form You can create rule sets that are independent of specific class names or image object level names feature types and so on 7 3 1 About Variables Scene Variables Scene variables are global variables that exist only once within a project They are inde pendent of the current image object Object Variables Object variables are local variables that may exist separately for each image object You can use object variables to attach specific values to image objects Class Variables Class Variables use classes as values In a rule set they can be used instead of ordinary classes to which they point Feature Variables Feature Variables have features as their values and return the same values as the feature to which they point Level Variables Level Variables have image object levels as their values Level variables can be used in processes as pointers to image object levels User Guide 27 September 2012 130 Developer XD 2 0 4 Image Layer and Thematic Layer Variables Image Layer and Thematic Layer Variables have layers as their values They can be se lected whenever layers can be selected for example in features domains and algorithms They can be passed as parameters in customized algorithms Region Variables Region Variables have regions as their values They ca
35. Yes 183 9 Automating Data Analysis 185 9 1 Loading and Managing Data saasaa e 185 9 1 1 Projects and Workspaces lt o c 2 ee ceritone 185 912 Data Mpo s ee ei eG ee GOB a a a 188 9 1 3 Collecting Statistical Results of Subscenes 196 9 1 4 Executing Rule Sets with Subroutines 196 OKS Totomals sie a ORO RRA OS Ee GO 196 gX Bach Processes lt oon ake ee fe Bo EE wee Oa bets ee eS 198 9 2 1 Submitting Batch Jobs to a Server 198 92 2 Tiling and Sutehing c lt sese ccas ee RA ee ee 201 9 2 3 Interactive Workflows lt c ss ssec cepere p arans 203 93 Exporting Data eere sewa reei e ea a ee ee eae ew 203 9 3 1 Automated Data Export oi ss gk eG Bk a 203 9 3 2 Reporting Data on a Single Project 0 203 9 3 3 Exporting the Contents of aWindow 208 10 Rule Sets for Definiens Architect XD 211 10 1 Acton LIBTATES lt oee e eo eRe R a a 211 10 1 1 Creating User Paramet rs soo co 5 24405 be ea Owe ere 211 10 1 2 Creating a Quick Test Button 2 2 2 2 medon mami 212 10 1 3 Maintaining Rule Sets for Actions 212 10 1 4 Workspace Automation o oaae 213 10 1 5 Creating a New Action Library aoea 213 10 1 6 Assembling and Editing an Action Library 213 10 1 7 Updating a Solution while Developing Actions 217 10 1 8 Building an Analysis Solution aaea 218 10 1 9 Editing Widgets for Action P
36. a container for other processes By default the algorithm drop down box displays Execute Child Processes Press OK You can then add subordinate processes by right clicking on your newly created parent and selecting Insert Child We recommend you keep automatic naming for these pro cesses as the names display information about the process Of course you can select child process and add further child processes that are subordinate to these me water with Ratio geen gt 0 2 Prepare for Expert owe isard ak Level_tie ua w Precees Tree Figure 4 4 Rule set sample showing parent and child processes 4 2 7 Editing a Rule Set You can edit a process by double clicking it or by right clicking on it and selecting Edit both options will display the Edit Process dialog box What is important to note is that when testing and modifying processes you will often want to re execute a single process that has already been executed Before you can do this however you must delete the image object levels that these processes have created In most cases you have to delete all existing image object levels and execute the whole process sequence from the beginning To delete image object levels use the Delete Levels button on the main toolbar or go to Image Objects gt Delete Level s via the main menu It is also possible to delete a level as part of a rule set and also to copy or rename one In the Algorithm field in the E
37. a preview of the attribute table that will be exported press the Preview button Exporting Results as Statistics To export statistics open the Export Results dialog box by choosing Export gt Export Results from the main menu Choose Statistics from the Export Type drop down box From the Content Type drop down box choose to export statistics for e Classes Export statistics of selected features per selected class Objects Export statistics of selected features per image object e Scenes Export statistics of selected features per scene 3 The format must be csv In the Options dialog box under the Output Format group you can define the decimal separator and the column delimiter 4 Select the image object level for which you want to export results in the Level drop down box If Scene has been selected as Content Type this option is not available 5 Change the default file name in the Export File Name field if desired 6 Click the Select classes button to open the Select Classes for Shape Export dialog box where you can add or remove classes to be exported This button is only active when choosing Class from the Content Type drop down list 7 Click the Select features button to open the Select Features for Export as Attributes dialog box where you can add or remove features to be exported 8 To save the statistics to disk press Export Ne 7 The rounding of floating point numbers depends on the operating system and runtime librar
38. a project that works as a good example for the whole workspace To define the general settings open the Analysis Builder window and select the General Settings button Some actions can be selected only once If such an action is already part of the analysis it does not appear in the Add Action dialog box User Guide 27 September 2012 W 222 Developer XD 2 0 4 Nucleus Stain 17_08_04_jeb15_plate2_AOT_s4_wi TIF 1 x Cetstan 1708 04 b15 pated A01 s4 w2 TIF gt Spot Stain 17 _08_04_jeb15_plate2_A01_s4_wA TIF 1 Masker 1 Stain 17_08_04_jcb15_plate2_A01_s4_w3 TIF 1 Maker 2 Stain enr assigned Figure 10 10 Sample properties of the General Settings of a solution General Settings You can define the bit depth and the pixel size manually or by loading a calibration from file Select one of the following bit depths for your project 8 bit images have a gray value range from 0 to 255 12 bit images have a gray value range from 0 to 4095 16 bit images have a gray value range from 0 to 65535 e Select the pixel size in um Calibrating Image Reader Settings Instead of manually defining the general settings of a solution you may load a calibration from file corresponding to an image reader and its image recording settings Loading a calibration sets the following General Settings properties e Bit depth e Pixel resolution in mm pixel e The scheme of Image Layers used for image analysis To load a calibra
39. and parameter set the remaining two transfer values between the parameter set and the rule set Update Action From Parameter Set always updates all instances of specific action To get all parameters from the action to the rule set before you execute a Quick Test you need a process sequence like this NOTE General settings must be updated if a rule set relies on them You should restore everything to the previous state when the quick test is done 10 1 3 Maintaining Rule Sets for Actions The developed rule set dcp file will probably be maintained by other developers There fore we recommend you structure the rule set clearly and document it using meaningful names of process groups or comments A development style guide may assure consis tency in the naming of processes classes variables and customized features and provide conventions for structuring rule sets 27 September 2012 User Guide Rule Sets for Definiens Architect XD 213 Process Tree Update parameter set GeneralSettingsParamSet from action General Settings Apply parameter set GeneralSettingsParamSet Update parameter set MyParamSet from action My action Apply parameter set MyParamSet lt ims RunMyQuickTestProcess a Put your stuff in here a Make sure you delete the image objects you created for the quick test Figure 10 2 Sample process sequence for a Quick Test button within actions 10 1 4 Workspace Automation
40. are displayed in the Analysis Builder window in the moment the project was saved Configured actions can only be restored properly if the open action library was open when saving because the action library provides corresponding action definitions Creating Calibration Parameter Set Files You can create a calibration to store the General Settings properties as a Parameter Set file Therefore you can save and provide common settings for common image readers for example as part of an application A calibration set stores the following General Settings properties e Bit depth e Pixel resolution in mm pixel e Zero based IDs of the Image Layers within the scene used to store the scheme of used image layers for image analysis Example of scene IDs If a scene consists of three image layers the first image layer has ID 0 the second image layer has ID 1 and the third image layer has ID 2 To create a calibration set the General Settings properties in the lower properties pane of the Analysis Builder window 27 September 2012 User Guide Rule Sets for Definiens Architect XD 225 For saving choose Library gt Save Calibration from the main menu By default calibra tion parameter set files with the extension psf are stored in C Program Files Definiens Developer XD 2 0 4 bin Applications Cell Calibration 10 1 9 Editing Widgets for Action Properties Widgets are user interface elements such as drop down lists radio buttons and
41. arrows or enter the value directly 4 Confirm with OK The distance will be attached as a number in brackets to the feature in the feature tree Number of Figure 4 16 Editing feature distance here the feature Number of Level Distance The level distance represents the hierarchical distance between image objects on different levels in the image object hierarchy Starting from the current image object level the level distance indicates the hierarchical distance of image object levels containing the respective image objects sub objects or superobjects User Guide 27 September 2012 58 Developer XD 2 0 4 Spatial Distance The spatial distance represents the horizontal distance between image objects on the same level in the image object hierarchy Feature distance is used to analyze neighborhood relations between image objects on the same image object level in the image object hierarchy It represents the spatial distance in the selected feature unit between the center of masses of image objects The default value of 0 represents an exception as it is not related to the distance between the center of masses of image objects only the neighbors that have a mutual border are counted Process Distance The process distance in the process hierarchy represents the upward distance of hierarchi cal levels in process tree between a process and the parent process It is a basic parameter of process related features In practice
42. between the feature value of an image object and the mean feature value of its neighbors of a selected class Note that for averaging the feature values are weighted with the area of the corresponding image objects Sum Calculates the sum of the feature values of the neighbors of a selected class Number Calculates the number of neighbors of a selected class You must select a feature in order for this feature to apply but it does not matter which feature you pick Min Returns the minimum value of the feature values of an image object and its neighbors of a selected class Max Returns the maximum value of the feature values of an image object and its neighbors of a selected class Mean difference to higher values Calculates the mean difference between the feature value of an image object and the feature values of its neighbors of a selected class which have higher values than the image object itself Note that the feature values are weighted by either by the border length distance 0 or by the area distance gt 0 of the respective image objects Mean difference to lower values Calculates the mean difference between the feature value of an image object and the feature values of its neighbors of a selected class which have lower values than the object itself Note that the feature values are weighted by either by the border length distance 0 or by the area distance gt 0 of the respective image objects Portion o
43. check boxes that the users of action libraries can use to adjust settings To create a widget first select an action definition in the upper pane of the Analysis Builder window You must structure the related parameters in at least one property group in the lower pane of the Analysis Builder window Right click the background of the lower pane and select Add Group Select a group or widget and right click it to add it the following widgets are available Checkbox Drop Down List Button Radio Button Row Toolbar Editbox Editbox with Slider Select Class Select Feature Select Multiple Features Select File Select Level Select Image Layer Select Thematic Layer Select Array Items Select Folder Slider Edit Layer Names Layer Drop Down List Manual Classification Buttons Choose one of the Add widget commands on the context menu The Widget Configura tion dialog box opens 1 2 Edit a Description text for each widget The Description text is displayed only Select a variable and configure any additional settings when the Edit Action Library mode is switched off and the mouse is located over the related widget area The new widget is added at the bottom of the selected group or below the selected item Save the edited action library by choosing Library gt Save Action Library from the main menu To move the widget within its group right click it and choose Move Up or Move Down on the context menu
44. color are available as features and can be added to the Thematic Layer Attribute Table window You can modify a thematic layer attribute table by adding editing or deleting table columns or editing table rows 7 2 4 Manually Editing Thematic Vector Objects A thematic object is the basic element of a thematic layer and can be a polygon line or point It represents positional data of a single object in the form of co ordinates and describes the object by its attributes The Manual Editing toolbar lets you manage thematic objects including defining regions of interest before image analysis and the verification of classifications after image analy sis 1 To display the Manual Editing toolbar choose View gt Toolbars gt Manual Editing from the main menu 2 For managing thematic objects go to the Change Editing Mode drop down list and change the editing mode to Thematic Editing 3 From the Select Thematic Layer drop down list box select an existing thematic layer or create a new one If you want to edit image objects instead of thematic objects by hand choose Image Object Editing from the drop down list Manual Editing Tools While editing image objects manually is not commonly used in automated image analysis it can be applied to highlight or reclassify certain objects or to quickly improve the 27 September 2012 User Guide Advanced Rule Set Concepts 123 analysis result without adjusting a rule set The primary manual edit
45. dialog box To select which classes are shown right click inside the dialog box and choose Select Classes to Display 27 September 2012 User Guide About Classification Til Navigating Samples To navigate to samples in the map view select samples in the Sample Editor window to highlight them in the map view 1 2 Before navigating to samples you must select a class in the Select Sample Informa tion dialog box To activate Sample Navigation do one of the following e Choose Classification gt Samples gt Sample Editor Options gt Activate Sample Navigation from the main menu e Right click inside the Sample Editor and choose Activate Sample Navigation from the context menu To navigate samples click in a histogram displayed in the Sample Editor window A selected sample is highlighted in the map view and in the Sample Editor window If there are two or more samples so close together that it is not possible to select them separately you can use one of the following e Select a Navigate to Sample button e Select from the sample selection drop down list Figure 6 31 For sample navigation choose from a list of similar samples Deleting Samples e Deleting samples means to unmark sample image objects They continue to exist as regular image objects e To delete a single sample double click or Shift click it e To delete samples of specific classes choose one of the following from the main menu
46. displaying everything as a solid color figure 2 7 If Classification View is active the Pixel View User Guide 27 September 2012 14 Developer XD 2 0 4 ee Figure 2 6 An image in normal Pixel View compared to the same image in Feature View with the Area algorithm selected from the Feature View window is displayed semi transparently through the classification Again you can customize the transparency in the same way as outlined in View Classification on page 12 Figure 2 7 Object displayed in Pixel View at 50 opacity left and 100 opacity right Show or Hide Outlines The Show or Hide Outlines button allows you to display the borders of image objects figure 2 8 that you have created by segmentation and classification The outline colors vary depending on the active display mode e In View Layer mode the outline colors are defined in the Edit Highlight Colors dialog box View gt Display Mode gt Edit Highlight Colors e In View Classification mode the outlines take on the colors of the respective classes Image View or Project Pixel View Image View or Project Pixel View is a more advanced feature which allows the compari son of a downsampled scene assuming you have created one with the original Pressing this button toggles between the two views 27 September 2012 User Guide Starting Developer 15 Figure 2 8 Images displayed with visible outlines The left hand image is displayed in Layer Vi
47. for an action The dependency item is forbidden for an action The dependency item is added created or assigned by an action The dependency item is removed or unassigned by an action To edit the dependencies go to the Edit Action Definition dialog box and click the Dependencies button The Edit Action Dependencies dialog box opens The Dependency Item tab gives an overview of which items are required forbidden added or removed To edit the dependencies click the ellipsis button located inside the value column which opens one of the following dialog boxes e Edit Classification Filter which allows you to configure classes e Select Levels to configure image object levels e Select Image Layers 27 September 2012 User Guide Rule Sets for Definiens Architect XD 217 Action Definition ects cells with diffuse stain Prior detection of nuclei is strongly ecommended but may be dispensable F cels have a bright center Icon ActionCeliDetection tif ie Version Action ID Detection of Cells Diffuse Stai Priority 0 Group ID Detection X Rule Set Parameter Set CytoplasmSettings Rule Set File DetectCytoplasm dep one Process to execute DetectCytoplasm Action Callbacks F Use only once Dependencies OK Cancel Figure 10 5 Action Definition dialog box is used for editing unconfigured actions e Select Thematic Layers 3 In the Item Error Messages tab you can edit messages that display in the propert
48. from the image object You can change the default name for new image object levels in Tools gt Options 27 September 2012 User Guide Basic Rule Set Editing 51 hierarchy Advanced users may want to switch off the confirmation message before dele tion To do so go to the Option dialog box and change the Ask Before Deleting Current Level setting Delete Level R Figure 4 11 Delete Level dialog box 4 5 Getting Information on Image Objects 4 5 1 The Image Object Information Window When analyzing individual images or developing rule sets you will need to investigate single image objects The Features tab of the Image Object Information window is used to get information on a selected image object Image objects consist of spectral shape and hierarchical elements These elements are called features in Definiens Developer XD 2 0 4 The Feature tab in the Image Object Information window displays the values of selected attributes when an image object is selected from within the map view The Image Object Information window is open by default but can also be selected from the View menu if required To get information on a specific image object click on an image object in the map view some features are listed by default To add or remove features right click the Image Object Information window and choose Select Features to Display The Select Displayed Features dialog box opens allowing you to select a feature of interes
49. from the main menu To select a class from which you want to collect samples do one of the following e Select the class in the Class Hierarchy window if available Select the class from the Active Class drop down list in the Sample Editor window This makes the selected class your active class so any samples you collect will be assigned to that class To define an image object as a sample for a selected class double click the image object in the map view To undo the declaration of an object as sample double click it again You can select or deselect multiple objects by holding down the Shift key As long as the sample input mode is activated the view will always change back to the Sample View when an image object is selected Sample View displays sample image objects in the class color this way the accidental input of samples can be avoided To view the feature values of the sample image object go to the Sample Editor window This enables you to compare different image objects with regard to their feature values Click another potential sample image object for the selected class Analyze its membership value and its membership distance to the selected class and to all other classes within the feature space Here you have the following options e The potential sample image object includes new information to describe the selected class low membership value to selected class low membership value to other classes e
50. information is used by the Definiens Server to configure the analysis engine software according to the job requirements An error message is generated if the installed packages do not meet the requirements specified The configuration information is of three types product version and configuration Start Analysis General Exports Configuration Exported Results ProjectFile C Documents and Settings pbrookes Desktop HE_TMA demo Tido Project Name _im Figure 9 11 Start Analysis Exports Plug Ins The plug ins that display initially are associated with the rule set that has been loaded in the General tab All the listed plug ins must be present for Definiens Server to process the rule set You can also edit the plug ins using the buttons at the top of the window To add a plug in first load a rule set on the General tab to display the associated plug ins Load a plug in by clicking the Add Plug in button or using the context menu to open the Add a Plug In dialog box Use the Name drop down box to select a plug in and version if needed Click OK to display the plug in in the list Drivers The listed drivers listed must be installed for the Definiens Server to process the tule set You might need to add a driver if it is required by the rule set and the wrong configuration is picked because of the missing information To add a driver first load a rule set on the General tab to display the associated drivers Load a driver by c
51. installed along with the optional integration components Please contact Aperio for information on obtaining and installing these components If you are using a 64 bit version of Windows only the 64 bit version of Internet Explorer supports this function If the Definiens Tissue Studio Analysis is not available in the drop down menu you may need to lower your browser s security settings to allow the display of Active X controls 253 254 Developer XD 2 0 4 Figure 13 1 Connection Manager 27 September 2012 User Guide Acknowledgments Portions of this product are based in part on the third party software components Definiens is required to include the following text with software and distributions The Visualization Toolkit VTK Copyright This is an open source copyright as follows Copyright 1993 2006 Ken Martin Will Schroeder and Bill Lorensen All rights reserved Redistribution and use in source and binary forms with or without modification are permitted provided that the following conditions are met e Redistributions of source code must retain the above copyright notice this list of conditions and the following disclaimer e Redistributions in binary form must reproduce the above copyright notice this list of conditions and the following disclaimer in the documentation and or other mate rials provided with the distribution e Neither name of Ken Martin Will Schroeder or Bill Lorensen no
52. internal thematic layer Each pixel is classified as one of the following classes no object ob ject in first layer object in second layer object in both layers and ignored by threshold Finally a chessboard segmentation is used to convert this thematic layer into an image object level In some cases you can use this algorithm as first step of your analysis to improve overall image analysis performance substantially The algorithm is particularly suited to fluores cent images where image layer information is well separated Contrast Split Segmentation Contrast split segmentation is similar to the multi threshold segmentation approach The contrast split segments the scene into dark and bright image objects based on a threshold value that maximizes the contrast between them The algorithm evaluates the optimal threshold separately for each image object in the image object domain Initially it executes a chessboard segmentation of variable scale and then performs the split on each square in case the pixel level is selected in the image object domain Several basic parameters can be selected the primary ones being the layer of interest and the classes you want to assign to dark and bright objects Optimal thresholds for splitting and the contrast can be stored in scene variables 4 3 2 Bottom up Segmentation Bottom up segmentation means assembling objects to create a larger objects It can but does not have to start with the p
53. it is displayed Process Tree Class Hierarchy or Class Description The Comment icon appears in a window when you hover over an item it also appears in the relevant editing dialog box The editing field is not available unless you have selected a rule set item Comments are automatically added to rule set items as soon as another tule set item or window is selected The up and down arrows allow you to navigate the comments attached to items in a hierarchy Paste and Undo functions are also available for this function 27 September 2012 User Guide Additional Development Tools 181 There is an option to turn off comments in the Process Tree in the Options dialog box Tools gt Options 8 2 2 The Rule Set Documentation Window The Rule Set Documentation window manages the documentation of rule sets To open it select Process gt Rule Set Documentation or View gt Windows gt Rule Set Documentation from the main menu Clicking the Generate button displays a list of rule set items in the window including classes customized features and processes The window also displays comments at tached to classes class expressions customized features and processes Comments are preceded by a double backslash You can add comments to rule set items in the window then click the Generate button again to view them It is possible to edit the text in the Rule Set Documentation window however changes made in the window will not be added to
54. multi scale map In contrast to workspace automation maps cannot be analyzed in parallel however they allow you to transfer the image object hierarchy This makes them valuable in the follow ing use cases e Multi scale and scene subset image analysis where the results of one map can be passed on to any other multi scale map e Comparing analysis strategies on the same image data in parallel enabling you to select the best results from each analysis and combine them into a final result e Testing analysis strategies on different image data in parallel When working with maps make sure that you always refer to the correct map in the image object domain The first map is always called main All child processes using a From Parent map will use the map defined in a parent process If there is none defined then the main map is used The active map is the map that is currently displayed and activated in Map View this setting is commonly used in Architect solutions The image object domain Maps allows you to loop over all maps fulfilling the set conditions Be aware that increasing the number of maps requires more memory and the Definiens client may not be able to process a project if it has too many maps or too many large maps in combination with a high number of image objects Using workspace automation splits the memory load by creating multiple projects 27 September 2012 User Guide Advanced Rule Set Concepts 159 7
55. object is then classified If the membership value of an image object is lower than the pre defined minimum mem bership value the image object remains unclassified If two or more class descriptions share the highest membership value the assignment of an object to one of these classes is random The three best classes are stored as the image object classification result Class related features are considered only if explicitly enabled by the corresponding parameter Unlike the Classification algorithm classes without a class description are assumed to have a membership value of 0 27 September 2012 User Guide About Classification 9 Using Hierarchical Classification With a Process Edit Process hams echa ciast ahon Algonthen Descrpton Evahuate the membership value of an maage otyect to a ist of selected ciscses Adgenthen parete Par areter Value Actree cistre Background Cell Nucleus Use chats seleted features Yes mage Otyect Domar mange otec bevel Parameter Vole Level Class hold condition Tive Map Per none From Pasert Regon Faam Parere M ya rember d mag d af Loops amp Cycles Number of cycles f3 Figure 6 8 Settings for the Hierarchical Classification algorithm In the Edit Process dialog box select Hierarchical Classification from the Algo rithm drop down list Define the Image Object Domain if necessary For the Algorithm Parameters select the active cla
56. of characters of a searched item e All variable parts of the search string can be defined by using blocks representing the search items which are sequenced in the search string see table 9 1 Search String Variables Project Naming in Workspaces Projects in workspaces have compound names that in clude the path to the image data Each folder within the Workspace window folder is part of the name that displays in the right hand pane with the name of the scene or tile included at the end You can understand the naming convention by opening each folder in the left hand pane of the Workspace window the Scene name displays in the Summary pane The name will also indicate any of the following e Whether the item is a tile e Whether the item is a subset The scale if the item has been rescaled e Whether the item is related to a well or a site 1 To view the entire name select List View from the drop down list in the right hand pane of the Workspace window 2 In the folder tree in the left hand pane select the root folder which is labeled by the workspace name The entire project names now display in the right hand pane In Windows 7 the location of this folder is C Users User AppData Roaming Definiens Version Number import When working with a complex folder structure in a workspace make sure that folder names are short This is important because project names are internally used for file names and must not be longer than 2
57. on two levels at the level of image objects created by segmentation or at the pixel level Whatever the object a process will run sequentially through each target applying an algorithm to each This section builds upon the tutorial in the previous chapter Process Tree 00 04 10 shape 0 5 compxt 0 5 creating Level 1 a Classification Figure 4 1 The Process Tree window displaying a simple rule set There are three ways to open the Edit Process dialog box figure 4 2 e Right click on the Process Tree window and select Append New e Select Process gt Process Commands gt Append New from the main menu e Use the keyboard shortcut Ctrl A The main areas in the Edit Process dialog box are listed in the following sections 4 1 1 Name Naming of processes is automatic unless the Automatic check box is unchecked and a name is added manually Processes can be grouped together and arranged into hierarchies which has consequences around whether or not to use automatic naming this is covered in Parent and Child Processes on page 40 4 1 2 Algorithm The Algorithm drop down box allows the user to select an algorithm or a related pro cess Depending on the algorithm selected further options may appear in the Algorithm Parameters pane 35 36 Developer XD 2 0 4 Edit Process Algonithen Descrpton Evahuste the mennbershe vake of an maage obyect to a ket of selected classes Algonthen parameters Parameter Value
58. or position of a frame click Move or Resize Core 2 In the map view move or resize the frame according to your needs 2 Frame adjustments of multiple cells do not affect fixed points and vertices that have been moved or selected for adjustment marked with a red or green rectangle You can remove a fixed point by holding down the Ctrl key while double clicking the red rectangle To unfix the position of a vertex double click the green rectangle User Guide 27 September 2012 238 Developer XD 2 0 4 e To delete a core mark the relevant cores in the map view 3 Then click Delete 4 e To accept your changes click Confirm To revert your changes click Roll back 3 To automatically define ROIs in all newly determined cores click Detect tissue in all empty cores You can manually adapt the ROIs after this process is finished 4 To manually define or change a core s ROI marked in green proceed as follows Click the ROI button If necessary activate ROI addition and deletion mode 1 To define a new ROI draw a polygon around the appropriate area using your mouse It is possible to define several ROIs within a core If however you define an ROI within another ROI the application excludes its area from analysis Use the Activate button 2 to change an existing ROI and adjust the shape of the polygon using the mouse To delete one or more ROIs click and mark the appropriate ROI in the map view 3 then click Delete 4 To accept
59. pixels Confirm with OK and for each scene to be tiled a new tiles folder will be created containing the created tile projects named tile lt number gt You can analyze tile projects in the same way as regular projects by selecting single or multiple tiles or folders that contain tiles Create Tiles Enter the size of the tiles Horizontal Size x 500 Vertical Size Y 500 Figure 7 39 The Create Tiles dialog box 7 10 3 Manually Stitch Scene Subsets and Tiles In the Workspace window select a project with a scene from which you created tiles or subsets These tiles must have already been analyzed and be in the processed state To open the Stitch Tile Results dialog box select Analysis gt Stitch Projects from the main menu or right click in the workspace window The Job Scheduler field lets you specify the computer that is performing the analysis It is set to http localhost 8184 by default which is the local machine However if you are running a Definiens Server over a network you may need to change this field Click Load to load a ruleware file for image analysis this can be a process dcp or solution dax file that contains a rule set to apply to the stitched projects For more details see Submitting Batch Jobs to a Server p 198 7 10 4 Processing Sub Scenes with Subroutines The concept of workspace automation is realized by structuring rule sets into subroutines that contain algori
60. priority the higher the action will be displayed in the list Load the rule set in the Rule Set File field as a dcp file Select the appropriate parameter set holding the related variables The Parameter Set combo box offers all parameter sets listed in the Manage Parameter Sets dialog box In Process to Execute enter the name and the path of the process to be executed by the action Process to Execute on Project Closing is usually used to implement a specific clean up operation when users close projects for example after sample input Denote the path by using a forward slash to indicate the hierarchy in the process tree The Callbacks field allows a rule set to react to certain events by executing a process Clear the Use Only Once check box to allow multiple actions of a solution Providing default actions for building solutions requires consideration of dependen cies on actions Click the Dependencies button to open the Edit Action Dependen cies dialog box Confirm with OK Editing Action Dependencies Providing action definitions to other users requires con sideration of dependencies because actions are often mutually dependent Dependency items are image layers thematic layers image object levels and classes To enable the usage of default actions for building solutions the dependencies on actions concerning dependency items have to be defined Dependencies can be defined as follows The dependency item is required
61. return true for the condition that no My Class objects exist in the neighborhood In the next block the two pieces of information defining the image object domain objects on Level 1 and no My Class objects exist in the neighborhood are split into two different lines 6 Execute the process at Level 1 Unclassified restore toremove the clas sification and return to the state after step 3 7 Execute the process try it with PPO a kind of internal loop The process if with Existence of My Class 0 0 My Class fig ure 7 21 applies the algorithm Assign Class to the image object that has been set in the parent process unclassified at Level 1 for all This has been invoked by selecting Current Image Object as image object domain Therefore all unclassified image objects will be called and each unclassified image object will be treated separately Execute the process and the result is a painted chessboard 9 In the first line all objects on image object Level are put in a list The process does nothing but pass on the identities of each of those image objects down to the next line one by one That second line the child process has only one object in the image object domain the current image object passed down from the parent process It then checks the feature condition which returns true for the first object tested But the next time this process is run with the next image object that image object is tested again and returns fal
62. saturation For inhibitory systems in which the response decreases with increasing concentration of the test substance this point is referred to as the JCsy concentration of half maximal inhibition For systems in which the response increases with increasing concentration this point is referred to as the ECs concentration of half maximal effect Because this concentration is a characteristic of the compound for the biological system being tested the goal of such an experiment is to determine the best estimate of this value 11 5 Accept and Reject Results To record your evaluation of a project you can mark it as Accepted or Rejected To mark a project select the Accept Project button or the Reject Project button on the File toolbar 27 September 2012 User Guide 12 Options The following options are available via Tools gt Options in the main menu General Show warnings as message box Yes Default Messages are displayed in a message box and additionally listed in the Message Console No Messages are displayed in the Message Console where a sequence of messages can be retraced Ask on closing project for saving project or tule set Yes Default Open a message box to prompt saving before closing No Close without asking for saving Save rule set minimized No Default Does not save features with the rule set Yes Save the features used in the Image Object Information windows with the rule set A
63. specific variable value settings They are mainly used when creating action libraries where they act as a transfer device between the values set by the action library user and the rule set behind the action Parameter sets can be created edited saved and loaded When they are saved they store the values of their variables these values are then available when the parameter set is loaded again Creating a Parameter Set To create a parameter set go to Process gt Manage Parameter Sets Manage Parameter Sets Paati w Hyliste POE LSE d temple 1G temps a BOT ht ag CELL Cel durai ieo npade Toe tempted T Lege ample Figure 7 16 Manage Parameter Sets dialog box In the dialog box click Add The Select Variable for Parameter Set dialog box opens After adding the variables the Edit Parameter Set dialog box opens with the selected variables displayed Edit Parameter Set Nome Test Pamete Sod Name Type Value tomo Vanstie SI CRESS BACKGROUND Verte Bachgound Adi Vaiatia DER Outs Unto Ay Figure 7 17 The Edit Parameter Set dialog box Insert a name for your new parameter set and confirm with OK Editing a Parameter Set You can edit a parameter set by selecting Edit in the Manage Parameter Sets dialog box 1 To add a variable to the parameter set click Add Variable The Select Variable for Parameter Set dialog box opens User Guide 27 September 2012 134 Developer XD 2 0 4 2 To edit
64. that you do not need to stitch the sub scenes results for result operations concerning the main scene To do this each sub scene analysis must have had at least one project or domain statistic exported All preceding sub scene analysis including export must have been processed completely before the Read Subscene Statistics algorithm starts any result summary cal culations Result calculations can be performed e In the main process tree after the Submit Scenes to Analysis algorithm e In a subroutine within a post processing step of the Submit Scenes to Analysis algorithm After processing all sub scenes the algorithm reads the exported result statistics of the sub scenes and performs a defined mathematical summary operation The resulting value representing the statistical results of the main scene is stored as a variable This variable can be used for further calculations or export operations concerning the main scene 7 11 Object Links 7 11 1 About Image Object Links Hierarchical image object levels allow you to derive statistical information about groups of image objects that relate to super neighbor or sub objects In addition you can derive statistical information from groups of objects that are linked to each other Use cases that require you to link objects in different image areas without generating a common super object include 1 Link objects between different timeframes of time series data in order to calculate a mo
65. the distance is the number of hierarchy levels in the Process Tree window above the current editing line where you find the definition of the parent object In the Process Tree hierarchical levels are indicated using indentation Process Tree Parert Process 2 Inserted Chiki Process Parent Process 2 3 Inserted Child Process Parent Process 3 4 Inserted Ch d Process 4 Appended Sibling Process 4 Appending Sibling Process Parent Process 4 S Insert Child Process 4 Appending Sibling Process 4 Appending Sibling Process 2 Appending Sibling Process 2 Appending Sibling Process 2 Appending Sibling Process 2 Appending Sibling Process Figure 4 17 Process Tree window displaying a prototype of a process hierarchy The pro cesses are named according to their connection mode Example e A process distance of one means the parent process is located one hierarchical level above the current process e A process distance of two means the parent process is located two hierarchical levels above the current process Put figuratively a process distance of two defines the grandparent process 27 September 2012 User Guide Basic Rule Set Editing 59 4 5 4 Comparing Objects Using the Image Object Table This feature allows you to compare image objects of selected classes when evaluating classifications To open it select Image Objects gt Image Object Table from the main menu To launch the Configure Im
66. the information of thematic raster layers is discrete Image layers and thematic layers must be treated differently in both segmentation and classifica tion 7 2 1 Importing Editing and Deleting Thematic Layers Typically unless you have created them yourself you will have acquired a thematic layer from an external source It is then necessary to import this file into your project Developer XD supports a range of thematic formats and a thematic layer can be added to a new project or used to modify an existing project Although vector data is rasterized when imported into Developer XD the original data remains unchanged Thematic layers can be specified when you create a new project via File gt New Project simply press the Insert button by the Thematic Layer pane Alternatively to import a layer into an existing project use the File gt Modify Existing Project function Once defined the Edit button allows you to further modify the thematic layer and the Delete button removes it When importing thematic layers ensure the image layers and the thematic layers have the same co ordinate systems and geocoding If they do not the content of the individual layers will not match As well as manually importing thematic layers using the File gt New Project or File gt Modify Open Project dialog boxes you can also import them using rule sets For more details look up the Create Modify Project algorithm in the Developer XD Referenc
67. then be displayed as the root folder in the Workspace window 185 186 Developer XD 2 0 4 Workspace undefined unc Export Specification E Definiens 7 0 dpr plate1 DO6 t02 v7 dpe 2 E Definiens 7 O vesute ProsectS tatistics csv Figure 9 1 Workspace window with Summary and Export Specification and drop down view menu If you need to define another output root folder it is preferable to do so before you load scenes into the workspace However you can modify the path of the output root folder later on using File gt Workspace Properties Importing Scenes into a Workspace Before you can start working on data you must import scenes in order to add image data to the workspace During import a project is created for each scene You can select different predefined import templates according to the image acquisition facility producing your image data If you only want to import a single scene into a workspace use the Add Project command To import scenes to a workspace choose File gt Predefined Import from the main menu or right click the left hand pane of the Workspace window and choose Predefined Import The Import Scenes dialog box opens Select a predefined template from the Import Template drop down box Browse to open the Browse for Folder dialog box and select a root folder that contains image data 3 The subordinate file structure of the selected image data root folder is displayed in the Preview field The plus
68. then select Execute The selected process tree is executed The application uses the current settings for all local variables during execution You can modify the value of all local variables including parameters in the Manage Variables dialog box If you use the Pass domain from calling process as a parameter domain handling mode you additionally have to specify the domain that should be used for manual execution Select the customized algorithm and do one of the following e Select Process gt Process Commands gt Edit Image Object Domain for stepwise execution from the main menu e Select Edit Image Object Domain for Stepwise Execution in the context menu The Edit Image Object Domain for dialog box opens Specify the image object domain that you want to be used for the from calling process domain during stepwise execution The Image Object Domain of the customized algorithm must be set to from calling process 7 8 8 Deleting a Customized Algorithm To delete a customized algorithm select it on the Customized Algorithms tab of the Process Tree window Do one of the following e Select Delete from the context menu Select Process gt Process Commands gt Delete from the main menu e Press Del on the keyboard The customized algorithm is removed from all processes of the rule set and is also deleted from the list of algorithms in the Edit Process dialog box Customized algorithms and all processes that use them are dele
69. to add data from a comma separated variable csv file After assigning an image and matching cores you can load an annota tions file Once imported labels will be visible in map view NOTE To check the possible matching results for grids other than the as signed select the relevant layout from the dropdown list under Grid Layout A preview is displayed in the TMA Grid View You can change its size and color range If you want to display a grid layout without matching results select Layout in the Show dropdown list You can return to the display of the assigned grid by clicking the Revert button 11 3 3 Changing the Grid After Matching To improve the results of automatic core detection and matching you can adjust the grid so that the individual cores can be better assigned to the cells in the grid 1 2 Activate the manual adaptation mode by clicking the Matching button To display the grid in the map view click Reset The initial grid comprises all cores that have been determined automatically or manually To change the grid manually do one of the following e To rescale or rotate the complete grid hold down the Ctrl key while double clicking the vertex of a cell The vertex is used as a fixed point for rescaling and rotation It is marked with a red rectangle You can only set one fixed point per grid Hold down the Ctrl key while clicking a different unfixed vertex and moving the mouse so that the resca
70. to determine the ICs9 or ECs of a test compound You can add compounds to plate rows then create a graph of the results and fit them to a curve The dose response curve is optimized for a 96 well plate but can be used with smaller and larger plates The general workflow is as follows 1 To open the Dose Response window select View gt Windows gt Dose Resp on the main menu Select the Result View preset layout by choosing View gt View Results View from the main menu 2 Input the selected compounds to a plate in selected sequences 3 Select a compound for which you want to see the dose response curve 27 September 2012 User Guide Advanced Data Visualizations 243 4 Select a feature for which a dose response curve is needed The dose response data points are automatically placed on the graph 5 Select a fitting model 6 As part of this process you may choose to alter the initial values of the model s parameters 7 After an initial fitting you may want to deal with outlying data points and then refit the curve 8 You can export both the image of the curve and the related data Displaying Dose Response Data Points Select a feature and a compound for the dose response to display data points on the graph in the Dose Response window Once you display the data points you can prepare to fit a dose response curve e To select a compound to display in a dose response curve select it from the drop down list of the Compound f
71. your changes click Confirm To revert your changes click Roll back 5 Select the Matching tab 6 Under Core Detection click Match Cores The application updates the TMA Grid View with the new core information 11 4 Cellenger 11 4 1 Plate View Plates are commonly used for automated image analysis in cellular biology Definiens Developer XD 2 0 4 provides specific controls and tools to develop ruleware for cellular image analysis To open the Plate View window choose View gt Windows gt Plate View from the main menu Viewing Results in Plate View The Results tab of Plate View window provides graphical information about the results of the analysis for each well Statistical distribution is indicated by colors ranging from blue to red blue indicates a low value for a selected parameter and red indicates a high value Color Value Range Blue Minimum value Green Lower half Yellow Mean value Orange Upper half Red Maximum value 27 September 2012 User Guide Advanced Data Visualizations 239 To open the Results tab of the Plate View window click the Results button Plate View 20050707 U20S ps 1883 GS Cl 1G11 1A9_0 000000000000 E 990000000000 Navigation Layout Dose Mean Total Intensity of Cell Spot Stain Automatically update heat map scale Selected wells 20 35346 GY 1135 9408 96 wells selected Figure 11 11 Analysis Results in the Plate View window with automatic scalin
72. 154 Developer XD 2 0 4 Customized Algorithm Properties Name Golgi Analysis E Used rule set items I Show reference ree Item name Scope B Classes Red local Black local E Levels chess boad level 1 global B Variables _lowerBoundaryF orBlack parameter _upperBoundaryF oBlack parameter counter parameter be Features gcd Brightness Desoiptio 110 lt double click here to edt descrip lt double click here to edit descrip 0 11331765 lt double click here to edit descrip Value Delete local results No Domain handing rvoke aigorithen foe each object Figure 7 33 Customized Algorithms Properties dialog box e Local The item is used internally Other processes outside this customized algorithm are unable to access it All occurrences of the original global item in the process sequence are replaced by a local item with the same name e Parameter The item is used as a parameter of the algorithm This allows the assignment of a specific value within the Algorithm parameters of the Edit Process dialog box whenever this customized algorithm is used 5 If you define the scope of a used a rule set item as a parameter it is listed in the Parameters section Modifying the parameter name renames the rule set item accordingly Furthermore you can add a description for each parameter When using the customized algorithm in the Edit Process dialog box the description is displayed in the parameter description fiel
73. 2 Click Save to open the Save Plate Layout dialog box 3 Browse to the desired folder and enter a name for the layout and confirm with Save 5 4 6 Load Plate Layout You can load an existing layout of a plate and also the input of compounds for the dose response curve Plate layouts are saved as dpl files 1 In the Plate View window click Load in the Layout tab to open the Open Plate Layout dialog box 2 Browse to the desired folder select a layout file and confirm with Open 27 September 2012 User Guide 6 About Classification 6 1 Key Classification Concepts 6 1 1 Assigning Classes When editing processes you can use the following algorithms to classify image objects e Assign Class assigns a class to an image object with certain features using a thresh old value e Classification uses the class description to assign a class e Hierarchical Classification uses the class description and the hierarchical structure of classes e Advanced Classification Algorithms are designed to perform a specific classifica tion task such as finding minimum or maximum values of functions or identifying connections between objects 6 1 2 Class Descriptions and Hierarchies You will already have a little familiarity with class descriptions and hierarchies from the basic tutorial where you manually assigned classes to the image objects derived from segmentation There are two views in the Class Hierarchy window which can be selected by
74. 20 orm OOSA 0558 Figure 11 2 Output of the Classification Stability statistics The difference between the best and the second best class assignment is calculated as a percentage The statistical output displays basic statistical operations number of image objects mean standard deviation minimum value and maximum value performed on the best to second values per class The Best Classification Result dialog box displays a statistic type used for accuracy as sessment Best Classification Result 01354 ouR 0282 5 3 0720 Paa Grarstard 0 01002 Pas Woodard 07753 Figure 11 3 Output of the Best Classification Result statistics The statistical output for the best classification result is evaluated per class Basic sta tistical operations are performed on the best classification result of the image objects 1 To display the comparable graphical output go to the View Settings window and select Mode 27 September 2012 User Guide Advanced Data Visualizations 229 assigned to a class number of image objects mean standard deviation minimum value and maximum value 11 1 2 Error Matrices The Error Matrix Based on TTA Mask dialog box displays a statistic type used for accu racy assessment Error Matrix based on TTA Mask Figure 11 4 Output of the Error Matrix based on TTA Mask statistics Test areas are used as a reference to check classification quality by comparing the clas sification with
75. 55 characters including the path backslashes names and file extension User Guide 27 September 2012 190 Developer XD 2 0 4 Table 9 1 Search String Variables Block Description Usage reverse Starts reading from the end instead part of a file name reverse of the beginning is recommended for reading file names because file name endings are usually fixed any Represents any order and number of Used as wildcard character for characters example any tif for TIFF files with an arbitrary name any folders Represents one or multiples of nested folders down the hierarchy under which the image files are stored root any folders any tif for all TIFF files in all folders below the root folder root Represents a root folder under Every search string has to start with which all image data you want to root import is stored folder Represents one folder under which root scene tif for TIFF files the image files are stored whose file names will be used as scene names scene Represents the name of a scene that root scene tif for TIFF files will be used for project naming whose file names will be used as within the workspace after import scene names layer Represents the name of an image layer slice Represents the slices of a 3D or 4D slice tif for all TIFF files or image data set It can be used for slice any tif for all TIFF files or folders files in a folder containing sl
76. 9 2 Adding a Map to a Project to Create Multi Project Maps Use cases that require different images to be loaded into one project so called multi project maps are commonly found e During rule set development for testing rule sets on different image data e During registration of two different images There are two ways to create a multi project e In the workspace select multiple projects with the status created not edited by holding down the Ctrl key then right click and choose Open from the context menu The New Multi Map Project Name dialog box opens Enter the name of the new project and confirm the new project is created and opens The first scene will be displayed as the main map e Open an existing project and go to File gt Modify Open Project in the main menu In the Modify Open Project dialog box go to Maps gt Add Map Type a name for the new map in the Map box and assign the image for the new map The new map is added to the Map drop down list 7 9 3 Copying a Map for Multi Scale Analysis Like workspace automation a copy of a map can be used for multiscale image analysis this can be done using the Copy Map algorithm The most frequently used options are e Defining a subset of the selected map using a region variable e Selecting a scale e Setting a resampling method e Copying all layers selected image layers and thematic layers e Copying the image object hierarchy of the source map When d
77. DEF NIENS Understanding Images Definiens Developer XD 2 0 4 User Guide DEEPER INSIGHTS FASTER RESULTS BETTER DECISIONS www definiens com Definiens Documentation Developer XD 2 0 4 User Guide Imprint 2012 Definiens AG All rights reserved This document may be copied and printed only in accordance with the terms of the Frame License Agreement for End Users of the related Definiens software Published by Definiens AG Bernhard Wicki StraBe 5 80636 Miinchen Germany Phone 49 89 2311 800 e Fax 49 89 2311 8090 Web www definiens com Dear User Thank you for using Definiens software We appreciate being of service to you with image intelligence solutions At Definiens we constantly strive to improve our products We therefore appreciate all comments and suggestions for improvements concerning our software training and documentation Feel free to contact us via web form on the Definiens support website www definiens com support Thank you Legal Notes Definiens Definiens Cellenger Definiens Cognition Network Technology DEFINIENS ENTERPRISE IMAGE INTELLIGENCE Tissue Studio and Understanding Images are registered trademarks of Definiens AG in Germany and other countries Cognition Network Technology Enterprise Image Intel ligence and Definiens Composer Technology are trademarks of Definiens AG in Germany and other countries All other product names company names and brand n
78. DEF NIENS Understanding images Select Portal oo Ht Tie Tissue Studio TMA Tissue Studio IF TMA 2 amp Call Tissue A Life Figure 2 2 Portals available for Developer Customers with Tissue Studio licenses 27 September 2012 User Guide Starting Developer 9 Portal Application Tissue Studio Brightfield whole tissue analysis Tissue Studio TMA Brightfield tissue micro array analysis Tissue Studio IF Fluorescence whole tissue analysis Tissue Studio IF TMA Fluorescence tissue micro array analysis 2 3 Starting Multiple Definiens Clients You can start and work on multiple Developer XD clients simultaneously this is helpful if you want to open more than one project at the same time However you cannot interact directly between two active applications as they are running independently for example dragging and dropping between windows is not possible 2 4 The Develop Rule Sets View se sie old MEO SP passaa ks JO ES eee it Rhee ep comm ir a x paes 2 Figure 2 3 The default workspace when a project or image is opened in the application in this case the Cell portal 1 The map view displays the image file Up to four windows can be displayed by se lecting Window gt Split Vertically and Window gt Split Horizontally from the main menu allowing you to assign different views of an image to each window The User Guide 27 September 2012 10 Developer
79. General QW serdodie 4 Waterbodes Link by name Uniink al Figure 6 34 Edit Conversion Table dialog box 1 To edit the conversion table choose Classification gt Samples gt Edit Conversion Table from the main menu User Guide 27 September 2012 114 Developer XD 2 0 4 2 The Linked Class list displays how classes of the map are linked to classes of the TTA mask To edit the linkage between the TTA mask classes and the classes of the current active map right click a TTA mask entry and select the appropriate class from the drop down list 3 Choose Link by name to link all identical class names automatically Choose Un link all to remove the class links 6 4 5 Creating Samples Based on a Shapefile You can use shapefiles to create sample image objects A shapefile also called an ESRI shapefile is a standardized vector file format used to visualize geographic data You can obtain shapefiles from other geo applications or by exporting them from Definiens maps A shapefile consists of several individual files such as shx shp and dbf To provide an overview using a shapefile for sample creation comprises the following steps e Opening a project and loading the shapefile as a thematic layer into a map e Segmenting the map using the thematic layer e Classifying image objects using the shapefile information Creating the Samples Edit Process agoen paraw Maem nbe of mage cbech Loops amp Oycies Looe while somet
80. Information window the Feature View window or the Select Displayed Features dialog box Manual Metadata Import Modify Project F Use geocoding Posi sine fur 2D Meters ca Geocoding Upper Right 0022871330688722 0 08976068738005 i Layer 1 Vig lmuc dapecects _Detirsens Academy Developer Advanced Tiare II 20 T Layer 2 WAglmuc deproects _Detinens Academy Developer Advanced Trang II 20 Tr Layer 3 WAg mus dapropects _Detivens Academg Developer Advanced Trane tl 20 Tr m 2 isle ke i Figure 4 22 The Modify Open Project dialog box 27 September 2012 User Guide Basic Rule Set Editing 63 Although it is not usually necessary you may sometimes need to link an open project to its associated metadata file To add metadata to an open project go to File gt Modify Open Project The lowest pane of the Modify Project dialog box figure 4 22 allows you to edit the links to metadata files Select Insert to locate the metadata file It is very important to select the correct file type when you open the metadata file to avoid error messages Once you have selected the file select the correct field from the Import Metadata box and press OK The filepath will then appear in the metadata pane To populate with metadata press the Edit button to launch the MetaData Conversion dialog box figure 4 23 Press Generate All to populate the list with metadata which will appear in th
81. Options Images are scanned in a specific order in the preview or workspace There are two options 1 Select the check box Search in Subfolders e Files in selected folder and all subfolders e Takes the first item in current folder e If this item is a folder then steps into this folder and continues search there User Guide 27 September 2012 78 Developer XD 2 0 4 2 Clear the check box Search in Subfolders e Only files directly in the folder e Alphabetical ascending For example one might import the following images with this folder struc ture selected folder gt 1 gt 5 gt 1 tif amp 8 tif selected folder gt 1 gt 8 gt 5 tif selected folder gt 1 gt 3 tif amp 7 tif selected folder gt 3 gt 6 tif selected folder gt 2 tif amp 4 tif 5 3 3 Importing Images with Annotations Definiens Developer XD 2 0 4 can import the following annotated formats but only via predefined import Aperio ScanScope svs afi Aperio ScanScope with resolution svs afi Aperio ScanScope FL svs afi Aperio ScanScope FL with resolution svs afi Bacus WebSlide ini Generic one file per scene with annotation jpg tif Generic one file per scene with resolution and annotation jpg tif Generic one scene per folder with annotation jpg tif Generic one scene per folder with ini metadata file and annotation jpg tif Hamamatsu ndpi
82. Server allows simultane ous analysis of the sub scenes submitted to a subroutine Each sub scene will then be processed by one of the available engines Creating a Subroutine To create a subroutine right click on either the main or subroutine tab in the Process Tree window and select Add New The new tab can be renamed deleted and duplicated The procedure for adding processes is identical to using the main tab Process Tree Figure 7 41 A subroutine in the Process Tree window Executing a Subroutine Developing and debugging open projects using a step by step execution of single pro cesses is appropriate when working within a subroutine but does not work across sub routines To execute a subroutine in Developer XD ensure the correct sub scene is open then switch to the subroutine tab and execute the processes When running a rule set on a Definiens Server subroutines are automatically executed when they are called by the Submit Scenes for Analysis algorithm for a more detailed explanation consult the Developer XD Reference Book Editing Subroutines Right clicking a subroutine tab of the Process Tree window allows you to select common editing commands 27 September 2012 User Guide Advanced Rule Set Concepts 167 a d gt Main A Suiram Berme Dughcate Figure 7 42 Subroutine commands on the context menu of the Process Tree window You can move a process including all child processes fr
83. The Generate Report dialog box creates an HTML page listing image objects each specified by image object features and optionally a thumbnail image Exporting Results as Raster Files Selecting raster file from the Export Type drop down box allows you to export image objects or classifications as raster layers together with attribute tables in csv format con taining parameter values Image objects or classifications can be exported together with their attributes Each image object has a unique object or class ID and the information is stored in an attached attribute table linked to the image layer Any geo referencing information used to create a project will be exported as well There are two possible locations for saving exported files e If a new project has been created but not yet saved the exported files are saved to the folder where the image data are stored e If the project has been saved recommended the exported files are saved in the folder where the project has been saved To export image objects or classifications open the Export Results dialog box by choos ing Export gt Export Results from the main menu 1 Select Raster file from the Export Type drop down box 2 In the Content Type drop down box choose one of the following e Image objects to export all image objects with individual object IDs and their attributes e Classification to export only the classification of image objects The attached attribute table c
84. The potential sample image object is really a sample of another class low membership value to selected class high membership value to other classes e The potential sample image object is needed as sample to distinguish the se lected class from other classes high membership value to selected class high membership value to other classes In the first iteration of selecting samples start with only a few samples for 27 September 2012 User Guide About Classification 109 g 10 11 12 each class covering the typical range of the class in the feature space Other wise its heterogeneous character will not be fully considered Repeat the same for remaining classes of interest Classify the scene The results of the classification are now displayed in the map view In the View Settings dialog box the mode has changed from Samples to Classification Note that some image objects may have been classified incorrectly or not at all All image objects that are classified are displayed in the appropriate class color If you hover the cursor over a classified image object a tool tip pops up indicating the class to which the image object belongs its membership value and whether or not it is a sample image object Image objects that are unclassified appear transparent If you hover over an unclassified object a tool tip indicates that no classification has been applied to this image object This information is also available in the Clas
85. User Guide 27 September 2012 60 Developer XD 2 0 4 Scatter Plot window navigate to View gt Windows gt 2D Scatter Plot 2D Scatter Pict Roundness i i i Coordinates 269 1527 Figure 4 20 2D Scatter Plot window The example figure 4 20 displays the roundness of image objects x axis compared to the mean value of the image layer w y axis The color coding refers to the colors of the classes Each dot in the 2D Scatter Plot represents an image object of the project in the map view Selecting an dot in the 2D Scatter Plot selects the corresponding image object in the map view and vice versa Configuring the 2D Scatter Plot To configure the display of the 2D Scatter Plot window 1 2 Select the General tab of the 2D Scatter Plot window To turn off automatic scaling clear the Auto Scale checkbox for either the x or the y axis Auto scaling adjusts either axis to the value range of the selected feature If you turn it off the current scale stays Further features that you select are displayed within this scale This can lead to distorted results when the range or value does not fit in the current scale By default the 2D Scatter Plot window displays a grid for both axes To turn it off clear the Show Grid checkbox for one or both axes Selecting Features for the 2D Scatter Plot You can select from a variety of features to be displayed in the 2D Scatter Plot window 1 2 3 Open the Features ta
86. Width Predefined Values Figure 2 15 The Window Leveling dialog box User Guide 27 September 2012 20 Developer XD 2 0 4 Image Equalization Image equalization is performed after all image layers are mixed into a raw RGB red green blue image If as is usual one image layer is assigned to each color the effect is the same as applying equalization to the individual raw layer gray value images On the other hand if more than one image layer is assigned to one screen color red green or blue image equalization leads to higher quality results if it is performed after all image layers are mixed into a raw RGB image There are several modes for image equalization None No equalization allows you to see the scene as it is which can be helpful at the beginning of rule set development when looking for an approach The output from the image layer mixing is displayed without further modification Linear Equalization with 1 00 is the default for new scenes Commonly it dis plays images with a higher contrast than without image equalization Standard Deviation Equalization has a default parameter of 3 0 and renders a dis play similar to the Linear equalization Use a parameter around 1 0 for an exclusion of dark and bright outliers Gamma Correction Equalization is used to improve the contrast of dark or bright areas by spreading the corresponding gray values Histogram Equalization is well suited for Landsat images but can lead t
87. XD 2 0 4 image can be enlarged or reduced using the Zoom functions on the main toolbar or from the View menu 2 The Process Tree Developer XD uses a cognition language to create ruleware These functions are created by writing rule sets in the Process Tree window 3 Class Hierarchy Image objects can be assigned to classes by the user which are displayed in the Class Hierarchy window The classes can be grouped in a hierar chical structure allowing child classes to inherit attributes from parent classes 4 Image Object Information This window provides information about the character istics of image objects 5 Feature View In Definiens software a feature represents information such as mea surements attached data or values Features may relate to specific objects or apply globally and available features are listed in the Feature View window 2 5 Customizing the Layout 2 5 1 Default Toolbar Buttons File Toolbar The File toolbars allow you to load image files open projects and open and create new workspaces as Oe View Settings Toolbar These buttons numbered from one to four allow you to switch between the four window layouts These are Load and Manage Data Configure Analysis Review Results and Develop Rule Sets Sl al EJEN As much of the User Guide centers around writing rule sets which organize and modify image analysis algorithms the view activated by button number four Develop Rule Sets is most
88. You can switch between degrees Deg or radians Rad 6 Click the Inv check box to invert the expression n User Guide 27 September 2012 146 Developer XD 2 0 4 Customized Features Athretc Raiasora Fere rare Figure 7 31 Creating an arithmetic feature in the Customized Features dialog box 7 To create a new customized feature do one of the following e Click Apply to create the feature without leaving the dialog box e Click OK to create the feature and close the dialog box 8 After creation the new arithmetic feature can be found in e The Image Object Information window e The Feature View window under Object Features gt Customized NOTE The calculator buttons are arranged in a standard layout In addi tion e signifies an exponent for example x 2 means x or a square root x 0 5 for x e Use abs for an absolute value e Use floor to round down to the next lowest integer whole value You can use floor 0 5 x to round up to the next integer value e Note that e is the Euler number and PI P is 7 7 7 3 Relational Customized Features The following procedure will assist you with the creation of a relational customized fea ture 1 Open the Manage Customized Features dialog box Tools gt Manage Customized 27 September 2012 User Guide Advanced Rule Set Concepts 147 Customized Features feses Tet coe Raimons to regon ohea
89. You can then select another group in which to display your customized feature In addition you can create your own group in the Feature Tree by selecting Create New Group This may be useful when creating solutions for another user Although it is possible to use variables as part or all of a customized feature name we would not recommend this practice as in contrast to features variables are not auto matically updated and the results could be confusing Customized features that are based on class related features cannot be saved by using the Save Customized Features menu option They must be saved with a rule set 27 September 2012 User Guide Advanced Rule Set Concepts 151 7 8 Customized Algorithms Defining customized algorithms is a method of reusing a process sequence in different rule sets and analysis contexts By using customized algorithms you can split compli cated procedures into a set of simpler procedures to maintain rule sets over a longer period of time You can specify any rule set item such as a class feature or variable of the selected process sequence to be used as a parameter within the customized algorithm A creation of configurable and reuseable code components is thus possible A rule set item is any object in a rule set Therefore a rule set item can be a class feature image layer alias level name or any type of variable Customized algorithms can be modified which ensures that code chan
90. You can use the settings in the Rule Set Options algorithm to change the way that poly gons display The settings for polygons in Project Settings group of the Options dialog box displays control how polygons are generalized 27 September 2012 User Guide Advanced Rule Set Concepts 177 7 12 2 Viewing Skeletons Skeletons are automatically generated in conjunction with polygons To display skeletons click the Show Hide Skeletons button and select an object You can change the skeleton color in the Edit Highlight Colors settings To view skeletons of multiple objects draw a polygon or rectangle using the Manual Editing toolbar to select the desired objects and activate the skeleton view Figure 7 50 Sample map with one selected skeleton the outline color is yellow the skeleton color is orange About Skeletons Skeletons describe the inner structure of an object By creating skeletons the object s shape can be described in a different way To obtain skeletons a Delaunay triangulation of the objects shape polygons is performed The skeletons are then created by identifying the mid points of the triangles and connecting them To find skeleton branches three types of triangles are created e End triangles one neighbor triangles indicate end points of the skeleton A e Connecting triangles two neighbor triangles indicate a connection point B e Branch triangles three neighbor triangles indicate branch points of the skele
91. a Pah _T onen Ee Furene GE ite Master Fie rusies POOO2 W Seach Sang boot iaryfokier layed soena if reverse Scere Name locas T Ceste wodcepace fokder bom search iang F Create workepace folder bom file ipsios Ver j Aetreera bc ah shave Dea Paean nosida Pood mios Figure 9 4 Customized Import dialog box 1 Click the Clear button before configuring a new import to remove any existing settings Choose a name in the Import Name field 2 The Root Folder is the folder where all the image data you want to import will be stored this folder can also contain data in multiple subfolders To allow a customized import the structure of image data storage has to follow a pattern which you will later define 3 Select a Master File within the root folder or its subfolders Depending on the file structure of your image data defined by your image reader or camera the master file may be a typical image file a metafile describing the contents of other files or both 4 The Search String field displays a textual representation of the sample file path used as a pattern for the searching routine The Scene Name text box displays a representation of the name of the scene that will be used in the workspace window after import 5 Press the Test button to preview the naming result of the Master File based on the Search String 27 September 2012 User Guide N gt Automating Data Analysis 189 Loading and Saving Templates Pr
92. a value or variable parameter it is possible to select an array item Array Features In Scene Features gt Rule Set Related three array variables are present rule set array values rule set array size and rule set array item For more information please consult the Reference Book In Customized Algorithms Rule set arrays may be used as parameters in customized algorithms on page 151 In Find and Replace Arrays may be selected in the Find What box in the Find and Replace pane 7 5 Image Objects and Their Relationships 7 5 1 Implementing Child Domains via the Execute Child Process Algorithm Through the tutorials in earlier chapters you will already have some familiarity with the idea of parent and child domains which were used to organize processes in the Process 27 September 2012 User Guide Advanced Rule Set Concepts 137 Tree In that example a parent object was created which utilized the Execute Child Processes algorithm on the child processes beneath it The child processes within these parents typically defined algorithms at the im age object level However depending on your selection Developer XD can apply algorithms to other objects selected from the Image Object Domain Current image object The parent image object itself Neighbor obj The distance of neighbor objects to the parent image object If distance is zero this refers to image objects that have a common border with the parent and lie on the sam
93. a variable select it and click Edit The Edit Value dialog box opens where you can change the value of the variable e If you select a feature variable the Select Single Feature dialog opens en abling you to select another value e If you select a class variable the Select Class dialog opens enabling you to select another value e If you select a level variable the Select Level dialog opens enabling you to select another value 3 To delete a variable from the parameter set select it and click Delete 4 Click Update to modify the value of the selected variable according to the value of the rule set 5 Click Apply to modify the value of the variable in the rule set according to the value of the selected variable 6 To change the name of the parameter set type in a new name NOTE Actions 4 and 5 may change your rule set Managing Parameter Sets To delete a parameter set select it and press Delete To save a parameter set to a psf file select it and click Save Click Save All when you want to save all parameter sets to one psf file Click Load to open existing parameter sets Click Update to modify the values of the variables in the parameter set according to the values of the rule set Click Apply to modify the values of the variables in the rule set according to the values of the parameter set Default Parameter Set Values In any project Developer XD creates the following parameters by default It is generally not ne
94. ad an already existing solution with all the analysis settings from a solution file extension dax to the Analysis Builder window go to Library gt Load Solution on the main menu To use a solution that was built with another action library open the action library before opening your solution The solution is displayed in the Analysis Builder window If you want to change a solution built with an older action library make sure that the corresponding action library is open before loading the solution gt Testing and Improving Solutions e Testing and improvement cycles might take some time Here are some tips to help you to improve the results e Use the Preview that some actions provide to instantly display the results of a certain setting in the map view e To execute all assembled actions click the Run Solution button on the Architect toolbar Alternatively choose Analysis gt Run Solution from the main menu e To execute all actions up to a certain step select an action and click the Run So lution Until Selected Action button on the Architect toolbar Alternatively choose Analysis gt Run Solution Until Selected Action from the main menu All actions above and including the selected action will be executed e To improve the test processing time you can test the actions on a subset of your project data To test and improve analysis e For faster testing use the Run Selected Action button on the Architect toolbar Al ternati
95. aded must not have an image object library the status should be set to cancelled In the right hand pane of the Workspace window select multiple projects by holding down the Ctrl or Shift key Right click and select Open from the context menu Type a name for the new multi map project in the opening New Multi Map Project Name dialog box Click OK to display the new project in the map view and add it to the project list If you select projects of different folders by using the List View the new multi map project is created in the folder with the last name in the alphabetical order Example If you select projects from a folder A and a folder B the new multi map project is created in folder B Working on Subsets and Copies of Scenes If you have to analyze projects with maps representing scenes that exceed the processing limitations you have to consider some preparations Projects with maps representing scenes within the processing limitations can be processed normally but some preparation is recommended if you want to accelerate the image anal ysis or if the system is running out of memory To handle such large scenes you can work at different scales If you process two dimensional scenes you have additional options e Definition of a scene subset e Tiling and stitching of large scenes e Tiling of large scenes For automated image analysis we recommend developing rule sets that handle the above methods automatically In the context
96. age Object Table dialog box double click in the win dow or right click on the window and choose Configure Image Object Table Configure Image Object Table Classes D Sxigord Gtopisim Mev tue O Goig Apparatus Complies Ode Geig Nuci O Nucet Select Classes Figure 4 18 Configure Image Object Table dialog box Upon opening the classes and features windows are blank Press the Select Classes button which launches the Select Classes for List dialog box Add as many classes as you require by clicking on an individual class or transferring the entire list with the All button On the Configure Image Object Table dialog box you can also add unclassified image objects by ticking the checkbox In the same manner you can add features by navigating via the Select Features button Image Object Table OIDU 2 17 333 0 m n75 0235 3 33 57 08777 282 177 S67 01y 2 1725833 0 E mo 204 633 Figure 4 19 Image Object Table window Clicking on a column header will sort rows according to column values Depending on the export definition of the used analysis there may be other tabs listing dedicated data Selecting an object in the image or in the table will highlight the corresponding object 4 5 5 Comparing Features Using the 2D Scatter Plot The 2D Scatter Plot provides graphical information on the comparison of two image objects and lets you select the features and classes to be compared To open the 2D
97. al scroll bar To zoom in and out hold down the Ctrl key and the right mouse button and move the mouse up or down Holding down the right mouse button and moving the pointer from left to right adjusts window leveling on page 18 Synchronizing Planar Projections Change the view settings image object levels and im age layers in one planar projection and then apply those settings to the other projections For the MPR Comparison view synchronization is only possible for XY projections with the same map You can also use this tool to synchronize the map view after splitting using the options available in the Window menu Select one of the planar projections and change any of the functions below Then click the Sync button in the 3D settings toolbar to synchronize the changes among all open projections Show or Hide Outlines Pixel View or Object Mean View View Classification View Layer Zoom options include Area Zoom Zoom In Center Zoom Out Center Zoom In Zoom Out Select Zoom Value Zoom 100 and Zoom to Window After zoom ing in one projection and then synchronizing you can refocus all projections by clicking on any point of interest Image layers and image object level mixing Image object levels Show Hide Polygons and Show Hide Skeletons for 2D connected image objects only Customizing the Window Layout To customize your window layouts and save them along with the selected view settings 1 2 3 4 Create a custo
98. ames mentioned in this document may be trademark properties of their respective holders Protected by patents EP0858051 W0O0145033 W0O2004036337 US 6 832 002 US 7 437 004 US 7 574 053 B2 US 7 146 380 US 7 467 159 B US 7 873 223 US 7 801 361 B2 Regulatory affairs Under certain circumstances the solutions and applications developed using Definiens Developer XD may fall under specific regulations e g medical de vice or IVD regulations in your country Please ensure that you check and follow local regulations before using or taking your solution or application into commerce If you require specific data about Definiens Developer XD please contact your dealer or our sales staff Typeset by Wikipublisher All rights reserved 2012 Definiens Documentation Miinchen Germany Day of print 27 September 2012 Contents 1 Key Concepts ol A EAVER e ea Se gs kw Boe Eady oe BAL Ege Ae wee L2 Image DataSet occi eek bee bs ROE Si oe Se 8 a 1 3 Segmentation and classification 6 64 5 5S ee ee ees 1 4 Image Objects Hierarchies and Domains L41 mage Objects ne ee ee a ee a ee Bd eg 1 4 2 Image Object Hierarchy ocs ee ceo a 1 4 3 Image ObjectDomain 2 1 5 Scenes Maps Projects and Workspaces 2 22 TOA BOGGS 6 kek ph ha y A ee ER Ae Se ee EE LO Maps and Projects od bs ee SEO He BEDE ws weed 133 WOTKSpaces i ep a OY eS eR de eR SS 2 Starting Developer 21 The Deve
99. an Image Object Domain 36 4 2 2 Adding an Algorithm o gt o s oe e e a 38 42 3 Loops amp Cycles co ectie 55 4 ae ewiri tunek 39 424 Executing a Process concas de ebb day eG e E es 39 4 2 5 Executing a Process on a Selected Object 39 4 2 6 Parent and Child Processes 40 42 Eoaumea Rule Set seder 6s a ee RHE ERE A OR eS 40 42 Mindome Gaus lt c sa rai e202 Se Hebe PRE OSS 40 4 2 9 Deleting a Processor Rule Set 0 41 4 2 10 Editing Using Drag and Drop 41 4 3 Creating Image Objects Through Segmentation 42 4 3 1 Top down Segmentation 0 42 4 3 2 Bottom up Segmentation osoo 44 4 3 3 Segmentation by Reshaping Algorithms 45 4 4 Object Levels and Segmentation saoo 47 4 4 1 About Hierarchical Image Object Levels 47 4 4 2 Creating an Image Object Level oaoa 47 4 4 3 Creating Object Levels With Segmentation Algorithms 48 4 4 4 Duplicating an Image Object Level nonoa 49 4 4 5 Editing an Image Object Level or Level Variable 49 4 4 6 Deleting an Image Object Level 0 50 4 5 Getting Information on Image Objects osoa 51 4 5 1 The Image Object Information Window 51 45 2 The Feature View Window o e s cc soc es aeo e e 52 4 5 3 Editing the Feature Distance o oo 57 4 5 4 Comparing Objects Using the Image Object Table
100. an be utilized to provide texture information about an image object for example the relative area covered by sub objects of a certain classification Further texture features are provided by Texture after Haralick These features are based upon the co occurrence matrix which is created out of the pixels of an object The calculation of Haralick texture features can require considerable processor power since for every pixel of an object a 256 x 256 matrix has to be calculated en wikipedia org wiki Co occurrence_matrix 27 September 2012 User Guide Basic Rule Set Editing 57 4 5 3 Editing the Feature Distance Some features may be edited to specify a distance relating two image objects There are different types of feature distances e The level distance between image objects on different image object levels in the image object hierarchy e The spatial distance between objects on the same image object level in the image object hierarchy e The process distance between a process and the parent process in the process hier archy The feature distance can be edited in the same way 1 Go to the Image Object Information window or the Feature View window 2 To change the feature distance of a feature right click it and choose Edit on the context menu The name of the feature dialog box with the same name as the feature opens 3 Select the Distance parameter and click in the Value column to edit the Distance box Use the
101. an close the current action library and open another to get access to another col lection of analysis actions To close the currently open action library choose Library gt Close Action Library from the main menu The action groups in the upper pane of the Analysis Builder window disappear When closing an action library with an assembled solution the solution is removed from the upper pane of the Analysis Builder window If it is not saved it must be reassembled User Guide 27 September 2012 220 Developer XD 2 0 4 Assembling a Solution from Actions in the Analysis Builder In the Analysis Builder window you assemble a solution from actions and configure them in order to analyze your data If not already visible open the Analysis Builder window Analysis Builder Cellenger Library General Settings 26 Detection of Nuclei DAPI Hoechs 26 Classify Nuckiin Populations by Brightness Add new Special Task Expodt Resuk Image Figure 10 8 Analysis Builder window displaying sample data of an application library 1 To add an action click the button with a plus sign on the sub section header or in an empty section click Add New The Add Action dialog box opens 2 Select an action from the Add Action dialog box and click OK The new action is added to the solution According to the type of the action it is sorted in the corresponding group The order of the actions is defined by the system and cannot be changed
102. anar Projection 3D Image Object MPR Comparison View The Multi Planar Preprojection MPR Comparison View is two vertically arranged displays of the same projection It is designed to enable you to view two different maps or to display different view settings If you are viewing only one map you can also access the split viewing modes available in the Window menu XY amp XZ displays a vertical side by side view XY amp YZ displays a vertical side by side view MPR Comparison View as previously summarized but displayed horizontally XY amp XZ displays horizontal side by side view XY amp YZ displays horizontal side by side view MPR displays the multi planar reprojection including 3D image objects Comparison View Displays two vertical groups with one of each planar projec tions in each group This display enables you to view a different map in each group The two groups synchronize independently of each other Displaying Image Objects in 3D Select one or more classes of image objects to display in the 3D image objects display This display renders the surface of the selected image objects in their respective class colors 1 To display image objects in 3D click the Window layout button in the 3D Settings toolbar and select the 3D Image Objects button or the Multi Planar Reprojection button to open the 3D image objects display User Guide 27 September 2012 26 Developer XD 2 0 4 2 Click the Class filter bu
103. and minus buttons expand and collapse folders 4 Click OK to import scenes The tree view on the left hand pane of the Workspace window displays the file structure of the new projects each of which administrate one scene Ne Supported Import Templates 27 September 2012 User Guide Automating Data Analysis 187 import Scenes Import Template Root Folder of image Oste O tWorling Fobder Acton te ary Action brary Preview Now Workspace biy Figure 9 2 Import Scenes dialog box Cell 1087 0 Processe S wt 1037 HT500367_0 Se Al fm At Figure 9 3 Folder structure in the Workspace window e You can use various import templates to import scenes Each import template is provided by a connector Connectors are available according to which edition of the Definiens Server you are using e Generic import templates are available for simple file structures of import data When using generic import templates make sure that the file format you want to import is supported e Import templates provided by connectors are used for loading the image data ac cording to the file structure that is determined by the image reader or camera pro ducing your image data e Customized import templates can be created for more specialized file structures of import data e A full list of supported and generic image formats is available in the accompanying volume Supported Connectors and Drivers Displaying Stat
104. as an individual project in the workspace Workspace automation can only be carried out in a workspace Scene Copy A scene copy is a duplicate of a project with image layers and thematic layers but without any results such as image objects classes or variables If you want to transfer results to a scene copy you might want to use maps Otherwise you must first export a thematic layer describing the results Scene copies are regular scene copies if they have been created at the same magnification or resolution as the original image top scene A rescaled scene copy is a copy of a scene at a higher or lower magnification or resolution To create a regular or rescaled scene copy you can e Use the Create Scene Copy dialog described in the next section for manual cre ation 27 September 2012 User Guide Advanced Rule Set Concepts 163 e Use the Create Scene Copy algorithm within a rule set for details see the Devel oper XD Reference Book The scene copy is created as a sub scene below the project in the workspace Scene Subset A scene subset is a project that contains only a subset area region of interest of the orig inal scene It contains all image layers and thematic layers and can be rescaled Scene subsets used in workspace automation are created using the Create Scene Subset algo rithm Depending on the selected image object domain of the process you can define the size and cutout position e Based on co ordi
105. ation Successful Nearest Neighbor classification usually requires several rounds of sample se lection and classification It is most effective to classify a small number of samples and then select samples that have been wrongly classified Within the feature space mis classified image objects are usually located near the borders of the general area of this class Those image objects are the most valuable in accurately describing the feature space region covered by the class To summarize 27 September 2012 User Guide About Classification 103 Class Description Name Display x class d E M Aways E Parent class foe display Modifiers class c X l Shared Abstract Inactive Al Contained Inherited Contained and fmin y Standard nearest neighbor generated Mean Layer 1 Mean Layer 2 Mean Layer 3 Mean Layer 4 Mean Layer 5 Mean Layer 6 Mean Layer 7 Figure 6 22 The Class Description Dialog Box 1 Insert Standard Nearest Neighbor into the class descriptions of classes to be con sidered 2 Select samples for each class initially only one or two per class 3 Run the classification process If image objects are misclassified select more sam ples out of those and go back to step 2 Optimizing the Feature Space Feature Space Optimization is an instrument to help you find the combination of features most suitable for separating classes in conjunction with a nearest neighbor classifier It
106. ation of an image object Linked Object Features Linked Object features are calculated by evaluating linked objects themselves Scene Features Scene features return properties referring to the entire scene or map They are global because they are not related to individual image objects and are grouped as follows e Variables are global variables that exist only once within a project They are inde pendent of the current image object e Class Related scene features provide information on all image objects of a given class per map e Scene Related features provide information on the scene Process Related Features Process related features are image object dependent features They involve the relation ship of a child process image object to a parent process They are used in local processing A process related features refers to a relation of an image objects to a parent process ob ject PPO of a given process distance in the process hierarchy Commonly used process related features include Border to PPO The absolute border of an image object shared with its parent pro cess object Distance to PPO The distance between two parent process objects Elliptic dist from PPO is the elliptic distance of an image object to its parent process object PPO Same super object as PPO checks whether an image object and its parent process object PPO are parts of the same superobject Rel border to PPO is the ratio of the border leng
107. atures Feature Type Ede Copy Delete Figure 7 30 Manage Customized Features dialog box Clicking the Add button launches the Customized Features dialog box which allows you to create a new feature The remaining buttons let you to edit copy and delete features 7 7 2 Arithmetic Customized Features The procedure below guides you through the steps you need to follow when you want to create an arithmetic customized feature Open the Manage Customized Features dialog box and click Add Select the Arithmetic tab in the Customized Features dialog box 1 Insert a name for the customized feature and click on the map pin icon to add any comments if necessary 2 The Insert Text drop down box lets you add patterns for ruleset objects allowing you to assign more meaningful names to customized features which reflect the names of the classes and layers involved The following feature values are avail able class name image layer name thematic layer name variable value variable name level name feature value Selecting lt automatic gt displays the arithmetic expression itself 3 Use the calculator to create the arithmetic expression You can e Type in new constants e Select features or variables in the feature tree on the right e Choose arithmetic operations or mathematical functions 4 To calculate or delete an arithmetic expression highlight the expression with the cursor and then click either Calculate or Del
108. ayed in the Generate Point window e Enter the point s x and y co ordinates in the Generate Point dialog box and click Add Point to generate the point The point objects can touch any existing image object To delete the point whose co ordinates are displayed in the Generate Point dialog box press Delete Point Generate Point x coordinate Y coordinate Figure 7 6 The Generate Point dialog box Generating Thematic Objects from Image Objects Thematic objects can be created from the outlines of selected image objects This function can be used to improve a thematic layer new thematic objects are added to the Thematic Layer Attribute Table Their attributes are initially set to zero 1 Select a polygon layer for thematic editing If a polygon layer does not exist in your map create a new thematic polygon layer 27 September 2012 User Guide Advanced Rule Set Concepts 125 2 Activate the Generate Thematic Object Based on Image Object button on the Man ual Editing toolbar 3 In the map view select an image object and right click it From the context menu choose Generate Polygon to add the new object to the thematic layer 4 To delete thematic objects select them in the map view and click the Delete Se lected Thematic Objects button NOTE Use the Classify Selection context menu command if you want to classify image objects manually Note that you have to Select a Class for Manual Classification with activat
109. ayers metadata or scaling geocoding is detected automatically go to File gt Load Image File in the main menu Import Image Layer a Drives Al Share on definiens local I IC Avo Imaces lt Local Disk C B lt Data D DVD RW Drive Network Drives IC Earth AG I Groups SS instaliinput on cox64 ey Life Hours S pbrookes on Dataimuc IE Marketina PS Workspaces Preview amp not avaigble Pubic Name M Folder 1 34Lanalysis test C11 w233734080 R Folder 1 84Lanalysis test C11 w3AOC26EE8 W Folder 1 94 Lanalysis test C11 w4046ACC13 M Folder 1 84Lanalysis test 002 w17A2SFF3A M Folder 1 841 analysis test D02 w2800FBA4C M Folder 1 84Lanalysis test D02 w33A9F9968 Mi Folder 1 841 analysis test D02 w4SEDAS6964 Ri Folder 1 841 analysis test D03 wi78C2FCFS4 M Folder 1 841 analysis test D03 w2607283EC Mi Folder 1 841 analysis test 003 w380450508 Mi Folder 1 841 analysis test D03 w4A6262899 M Folder 1 841 analysis test 004 wiASESA6S7 4 M Folder 1 841 analysis test D04 w27A4A 1690 M Folder 1 84 Lanalysis test D04 w384657882 M Folder 1 841 analysis test D04 w442E2924 lt Mi Folder 1 841 analysis test DOS w1AC72A4854 M Folder 1 34 Lanalysis test DOS w2306530C8 Ri Folder 1 841 analysis test DOS w3A66B1F3A M Folder 1 84 Lanalysis test DOS w43 S6F320 W Folder 1 841 enalysis test DOS w105800896 t M Folder 1 841 analysis test D06 w22 204105 M Folder 1 841 anal
110. b objects of an object and the feature values of a selected class Note that the feature values are weighted by either by the border length distance 0 or by the area distance gt 0 of the respective image objects 7 7 4 Saving and Loading Customized Features You can save customized features separately for use in other rule sets 3 e Open the Tools menu in the main menu bar and select Save Customized Features to open the Save Customized Features dialog box Your customized features are saved as a duf file e To load customized features that have been saved as a duf file open the Tools menu and select Load Customized Features to open the Load Customized Features dialog box 7 7 5 Finding Customized Features You can find customized features at different places in the feature tree depending on the features to which they refer For example a customized feature that depends on an object feature is sorted below the group Object Features gt Customized If a customized feature refers to different feature types they are sorted in the feature tree according to the interdependencies of the features used For example a customized feature with an object feature and a class related feature displays below class related features 7 7 6 Defining Feature Groups You may wish to create a customized feature and display it in another part of the Feature Tree To do this go to Manage Customized Features and press Edit in the Feature Group pane
111. b of the 2D Scatter Plot window In the tree view select the feature you want to display on the x axis Click X Axis The value of the image objects for the selected feature is displayed in the 2D Scatter Plot Select the feature for the Y Axis and click the respective button You can change the selection any time by selecting a new feature and placing it on either axis 27 September 2012 User Guide Basic Rule Set Editing 61 6 To switch axes select the feature currently displayed on the x axis and click the Y Axis button Do likewise for the feature on the other axis Filtering the 2D Scatter Plot by Classes By default the 2D Scatter Plot displays all classes You can select or deselect classes to reduce the number value dots on the 2D Scatter Plot Open the Classes tab of the 2D Scatter Plot window From the Level list select a specific level or leave the entry to All Levels Click Select Classes to open the Edit Classification Filter dialog box Select a class To select more than one class press the Ctrl key while clicking Click OK to apply the filter The 2D Scatter Plot displays only the selected classes To view all classes available in the project select Always Use All Classes To show all classes again press the Deselect All button in the Edit Classification Filter dialog box NYDN WN KF 4 5 6 Comparing Features Using the 2D Feature Space Plot This feature allows you to analyze the correlation of
112. ble Editing Image Layer Mixing for Thumbnails You can change the way thumbnails display in the Heat Map window and in the Thumbnail Views of the workspace 1 2 Right click on the Heat Map window or go to View gt Thumbnail Settings to open the Thumbnail Settings dialog box figure 2 12 Choose among different layer mixes in the Layer Mixing drop down list The One Layer Gray preset displays a layer in grayscale mode with the red green and blue together The three layer mix displays layer 1 in the red channel layer 2 in green and layer 3 in blue Choose six layer mix to display additional layers User Guide 27 September 2012 18 Developer XD 2 0 4 Figure 2 11 Layer Mixing presets from left to right One Layer Gray Three Layer Mix Six Layer Mix Thumbnail Settings Figure 2 12 Thumbnail Settings dialog box 3 Using the Equalizing drop down box and select a method that gives you the best display of the objects in the thumbnails 4 If you select an equalization method you can also click the Parameter button to changing the equalizing parameters The Layer Visibility Flag It is also possible to change the visibility of individual layers and maps The Manage Aliases for Layers dialog box is shown in figure 2 13 on the next page To display the dialog go to Process gt Edit Aliases gt Image Layer Aliases or Thematic Layer Aliases Hide a layer by selecting the alias in the left hand column and unchecking the
113. border of a superobject is consistent with the borders of its sub objects The area represented by a specific image object is defined by the sum of its sub objects areas Definiens technology accomplishes this quite easily because the segmentation techniques use region merging algorithms For this reason not all the algorithms used to analyze images allow a level to be created below an existing one Each image object level is constructed on the basis of its direct sub objects For example the sub objects of one level are merged into larger image objects on level above it This merge is limited by the borders of exiting superobjects adjacent image objects cannot be merged if they have different superobjects 4 4 3 Creating Object Levels With Segmentation Algorithms You can create an image object level by using some segmentation algorithms such as multiresolution segmentation multi threshold or spectral difference segmentation The relevant settings are in the Edit Process dialog box e Go to the drop down list box within the Image Object Domain group box and select an available image object level To switch to another image object level select the 27 September 2012 User Guide Basic Rule Set Editing 49 currently active image object level and click the Parameters button to select another image object level in the Select Level dialog box e Insert the new image object level either above or below the one selected in the image object l
114. by thematic layers if these are present Class Related Features Class related features are dependent on image object features and refer to the classes assigned to image objects in the image object hierarchy This location is specified for superobjects and sub objects by the levels separating them For neighbor image objects the location is specified by the spatial distance Both these distances can be edited Class related features are grouped as follows e Relations to Neighbor Objects features are used to describe an image object by its relationships to other image objects of a given class on the same image object level e Relations to Sub Objects features describe an image object by its relationships to other image objects of a given class on a lower image object level in the image User Guide 27 September 2012 54 Developer XD 2 0 4 object hierarchy You can use these features to evaluate sub scale information be cause the resolution of image objects increases as you move down the image object hierarchy Relations to Superobjects features describe an image object by its relations to other image objects of a given class on a higher image object level in the image object hi erarchy You can use these features to evaluate super scale information because the resolution of image objects decreases as you move up the image object hierarchy Relations to Classification features are used to find out about the current or poten tial classific
115. can be edited everywhere where the feature is listed but always applies to every use of this feature for example in rule sets image object information and classes All geometry related features such as distance to let you specify units for exam ple pixels metrics or the same as project unit value When using Object Features gt Position you can choose to display user co ordinates same as project unit or co ordinates Selecting pixel uses the pixel image co ordinate system In Customized Arithmetic Features the set calculation unit applies to numbers not the used features Be aware that customized arithmetic features cannot mix co ordinate features with metric features for example m 00 Amin 0er Would Length m require two customized arithmetic features Since same as project unit might vary with the project we recommend using absolute units 119 120 Developer XD 2 0 4 7 2 Thematic Layers and Thematic Objects Thematic layers are raster or vector files that have associated attribute tables which can add additional information to an image For instance a satellite image could be combined with a thematic layer that contains information on the addresses of buildings and street names They are usually used to store and transfer results of analyses Thematic vector layers comprise only polygons lines or points While image layers con tain continuous information
116. cannot be undone e The Delete command can be used to delete individual processes If you delete a parent process you will be asked whether or not you wish to delete any sub processes child processes as well CAUTION Delete Rule Set eliminates all classes variables and cus tomized features in addition to all single processes Consequently an existing image object hierarchy with any classification is lost 4 2 10 Editing Using Drag and Drop You can edit the organization of the Process Tree by dragging and dropping with the mouse Bear in mind that a process can be connected to the Process Tree in three ways e As a parent process on a higher hierarchical level e As a child process on a lower hierarchy level e As an appended sibling process on the same hierarchy level To drag and drop go to the Process Tree window e Left click a process and drag and drop it onto another process It will be appended as a sibling process on the same level as the target process e Right click a process and drag and drop it onto another process It will be inserted as a child process on a lower level than the target process User Guide 27 September 2012 42 Developer XD 2 0 4 4 3 Creating Image Objects Through Segmentation Commonly the term segmentation means subdividing entities such as objects into smaller partitions In Developer XD it is used differently segmentation is any opera tion that creates new image objects or alte
117. cases We recommend using the default settings when importing the data rather than trying to modify them 7 9 5 Displaying Maps In order to display different maps in the Map View switch between maps using the drop down box at the top of the Developer XD client to display several maps at once use the Split commands available under Window in the main menu 7 9 6 Synchronizing Maps When working with multi scale or multi project maps you will often want to transfer a segmentation result from one map to another The Synchronize Map algorithm allows you to transfer an image object hierarchy using the following settings e The source map is defined in the image object domain Select the image object level map and if necessary classes conditions and source region e With regard to the target map set the map name target region level class and condition If you want to transfer the complete image object hierarchy set the value to Yes 27 September 2012 User Guide Advanced Rule Set Concepts 161 Synchronize Map is most useful when transferring image objects of selected image object levels or regions When synchronizing a level into the position of a super level then the relevant sub objects are modified in order to maintain a correct image object hierarchy Image layers and thematic layers are not altered when synchronizing maps 7 9 7 Saving and Deleting Maps Maps are automatically saved when saving the project Maps are del
118. cessary to edit these parameters These are necessary for integration with the Definiens Image Miner product Rule Set Name Rule Set Description Rule Set Author Rule Set Version It is possible to add scene variables to the default parameter set when you open a De veloper XD workspace in Image Miner these will appear as editable parameters in the Submit Analysis algorithm in Image Miner 27 September 2012 User Guide Advanced Rule Set Concepts 135 7 4 Arrays The array functions in Developer XD let you create lists of features which are accessi ble from all rule set levels This allows rule sets to be repeatedly executed across for example classes levels and maps 7 4 1 Creating Arrays The Manage Arrays dialog box figure 7 18 can be accessed via Process gt Manage Ar rays in the main menu The following types of arrays are supported numbers strings classes image layers thematic layers levels features regions map names To add an array press the Add Array button and select the array type from the drop down list Where arrays require numerical values multiple values must be entered individually by row Using this dialog array values made up of numbers and strings can be repeated several times other values can only be used once in an array Additional values can be added using the algorithm Update Array which allows duplication of all array types When selecting arrays such as level and image lay
119. ch Detailed Analysis of Tiles Detailed Analysis If you want to transfer result information from one sub scene to another you can do so by exporting the image objects to thematic layers and adding this thematic layer then to the new scene copy Here you either use the Export Vector Layer or the Export Thematic Raster Files algorithm to export a geocoded thematic layer Add features to the thematic layer in order to have them available in the new scene copy After exporting a geocoded thematic layer for each subset copy add the export item names of the exported thematic layers in the Additional Thematic Layers parameter of the Create Scene Tiles algorithm The thematic layers are matched correctly to the scene tiles because they are geocoded Using the submit scenes for analysis algorithm you finally submit the tiles for further pro User Guide 27 September 2012 172 Developer XD 2 0 4 cessing to the subsequent subroutine Here you can utilize the thematic layer information by using thematic attribute features or thematic layer operations algorithms Likewise you can also pass parameter sets to new sub scenes and use the variables from these parameter sets in your image analysis Getting Sub Project Statistics in Nested Workspace Automation Sub scenes can be tiles copies or subsets You can export statistics from a sub scene analysis for each scene and collect and merge the statistical results of multiple files The advantage is
120. ck Open the new project is added to the right hand Workspace pane Creating a New Project Within a Workspace To add multiple projects to a workspace use the Import Scenes command To add an existing projects to a workspace use the Import Existing Project command To create a new project separately from a workspace close the workspace and use the Load Image File or New Project command 1 To create a new project within a workspace do one of the following e Go to the left pane of the Workspace window Right click a folder and if available choose Add Project from the context menu e Choose File gt New Project from the main menu e Choose File gt Load Image File from the main menu The Import Image Layers dialog box opens 2 Proceed in the same way as for creating separate projects 3 Click OK to create a project The new project is displayed in the right pane of the Workspace In the event of an unexpected processing failure the project automatically rolls back to the last workflow state This operation is documented as Automatic Rollback in the Remarks column of the Workspace window and as Roll Back Operation in the History dialog box 27 September 2012 User Guide Automating Data Analysis 195 Loading Scenes as Maps into a New Project Multi map projects can be created from multiple scenes in a workspace The preconditions to creating these are e Individual scenes to be loaded must include only one map e Scenes to be lo
121. clicking the tabs at the bottom of the window e Groups view allows you to assign a logical classification structure to your classes In the figure below a geographical view has been subdivided into land and sea the land area is further subdivided into forest and grassland Changing the organization of your classes will not affect other functions e Inheritance view allows class descriptions to be passed down from parent to child classes Double clicking a class in either view will launch the Class Description dialog box The Class Description box allows you to change the name of the class and the color assigned to it as well as an option to insert a comment Additional features are e Select Parent Class for Display which allows you to select any available parent classes in the hierarchy 83 84 Developer XD 2 0 4 Figure 6 1 The Class Hierarchy window displaying Groups and Inheritance views e Display Always which enables the display of the class for example after export even if it has not been used to classify objects e The modifier functions are Shared This locks a class to prevent it from being changed Shared image objects can be shared among several rule sets Abstract Abstract classes do not apply directly to image objects but only inherit or pass on their descriptions to child classes in the Class Hierarchy window they are signified by a gray ring around the class color Inactive classes are ignored in th
122. commonly used BEB This group of buttons allows you to select image view options offering views of layers classifications and any features you wish to visualize EE This group is concerned with displaying outlines and borders of image objects and views of pixels mi i l Y 27 September 2012 User Guide Starting Developer Il These toolbar buttons allow you to visualize different layers in grayscale or in RGB They also allow you to switch between layers and to mix them Zoom Functions Toolbar This region of the toolbar offers direct selection and the ability to drag an image along with several zoom options k Melo ojos AA View Navigate Toolbar The View Navigate folder allows you to delete levels select maps and navigate the object hierarchy B man Level 1 X t 4 Tools Toolbar The Tools toolbar allow access to advanced dialog boxes s Y P N m PE Cur Ba The buttons on the Tools toolbar launch the following dialog boxes and toolbars The Manual Editing Toolbar Manage Customized Features Manage Variables Manage Parameter Sets e Undo e Redo Save Current Project State Restore Saved Project State 2 5 2 Splitting Windows There are several ways to customize the layout in Developer XD allowing you to display different views of the same image For example you may wish to compare the results of a segmentation alongside the original image Selecting Window gt Split allows you to split
123. compares the features of selected classes to find the combination of features that pro duces the largest average minimum distance between the samples of the different classes Using Feature Space Optimization The Feature Space Optimization dialog box helps you optimize the feature space of a nearest neighbor expression To open the Feature Space Optimization dialog box choose Tools gt Feature Space Op timization or Classification gt Nearest Neighbor gt Feature Space Optimization from the main menu 1 To calculate the optimal feature space press Select Classes to select the classes you want to calculate Only classes for which you selected sample image objects are available for selection 2 Click the Select Features button and select an initial set of features which will later be reduced to the optimal number of features You cannot use class related features in the feature space optimization 3 Highlight single features to select a subset of the initial feature space User Guide 27 September 2012 104 Developer XD 2 0 4 Feature Space Optimization O Grassland General impervious General Weterbodies Woodland General 3 Standard deviation Layer 1 Standard deviation Layer 2 Standard deviation Layer 3 Max dit Raho Layer 1 Raho Layer 2 Ratin anar Select Features Show Distance Manie Number of selected features 12 v Optimization Image obiectievet Levelt asf Maximum dimension 5 Cakuste C
124. ct Classification gt Samples gt Create Samples from TTA Mask The Apply TTA Mask to Level dialog box opens 7 Select which level you want to apply the TTA mask information to If the project contains only one image object level this level is preselected and cannot be changed 8 In the Create Samples dialog box enter the Minimum Overlap for Sample Objects and click OK The default value is 0 75 Since a single training area of the TTA mask does not necessarily have to match an image object the minimum overlap decides whether an image object that is not 100 within a training area in the TTA mask should be declared a sample The value 0 75 indicates that 75 of an image object has to be covered by the sample area for a certain class given by the TTA mask in order for a sample for this class to be generated The map view displays the original map with sample image objects selected where the test area of the TTA mask have been 6 4 4 The Edit Conversion Table You can check and edit the linkage between classes of the map and the classes of a Train ing and Test Area TTA mask You must edit the conversion table only if you chose to keep your existing class hierarchy and used different names for the classes A TTA mask has to be loaded and the map must contain classes z Edit Conversion Table TTA Mask entry 1D Linked Class WoodandGeneral 1 Woodland General O GiasslandGereral 2 Grassland General impervious General 3 Impervious
125. ct can be displayed in the map view an image must be loaded and a segmentation must be applied to the map 1 To create a new feature right click in the Feature View window and select Man age Customized Features In the dialog box click Add to display the Customized Features box then click on the Relational tab 2 In this example we will create a new feature based on Min Pixel Value In the Feature Selection box this can be found by selecting Object Values gt Layer Values gt Pixel based gt Min Pixel Value 3 Under Min Pixel Value right click on Create New Min Pixel Value and select Create The relevant dialog box in this case Min Pixel Value figure 4 15 will open In this example the parameter value will be set to Nuclei 4 Depending on the feature and your project you must set parameter values Pressing OK will list the new feature in the feature tree The new feature will also be loaded into the Image Object Information window 5 Some features require you to input a unit which is displayed in parentheses in the feature tree By default the feature unit is set to pixels but other units are available You can change the default feature unit for newly created features Go to the Options dialog box and change the default feature unit item from pixels to same as project unit The project unit is defined when creating the project and can be checked and modified in the Modify Project dialog box User Gui
126. cted area shows the number of selected wells 2 To change the plate select the plate number or name from the Plate list 3 If existing you can change the site Click the up or down arrow of the Site list or enter the number of the desired site directly 4 To deselect all selected wells click on the plate between the wells Changing the selection of plates changes the display of the graph simultaneously 5 4 4 Define Plate Layout Define the wells used for negative and positive control or inactive wells which will be excluded from the analysis 1 To edit the layout of a plate click Layout tab in the Plate View window 2 Mark your controls and inactive wells e Click Negative Control or Positive Control to mark the selected wells respec tively Negative Control wells are displayed in red color positive control wells are blue e Click Inactive to exclude the selected wells from the analysis Inactive wells are displayed in gray color 3 To remove marks from a well select them and select Clear Marks User Guide 27 September 2012 82 Developer XD 2 0 4 6 7 S000000 N0000 OO0000 OO0000 000000 8 O s O O O O eeeeeee mwaOO000 moOOOO000 mOOO000 OO OO OO OO OO OO OO O0O00 800000000000 Figure 5 18 A sample plate map with marked wells 5 4 5 Save Plate Layout You can save the layout of a plate to a dp file 1 In the Plate View window define the layout as you wish
127. d a process with the algorithm submit scenes for analysis to the end of the main process tree It executes a subroutine that defines the detailed image analysis processing on a separate tab Process Tree BE chess board 50 creating New Level PL with Brightness lt 220 at New Level no_background sew loop no_background at New Level merge region no_background at New Level create subset process subsets with Subroutine Figure 9 8 The Main process tree in the Process Tree window Process Tree Detaled Image Analyses Processes a 4 p Mein A Subroutine Figure 9 9 A subroutine in the Process Tree window Use Case Advanced Transfer Results Transfer intermediate result information by exporting to thematic layers and reloading them to a new scene copy This subroutine use case presents an alternative for using the merging results parameters of the submit scenes for analysis algorithm because its intersection handling may result in performance intensive operations Here you use the export thematic raster files algorithm to export a geocoded thematic layer for each scene or subset containing classification information about intermediate results This information stored in a thematic layers and an associated attribute table is a description of the location of image objects and information about the classification of image objects After exporting a geocoded thematic layer for each subset copy you reload all the
128. d by the user of the action library 1 To create an action definition go to the Analysis Builder window select and right click any action group or the background and choose Add Action Definition or one of the standard export action definitions e Add Export Domain Statistics Standard export actions are predefined Therefore the underlying processes cannot be edited and some of the following options are unavailable User Guide 27 September 2012 216 Developer XD 2 0 4 11 e Add Export Object Data e Add Export Project Statistics e Add Export Result Image The new action definition item is added at the bottom of the selected action group If you have sequenced two actions or more in an action group you may rearrange them using the arrow buttons on the right of each action item To edit an item right click it and choose Edit Action Definition or double click the item The Action Definition dialog box opens The first two fields let you add a name and description and the Icon field gives an option to display an icon on the action user interface element Action ID allows a rule set to keep track of the structure of the analysis and returns the number of actions in the current analysis with a given ID The Group ID reflects the current group the action belongs to To move it select another group from the drop down list box Priority lets you control the sorting of action lists the higher the
129. d if it is selected in the parameters list For parameters based on scene variables you can also specify a default value This value is used to initialize a parameter when the customized algorithm is selected in the Edit Process dialog box 6 Configure the general properties of the customized algorithm in the Settings list e Delete Local Results specifies if local rule set items are deleted from the 27 September 2012 User Guide Advanced Rule Set Concepts 155 image object hierarchy when the customized algorithm terminates If set to No references from the image object hierarchy to local rule set objects are not automatically deleted This will result in a faster execu tion time when the customized algorithm is called Make sure that you clean up all references to local objects in the code of your customized algorithm to avoid references to local objects in the image object hierar chy If set to Yes all references from local image objects are automatically deleted after execution of the customized algorithm This applies to clas sifications with local classes local image object levels and local image object layers e Domain Handling specifies the handling of the selected image object domain by the calling process Invoke algorithm for each object The customized algorithm is called for each image object in the image object domain of the calling process This setting is recommended for customized algorithms designed to b
130. de 27 September 2012 7 8 56 Developer XD 2 0 4 Min pixel value Parameter Valse DES EALE TE Layer 1 Microtubules L 2 Golg Apparatus Layer 3 Nucle Figure 4 15 Feature dialog box for creating a new feature from the Select Displayed Fea tures dialog box Thematic Attributes Thematic attributes can only be used if a thematic layer has been imported into the project If this is the case all thematic attributes in numeric form that are contained in the attribute table of the thematic layer can be used as features in the same manner as you would use any other feature Object Oriented Texture Analysis Object oriented texture analysis allows you to describe image objects by their texture By looking at the structure of a given image object s sub objects an object s form and texture can be determined An important aspect of this method is that the respective segmentation parameters of the sub object level can easily be adapted to come up with sub objects that represent the key structures of a texture A straightforward method is to use the predefined texture features provided by Definiens Developer XD 2 0 4 They enable you to characterize image objects by texture deter mined by the spectral properties contrasts and shape properties of their sub objects Another approach to object oriented texture analysis is to analyze the composition of classified sub objects Class related features relations to sub objects c
131. dialog box figure 6 7 You can then right click on this window select Insert Class then create a new class using the same method outlined in the preceding section The Assign Class Algorithm The Assign Class algorithm is a simple classification algo rithm which allows you to assign a class based on a threshold condition for example brightness e Select Assign Class from the algorithm list in the Edit Process dialog box e Select a feature for the condition via the Threshold Condition parameter and define your feature values In the Algorithm Parameters pane opposite Use Class select a class you have previously created or enter a new name to create a new one this will launch the Class Description dialog box User Guide 27 September 2012 86 Developer XD 2 0 4 Editing the Class Description You can edit the class description to handle the features describing a certain class and the logic by which these features are combined 1 Open a class by double clicking it in the Class Hierarchy window 2 To edit the class description open either the All or the Contained tab 3 Insert or edit the expression to describe the requirements an image object must meet to be member of this class Inserting an Expression A new or an empty class description contains the and min operator by default s e not wa Insert new Expression EZ Rel b Edit Expression Evaluate undefined Invert Expression Figure 6 4 Con
132. dit Process box select Delete Image Object Level and enter your chosen parameters 4 2 8 Undoing Edits It is possible to go back to a previous state by using the undo function which is located in Process gt Undo a Redo command is also available These functions are also available 27 September 2012 User Guide Basic Rule Set Editing 41 as toolbar buttons using the Customize command You can undo or redo the creation modification or deletion of processes classes customized features and variables However it is not possible to undo the execution of processes or any operations relating to image object levels such as Copy Current Level or Delete Level In addition if items such as classes or variables that are referenced in rule sets are deleted and then undone only the object itself is restored not its references It is also possible to revert to a previous version p 194 Undo Options You can assign a minimum number of undo actions by selecting Tools gt Options in addition you can assign how much memory is allocated to the undo function although the minimum number of undo actions has priority To optimize memory you can also disable the undo function completely 4 2 9 Deleting a Process or Rule Set Right clicking in the Process Tree window gives you two delete options e Delete Rule Set deletes the entire contents of the Process Tree window a dialog box will ask you to confirm this action Once performed it
133. e Book Importing Polygon Shapefiles The polygon shapefile shp which is a common format for geo information systems will import with its corresponding thematic attribute table file dbf file automatically For all other formats the respective attribute table must be specifically indicated in the Load Attribute Table dialog box which opens automatically Polygon shapefiles in 2D and 3D scenes are supported From the Load Attribute Table dialog box choose one of the following supported formats e txt ASCII text files e dbf Dbase files e csv comma separated values files When loading a thematic layer from a multi layer image file for example an img stack file the appropriate layer that corresponds with the thematic information is requested in 27 September 2012 User Guide Advanced Rule Set Concepts 121 the Import From Multi Layer Image dialog box Additionally the attribute table with the appropriate thematic information must be loaded If you import a thematic layer into your project and Developer XD does not find an appropriate column with the caption ID in the respective attribute table the Select ID Column dialog box will open automatically Select the caption of the column containing the polygon ID from the drop down menu and confirm with OK Select ID column dg Cannot find 1D column in attribute table yokosuka_ms IMG Pleate insert ID column heading ROW NUMBER lt Cro Figure 7 1 The
134. e used with the execute image object domain Pass domain from calling process as parameter The customized al gorithm is called only once from the calling process The selected image object domain can be accessed by the special from calling process do main within processes of the customized algorithm 7 Confirm with OK The processes of the customized algorithm are displayed on a separate Customized Algorithms tab of the Process Tree window figure 7 34 8 Customized algorithms can be selected at the bottom of the algorithm drop down list box in the Edit Process dialog box The local classes are displayed in explicit sections within the Class Hierarchy window whenever the customized algorithm is selected figure 7 35 9 The map pin symbol at the top right of the dialog box lets you add a comment to the customized algorithm This comment will be visible in the Process Tree It will also be visible in the Algorithm Description field of the Edit Process dialog when the customized algorithm is selected in the algorithm drop down box auto threshold segment adon using Gomera onvat New Level ote tretreauto threshold on Layer 1 ety at Mew Levent dark lt m hitrih lt bright on Layer 1 tty wath Number of paeis lt man da site of New Levelt remove atjects aE auto thresheld segmentation using Gomara Layer layer Class Sark Class Bright Variable Wan object see trom calling process obi Irsh ate tweshokd on la
135. e Feature Space with Nearest Neighbor Expressions To define feature spaces Nearest Neighbor NN expressions are used and later applied to classes Developer XD distinguishes between two types of nearest neighbor expressions User Guide 27 September 2012 100 Developer XD 2 0 4 Membership value Membership value 0 9 0 8 0 7 0 6 Assigned Membership Value 0 5 5 04 0 3 0 2 0 1 0 0 2 0 4 0 6 08 1 1 2 1 4 1 6 1 8 2 Feature 1 Feature space distance of image object to be classified to sample Figure 6 17 Membership function created by Nearest Neighbor classifier 0 9 0 8 0 7 0 6 0 5 pect to class blue 0 4 0 3 0 2 0 1 Sample Sample Image Object Sample Feature 1 Figure 6 18 Membership function showing Class Assignment in one dimension e Standard Nearest Neighbor where the feature space is valid for all classes it is assigned to within the project e Nearest Neighbor where the feature space can be defined separately for each class by editing the class description 1 From the main menu choose Classification gt Nearest Neighbor gt Edit Standard NN Feature Space The Edit Standard Nearest Neighbor Feature Space dialog box opens 2 Double click an available feature to send it to the Selected pane Class related features only become available after an initial classification 3 To remove a feature double click it in the Selected pane 4 Use feature spac
136. e any other algorithm you use them in processes added to your rule set in the same way and you can delete them in the same ways They are grouped as Customized in the Algorithm drop down list of the Edit Process dialog box You use them in processes added to your rule set in the same way and you can delete them in the same ways They are grouped as Customized in the Algorithm drop down list of the Edit Process dialog box If a customized algorithm contains parameters you can set the values in the Edit Process dialog box 7 8 6 Modifying a Customized Algorithm You can edit existing customized algorithms like any other process sequence in the soft ware That is you can modify all properties of the customized algorithm using the Cus tomized Algorithm Properties dialog box To modify a customized algorithm select it on the Customized Algorithms tab of the Process Tree window Do one of the following to open the Customized Algorithm Properties dialog box e Double click it e Select Process gt Process Commands gt Edit Customized Algorithm from the main menu e In the context menu select Edit Customized Algorithm 27 September 2012 User Guide Advanced Rule Set Concepts 157 7 8 7 Executing a Customized Algorithm for Testing You can execute a customized algorithm or its child processes like any other process sequence in the software Select the customized algorithm or one of its child processes in the Customized Algo rithm tab
137. e classification process in the Class Hierar chy window they are denoted by square brackets Use Parent Class Color activates color inheritance for class groups in other words the color of a child class will be based on the color of its parent When this box is selected clicking on the color picker launches the Edit Color Brightness dialog box where you can vary the brightness of the child class color using a slider Class Description Figure 6 2 The Class Description Dialog Box 27 September 2012 User Guide About Classification 85 Creating and Editing a Class There are two ways of creating and defining classes directly in the Class Hierarchy win dow or from processes in the Process Tree window Creating a Class in the Class Hierarchy Window To create a new class right click in the Class Hierarchy window and select Insert Class The Class Description dialog box will appear Class Description Nome Paver class tor daphay Nucia AJ Cortsined s Inherted Contaned Figure 6 3 The Class Description Window Enter a name for your class in the Name field and select a color of your choice Press OK and your new class will be listed in the Class Hierarchy window Creating a Class as Part of aProcess Many algorithms allow the creation of a new class When the Class Filter parameter is listed under Parameters clicking on the value will display the Edit Classification Filter
138. e image object level If a value is specified it refers to the distance between an object s center of mass and the parent s center of mass up to that specified threshold Sub objects Objects whose image area covers all or part of the parent s image area and lie a specified number of image object levels below the parent s image object level Super objects Objects whose image area covers some or all of the parent s image area and lie a specified number of image object levels above the parent s image object level Note that the child image object is on top here 7 5 2 Child Domains and Parent Processes Terminology Below is a list of terms used in the context of process hierarchy Parent process A parent process is used for grouping child processes together in a process hierarchy Child process A child process is grouped on a level beneath a parent process in the hierarchy Child domain subdomain An image object domain defined by using one of the four local processing options Parent process object PPO A parent process object PPO is the object defined in the parent process Parent Process Objects A parent process object PPO is an image object to which a child process refers and must first be defined in the parent process An image object can be called through the respective selection in the Edit Process dialog box go to the Image Object Domain group box and select one of the four local processing options from
139. e optimization to combine the best features 27 September 2012 User Guide About Classification 101 Sample of class blue Sample of class red Area in which image objects will be classified Feature 2 blue Shading corresponds to Nearest Neighbor membership value Feature 1 Figure 6 19 Membership function showing Class Assignment in two dimensions Samples are represented by small circles Membership values to red and blue classes correspond to shading in the respective color whereby in areas in which object will be classified red the blue membership value is ignored and vice versa Note that in areas where all membership values are below a defined threshold 0 1 by default image objects get no classification those areas are colored white in the graph Edit Standard Nearest Neighbor Feature Space Object features Clase Related features Linked Object features Linked objects count Linked objects statistics Link weight to PPO Scene features Variables T Class Related Scene Related Process Related features Region features Image Registration features Metadata Feature Variables see e e POG eee oe Figure 6 20 The Edit Standard Nearest Neighbor Feature Space dialog box User Guide 27 September 2012 102 Developer XD 2 0 4 Applying the Standard Nearest Neighbor Classifier Apply Standard Nearest Neighbor to Classes Selected classes dones ta Cogis
140. e procedure as shown before with the PPO 0 gt Features A Cisssification te new Rel border to PPO ew Boeder to PPO ed e new ratio PPO new Gif PPO Mean Layer 2 diff PPO 0 Mean Layer 3 diff PPO 1 Mean Diff to neighbors abs legacy feature up to V4 0 Layer 1 0 diff PPO 1 Mean Layer 3 dif PPO 2 Figure 7 26 Compare the difference between the red highlighted image object and the green highlighted parent process object PPO 7 7 Customized Features Customized features can be arithmetic or relational relational features depend on other features All customized features are based on the features shipped with Definiens De veloper XD 2 0 4 e Arithmetic features are composed of existing features variables and constants which are combined via arithmetic operations Arithmetic features can be com posed of multiple features e Relational features are used to compare a particular feature of one object to those of related objects of a specific class within a specified distance Related objects are surrounding objects such as neighbors sub objects superobjects sub objects of a superobject or a complete image object level Relational features are composed of only a single feature but refer to a group of related objects User Guide 27 September 2012 144 Developer XD 2 0 4 Edit Process s E Define o weity ct goning and maring methods and wpecly in dete ha condors ko
141. e right hand column You can also load or save metadata in the form of XML files MeteData Conversion Metadata name Metadate F Inet Value Conrvernon External 8 8 SUDE_VERSION SUDE NAME PROJECT NAME SUDE_ID IMAGE NUMBER IMAGENUMBER_Y CURRENT SUDE VERSION IMAGE_OVERLAP_MICROMETERS_ gt IMAGE_OVERLAP_MICROMETERS_Y SUDE_POSITION_X SUDE POSTION Y SUDE CONTENT SUDE_CREATIONDATE TIME PHISICAL_ MAGNIFY CAMERA_TYPE ADAPTER_SCE OPTOVAR_SCE OBJECTIVE MAGNIFICATION SUDE_TYPE Camersinage Omron Perde VIMSUDE CP BRIGHTNESS ALL SeanMetaData Gormsen Load Seve Figure 4 23 The MetaData Conversion dialog box Customized Metadata Import If you are batch importing large amounts of image data then you should define metadata via the Customized Import dialog box figure 4 24 On the Metadata tab of the Customized Import dialog box you can load Metadata into the projects to be created and thus modify the import template with regard to the following options e Add and remove metadata e Define a special search string for metadata files for an explanation of search strings see Editing Search Strings and Scene Names If the image data contains User Guide 27 September 2012 64 Developer XD 2 0 4 Customized import Workspace image Layers Thematic Layers Metadata Scene ingot Name Customned inpor Poot Folder treme Developer Advanced Tharwg E 20 Moduse 3 image Rep
142. e same object are taken by different devices If you do not want to work with the image results of the image registration you can specify a parameter set defining an affine transformation between the source and target domains of the form ax b where a is the transformation matrix and b is the translation vector In case the transformation parameters are unknown to you you can create the corresponding parameter set using the image registration algorithm with affine transformation automatic by brightness Figure 7 46 Incoming and outgoing links over multiple time frames The red circles represent objects and the green arrows represent links Displaying Object Links By default all object links of an image object are outlined when selecting the image object in the Map View You can display a specific link class link direction or links within a maximal distance using the Edit Linked Object Visualization dialog Access the dialog in the Menu View Display Mode Edit Linked Object Visualization Deriving Object Link Statistics For creating statistics about linked objects Definiens Developer XD 2 0 4 provides Linked Objects Features e Linked Objects Count counts all objects that are linked to the selected object and that match the link class filter link direction and max distance settings e Statistics of Linked Objects provides statistical operations such as Sum or Mean over a Selected feature taking the set object link param
143. ed Image field and highlight the corresponding tile in the right side of the Workspace window e Double click a tile thumbnail to open it in the map view and highlight it in the right side of the Workspace window e Click the Show Group button to return to a display of the project thumbnails 7 Use the Display drop down list to view project or tile statistics 8 The Overview and Details buttons are used when there are workplace subsets Press Details to display subsets and Overview to move back up one level W 27 September 2012 User Guide Advanced Data Visualizations 231 Heat Map Large Squares Overview Dotais Figure 11 6 Heat Map window display with thumbnails of scenes Comparing Scene Statistics If you have an analyzed workspace open you can use the Heat Map window to compare scene statistics 1 Click the drop down arrow next to the Display field and select a result Result values will display as colors in the Heat Map window for each scene in the group You can adjust the transparency of the color overlay by moving the vertical slider at the bottom right of the window The features displayed are the features that have been configured for export 2 To change the range of values for the Heat Map enter numbers in the fields at either end of the color range at the bottom of the window or use the up and down arrows Select another result and the Heat Map will update automatically 4 If the selected scene is
144. ed Image object editing mode before hand Selecting Thematic Objects Manually by a I ah Image objects or thematic objects can be selected using these buttons on the Manual Editing toolbar From left to right e Single Selection Mode selects one object with a single click e Rectangle Selection selects all objects within a rectangle that you drag in the map view By default all objects that touch the selection polygon outline are included If you want to only include objects that are completely within the selection polygon change the corresponding setting in the Options dialog box Polygon Selection selects all objects that are located within the border of a polygon Click in the map view to set each vertex of the polygon with a single click To close an open polygon right click and choose Close Polygon By default all objects that touch the selection polygon outline are included Again if you only want objects within the selection change the corresponding setting in Options Line Selection selects all objects along a line A line can also be closed to form a polygon by right clicking and choosing Close Polygon All objects touching the line are selected Merging Thematic Objects Manually You can merge objects manually although this function only operates on the current image object level To merge neighboring objects into a new single object choose Tools gt Manual Editing gt Merge Objects from the main menu or pr
145. ed to vector shapefiles This enables them to be used with other maps or projects In the manual editing toolbar select Save Thematic Layer As which exports the layer in shp format Alternatively you can use the Export Results dialog box User Guide 27 September 2012 128 Developer XD 2 0 4 7 2 5 Using a Thematic Layer for Segmentation In contrast to image layers thematic layers contain discrete information This means that related layer values can carry additional information defined in an attribute list The affiliation of an object to a class in a thematic layer is clearly defined it is not possible to create image objects that belong to different thematic classes To ensure this the borders separating different thematic classes restrict further segmentation whenever a thematic layer is used during segmentation For this reason thematic layers cannot be given different weights but can merely be selected for use or not If you want to produce image objects based exclusively on thematic layer information you have to switch the weights of all image layers to zero You can also segment an image using more than one thematic layer The results are image objects representing proper intersections between the layers 1 To perform a segmentation using thematic layers choose one of the following seg mentation types from the Algorithms drop down list of the Edit Process dialog box e Multiresolution segmentation e Spectral differe
146. ee Options p 247 65 66 Developer XD 2 0 4 You can filter file names or file types using the File Name field To combine different conditions separate them with a semicolon for example tif 1las The File Type drop down list lets you select from a range of predefined file types The buttons at the top of the dialog box let you easily navigate between folders Pressing the Home button returns you to the root file system There are three additional buttons available The Add to Favorites button on the left lets you add a shortcut to the left hand pane which are listed under the Favorites heading The second button Restore Layouts tidies up the display in the dialog box The third Search Subfolders additionally displays the contents of any subfolders within a folder You can by holding down Ctrl or Shift select more than one folder Files can be sorted by name size and by date modified In the Load Image File dialog box you can 1 Select multiple files by holding down the Shift or Ctrl keys as long as they have the same number of dimensions 2 Access a list of recently accessed folders displays in the Go to Folder drop down list You can also paste a filepath into this field which will also update the folder buttons at the top of the dialog box 5 2 Creating a Project with Predefined Settings When you create a new project the software generates a main map representing the image data of a scene To prepare this y
147. ee into what other classes this image object would fit and possibly fine tune your settings To apply this function 1 In the Edit Process dialog box select classification from the Algorithm list and define the image object domain User Guide 27 September 2012 a 90 Developer XD 2 0 4 2 From the algorithm parameters select active classes that can be assigned to the image objects 3 Select Erase Old Classification to remove existing classifications that do not match the class description 4 Select Use Class Description if you want to use the class description for classifica tion Class descriptions are evaluated for all classes An image object is assigned to the class with the highest membership value 6 2 3 The Hierarchical Classification Algorithm The Hierarchical Classification algorithm is used to apply complex class hierarchies to image object levels It is backwards compatible with eCognition 4 and older class hierar chies and can open them without major changes The algorithm can be applied to an entire set of hierarchically arranged classes It applies a predefined logic to activate and deactivate classes based on the following rules 1 Classes are not applied to the classification of image objects whenever they contain applicable child classes within the inheritance hierarchy Parent classes pass on their class descriptions to their child classes These child classes then add additional feature descriptions and if
148. efining the source map to be copied you can e Copy the complete map e Copy a specific region source region e Copy a defined image object The third option creates a map that has the extent of a bounding box drawn around the image object You can create copies of any map and make copies of copies Developer XD maps can be copied completely or 2D subsets can be created Copying image layer or image objects to an already existing map overwrites it completely This also applies to the main map when it is used as target map Therefore image layers and thematic layers can be modified or deleted if the source map contains different image layers Use the Scale parameter to define the scale of the new map Keep in mind that there are absolute and relative scale modes For instance using magnification creates a map with a set scale for example 2x with reference to the original project map Using the Percent parameter however creates a map with a scale relative to the selected source map When downsampling maps make sure to stay above the minimum size which is 4x4x 1x1 x y z t In case you cannot estimate the size of your image data use a scale variable with a precalculated value in order to avoid inadequate map sizes User Guide 27 September 2012 160 Developer XD 2 0 4 Resampling is applied to the image data of the target map to be downsampled The Resampling parameter allows you to choose between the following two methods e Fast
149. egmentation Quadtree based segmentation is similar to chessboard segmentation but creates squares of differing sizes You can define an upper limit of color differences within each square using Scale Parameter After cutting an initial square grid the quadtree based segmenta tion continues as follows e Cut each square into four smaller squares if the homogeneity criterion is not met Example The maximal color difference within the square object is larger than the defined scale value e Repeat until the homogeneity criterion is met at each square gt Legend W Criterionnotmet DO Criterion met Figure 4 6 Quadtree based segmentation Following a quadtree based segmentation very homogeneous regions typically produce larger squares than heterogeneous regions Compared to multiresolution segmentation quadtree based segmentation is less heavy on resources Contrast Filter Segmentation Contrast filter segmentation is a very fast algorithm for initial segmentation and in some cases can isolate objects of interest in a single step Because there is no need to initially create image object primitives smaller than the objects of interest the number of image objects is lower than with some other approaches User Guide 27 September 2012 44 Developer XD 2 0 4 An integrated reshaping operation modifies the shape of image objects to help form coher ent and compact image objects The resulting pixel classification is stored in an
150. eir automatically determined regions of interest on the Editing tab for more information see Editing Cores on page 237 Check whether all cores have been correctly inserted into the grid The application automatically assigns each core to the cell containing its center An additional row marked with is created for all cores that couldn t be matched for example User Guide 27 September 2012 236 Developer XD 2 0 4 because the centers of two different cores can be found in the same cell You can correct the results by doing one of the following e Moving the cores within the grid When you select one of the cells in the TMA Grid View the corresponding core is automatically selected in the map view If the core has not been inserted at the correct place you can drag it into the correct position e Adjusting the grid on the slide by manually changing its size position or layout If you have made any changes to the grid or to the cores select Match Cores The TMA Grid View is updated with the new grid and core information To save the matching to a file select Save Matching under Save and Load Matching Matchings can be imported for other slides using the Load Matching button The Delete Unmatched function deletes all cores that are not matched signified by a In addition When creating cores those that would fall into cells with the label empty are directly moved to a row The Annotations pane allows you
151. eld and click Rename Nn Using Predefined Names In some cases it is helpful to define names of image object levels before they are assigned to newly created image object levels during process execution To do so use the Add Level button within the Edit Level Aliases dialog box e Depending on the selected algorithm and the selected image object domain you can alternatively use one of the following parameters e Level parameter of the image object domain group box e Level Name parameter in the Algorithm Parameters group box Instead of selecting any item in the drop down list just type the name of the image object level to be created during process execution Click OK and the name is listed in the Edit Level Aliases dialog box 4 4 6 Deleting an Image Object Level When working with image object levels that are temporary or are required for testing processes you will want to delete image object levels that are no longer used To delete an image object level do one of the following e Create a process using the Delete Image Object Level algorithm e Choose Image Objects gt Delete Levels from the main menu or use the button on the toolbar The Delete Level dialog box figure 4 11 will open which displays a list of all image object levels according to the image object hierarchy Select the image object level to be deleted you can press Ctrl to select multiple levels and press OK The selected image object levels will be removed
152. elect yes to activate window leveling p 18 by dragging the mouse with the right hand button held down Show hidden layer names Select yes or no to display hidden layers This setting also applies to any action libraries that are opened using other portals such as Architect XD and Tissue Studio 27 September 2012 User Guide Options 249 Show hidden layer Select yes or no to display hidden maps This setting also applies to maps any action libraries that are opened using other portals such as Architect XD and Tissue Studio Manual Editing Mouse wheel operation 2D images only Choose between zooming where the wheel will zoom in and out of the image and panning where the image will move up and down Snapping tolerance pxl Set the snapping tolerance for manual object selection and editing The default value is 2 Include objects on selection polygon outline Yes Include all objects that touch the selection polygon outline No Only include objects that are completely within the selection polygon Image view needs to be activated before mouse input Output Format Defines how mouse clicks are handled in the inactive image view If the value is set to Yes inactive image view is activated when clicked in the previously inactive image view If the value is No image view is activated and the currently active input operation is applied immediately for example image object is selected
153. eloper 13 Figure 2 4 Two images displayed using Layer View The left hand image is displayed in RGB while the right hand image displays the red layer only its RGB layers as outlined in the previous section against its appearance when View Classification is selected Clicking the Pixel View or Object Mean View button toggles between an opaque overlay in Object Mean View and a semi transparent overlay in Pixel View When in Pixel View a button appears at the bottom of the image window clicking on this button will display a transparency slider which allows you to customize the level of transparency Figure 2 5 An object for analysis displayed with all layers in Pixel View next to the same image in Classification View The colors in the right hand image have been assigned by the user and follow segmentation and identification of image objects Feature View The Feature View button may be deactivated when you open a project It becomes active when you select a feature in the Feature View window by double clicking on it Image objects are displayed as grayscale according to the feature selected figure 2 6 Low feature values are darker while high values are brighter If an object is red it has not been defined for the evaluation of the chosen feature Pixel View or Object Mean View This button switches between Pixel View and Object Mean View Object Mean View creates an average color value of the pixels in each object
154. ended for single image layers to display a visualization in rainbow colors Here the regular color range is converted to a color range between blue for darker pixel intensity values and red for brighter pixel intensity values Three Layer Mix displays layer one in the red channel layer two in green and layer three in blue e Six Layer Mix displays additional layers Change these settings to your preferred options with the Shift button or by clicking in the respective R G or B cell One layer can be displayed in more than one color and more than one layer can be displayed in the same color Individual weights can be assigned to each layer Clear the No Layer Weights check box and click a color for each layer Left clicking increases the layer s color weight while right clicking decreases it The Auto Update checkbox refreshes the view with each change of the layer mixing settings Clear this check box to show the new settings after clicking OK With the Auto Update check box cleared the Preview button becomes active Compare the available image equalization methods and choose one that gives you the best visualization of the objects of interest Equalization settings are stored in the workspace and applied to all projects within the workspace or are stored within a separate project In the Options dialog box you can define a default equalization setting Click the Parameter button to changing the equalizing parameters if availa
155. ene scale compared to that of the currently selected project that way you can work on the scene copy at a different resolution If you enter an invalid scale factor it will be changed to the closest valid scale and displayed in the table Reconfirm with OK In the workspace window a new project item appears within the folder corresponding to the scale for example 100 5 The current scale mode cannot be modified in this dialog box Click the Image View or Project Pixel View button on the View Settings toolbar to display the map at the original scene scale Switch between the display of the map at the original scene scale button activated and the rescaled resolution button released Create Scene Copy with Scale Value Description Absolute value Relative to original scene sze Absolute value Relative to original scene size Absolute value CE eme Figure 7 38 Create Scene Copy with Scale dialog box Creating Tiles Manually created scene tiles are added into the workspace as sub scenes of the originating project Image objects or other results are not copied into these scene copies 1 To create scene tiles right click on a project in the right hand pane of the Workspace window 2 From the context menu select Create Tiles on the context menu The Create Tiles dialog box opens figure 7 39 27 September 2012 User Guide Advanced Rule Set Concepts 165 3 Enter the tile size in x and y the minimum tile size is 100
156. ens Server Rule sets that include subroutines cannot be processed on a local machine 9 1 5 Tutorials To give you practical illustrations of structuring a rule set into subroutines have a look at some typical use cases including samples of rule set code For detailed instructions see the related instructional sections and the Reference Book listing all settings of algorithms Use Case Basic Create a Scene Subset Find regions of interest ROIs create scene subsets and submit for further processing 27 September 2012 User Guide Automating Data Analysis 197 In this basic use case you use a subroutine to limit detailed image analysis processing to subsets representing ROIs The image analysis processes faster because you avoid detailed analysis of other areas Commonly you use this subroutine use case at the beginning of a rule set and therefore it is part of the main process tree on the Main tab Within the main process tree you sequence processes in order to find regions of interest ROI on a bright background Let us say that the intermediate results are multiple image objects of a class no_background representing the regions of interest of your image analysis task Still editing within the main process tree you add a process applying the create scene subset algorithm on image objects of the class no_background in order to analyze regions of interest only The subsets created must be sent to a subroutine for analysis Ad
157. er hold down the Ctrl or Shift key to enter more than one value Values can be edited either by double clicking them or by using the Edit Values button Manage Arrays Name Type Value dbl_array double 3 2 45 4 6 1 0 stt_array string 1 2 lvl_array level Cell Level lvl_array2 level Cell Level clss_array class Cell unclassified rol_array region roi_vrbl lyr image layer fg map name Numbers Strings Classes Image layers Thematic layers Levels Features Regions Map names Figure 7 18 The Manage Arrays dialog box User Guide 27 September 2012 136 Developer XD 2 0 4 7 4 2 Order of Array Items Initially string double map and region arrays are executed in the order they are entered However the action of rule sets may cause this order to change Class and feature arrays are run in the order of the elements in the Class Hierarchy and Feature Tree Again this order may be changed by the actions of rule sets for example a class or feature array may be sorted by the algorithm Update Array then the array edited in the Manage Array dialog at a later stage this will cause the order to be reset and duplicates to be removed 7 4 3 Using Arrays in Rule Sets From the Image Object Domain Array can be selected in all Process Related Operations other than Execute Child Se ries From Variables and Values In any algorithm where it is possible to enter
158. er Guide 3 An Introductory Tutorial 3 1 Identifying Shapes As an introduction to Definiens image analysis we ll analyze a very simple image The example is very rudimentary but will give you an overview of the working environment The key concepts are the segmentation and classification of image objects in addition it will familiarize you with the mechanics of putting together a rule set Ki Definiens Developer My first project Pixels Q ge Yew rage Ctpects Ass boy Clesatication Process pos Dpot Window Heb eeu tie eS DESEA k Figure 3 1 Screenshot displaying shapes tif Download the image shapes tif and open it by going to File gt New Project When you press Save or Save As Developer XD uses this image to create a project an additional file will be created with the extension dpr and the Create Project dialog will appear Name the new project Shape Recognition keep the default settings and press OK Of course shapes tif is a raster image and to start any meaningful analysis we have to instruct the software to recognize the elements as objects after we ve done this we can then add further levels of classification In Definiens software these instructions are called rule sets and they are written and displayed in the Process Tree window 29 30 Developer XD 2 0 4 3 1 1 Divide the Image Into Basic Objects The first step in any analysis is for the software to divide up the image into defined areas
159. ership functions is based on user defined functions of object features whereas Nearest Neighbor classification uses a set of samples of different classes to assign membership values The procedure consists of two major steps 1 Teaching the system by giving it certain image objects as samples 2 Classifying image objects in the image object domain based on their nearest sample neighbors The Nearest Neighbor classifier returns a membership value of between zero and one based on the image object s feature space distance to its nearest neighbor The member ship value has a value of one if the image object is identical to a sample If the image object differs from the sample the feature space distance has a fuzzy dependency on the feature space distance to the nearest sample of a class The user can select the features to be considered for the feature space For an image object to be classified only the nearest sample is used to evaluate its mem bership value The effective membership function at each point in the feature space is a combination of fuzzy function over all the samples of that class When the membership function is described as one dimensional this means it is related to one feature In higher dimensions depending on the number of features considered it is harder to depict the membership functions However if you consider two features and two classes only it might look like the graph on figure 6 19 on page 101 Defining th
160. es you several options These options can be edited at any time by selecting File gt Modify Open Project e Change the name of your project in the Project Name field The Map selection is not active here but can be changed in the Modify Project dialog box after project creation is finished e If you load two dimensional image data you can define a subset using the Subset Selection button If the complete scene to be analyzed is relatively large subset selection enables you to work on a smaller area to save processing time e If you want to rescale the scene during import edit the scale factor in the text box corresponding to the scaling method used resolution m pxl magnification x percent or pixel px pxl e To use the geocoding information from an image file to be imported select the Use Geocoding checkbox e For feature calculations value display and export you can edit the Pixels Size Unit If you keep the default auto the unit conversion is applied according to the unit of the co ordinate system of the image data as follows If geocoding information is included the pixel size is equal to the resolution In other cases pixel size is 1 In special cases you may want to ignore the unit information from the included geocoding information To do so deactivate Initialize Unit Conversion from Input File item in Tools gt Options in the main menu e The Image Layer pane allows you to insert remove and edit i
161. ess Save to save a template as an XML file Tem plates are saved in custom folders that do not get deleted if Developer XD is unin stalled Selecting Load will open the same folder in Windows XP the location of this folder is C Documents and Settings User Application Data Definiens Version Number Import Editing Search Strings and Scene Names Editing the Search String and the Scene Name if the automatically generated ones are unsatisfactory is often a challenge for less experienced users There are two types of fields that you can use in search strings static and variable A static field is inserted as plain text and refers to filenames or folder names or parts of them Variable fields are always enclosed in curly brackets and may refer to variables such as a layer folder or scene Variable fields can also be inserted from the Insert Block drop down box For example the expression scene 001 tif will search for any scene whose filename ends in 001 tif The expression scene _x_ scene jpg will find any JPEG file with _x_ in the filename For advanced editing you can use regular expressions such as and OR You must comply with the following search string editing rules e The search string has to start with root this appears by default e All static parts of the search string have to be defined by normal text e Use a backslash between a folder block and its content e Use block name n to specify number
162. ess the Merge Objects Manually button on the Manual Editing toolbar to activate the input mode Select the neighboring objects to be merged in map view Selected objects are displayed with a red outline the color can be changed in View gt Display Mode gt Edit Highlight Colors To clear a selection click the Clear Selection for Manual Object Merging button or de select individual objects with a single mouse click To combine objects use the Merge Selected Objects button on the Manual Editing toolbar or right click and choose Merge Selection User Guide 27 September 2012 126 Developer XD 2 0 4 Figure 7 7 Left selected image objects Right merged image objects NOTE If an object cannot be activated it cannot be merged with the al ready selected one because they do not share a common border In addition due to the hierarchical organization of the image objects an object cannot have two superobjects This limits the possibilities for manual object merg ing because two neighboring objects cannot be merged if they belong to two different superobjects Merging Thematic Objects Based on Image Objects You can create merge the outlines of a thematic object and an image object while leaving the image object unchanged 1 Press the Merge Thematic Object Based on Image Object button 2 Select a thematic object and then an adjoining image object 3 Right click and choose Merge to Polygon Figure 7 8 In the left
163. eted using the Delete Map algorithm You can delete each map individually using the image object domain Execute or delete all maps with certain prefixes and defined conditions using the image object domain maps 7 9 8 Working with Multiple Maps Multi Scale Image Analysis Creating a downsampled map copy is useful if working on a large image data set when looking for regions of interest Reducing the resolution of an image can improve perfor mance when analyzing large projects This multi scale workflow may follow the follow ing scheme e Create a downsampled map copy to perform an overview analysis e Analyze this map copy to find regions of interest e Synchronize the regions of interest as image objects back to the original map Likewise you can also create a scene subset in a higher scale from the downsampled map For more information on scene subsets refer to Workspace Automation One Map Per Object In some use cases it makes sense to refine the segmentation and classification of indi vidual objects The following example provides a general workflow It assumes that the objects of interest have been found in a previous step similar to the workflow explained in the previous section In order to analyze each image object individually on a separate map do the following e Ina parent process select an image object domain at new level e Add a Copy Map process set the image object domain to current image object and define you
164. eters into account 27 September 2012 User Guide Advanced Rule Set Concepts 175 e Link weight to PPO computes the overlap area of two linked objects to each other 7 12 Polygons and Skeletons Polygons are vector objects that provide more detailed information for characterization of image objects based on shape They are also needed to visualize and export image object outlines Skeletons which describe the inner structure of a polygon help to describe an object s shape more accurately Polygon and skeleton features are used to define class descriptions or refine segmenta tions They are particularly suited to studying objects with edges and corners A number of shape features based on polygons and skeletons are available These features are used in the same way as other features They are available in the feature tree under Object Features gt Geometry gt Based on Polygons or Object Features gt Geometry gt Based on Skeletons NOTE Polygon and skeleton features may be hidden to display them go to View gt Customize and reset the View toolbar 7 12 1 Viewing Polygons Polygons are available after the first segmentation of a map To display polygons in the map view click the Show Hide Polygons button For further options open the View Settings View gt View Settings window View Settings Class icaton Image Data Image Data Prel Scale Parameter Analysis Figure 7 47 View Settings
165. evel Go to the Algorithm Parameters group box and look for a Level Usage parameter If available you can select from the options if not available the new image object level is created above the current one Using Segmentation to Create an Image Object Hierarchy Because a new level produced by segmentation uses the image objects of the level beneath it the function has the following restrictions e An image object level cannot contain image objects larger than its superobjects or smaller than its sub objects e When creating the first image object level the lower limit of the image objects size is represented by the pixels the upper limit by the size of the scene This structure enables you to create an image object hierarchy by segmenting the image multiple times resulting in different image object levels with image objects of different scales 4 4 4 Duplicating an Image Object Level It is often useful to duplicate an image object level in order to modify the copy To duplicate a level do one of the following e Choose Image Objects gt Copy Current Level from the main menu The new image object level will be inserted above the currently active one e Create a process using the Copy Image Object Level algorithm You can choose to insert the new image object level either above or below an existing one 4 4 5 Editing an Image Object Level or Level Variable Edit Level Aliases Alas Level Var Add Variable Remove Rename Na
166. evel for the image object domain you must select an image object level name or a variable If you choose pixel level for the image object domain you can specify the name of a new image object level e Class filter If you already classified image objects you can select classes to focus on the image objects of these classes e Threshold condition You can use a threshold condition to further narrow down the number of image objects When you have added a threshold condition a second drop down box appears which allows you to add another threshold condition e Max number of image objects Enter the maximum number of image objects to be processed Technically the image object domain is a set of image objects Every process loops through the set of image objects in the image object domain one by one and applies the algorithm to each image object The set of domains is extensible using the Developer XD SDK To specify the image object domain select an image object level or another basic domain in the drop down list Available domains are listed in table 4 1 on the current page Image Object Domains Table 4 1 Image Object Domains Basic Domain Usage Parameters Execute A general domain used to execute an algorithm It will activate any commands you define in the Edit Process dialog box but is independent of any image objects It is commonly used to enable parent processes to run their subordinate processes Execute Child Pr
167. evelopment Tools 183 Snippets Figure 8 5 Snippets window processes Alternatively you can right click process or snippets for copying and pasting You can also copy snippets from the Snippets window to any position of the Process Tree window To save all listed snippets in a snippets library right click in the Snippets window and select Export Snippets All process snippets are saved as a snippet slb file To import Snippets from a snippets library right click in the Snippets window and select Import Snippets You cannot add customized algorithms to the Snippets window but snippets can include references to customized algorithms 8 5 1 Snippets Options e You can rename the processes in the Snippets window by clicking twice on the name and entering a new one However when you paste it back into the Process Tree window it will revert to its original name e The contents of the Snippets window will remain there until deleted To delete right click on a process snippet and select Delete or Delete All from the context menu User Guide 27 September 2012 9 Automating Data Analysis 9 1 Loading and Managing Data 9 1 1 Projects and Workspaces A project is the most basic format in Definiens Developer XD 2 0 4 A project contains one or more maps and optionally a related rule set Projects can be saved separately as a dpr project file but one or more projects can also be stored as part of a workspace For more advanced a
168. ew The right hand image is displayed with View Classification selected and the outline colors are based on user classification colors 2 5 6 Image Layer Display Single Layer Grayscale Scenes are automatically assigned RGB red green and blue colors by default when image data with three or more image layers is loaded Use the Single Layer Grayscale button on the View Settings toolbar to display the image layers separately in grayscale In general when viewing multilayered scenes the grayscale mode for image display provides valuable information To change from default RGB mode to grayscale mode go to the toolbar and press the Single Layer Grayscale button which will display only the first image layer in grayscale mode Figure 2 9 Layer 1 single grayscale map view of a sample scene of microtubules Image data courtesy of EMBL Heidelberg Three Layers RGB Display three layers to see your scene in RGB By default layer one is assigned to the red channel layer two to green and layer three to blue The color of an image area informs the viewer about the particular image layer but not its real color These are additively mixed to display the image in the map view You can change these settings in the Edit Image Layer Mixing dialog box User Guide 27 September 2012 16 Developer XD 2 0 4 Show Previous Image Layer In Grayscale mode this button displays the previous image layer The number or name of the displayed image layer
169. f a plate are exported into one file The Fitting Models The following fitting models are available Fai _ Ymin T Ymax Ymin Logistic Four Parameters y 1 10UBEC 1 xb cous _ Ymin T Ymax Ymin Logistic Three Parameters y 1 100g Eaa Hill Three Parameters y 2 EC50 x Sigmoid Three Parameters y a l e f b o XX Hyperbola Two Parameters y UEL ECs9 x Hyperbola Single I Three Y Ymin Ymax Ymin X a ECs9 x Parameters Ymax X X Hyperbola Single II Three y Parameters G oes Ymax x Ymax x Hyperbola Double Four x x ap Z 2 or 2 assists Parameters Linear y yx 0 b x log x The returned Max value for Hyperbola Single II Three Parameters is for the compound specific response Because a non specific response is assumed here the actual maximal response may greatly extend the returned Max value The returned slope c is the slope of this nonspecific response Variables ymin is the minimum value of response e Ymax is the maximum value of response e ECs is the concentration with half effect e log ECs9 is the logarithmic value of concentration with half effect e bis the slope of curve e cis the slope of non specific reaction User Guide 27 September 2012 246 Developer XD 2 0 4 About Dose Response Experiments and Curve Fitting A dose response curve DRC or concentration response curve describes the relationship between the amount or concentration of a drug or
170. f higher value area Calculates the portion of the area of the neighbors of a selected class which have higher values for the specified feature than the object itself to the area of all neighbors of the selected class Portion of lower value area Calculates the portion of the area of the neighbors of a selected class which have lower values for the specified feature than the object itself to the area of all neighbors of the selected class Portion of higher values Calculates the feature value difference between an image object and its neighbors of a selected class with higher feature values than the object itself divided by the difference of the image object and all its neighbors of the selected class Note that the features are weighted with the area of the corresponding image objects Portion of lower values Calculates the feature value difference between an image object and its neighbors of a selected class with lower feature values than the object itself divided by the difference of the image object and all its neighbors of the selected class Note that the features are weighted with the area of the corresponding image object Continues User Guide 27 September 2012 w 150 Developer XD 2 0 4 Function Description Mean absolute Available only if sub objects is selected for Relational function difference to concerning Calculates the mean absolute difference between the feature neighbors value of su
171. f using class descriptions lies in combining several conditions The concept of threshold conditions is also available for process based classification in this case the threshold condition is part of the image object domain and can be added to most algo rithms This limits the execution of the respective algorithm to only those objects that fulfill this condition To use a threshold e Go to the Class Hierarchy dialog box and double click on a class Open the Con tained tab of the Class Description dialog box In the Contained area right click the initial operator and min and choose Insert New Expression on the context menu From the Insert Expression dialog box select the desired feature Right click on it and choose Insert Threshold from the context menu The Edit Threshold Condition dialog box opens where you can define the threshold expression In the Feature group box the feature that has been selected to define the threshold is displayed on the large button at the top of the box To select a different feature click this button to reopen the Select Single Feature dialog box Select a logical operator Enter the number defining the threshold you can also select a variable if one exists For some features such as constants you can define the unit to be used and the feature range displays below it Click OK to apply your settings The resulting logical expression is displayed in the Class Description box 6 3 2 About the Class Descr
172. from the parent process There fore you must execute the parent process itself or in between a superordinated parent process User Guide 27 September 2012 140 Developer XD 2 0 4 Process Tree e Tryot PPro Jeg use segnertation counting end numbering of each object paint chessboard using a kind of PPO that happens without PPO DL unclassified with Existence of MyClass 0 0 ot Level t MyClass As amp Level t unclassified restore try t with PPO kind of internal loop unclassified at Level 1 LA if with Existence of M more complex referring to Edit Process Name Algorithm Description ti 7 Aut ee ee to he class specified by the Use class E with Exostence of MyClass 0 0 MyClass Algorithm parameters Algoth Parameter fession class gp eae mage Object Domain curent mage object z Parameter Value Class fiter none Theeshoki condition Existence of MyClass 0 Max number of mage obj all Loops amp Cycles Number of cycles 1 Figure 7 21 Setting with parent process object PPO a kind of internal loop Figure 7 22 Result with parent process object PPO a kind of internal loop 27 September 2012 User Guide Advanced Rule Set Concepts 141 Process Tree e Omis try oe PPO Oits urele we i yetin dim oig lt in part Combowd wre sind d PPO O63le more complex referring to 4 gt ne Process tree
173. fy the path of the output root folder choose File gt Workspace Properties from the main menu Clear the Use Workspace Folder check box and change the path of the output root folder by editing it or click the Browse for Folders button and browse to an output root folder This changes the location where image results and statistics will be stored The workspace location is not changed Workspace Properties Name New Workspace Output root D remp Workspace file C Documents and Settings rthomson Desktop New Wor Use workspace folder for output CE a Figure 9 6 Workspace Properties dialog box Opening Projects and Workspace Subsets Open a project to view and investigate its maps in the map view 1 Go to the right hand pane of the Workspace window that lists all projects of a workspace 2 Do one of the following e Right click a project and choose Open on the context menu e Double click a project e Select a project and press Enter 3 The project opens and is displayed its main map in the map view If another project is already open it is closed before opening the other one If maps are very large you can open and investigate a subset of the map e Go to the right pane of the Workspace window that lists all projects of a workspace e Right click a project and choose Open Subset The Subset Selection dialog box opens e Define a subset and confirm with OK The subset displays in the map view This subset is not saved with t
174. g option acti vated 1 Select a parameter from the Parameter list The list contains parameters that were processed during the analysis and exported using the actions Export Project Statis tics or Export Population Data 2 The Heat Map scale marks the minimum left blue color and maximum value right red color of the selected parameter 3 Select Automatically Update Heat Map Scale to automatically adjust the minimum and maximum value to the distribution of the selected parameter 4 To adjust the distribution of the colors manually enter the desired values for min imum or maximum To preserve your settings when you select another parameter first clear the Automatically Update Heat Map Scale checkbox 5 To open the image of a specific well double click it gt gt nm moo Q m O0000000 00000000 00000000 00000000 00000000 O0000000 0000000 00000000 0000000 OO080080 gt LH Figure 11 12 Analysis Results in the Plate View window with manual scaling settings Diagrams such as the Graph window or the 2D Scatter Plot window provide an alternative User Guide 27 September 2012 240 Developer XD 2 0 4 view of the statistical distribution You can use the Dose Response window in conjunction with the Plate View window to generate a dose response curve View Result Values in the Graph Results for features of selected wells can be displayed graphical
175. ge Each square represents a scene tile In order to put the individually analyzed tiles back together stitching is required A complete workflow and implementation in the Process Tree window is illustrated in fig ure 7 44 on the next page 1 Select the Create Scene Tile algorithm and define the tile size When creating tiles the following factors should be taken into account e The larger the tile the longer the analysis takes however too many small tiles increases loading and saving times User Guide 27 September 2012 168 Developer XD 2 0 4 EFTTEXVE f 10 sstl4_ Ro ARP bie Figure 7 43 Schematic presentation of a tiled image Process Tree O C create 290x 100 ties E crocess thes mih Subroutine T and stich delete tes Export Stetetes for Top Scene BB expert project statetes Figure 7 44 Stitching and tiling ruleset e When stitching is requested bear in mind that there are limitations for the number of objects over all the tiles depending on the number of available image layers and thematic layers 2 Tiles are handed over to the subroutine analyzing the scene tiles by the Submit Scenes for Analysis algorithm e In the Type of Scenes field select Tiles e Set the Process Name to Subroutine 1 e Use Percent of Tiles to Submit if you want a random selection to be analyzed for example if you want a statistical overview e Set Stitching to Yes in order to stitch the analy
176. ges take effect immediately in all relevant places in your rule set When you want to modify a dupli cated process sequence you need to perform the changes consistently to each instance of this process Using customized algorithms you only need to modify the customized algorithm and the changes will affect every instance of this algorithm A rule set item is any object in a rule set other than a number of a string Therefore a rule set item can be a class feature image layer alias level name or any type of variable To restrict the visibility and availability of rule set items to a customized algorithm local variables or objects can be created within a customized algorithm Alternatively global variables and objects are available throughout the complete rule set A rule set item in a customized algorithm can belong to one of the following scope types e Local scope Local rule set items are only visible within a customized algorithm and can only be used in child processes of the customized algorithm For this scope type a copy of the respective rule set item is created and placed in the local scope of the customized algorithm Local rule set items are thus listed in the relevant con trols such as the Feature View or the Class Hierarchy but they are only displayed when the customized algorithm is selected e Global scope Global rule set items are available to all processes in the rule set They are accessible from anywhere in the rule se
177. gorithm to all sub objects of the Class filter Threshold current internally selected image object of condition Level distance the parent process The number of levels Max number of image down the image objects level hierarchy is objects defined by the Level Distance parameter Linked objects Applies the algorithm to the linked object of Link class filter Link the current internally selected image object direction Max distance of the parent process Use current image object Class filter Threshold condition Max number of image objects Maps Applies the algorithm to all specified maps of Map name prefix a project You can select this domain in Threshold condition parent processes with the Execute child process algorithm to set the context for child processes that use the Map parameter From Parent Image object list A selection of image objects created with the Image object list Class Update Image Object List algorithm filter Threshold condition Max number of image objects This set of domains is extensible using the Developer SDK 4 2 2 Adding an Algorithm Algorithms are selected from the drop down list under Algorithms detailed descriptions of algorithms are available in the Reference Book By default the drop down list contains all available algorithms You can customize this list by selecting more from the drop down list which opens the Select Process Algo rithms box figure 4 3 By default the
178. h them from other classes To optimize the thresholds for evaluation classes click on the Class Evaluation tab in the Image Object Information window Clicking on an object returns all of its defined values allowing you to adjust them as necessary Image Object Information Term Feature Value Wei Evaluation of Clas mean geom Bnghiness 139 33 10 sification Class Evaluation Figure 6 15 Optimize thresholds for evaluation classes in the Image Object Information win dow Using Evaluation Classes In the above example the rule set developer has specified a threshold of 0 55 Rather than use this value in every rule set item new processes simply refer to this evaluation class when entering a value for a threshold condition if developers wish to change this value they need only change the evaluation class TIP When using this feature with the geometrical mean logical operator ensure that no classifications return a value of zero as the multiplication of values will also result in zero If you want to return values between 0 and 1 use the arithmetic mean operator 27 September 2012 User Guide About Classification 99 Edit threshold condition Threshold settings sea eal al eal em gt oss v No Unit Entire range of Delete condition Figure 6 16 Example of an evaluation class 6 4 Supervised Classification 6 4 1 Nearest Neighbor Classification Classification with memb
179. h to display The drop down boxes at the bottom let you edit the attributes of the text Note that the two left hand corners always display left justified text and the right hand corners show right justified text Text rendering settings can be saved or loaded using the Save and Load buttons these settings are saved in files with the extension dtrs If you wish to export an image as part of a rule set with the text displayed it is necessary to use the Export Current View algorithm with the Save Current View Settings parameter Image object information is not exported If a project contains multiple slices all slices will be labelled User Guide 27 September 2012 22 Developer XD 2 0 4 Edit Top Right Corner Text Settings Name of Image inset Map Nane 8Shee Pos Bnaptre Name SBnghines Vake Irnest Sce Pos ircect Feature Figure 2 19 The Edit Text Settings dialog box Changing the Default Text It is possible to specify the default text that appears on an image by editing the file default_image_view xml It is necessary to put this file in the appropriate folder for the portal you are using these folders are located in C Program Files Definiens Developer XD 2 0 4 bin application assuming you installed the program in the default location By default there are copies of default_image_view xml in the Life and Tissue folders figure 2 20 if you wish to use this file for another portal simply copy it into
180. hand image a thematic object outlined in blue and a neighboring image object outlined in red are selected 27 September 2012 User Guide Advanced Rule Set Concepts 127 Cutting a Thematic Object Manually To cut a single image object or thematic object 1 2 Draw the cut line which can consist of several sections Depending on the object s Activate the manual cutting input mode by selecting Tools gt Manual Editing gt Cut Objects from the main menu To cut an object activate the object to be split by clicking it shape the cut line can touch or cross the object s outline several times and two or more new objects will be created Right click and select Perform Split to cut the object or Close and Split to close the cut line before cutting The small drop down menu displaying a numerical value is the Snapping Tolerance which is set in pixels When using Manual Cutting snapping attracts object borders magnetically NOTE If you cut image objects note that the Cut Objects Manually tool cuts both the selected image object and its sub objects on lower image object levels Figure 7 9 Choosing Perform Split left will cut the object into three new objects while Close and Split right will cause the line to cross the object border once more creating four new objects Saving Thematic Objects to a Thematic Layer Thematic objects with their accompanying thematic layers can be export
181. hange the number of the first no influence 0 displayed slice Number of The number of Click the Calc button to 1 frames two dimensional images each calculate the rounded ratio of representing a single film width and height of the internal picture frame of a scene with map time dimension Frame distance Change the temporal distance no influence 1 between slices Frame start Change the number of the first no influence 0 27 September 2012 displayed frame Assign No Data Values Global No Data Value F Use preje vaise tor al layers kurson Individual No Data Vaks T Use pivi walues for each layer Your lrtertecton T Uron I Diabie Ho Data Vakt 0 000000 NoDstaVae 0 Las Cheat Vaive Figure 5 6 The Assign No Data Values Dialog Box User Guide Projects and Workspaces 71 No data values can be assigned to image pixel values or combinations of values to save processing time These areas will not be included in the image analysis Typical examples for no data values are bright or dark background areas The Assign No Data Value dialog box can be accessed when you create or modify a project After preloading image layers press the No Data button The Assign No Data Values dialog box opens figure 5 6 Selecting Use Single Value for all Layers Union lets you set a single pixel value for all image layers To set individual pixel values for each image layer select the Use Individual Values f
182. hat happens without PPO WL unclassified with Existence of MyClass 0 0 at Level 1 MyClass RL ot Level 1 unclassfied restore tryit with PPO a kind of internal bop more complex referring to Figure 7 19 Process Tree window of the example project ParentProcessObjects dpr Figure 7 20 Result without parent process object image data courtesy of EMBL Heidelberg 1 Open the test project ParentProcessObjects dpr which is included in the installation The path is C Program Files Definiens Developer version number Examples ParentProcessObjectPPO ParentProcessObjects dpr The rule set can be seen in figure 7 19 on the current page This project was created for presentation purposes only so it is not structured for solving an image analysis problem Image data courtesy of European Molecular Biology Laboratory EMBL Heidelberg 2 Using the first parent process named simple use you can compare the results of the Assign Class algorithm with figure 7 22 and without figure 7 20 the parent process object PPO 3 Execute the segmentation process 27 September 2012 User Guide Advanced Rule Set Concepts 139 4 Execute the process counting and numbering of each object 5 Execute the that happens without PPO process using the Assign Class algorithm Without a PPO the whole image is classified This is because before processing the line no objects of class My Class existed so all objects in Level
183. he Rule Set From the Feature View tree select Object Features gt Layer Values gt Mean then double click on the Brightness tag A Brightness value now appears in the Image Object Informa tion window Clicking on our new object primitives now gives a value for brightness and the values are all in the region of 254 Conversely the shapes have much lower brightness values between 80 and 100 So for example what we can now do is define anything with a brightness value of more than 250 as background Right click on the sibling you just created the 200 shape 0 1 process and select Append New this will create a new rule at the same level Once we ve isolated the background we re going to stick the pieces together and give it the value Background In the Algorithm drop down box select Assign Class We need to enter the brightness attributes we ve just identified by pressing the ellipsis in the value column next to Threshold Condition which launches the Select Single Feature window This has a similar structure to the Feature View box so as previously select Object Features gt Layer Values gt Mean and double click on Brightness We can define the background as anything with a brightness over 230 so select the greater than button gt and enter 230 in the left hand field Press OK The final thing to do is to classify our new criteria In the Use Class parameter of Algo rithm Parameters on the r
184. he project and does not modify the project After closing the map view of the subset the subset is lost however you can save the subset as a separate project Inspecting the State of a Project For monitoring purposes you can view the state of the current version of a project Go to the right hand pane of the Workspace window that lists the projects The state of a current version of a project is displayed behind its name 27 September 2012 User Guide Automating Data Analysis 193 Processing States Related to User Workflow Created Canceled Edited Processed Skipped Stitched Accepted Rejected Deleted Project has been created Automated analysis has been canceled by the user Project has been modified automatically or manually Automated analysis has finished successfully Tile was not selected randomly by the submit scenes for analysis algorithm with parameter Percent of Tiles to Submit defined smaller than 100 Stitching after processing has been successfully finished Result has been marked by the user as accepted Result has been marked by the user as rejected Project was removed by the user This state is visible in the Project History Other Processing States Unavailable The Job Scheduler a basic element of Definiens software where the job was Waiting Processing Failed Timeout Crashed submitted is currently unavailable It might have been disconnected or restarted Project is waiting for automated anal
185. he shapes Press OK to close the box then press Execute The background is now a single object TIP To view the classification of an image object within an image you must have the View Classification button selected on the horizontal toolbar The classification is displayed when you hover over the object with the cursor 3 1 3 Shapes and Their Attributes Some properties of circles e Small circumference in relation to area e Constant degree of curvature e No straight edges Some properties of squares e A ratio of length to width of 1 1 e All sides are of equal length Some properties of stars e Relatively long borders compared to area e No curved edges Isolating the Circles Developer XD has a built in algorithm called Elliptic Fit it basically measures how closely an object fits into an ellipse of a similar area Elliptic Fit can also be found in Feature View and can be found by selecting Object Features gt Geometry gt Shape then double clicking on Elliptic Fit Of course a perfect circle has an elliptic fit of 1 the max imum value so at least in this example we don t really need to check this But you might want to practice using Feature View anyway To isolate the circles we need to set up a new rule We want this rule to be in the same hierarchical level as our first Create objects rule set and the easiest way to do this is to right click on the Create objects rule set and
186. he total distribution of this feature over one or all image object levels Use this tool to assign samples using a Nearest Neighbor classification or to compare an image object to already existing samples in order to determine to which class an image object belongs If you assign samples features can also be compared to the samples of other classes Only samples of the currently active map are displayed 1 Open the Sample Editor window using Classification gt Samples gt Sample Editor from the main menu 2 By default the Sample Editor window shows diagrams for only a selection of fea tures To select the features to be displayed in the Sample Editor right click in the Sample Editor window and select Select Features to Display 3 In the Select Displayed Features dialog box double click a feature from the left hand pane to select it To remove a feature click it in the right hand pane 4 To add the features used for the Standard Nearest Neighbor expression select Dis play Standard Nearest Neighbor Features from the context menu 27 September 2012 User Guide About Classification 107 Active class Compare class Waterbodes v impervacnss Geneal X Mean Layer 1 MN 58 7 67 3 StdDew 2 40 71 9 93 7 StdDew 7 35 6 0 684 ML 021 1055 1179 192 1426 155 0 Ovenap 0 00 Mean Layer 1 NN Mire a 50 4 154 2 Std Dev 9 90 560 64 8S 931 1055 1179 133 1426 1550 Mean Layer 1 NN 56 0 155 0 Std De
187. hen you want a series of processes to create a particular outcome You can achieve this by adding sibling processes to the parent process us ing the Insert Child command For more information on segmentation see Multiresolution Segmentation p 44 for more detailed information consult the Reference Book 3 1 2 Identifying the Background Overview The obvious attribute of the background is that it is very homogeneous and in terms of color distinct from the shapes within it In Developer XD you can choose from a huge number of shape texture and color vari ables in order to classify a particular object or group of objects In this case we re going to use the Brightness feature as the background is much brighter then the shapes You can take measurements of these attributes by using the Feature View window The Feature View window essentially allows you test algorithms and change their parameters double click on a feature of interest then point your mouse at an object to see what 27 September 2012 User Guide An Introductory Tutorial 31 numerical value it gives you This value is displayed in the Image Object Information window You can then use this information to create a rule TIP Running algorithms and changing values from the Feature View tree does not affect any image settings in the project file or any of the rule sets It is safe to experiment with different settings and algorithms Writing t
188. ice files frame Represents the frames of a time frame tif for all TIFF files or series or 4D image data set It can frame any tif for all TIFF be used for files or folders files in a folder containing frame files row Same as slice Same as slice column Same as frame Same as frame 27 September 2012 User Guide Automating Data Analysis 191 Workspace IS colon Rat 1001_6 1a_Cec 1001_6 1a_Cec 1 2 Me 1001 _6 1a_Cec 1 2 10x g 10x 1001 _6 1a_Cec 1 2 10x tiles tie000 ties 1001_6 1a_Cec 1 2 10x tiles tle001 1001 6 13 Cec 1 2 10x tiles tdeO02 1001 _6 la Cec 1 2 10x tiles tikeO0S 1001_6 14_Cec 1 2 10x tiles theO04 1001_6 1a_Cec 1 2 10x tiles the005 1001 _6 1a_Cec 1 2 10x tiles tie005 1001_6 1a_Cec 1 2 10x tiles the007 1001 _6 14_Cec 1 2 10x tiles tde008 1001_6 ta_Cec 1 2 10x tiles tke009 1001 _6 1a_Cec 1 2 10x tiles tie010 1001_6 1a_Cec 1 2 10x tiles tie011 1001 _6 1a_Cec 1 2 10x tiles tie012 1001_6 1a_Cec 1 2 10x tiles t e013 1001 _6 1a_Cec 1 2 10x tiles tie014 1001_6 1a_Cec 1 2 10x tiles tle015 1001_6 1a_Cec 1 2 10x tiles tie016 1001_6 1a_Cec 1 2 10x tiles tie017 Summary e003 Processed 00 00 17 Figure 9 5 Workspace window with folders open to display project naming Managing Folders in the Workspace Tree View Add move and rename folders in the tree view on the left pane of the Workspace window Depending on the import template these folders may represent different items such as Assay
189. ield of the Dose Response window If the window is not already open open it by selecting View gt Windows gt Dose Response Curve from the main menu The compounds available have already been added to plate TOws Select a feature by clicking the Results button in the Plate View and making a selection from the drop down list for the Parameter field The data points for the rows where the compound was added display on the graph in the Dose Response window Fitting the Dose Response Curve After the data points are loaded a curve can be created to link the values and Developer XD offers several fitting models and assay types for the dose response curve As options you can choose initial values for the curve and deal with outlying values before fitting the curve or edit them later and fit the curve again To fit a dose response curve to the data points 1 Go to View gt Windows gt Dose Resp Curve to open the Dose Response window Click the Curve Data button if the tab is not already selected If a compound has been assigned to a plate the compound name and dilution sequence display in the Compound field 2 Select a fitting model from the Model drop down list 3 Select the assay type e ECso concentration of half maximal effect has a curve with a positive slope e ICso concentration of half maximal inhibition has a curve with a negative slope 4 The dose response curve can now be fitted to the data by clicking the Fit button The
190. ies Therefore the results of statistical calculations between Linux and Windows may be slightly different User Guide 27 September 2012 206 Developer XD 2 0 4 9 To view a preview of the attribute table that will be exported press the Preview button Generating Reports Generate Report creates a HTML page containing information about image object fea tures and optionally a thumbnail image To open the Generate Report dialog box choose Export gt Generate Report from the main menu Generate Report Select festres W Update Oty Table Save Report Cove Figure 9 14 Generate Report dialog box 1 Select the Image object level for which you want to create the report from the drop down box 2 The Table header group box allows you to choose from the following options e User Info Include information about the user of the project e Project Info Include co ordinate information resolution and units of the map 3 From the Table body group box choose whether or not to include thumbnails of the image objects in jpeg format 4 Click the Select Classes button to open the Select Classes for Report dialog box where you can add or remove classes to be included in the report 5 Click the Select features button to open the Select Features for Report dialog box where you can add or remove features to be included in the report 6 Change the default file name in the Export File Name text field if desired 7 Clear the Update Obj Tab
191. ies panel to the users of action libraries in cases where the dependency on actions cause problems If you do nothing a default error message is created Loading Rule Sets for Use in Action Libraries If your action library requires a rule set to be loaded it is necessary to edit the dix file which is created automatically when a new action library is constructed Insert a link to the rule set file using the following structure using a text editor such as Notepad The lt Preload gt opening and closing tags will already be present in the file lt Preload gt lt Ruleset name ruleset dcp gt lt Preload gt 10 1 7 Updating a Solution while Developing Actions A configured solution can be automatically updated after have you have changed one or more actions in the corresponding action library This option enables rule set developers to make changes to actions in an action library and then update a solution without reassembling actions as a solution The menu item is only active when a solution is loaded in the Analysis Builder window 1 To update the open solution choose Library gt Update Solution from the main menu All loaded processes are deleted and reloaded from the open action library All the solution settings displayed in the Analysis Builder are preserved User Guide 27 September 2012 218 Developer XD 2 0 4 Edit Action Dependencies Dependency Items Item Ence Messages Parameter Value B Required Clas
192. ight of the Edit Process window overwrite unclassified enter Background and press Enter The Class Description box will appear where you can change the color to white Press OK to close the box then press Execute in the Edit Process dialog TIP It s very easy at this stage to miss out a function when writing rule sets Check the structure and the content of your rules against the screen capture of the Process Tree window at the end of this section As a result when you point your mouse at a white region the Background classification we have just created appears under the cursor In addition Background now appears in the Class Hierarchy window at the top right of the screen Non background objects all the shapes have the classification Unclassified Joining the Background Pieces As we ve now got several pieces of background with a Background classification we can merge all the pieces together as a single object User Guide 27 September 2012 32 Developer XD 2 0 4 Again right click on the last rule set in the Process Tree and select Append New to create the third rule in the Create objects and remove background parent process In the Algorithm drop down box select Merge Region In the Class Filter parameter which launches the Edit Classification Filter box select Background we want to merge the background objects so we can later sub divide the remaining objects t
193. igure 10 4 Edit Group dialog box 1 To create an action group go to upper pane of the Analysis Builder window now called Edit Library Name of the Loaded Action Library and right click any item or the background and choose Add Group The new action group is added at the bottom of the existing action group list 2 To modify an action group double click it or right click it and select Edit Group The Edit Group dialog box opens 3 Edit the name ID and label color of the action group After adding any action definition the ID cannot be modified 4 Before changing the ID or deleting an action group you have to delete all contained action definitions 5 To move an action group right click it and select Move Group Up or Move Group Down 6 To delete an action group right click it and select Delete Group Editing Action Definitions Action definitions are unconfigured actions which enable users of action libraries to spec ify actions that act as building blocks of a specific solution You can define an action def inition by transforming a rule set related to a specified part of the solution Alternatively you can import an action definition from an xml file to an action library To edit action definitions you ll need to have loaded a rule set file dcp file into the Process Tree window which contains a rule set related to a specified part of the solution The rule set must include a parameter set providing variables to be adjuste
194. igure 7 24 A more complex usage of parent process object PPO creating customized par ent process objects 1 In the ParentProcessObjects dpr project figure 7 24 execute each child pro cess from the process more complex referring to After executing the Ba sic Segmentation parent switch to the outline view In this rule set the PPO O pro cedure is used to merge the image objects with the brightest image object classified as _active in the nucleus image layer Layer 2 For this purpose a difference range gt 50 to the _act ive image object is used 2 The red bordered image object _act ive is the brightest image object in this im age layer To find out how it is different from the similar image objects you might want to merge with select it using the Ctrl key Doing that you have to manu ally set your parent process object PPO The PPO will be highlighted in green figure 7 25 User Guide 27 September 2012 142 Developer XD 2 0 4 Figure 7 25 The brightest image object in this image layer Image data Courtesy of EMBL Heidelberg 3 Hide the outlines and go to the Feature View window in the Mean Layer 2 diff PPO 0 feature Check the values in the Image Object Information window figure 7 26 to find the best fitting range for the difference to the brightest object _act ive The green highlighted image object displays the PPO All other image objects that are selected will be highlighted in red and yo
195. ing Changes tartar of cycles Thematic Layer usage Thematic Layer weage tags Figure 6 35 Edit a process to use a shapefile Add a shapefile to an existing project e Open the project and select a map e Select File gt Modify Open Project from the main menu The Modify Project dialog box opens e Insert the shapefile as a new thematic layer Confirm with OK 27 September 2012 User Guide About Classification 115 Add a Parent Process e Go to the Process Tree window e Right click the Process Tree window and select Append New e Enter a process name From the Algorithm list select Execute Child Processes then select Execute in the Image Object Domain list Add segmentation Child Process e In the Process Tree window right click and select Insert Child from the context menu e From the Algorithm drop down list select Multiresolution Segmentation Under the segmentation settings select Yes in the Thematic Layer entry The segmentation finds all objects of the shapefile and converts them to image objects in the thematic layer Classify objects using shapefile information e For the classification create a new class for example Sample e In the Process Tree window add another process The child process identifies image objects using information from the thematic layer use the threshold classifier and a feature created from the thematic layer attribute table for example Image Object ID or Class
196. ing tools are for merging classifying and cutting manually To display the Manual Editing toolbar go to View gt Toolbars gt Manual Editing from the main menu Ensure the editing mode displayed in the Change Editing Mode drop down list is set to Image Object Editing Image object editing M v Image object editing Thematic editing Figure 7 4 The Change Editing Mode drop down list If you want to edit thematic objects by hand choose Thematic Editing from the drop down list Creating a New Thematic Layer If you do not use an existing layer to work with thematic objects you can create a new one For example you may want to define regions of interest as thematic objects and export them for later use with the same or another project On the Select Thematic Layer drop down list box select New Layer to open the Create New Thematic Layer dialog box Enter an name and select the type of thematic vector layer polygon line or point layer Generating Thematic Objects There are two ways to generate new thematic objects either use existing image objects or create them yourself This may either be on an existing layer or on a new thematic layer you have created For all objects the selected thematic layer must be set to the appropriate selection poly gon line or point Pressing the Generate Thematic Objects button on the Manual Editing toolbar will then open the appropriate window for shape creation The Single Selection
197. ingle Project e Data export initiated by various Export menu commands applies only to the cur rently active map of a project The Export Current View dialog box is used to Most export functions automatically generate csv files containing attribute information To obtain correct export results make sure the decimal separator for csv file export matches the regional settings of your oper ating system In Definiens Developer XD 2 0 4 these settings can be changed under Tools gt Options If geo referencing information of supported co ordinate systems has been provided when creating a map it should be exported along with the classification results and additional information if you choose Export Image Objects or Export Classification User Guide 27 September 2012 204 Developer XD 2 0 4 export the current map view to a file Copy the current map view to the clipboard and choose Export gt Copy Current View to Clipboard from the main menu e Class object or scene statistics can be viewed and exported They are calculated from values of image object features e Image objects can be exported as a thematic raster layer together with an attribute table providing detailed parameter values The classification of a current image ob ject level can be exported as an image file with an attribute table providing detailed parameter values e Polygons lines or points of selected classes can be exported to the shapefile format on page 206
198. ion Layer Properties Layer Abas Tk Geocoding Lower leitX Px 0 Lower leit Y Px 0 Pixel size Pd fi Geocoding V coe Figure 5 8 The Layer Properties dialog box allows you to edit the geocoding information 5 2 7 Multisource Data Fusion If the loaded image files are geo referenced to one single co ordinate system image layers and thematic layers with a different geographical coverage size or resolution can be inserted This means that image data and thematic data of various origins can be used simultane ously The different information channels can be brought into a reasonable relationship to each other 27 September 2012 User Guide Projects and Workspaces 73 Figure 5 9 Layers with different geographical coverage 5 3 Creating Saving and Loading Workspaces The Workspace window lets you view and manage all the projects in your workspace along with other relevant data You can open it by selecting View gt Windows gt Workspace from the main menu Workspace Export Specification 1 E Definiens 7 0 dpe plate1 DO6 102 v7 dpe 2 i Figure 5 10 Workspace window with Summary and Export Specification and drop down view menu The Workspace window is split in two panes User Guide 27 September 2012 74 Developer XD 2 0 4 e The left hand pane contains the Workspace tree view It represents the hierarchical structure of the folders that contain the projects e In the righ
199. iption The class description contains class definitions such as name and color along with several other settings In addition it can hold expressions that describe the requirements an image object must meet to be a member of this class when class description based classification is used There are two types of expressions e Threshold expressions define whether a feature is fulfills a condition or not for example whether it has a value of one or zero e Membership functions apply fuzzy logic to a class description You can define the degree of membership for example any value between one true and zero not true There are also several predefined types of membership functions that you can adapt Use Samples for Nearest Neighbor Classification this method lets you de clare image objects to be significant members of a certain class The Nearest Neighbor algorithm then finds image objects that resemble the samples Similarities allow you to use class descriptions of other classes to define a class Similarities are most often expressed as inverted expressions 27 September 2012 User Guide About Classification 93 You can use logical operators to combine the expressions and these expressions can be nested to produce complex logical expressions 6 3 3 Using Membership Functions for Classification Membership functions allow you to define the relationship between feature values and the degree of membership to a class using fuzzy l
200. is indicated in the middle of the status bar at the bottom of the main window In Three Layer Mix the color composition for the image layers changes one image layer up for each image layer For example if layers two three and four are displayed the Show Previous Image Layer Button changes the display to layers one two and three If the first image layer is reached the previous image layer starts again with the last image layer Show Next Image Layer In Grayscale mode this button displays the next image layer down In Three Layer Mix the color composition for the image layers changes one image layer down for each layer For example if layers two three and four are displayed the Show Next Image Layer Button changes the display to layers three four and five If the last image layer is reached the next image layer begins again with image layer one The Edit Image Layer Mixing Dialog Box Edit Image Layer Mixing Presets Shit Equalizing Urea 1 00 Parameter E E V Auto update IW No layer weights view _ Corcel Figure 2 10 Edit Image Layer Mixing dialog box Changing the layer mixing and equalizing options affects the display of the image only You can define the color composition for the visualization of image layers for display in the map view In addition you can choose from different equalizing options This enables you to better visualize the image and to recognize the visual structures with
201. istics in Folder View Selecting Folder View gives you the option to display project statistics Right click in the right hand pane and Select Folder Statistics Type from the drop down menu The available options are Sum Mean Standard Deviation Minimum and Maximum 1 By default the connectors for predefined import are stored in the installation folder under bin drivers import If you want to use a different storage folder you can change this setting under Tools gt Options gt General User Guide 27 September 2012 188 Developer XD 2 0 4 9 1 2 Data Import Creating Customized Imports Multiple scenes from an existing file structure can be imported into a workspace and saved as an import template The idea is that the user first defines a master file which functions as a sample file and allows identification of the scenes of the workspace The user then defines individual data that represents a scene by defining a search string A workspace must be in place before scenes can be imported and the file structure of image data to be imported must follow a consistent pattern To open the Customized Import dialog box go to the left hand pane of the Workspace window and right click a folder to select Customized Import Alternatively select File gt Customized Import from the main menu Customized Import Workspace image Layers Thematic Layers Metadata TMA Anrctation Scene imgot Name Custer inport Pomot F ohjes deiran duae D
202. iwo Figure 6 21 The Apply Standard Nearest Neighbor to Classes dialog box 1 From the main menu select Classification gt Nearest Neighbor gt Apply Standard NN to Classes The Apply Standard NN to Classes dialog box opens 2 From the Available classes list on the left select the appropriate classes by clicking on them 3 To remove a selected class click it in the Selected classes list The class is moved to the Available classes list 4 Click the All gt button to transfer all classes from Available classes to Selected classes To remove all classes from the Selected classes list click the lt All button Click OK to confirm your selection 6 In the Class Hierarchy window double click one class after the other to open the Class Description dialog box and to confirm that the class contains the Standard Nearest Neighbor expression Nn NOTE The Standard Nearest Neighbor feature space is now defined for the entire project If you change the feature space in one class descrip tion all classes that contain the Standard Nearest Neighbor expression are affected The feature space for both the Nearest Neighbor and the Standard Nearest Neighbor clas sifier can be edited by double clicking them in the Class Description dialog box Once the Nearest Neighbor classifier has been assigned to all classes the next step is to collect samples representative of each one Interactive Workflow for Nearest Neighbor Classific
203. ixels of the image Examples are multiresolution segmentation and classification based segmentation Multiresolution Segmentation The Multiresolution Segmentation algorithm consecutively merges pixels or existing image objects Essentially the procedure identifies single image objects of one pixel in size and merges them with their neighbors based on relative homogeneity criteria This homogeneity criterion is a combination of spectral and shape criteria You can modify this calculation by modifying the scale parameter Higher values for the scale parameter result in larger image objects smaller values in smaller ones With any given average size of image objects multiresolution segmentation yields good abstraction and shaping in any application area However it puts higher demands on the processor and memory and is significantly slower than some other segmentation tech niques therefore it may not always be the best choice Benz UC Hofmann P Willhauck G Lingenfelder M 2004 Multi Resolution Object Oriented Fuzzy Analysis of Remote Sensing Data for GIS Ready Information SPRS Journal of Photogrammetry amp Remote Sensing Vol 58 pp239 258 Amsterdam Elsevier Science 27 September 2012 User Guide N w Basic Rule Set Editing 45 The Homogeneity Criterion The homogeneity criterion of the multiresolution segmenta tion algorithm measures how homogeneous or heterogeneous an image object is within itself It is ca
204. ject If distance is zero this refers to image objects that have a common border with the parent and lie on the same image object level If a value is specified it refers to the distance between an object s center of mass and the parent s center of mass up to that specified threshold Sub objects Objects whose image area covers all or part of the parent s image area and lie a specified number of image object levels below the parent s image object level Super objects Objects whose image area covers some or all of the parent s image area and lie a specified number of image object levels above the parent s image object level Note that the child image object is on top here 7 11 3 Creating and Saving Image Object Links Object Links are created using the Create Links algorithm Links may link objects on different hierarchical levels different slices or frames or on different maps Therefore an image object can have any number of object links to any other image object A link belongs to the level of its source image object The direction of a link is always directed towards the target object so is defined as an incoming link The example in the figure below shows multiple time frames TO to T4 The object red in T2 has one incoming link and two outgoing links In most use cases multiple links are created in a row defined as a path If multiple links are connected to one another the link direction is defined as e In Onl
205. jections and 3D image objects Image data courtesy of Merck amp Co Inc The 3D Toolbar ew Bet perme From left to right you can use the toolbar buttons to perform the following functions Class Filter Select classes to display as 3D objects 3D Visualization Options Adjust the surface detail of 3D image objects Window Layout Select a layout for planar projections and 3D image objects Navigation Use sliders to navigate in the planar projections Crosshairs Display crosshairs in the planar projections Start Stop Animation Start and stop animation of a time series Show Next Slice Display next slice in the planar projections Show Previous Slice Display previous slice in the planar projections Show Next Time Frame Display next time frame in the planar projections Show Previous Time Frame Display next time frame in the planar projections Synchronize Views Synchronize view settings across planar projections TIP If 3D rendering is taking too long you can stop it by unchecking the classes in the Class Filter dialog Selecting a Window Layout The Window Layout button in the 3D Toolbar allows you to choose from the available viewing options Standard XYZ co ordinates are used fig ure 2 22 From left to right the following views are available 27 September 2012 User Guide Starting Developer 23 Figure 2 22 Standard XYZ co ordinates for 3D objects XY Planar Projection XZ Planar Projection YZ Pl
206. k the selected item and choose Analyze The Start Analysis dialog box opens with the General tab active 1 The Submit as Run checkbox always shows the last state of the workspace in the case of Developer XD workspaces it will always be checked However if a workspace was recently processed in Definiens Tissue Studio which does not use the run concept this box will be unchecked If you wish to run new non Tissue Studio rulesets on it you can check this box to do so 2 Enter a name for the run in the Run Name field Selecting the Automatic Name checkbox will automatically assign a name for you based on the name of the rule set file e Selecting Add on Run will add the results of the new run to the previous run 3 In the Ruleset field click Load to load a ruleware file for the image analysis this can be a process file extension dcp or a solution file extension dax 4 Enter the address of the server if it is hosted on another machine The default is localhost You can check the connection using the Test button 5 The Package field contains server configuration last denotes that the latest in stalled software package is in use It is normally not necessary to change this 27 September 2012 User Guide Automating Data Analysis 199 Start Analysis General Exports Configuration Run Settings F Submit as Run Run Name ImageMiner_run3 Analysis Settings Ruleset D LocalData HE_TMA mageMiner_ru
207. kspace However you can modify the path of the output root folder later on using File gt Workspace Properties 27 September 2012 User Guide Projects and Workspaces 75 User Permissions The two checkboxes at the bottom left of the Open Workspace dialog box determine the permissions of the user who opens it e If both boxes are unchecked users have full user rights Users can analyze roll back and modify projects and can also modify workspaces add and delete projects However they cannot rename workspaces e If Read Only is selected users can only view projects and use History View The title bar will display Read Only e If Edit Only is selected the title bar will display Limited and the following principles apply Projects opened by other user are displayed as locked Users can open modify history name layers segmentation thematic lay ers Save projects and create new multi map projects Users cannot analyze rollback all cancel rename modify workspaces up date paths or update results If a Project Edit user opens a workspace before a full user the Workspace view will display the status locked Users can use the Project History function to show all modi fications made by other users Multiple access is not possible in Data Management mode If a workspace is opened using an older software version it cannot be opened with Definiens Developer XD 2 0 4 at the same time 5 3 2 I
208. l Waterbockes lcodand Gener 0 000000 BIANI THS 5 847053 Geassland Gons 6 1271763 0 000000 15 204904 Inperio General 3142396 5530417 4 432606 steeds 5847053 15284304 0 000000 Cire expend Figure 6 24 Class Separation Distance Matrix for Selected Features Viewing Advanced Information The Feature Space Optimization Advanced Information dialog box provides further information about all feature combinations and the separabil ity of the class samples Feature Space Optimization Adva A Distance 6726705 Apply to Std NN M Chasty Project M Figure 6 25 The Feature Space Optimization Advanced Information dialog box 1 The Result List displays all feature combinations and their corresponding distance values for the closest samples of the classes The feature space with the highest result is highlighted by default 2 The Result Chart shows the calculated maximum distances of the closest samples along the dimensions of the feature spaces The blue dot marks the currently se lected feature space 3 Click the Show Distance Matrix button to display the Class Separation Distance Matrix window This matrix shows the distances between samples of the se lected classes within a selected feature space Select a feature combination and re calculate the corresponding distance matrix User Guide 27 September 2012 106 Developer XD 2 0 4 Class Separation Distance Matrix Weodand Gereral Graceland Gereeal
209. l cores or mark cells that you want to leave empty Assigns a postive control core Assigns a negative control care Assigns an empty cell Hebe Removes an assignment To save a layout within a workspace select Confirm To revert your changes click Re vert To save your layout to a file select Save to File under Save Load Layout Layout files can be imported into other workspaces using the Load from File button Follow ing confirmation newly defined grid layouts are available in the workspace and can be assigned to one or more slides before you proceed with core detection and matching Ex isting assignments of changed grid layouts to slides remain unchanged although it may be necessary to repeat the matching of the cores to the grid If a layout is no longer needed you can delete it at any time using the Delete button under Grid Layout Templates You can change the size of the thumbnail display in the grid by selecting an entry from the Size dropdown list in the TMA Grid View 11 3 2 Matching Cores to the Grid The cores of a slide can be determined automatically and manually You can match them to any of the available grids in a workspace 27 September 2012 User Guide Advanced Data Visualizations 235 D E F G H I J K t M N 0 P Q pre IRE ars abdi ut dee Show Thuntraty See Meda Sa er Figure 11 10 TMA Grid view in Matching mode Open a workspace containing the slides
210. l require more processing performance and time but it also allows a more detailed analysis Finally submit the newly created rescaled subset copies of regions of interest for further processing to the next subroutine Use the Submit Scenes for Analysis algorithm for such connections of subroutines Create Rescaled Subsets of ROI Find Regions of Interest ROI ROI at ROI_Level create subset ROI_Subset with scale 40x process ROI_Subset subsets with Tilingt Stitching of Subsets and stitch with Export Results of Main Scene Multi Scale 3 Use Tiling and Stitching Create tiles submit for processing and stitch the result tiles for post processing In this step you create tiles using the Create Scene Tiles algorithm In this example the Submit Scenes for Analysis algorithm subjects the tiles to time and performance consuming processing which in our example is a detailed image analysis at a higher scale Generally creating tiles before processing enables the distribution of the analysis processing on multiple instances of Analysis Engine software Here following processing of the detailed analysis within a separate subroutine the tile results are stitched and submitted for post processing to the next subroutine Stitching settings are done using the parameters of the Submit Scenes for Analysis algorithm Tiling Stitching Subsets create 500x500 tiles process tiles with Detailed Analysis of Tiles and stit
211. lculated as a combination of the color and shape properties of the initial and resulting image objects of the intended merging Color homogeneity is based on the standard deviation of the spectral colors The shape homogeneity is based on the deviation of a compact or smooth shape Homogeneity criteria can be customized by weighting shape and compactness criteria e The shape criterion can be given a value of up to 0 9 This ratio determines to what degree shape influences the segmentation compared to color For example a shape weighting of 0 6 results in a color weighting of 0 4 e In the same way the value you assign for compactness gives it a relative weighting against smoothness Multi Threshold Segmentation and Auto Thresholds The Multi Threshold Segmentation algorithm is a new feature in Definiens Developer XD 2 0 4 It splits the image object domain and classifies the resulting image objects based on a defined pixel value threshold This threshold can be user defined or can be auto adaptive when used in combination with the Automatic Threshold algorithm The threshold can be determined for an entire scene or for individual image objects this determines whether it is stored in a scene variable or an object variable dividing the se lected set of pixels into two subsets so that heterogeneity is increased to a maximum The algorithm uses a combination of histogram based methods and the homogeneity measure ment of multi resolution segme
212. le check box if you don t want to update your object table when saving the report 8 To save the report to disk press Save Report Exporting Results as Shapefiles Polygons lines or points of selected classes can be exported as shapefiles As with the Export Raster File option image objects can be exported together with their attributes 27 September 2012 User Guide Automating Data Analysis 207 and classifications Any geo referencing information as provided when creating a map is exported as well The main difference to exporting image objects is that the export is not confined to polygons based on the image objects Polygons in 2D and 3D scenes are supported You can choose between three basic shape formats points lines and polygons To ex port results as shapes open the Export Results dialog box by choosing Export gt Export Results on the main menu 1 Choose Shape file from the Export Type drop down list 2 From the Content Type drop down list choose from the following formats e Polygon raster to export non overlapping polygons following the raster out line The exported shapefile describes the border of the image objects along the pixel raster Polygon smoothed not overlapping to export non overlapping polygons fol lowing the smoothed outline as defined by the polygonization Polygon smoothed individual to export the shape polygons following the smoothed outline as defined by the polygonization Here overlap
213. le sets as action definitions and give them a user interface Later you may modify an existing action library 1 To activate the action library editing mode on your newly created or open library choose Library gt Edit Action Library from the main menu The Analysis Builder User Guide 27 September 2012 214 Developer XD 2 0 4 window changes its title bar to Edit Library Name of the Loaded Action Library Additionally a check mark left of the menu command indicates the editing mode 2 Go to the Analysis Builder window and right click any item or the background for available editing options Depending on the right clicked item you can add edit or delete one of the following e General settings definition e Action groups grouping actions e Action definitions including various Export actions e Widgets user interface components for the properties of action 3 Save the edited action library using Library gt Save Action Library on the main menu then close it using Library gt Close Action Library 4 To deactivate the editing mode go to Library gt Edit Action Library The window title bar reverts to Analysis Builder Editing the General Settings Definition A general settings definition enables users of action libraries to associate their image data with the appropriate actions General settings definitions may include interface compo nents widgets for defining parameters such as the image size and bit depth as well as co
214. levels Specify the image object level of interest by using the Image object level drop down menu In the Classes window all classes and their inheritance structures are displayed 227 228 Developer XD 2 0 4 3 To select classes for assessment click the Select Classes button and make a new selection in the Select Classes for Statistic dialog box By default all available classes are selected You can deselect classes through a double click in the right frame 4 In the Statistic type drop down list select one of the following methods for accu racy assessment e Classification Stability e Best Classification Result e Error Matrix based on TTA Mask e Error Matrix based on Samples 5 To view the accuracy assessment results click Show statistics To export the statis tical output click Save statistics You can enter a file name of your choice in the Save filename text field The table is saved in comma separated ASCII txt format the extension txt is attached automatically 11 1 1 Classification Stability The Classification Stability dialog box displays a statistic type used for accuracy assess ment Classification Stability Om Objects Mean StDev Mrama Mavereue Padingeroon 59 DOSIA Ores rs Leben ingeniosa SR ox omg 9 UEDA Waebose 3 0R 02433 0009733995003 07231 Uban Genssland 45 027 02315 0003000373609 1 Urban Weedand 23 o133 01006 OSS 039 Raa Granad S37 O2616 ors 00003220630547 1 Rud Wooded 820 02
215. lgorithms are referred to as classification based segmentation algorithms because they commonly use information about the class of the image objects to be merged or cut Although this is not always true Definiens Developer XD 2 0 4 uses this terminology The two most basic algorithms in this group are Merge Region and Grow Region The more complex Image Object Fusion is a generalization of these two algorithms and offers additional options Merge Region The Merge Region algorithm merges all neighboring image objects of a class into one large object The class to be merged is specified in the image object domain 4 Figure 4 7 Red image objects are merged Classifications are not changed only the number of image objects is reduced Grow Region The Grow Region algorithm extends all image objects that are specified in the image object domain and thus represent the seed image objects They are extended by neigh boring image objects of defined candidate classes For each process execution only those candidate image objects that neighbor the seed image object before the process execution are merged into the seed objects The following sequence illustrates four Grow Region processes 4 The image object domain of a process using the Merge Region algorithm should define one class only Other wise all objects will be merged irrespective of the class and the classification will be less predictable 5 Grow region proce
216. lick Save to save the sequence to the client software The dialog remains open and a default duplicate sequence is automatically generated so you can quickly create a series of dilution sequences 3 To create or edit single concentrations double click to the right of a concentration and enter a number Exponent notation is supported for example enter 3e 4 to display the dilution 3 x 10 0 0003 after the dilution sequence is saved Assigning and Unassigning Compounds to a Plate To assign compounds to a plate User Guide 27 September 2012 242 Developer XD 2 0 4 New Dilution Sequence Name Seq 09 Unit moli Automatic Number of concentrations 12 X Starting wth 1000 X Series 1 3 10 Steps Generate Manual Figure 11 15 Dilution Sequence dialog box 1 Select the rows in the Plate View where you want to apply compounds The number of wells selected displays under Selected wells 2 Use the controls in the Assign Compound to Wells group box to change the direc tion and order of assignment 3 Click Assign to Selection to assign the compound e The compound displays as the assigned color in the plate wells e Click any well to display the compound and concentration under Selected Wells 4 To unassign select the compound and sequence you want to unassign and click Delete This action does not delete sequences that have been saved to a file 11 4 2 Creating Dose Response Curves Use the Dose Response window
217. licking the Add Driver button or using the context menu to open the Add a Driver dialog box Use the drop down Name list box to select a driver and optionally a version if needed Click OK to display the driver in the list You can also edit the version number in the list For automatic selection of the correct version of the selected driver delete the version number 27 September 2012 User Guide Automating Data Analysis 201 Start Analysis General Exports Configuration DAEX X Name Plugins Definiens Basic Process Aigonthms Definiens intemal Process Algorithms Defiriens Thematic Layer Algorthms Definiens Advanced Features Definiens Basic Features Definiens Vector Features Defiriens Contrast Fiter Segmentation Process fegacy up to 5 0 Defirtens intemal Export Process Algorthms Defiriens Fiering Algorithms Definiens interactive Process Algorithms Pree eee eee Maw dtheans Figure 9 12 Start Analysis Configuration Extensions The Extension field displays extensions and applications if available To add an extension first load a rule set on the General tab Load an extension by clicking the Add Extension button or using the context menu to open the Add an Extension dialog box Enter the name of the extension in the Name field Click OK to display the extension in the list Changing the Configuration To delete an item from the list select the item and click the Delete Item button or use the context menu You ca
218. ling or rotation is performed according to your needs To adjust the position of the complete grid hold down the Ctrl key while moving the grid into the appropriate position It is only possible to move the complete grid if no fixed point is set To adjust the size of a single cell double click on the core within the cell The cell is adapted so that it fits the size of the complete core 27 September 2012 User Guide Advanced Data Visualizations 237 e To adjust the frame of a single cell click a vertex of the relevant cell and move it into the appropriate position The vertex is marked with a green rectangle and kept in a fixed position e To adjust the frames of all cells in a row and all cells in a column click a vertex of the relevant cell Hold down the Shift key while moving it into the appropriate position The vertex is marked with a green rectangle and kept in a fixed position e To adjust the frames of all cells within the grid click a vertex of any cell Hold down the Ctrl and Shift keys while moving it into the appropriate position It is marked with a green rectangle 4 To automatically optimize the layout of the grid click Optimize The application works along the columns to adjust the grid to the position of the cores on the current slide We therefore recommend that you prepare the optimizing by manually adjusting the grid for the top and bottom rows of cores 5 To confirm your changes and update the TMA Grid View wi
219. ll functions existing in the drop down list under the relational function section is shown in table 7 2 on the current page Relational functions Table 7 2 Relational functions Function Description Mean Calculates the mean value of selected features of an image object and its neighbors You can select a class to apply this feature or no class if you want to apply it to all image objects Note that for averaging the feature values are weighted with the area of the image objects Standard Calculates the standard deviation of selected features of an image object deviation and its neighbors You can select a class to apply this feature or no class if you want to apply it to all image objects Mean difference Calculates the mean difference between the feature value of an image object and its neighbors of a selected class Note that the feature values are weighted by either by the border length distance 0 or by the area distance gt 0 of the respective image objects Mean absolute difference Calculates the mean absolute difference between the feature value of an image object and its neighbors of a selected class Note that the feature values are weighted by either by the border length distance 0 or by the area distance gt 0 of the respective image objects 27 September 2012 Continues User Guide Advanced Rule Set Concepts 149 Function Description Ratio Calculates the proportion
220. loper XD Portal ce ee ee ew ee eas 2 2 Developer Portal with Tissue Studio License 2 3 Starting Multiple Definiens Clients 24 The Develop Rule Sets VieW 25 55 sreco meree ey areni 235 Customizing the LAVvGUue es Sa Ae RE ERY ee eS Zo Default Toolbar Buttons sme c eo4 ead ae be Ye 25 2 Splits Wimdews s css paca slee BP Se Re YE EE 2 0 IMAGINE 224 6 2 tie ek eee Bee he Se Ghee eA 234 Dookie gt renean et y Ree eA Eee GS 299 Developer XD VIEWS s cida 525 4 ea aeee A 2 3 6 Image Layer Display poes socie AG e a ee 2 5 7 Adding Text to an Image oaaae 2 2 0 Navigatingin2D gt o cascca eee a ee 259 3D and4D Viewime scenes a ew a ew a ee a 3 An Introductory Tutorial St Identryine Shapes lt 65 oe hd 2a a bewd Bee se SES ES 3 1 1 Divide the Image Into Basic Objects 3 1 2 Identifying the Background 3 1 3 Shapes and Their Attributes lt s socre ew a a S14 The Complete Rule Set roco 44440566 Ga 4 eed des 4 Basic Rule Set Editing 4 1 Creating and Editing Processes in the Process Tree Window AA IMG oc he RR ER Pw ORE aE Se E 29 29 30 30 32 33 35 35 35 iii iv Developer XD 2 0 4 CA GSO 6 hobs oe Gli eh eee dette ie oh aegis 35 4 1 3 Image Object Domain lt s s es epres atris ee i 36 4 1 4 Algorithm Parameters aoaaa 36 42 Adding a Process c soe scoe darem ia A Re eR 36 4 2 1 Selecting and Configuring
221. lose Figure 6 23 The Feature Space Optimization dialog box 4 Select the image object level for the optimization 5 Enter the maximum number of features within each combination A high number reduces the speed of calculation 6 Click Calculate to generate feature combinations and their distance matrices 7 Click Show Distance Matrix to display the Class Separation Distance Matrix for Selected Features dialog box The matrix is only available after a calculation e The Best Separation Distance between the samples This value is the min imum overall class combinations because the overall separation is only as good as the separation of the closest pair of classes 8 After calculation the Optimized Feature Space group box displays the following results e The Dimension indicates the number of features of the best feature combina tion 9 Click Advanced to open the Feature Space Optimization Advanced Information dialog box and see more details about the results 2 TIP When you change any setting of features or classes you must first click Calculate before the matrix reflects these changes 2 The distance calculation is only based upon samples Therefore adding or deleting samples also affects the separability of classes 27 September 2012 User Guide About Classification 105 Class Separation Distance Matrix For Selected Features Chats Chats Woodland General Grassland General Impervious Genera
222. ltiple Maps 161 7 10 Workspace Automation 2 lt s socs cow mond sanp koade E o 162 TTIQI OVEIIEW ee coeg eom eh AERA ee E 162 7 10 2 Manually Creating Copies and Tiles 164 7 10 3 Manually Stitch Scene Subsets and Tiles 165 7 10 4 Processing Sub Scenes with Subroutines 165 7105 Multi Scale Workflows lt c s 0 5 55 54564 05 8b pe ews 167 Polk OBEST LINES 5 2556 b4455 2459 bbe ew beets BA BAS ES ws 172 7 11 1 About Image Object Links 172 7 11 2 Image Objects and their Relationships 173 7 11 3 Creating and Saving Image Object Links 173 7 12 Polygons and Skeletons s oe 2 bee ee eS 175 7 12 1 Viewing Polygons ooo scosse aope ee eR 175 712 2 Viewing Skeletons 406445 4464 484 4 4 Moe wd 177 7 13 Encrypting and Decrypting Rule Sets 0 178 8 Additional Development Tools 179 8 1 The Find and Replace Bar o 0c ee ee E 179 8 1 1 Find and Replace Modifiers 180 2 Rule Set Documentation 2 cc eoe AG Se oe Rs 180 8 2 1 Adding Comments ss 6 ee ee 180 8 2 2 The Rule Set Documentation Window 181 OS Process PAs sok sk A eh ew b EEA GORY Bee ER aes 181 8 4 Improving Performance with the Process Profiler 181 Moo PMID ss a eke SOA oe So eR eRe ee eRe doe eS 182 27 September 2012 User Guide CONTENTS vii Bol BiIppets OPHION e ecrini e a a ag dhe a aE a
223. ly information can also be displayed across projects To use this function the plate and site of the plate must be selected In the Navigation or Result tab of the Plate View and a parameter selected in the Results tab To open the Graph window select View gt Windows gt Graph from the main menu The Graph window opens with an empty diagram frame In Plate View select those wells of the plate map you want to see in the diagram Change to the Results tab and select the parameter The graph now displays the values of the parameter for the selected wells on the y axis The x axis indicates the co ordinates of the selected wells When you select different wells or a new parameter the graph updates automatically B L 2i Wells site 8 Figure 11 13 Graph window for selected wells Input Compounds to Plate Rows Plate View allows you to add compounds to the plate rows The idea is to create com pounds or edit existing ones customize your dilution sequences then assign and unassign the compound and sequence as needed The compounds and dilution sequences can be created edited saved and edited again If desired single concentrations can be assigned arbitrarily or to selected rows or columns Creating Compounds To create or edit compounds to add to a plate 1 To add compounds to plate rows first set positive and negative controls and select any inactive rows on the Layout tab 27 September 2012 User Guide Advanced Da
224. ly make sense in processes that need more than one image object as an input for example image object fusion You may have a PPO O feature evaluated for the candidate or for the target image object That feature is then compared or set to relation to the image object in the im age object domain of the same line that is the seed image object of the image object fusion Go to the Feature View window figure 7 29 to create a process related fea ture sometimes referred to as PPO feature Expand the process related fea tures group 27 September 2012 User Guide Advanced Rule Set Concepts 143 To create a process related feature PPO feature double click on the feature you want to create and add a process distance to the parent process object The process distance is a hierarchical distance in the process tree for exam ple e PPO O has the process distance 0 which refers to the image object in the current process that is mostly used in the image object fusion algorithm e PPO 1 has the process distance 1 which refers to the image object in the parent process one process hierarchy level above e PPO 2 has the process distance 2 which refers to the parent process two hierarchy levels above in the process hierarchy If you want to create a customized parent process object you also have to choose a feature 5 The following processes in the sample rule set are using different parent process object hierarchies Applying them is the sam
225. mage layers The order of layers can be changed using the up and down arrows User Guide 27 September 2012 68 Developer XD 2 0 4 Create Project Project Image Layers Thematk Leyers Metadata Project Name ME a Geocoding Lowe Let 0 0 Geocoding Uroa Right RII 50 ima Fle Location A Um iye lt imet Lam CDocument and Setting gtrockar Deckion Arch ie pno 1 Poet tung 7 Lyn C Documents and Setingr gtrocker Deckiog Arch ie ong 2 Poet St uneg 1 1 Layer 3 C Documents and Seting gtrocker Dechion Archie org 3 1 Pack Stung fe 1 Layer 4 CWDocuments and Setting gtrook er Desk top Arch ie prg 4 Peel S82 uneg No Das Eeteece Ming lt gt Thematic Layer Akat aj Insert 7 Renove Ea J J Ea Prevew CE re Figure 5 4 Create Project dialog box If you use multidimensional image data sets you can check and edit multi dimensional map parameters You can set the number the distance and the starting item for both slices and frames If you load two dimensional image data you can set the value of those pixels that are not to be analyzed Select an image layer and click the No Data button to open the Assign No Data Values dialog box If you import image layers of different sizes the largest image layer dimen sions determine the size of the scene When importing without using geocod ing the smaller image layers keep their size if the Enforce Fitting check box
226. mage object levels store image objects which are representative of this data The scene below is represented at the pixel level and is an image of a cell Each level has a super level above it where multiple objects may become assigned to single classes for example the cell level is the super level containing the cell body and nucleus whose objects comprise it Every image object is networked in a manner that each image object knows its context who its neighbors are which levels and objects superobjects are above it and which are below it sub objects No image object may have more than one superobject but it can have multiple sub objects 1 4 3 Image Object Domain The image object domain describes the scope of a process in other words which image objects or pixels an algorithm is applied to For example an image object domain is created when you select objects based on their size A segmentation classification segmentation cycle is illustrated in figure 1 2 on page 4 The square is segmented into four and the regions are classified into A and B Region B then undergoes further segmentation The relevant image object domain is listed under neath the corresponding algorithm 27 September 2012 User Guide Key Concepts 3 Cell Colleve AL j FD Cell body amp Ge Nucleus Nucleusleve veo Spots in Nucleus 2 Spotleve j differently colored pixels Pivellevel Figure 1 1 The hierarch
227. mage objects 3 Classify review the results and optimize your classification Defining Sample Image Objects For the Nearest Neighbor classification you need sam ple image objects These are image objects that you consider a significant representative of a certain class and feature By doing this you train the Nearest Neighbor classification algorithm to differentiate between classes The more samples you select the more con sistent the classification You can define a sample image object manually by clicking an image object in the map view You can also load a Test and Training Area TTA mask which contains previously manu ally selected sample image objects or load a shapefile which contains information about image objects For information on TTA masks to find out about shapefiles Adding Comments to an Expression Comments can be added to expressions using the same principle described in Adding Comments to Classes 6 1 3 The Edit Classification Filter The Edit Classification Filter is available from the Edit Process dialog for appropriate algorithms and can be launched from the Class Filter parameter The buttons at the top of the dialog allow you to e Select classes based on groups e Select classes based on inheritance e Select classes from a list this option has a find function The Use Array drop down box lets you filter classes based on arrays p 135 27 September 2012 User Guide About Classification 89 Edit
228. mask If your samples are all in one image object level it is selected automatically and cannot be changed 3 Click OK to save your changes Your selection of sample image objects is now converted to a TTA mask 4 To save the mask to a file select Classification gt Samples gt Save TTA Mask Enter a file name and select your preferred file format Loading and Applying a TTA Mask To load samples from an existing Training and Test Area TTA mask Apply TTA Mask to PX Figure 6 33 Apply TTA Mask to Level dialog box 1 From the main menu select Classification gt Samples gt Load TTA Mask 2 In the Load TTA Mask dialog box select the desired TTA Mask file and click Open 27 September 2012 User Guide About Classification 113 3 In the Load Conversion Table dialog box open the corresponding conversion table file The conversion table enables mapping of TTA mask classes to existing classes in the currently displayed map You can edit the conversion table 4 Click Yes to create classes from the conversion table If your map already contains classes you can replace them with the classes from the conversion file or add them If you choose to replace them your existing class hierarchy will be deleted If you want to retain the class hierarchy you can save it to a file 5 Click Yes to replace the class hierarchy by the classes stored in the conversion table 6 To convert the TTA Mask information into samples sele
229. mate rials provided with the distribution e Neither the name of the Insight Software Consortium nor the names of its con tributors may be used to endorse or promote products derived from this software without specific prior written permission THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CON TRIBUTORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES INCLUD ING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABIL ITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT INDIRECT INCIDENTAL SPECIAL EXEMPLARY OR CONSE QUENTIAL DAMAGES INCLUDING BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES LOSS OF USE DATA OR PROFITS OR BUSINESS INTERRUPTION HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY WHETHER IN CONTRACT STRICT LIABILITY OR TORT INCLUD ING NEGLIGENCE OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAM AGE 2012 Definiens AG Page collection published 27 September 2012 Typeset by Wikipublisher 27 September 2012 User Guide
230. matic User Guide 27 September 2012 198 Developer XD 2 0 4 layers to a new copy of the complete scene This copy is created using the create scene copy algorithm The subset thematic layers are matched correctly to the complete scene copy because they are geocoded Consequently you have a copy of the complete scene with intermediate result information of preceding subroutines Using the submit scenes for analysis algorithm you finally submit the copy of the com plete scene for further processing to a subsequent subroutine Here you can use the inter mediate information of the thematic layer by using thematic attribute features or thematic layer operations algorithms Advanced Transfer Results of Subsets at ROI_Level export classification to ExportObjectsThematicLayer create scene copy MainSceneCopy process MainSceneCopy subsets with Further Further Further Processing wg mr mr 9 2 Batch Processing 9 2 1 Submitting Batch Jobs to a Server Definiens Developer XD 2 0 4 enables you to perform automated image analysis jobs that apply rule sets to single or multiple projects It requires a rule set or existing ruleware file which may be arule set dcp or a solution dax Select one or more items in the Workspace window you can select one or more projects from the right hand pane or an entire folder from the left hand pane Choose Analysis gt Analyze from the main menu or right clic
231. me Vale B Level Names Level 1 Level 1 Level 2 Level 2 6 Variables not assigned Figure 4 10 The Edit Level Aliases dialog box User Guide 27 September 2012 a 50 Developer XD 2 0 4 You may want to rename an image object level name for example to prepare a rule set for further processing steps or to follow your organization s naming conventions You can also create or edit level variables and assign them to existing levels 1 To edit an image object level or level variable select Image Objects gt Edit Level Names from the main menu The Edit Level Aliases dialog box opens figure 4 10 2 Select an image object level or variable and edit its alias 3 To create a new image object level name type a name in the Alias field and click the Add Level or Add Variable button to add a new unassigned item to the Level Names or Variable column Select not assigned and edit its alias or assign another level from the drop down list Click OK to make the new level or variable available for assignment to a newly created image object level during process execution 4 To assign an image object level or level variable to an existing value select the item you want to assign and use the drop down arrow to select a new value To remove a level variable alias select it in the Variables area and click Remove 6 To rename an image object level or level variable select it in the Variables area type a new alias in the Alias fi
232. memory allowed for operation items MB Sample Brush Assign a maximum of memory allowed for undo items However a minimum number of operation items will be available as defined in Min length of undo stack above Default is 25 Replace existing samples Yes Replace samples that have already been selected when the sample brush is reapplied No Do not replace samples when the sample brush is reapplied Exclude objects that are already classified as sample class Unit Handling No Applying the sample brush to classified objects will reclassify them according to the current sample brush Yes Applying the sample brush to classified objects will not reclassify them Initialize unit conversion from input files Miscellaneous Used for image files with geocoding information Yes Use the unit in the image file No Ignore the unit in the image file and use the last settings selected in the Create Projects dialog box Automatically send crash reports to Definiens Engine No Default Do not send crash report Yes Send crash report supporting Definiens in improving its products Raster data access Direct Access image data directly where they are located Internal copy Create an internal copy of the image and accesses data from there User Guide 27 September 2012 252 Developer XD 2 0 4 Project Settings These values display the status after the last execution of the project They
233. ments typically used for image analysis within an industry or science domain However most tools and user interface elements that are hidden by default are still available 2 1 The Developer XD Portal The following portals are available e Cell recommended for cell based image analysis Standard portal for Definiens Cellenger application e Tissue recommended for tissue based image analysis Standard portal for Definiens TissueMap application e TMA recommended for the analysis of tissue micro arrays Standard portal for Definiens TMA application e Life standard portal for the life sciences domain We recommend you do not use the Cell Tissue or TMA portals for rule set development as this will create unwanted layers Users should use the Life portal in this case Open Definiens Developer XD 2 0 4 from the Windows Start menu and select a portal Click any portal item to stop automatic opening If you do not click a portal within three seconds the most recently used portal will start To start a different portal close the client and start again 2 2 Developer Portal with Tissue Studio License Customers who have also purchased Definiens Tissue Studio licenses will see further start up options relating to this product For more details see the Tissue Studio User Guide 8 Developer XD 2 0 4 DEF INIENS Select Portal Cel Tissue Figure 2 1 Start up options for Definiens Developer XD 2 0 4
234. mized window layout by opening a window layout and choosing the view settings you want to keep for each projection Select View gt Save Current Splitter Layout in the main menu to open the Save Custom Layout dialog box Choose a layout label Custom through Custom 7 and choose synchronization options for planar projections The options are e None The Sync button is inoperative it will not synchronize view settings crosshairs or zoom settings in any of the projections e By rows The Sync button operates only across rows of the display e By columns The Sync button operates only across columns of the display e All The Sync button synchronizes all planar projections displayed Click OK to save the layout It is saved to the user information on the computer Viewing a Time Series Image data that includes a time series can be viewed as an anima tion You can also step though frames one at a time The current frame number displays in the bottom right corner of the map view User Guide 27 September 2012 28 Developer XD 2 0 4 To view an animation of an open project click the play button in the Animation toolbar to stop click again You can use the slider in the Animation toolbar to move back and forth through frames Either drag the slider or click it and then use the arrow keys on your keyboard to step through the frames You can also use buttons in the 3D Settings toolbar to step back and forth through frames 27 September 2012 Us
235. monly called film A time series data set consists of a series of frames where each frame is a 2D image Its co ordinates are x y t Its elementary unit is a pixel series 2 Developer XD 2 0 4 1 3 Segmentation and classification The first step of a Definiens image analysis is to cut the image into pieces which serve as building blocks for further analysis this step is called segmentation and there is a choice of several algorithms to do this The next step is to label these objects according to their attributes such as shape color and relative position to other objects This is typically followed by another segmentation step to yield more functional objects This cycle is repeated as often as necessary and the hierarchies created by these steps are described in the next section 1 4 Image Objects Hierarchies and Domains 1 4 1 Image Objects An image object is a group of pixels in a map Each object represents a definite space within a scene and objects can provide information about this space The first image objects are typically produced by an initial segmentation 1 4 2 Image Object Hierarchy This is a data structure that incorporates image analysis results which have been extracted from a scene The concept is illustrated in figure 1 1 on the facing page It is important to distinguish between image object levels and image layers Image layers represent data that already exists in the image when it is first imported I
236. more processes to it and they can be encrypted separately if you wish Decrypting a rule set is essentially the same process first load it into the Process Tree window then open the Process menu in the main menu bar and select Decrypt Rule Set to open the Decrypt Data dialog box When you enter your password the padlock icon will disappear and you will be able to read and modify the processes If the rule set is part of a project and you close the project without saving changes the tule set will be decrypted again when you reopen the project The License id field of the Encrypt Data dialog box is used to restrict use of the rule set to specific Definiens licensees Simply leave it blank when you encrypt a rule set 27 September 2012 User Guide 8 Additional Development Tools 8 1 The Find and Replace Bar Find and Replace is a useful method to browse and edit rule set items allowing you to replace them by rule set items of the same category This is helpful especially for maintaining large rule sets and for development in teams Within a rule set you can find and replace all occurrences the following rule set items algorithms within an rule set loaded in the Process Tree window classes class vari ables features feature variables image layers image object levels level variables map variables object variables region variable scene variables text and thematic layers To open the Find and Replace window do one of the follo
237. mple Simply right click in the right or left hand pane of the Workspace Window and select Copy to Clipboard 9 1 3 Collecting Statistical Results of Subscenes Subscenes can be tiles or subsets You can export statistics from a subscene analysis for each scene and collect and merge the statistical results of multiple files The advantage is that you do not need to stitch the subscenes results for result operations concerning the main scene To do this each subscene analysis must have had at least one project or domain statistic exported All preceding subscene analysis including export must have been processed completely before the Read Subscene Statistics algorithm starts any result summary cal culations To ensure this result calculations are done within a separate subroutine After processing all subscenes the algorithm reads the exported result statistics of the subscenes and performs a defined mathematical summary operation The resulting value representing the statistical results of the main scene is stored as a variable This variable can be used for further calculations or export operations concerning the main scene 9 1 4 Executing Rule Sets with Subroutines A rule set with subroutines can be executed only on data loaded to a workspace This enables you to review all projects of scenes subset and tiles They all are stored in the workspace A rule set with subroutines can only be executed if you are connected to a Defini
238. mple of an image with one layer whereas the most common single layers are the red green and blue RGB layers that go together to create a color image In addition image layers can contain information such as the intensity values of biomarkers used in life sciences or the near infrared NIR data contained in remote sensing images Image layers can also contain a range of other information such as geographical elevation models Definiens Developer XD 2 0 4 allows the import of these image raster layers It also supports what are known as thematic raster layers which can contain qualitative and categorical information about an area an example is a layer that acts as a mask to identify a particular region 1 2 Image Data Set Definiens software handles two dimensional images and data sets of multidimensional visual representations e A 2D image is set of raster image data representing a two dimensional image Its co ordinates are x y Its elementary unit is a pixel e A 3D data set is a set of layered 2D images called slices A 3D data set consists of a stack of slices representing a three dimensional space Its co ordinates are x y z Its elementary unit is a voxel A 4D data set is a temporal sequence of 3D data sets A 4D data set consists of a series of frames each frame consisting of a 3D data set Its co ordinates are x y z t Its elementary unit is a voxel series e A time series data set is a sequence of 2D images com
239. mporting Scenes into a Workspace import Scenes Rock Folder of Image Oste Dworkin Folder AcbonLte aryl Acon Be ary Gelete mais DICOM import eCognition harg_detect hang_macs mch massi cut shatnbcs I Search in ablolders Figure 5 12 Import Scenes dialog box Before you can start working on data you must import scenes in order to add image data to the workspace During import a project is created for each scene You can select different predefined import templates according to the image acquisition facility producing your image data User Guide 27 September 2012 76 Developer XD 2 0 4 If you only want to import a single scene into a workspace use the Add Project command To import scenes to a workspace choose File gt Predefined Import from the main menu or right click the left hand pane of the Workspace window and choose Predefined Import The Import Scenes dialog box opens figure 5 12 1 Select a predefined template from the Import Template drop down box 2 Browse to open the Browse for Folder dialog box and select a root folder that contains image data 3 The subordinate file structure of the selected image data root folder is displayed in the Preview field The plus and minus buttons expand and collapse folders 4 Click OK to import scenes The tree view on the left hand pane of the Workspace window displays the file structure of the new projects each of which administrate one scene Cell
240. must be saved with the rule set in order to display after loading it These settings can be changed by using the Set Rule Set Options algorithm Update topology Yes default Object neighbor list is created If No object neighbor list is created on demand Polygon compatibility mode Several improvements were made to polygon creation after version 7 0 6 These improvements may cause differences in the generation of polygons when older files are opened Polygon compatibility mode ensures backwards compatibility By default compatibility mode is set to none for rule sets created with version v7 0 6 and older the value is v7 0 This option is saved together with the rule set Resampling compatibility mode The rendering of resampled scenes has been improved in this software version This mode enables old rule sets to deliver same analysis result as previous versions Current resampling method The current resampling method Default is Center of Pixel Distance calculation The current distance calculation Default is Smallest Enclosing Rectangle Evaluate conditions on undefined features as 0 The current value Default is Yes No means ignore Polygons base polygon threshold Display the degree of abstraction for the base polygons Default is 1 25 Polygons shape polygon threshold Display the degree of abstraction for the shape polygons Default is 1 00 Polygons remove
241. n Process 6972 3 1 6972s Figure 8 3 The Process Profiler window e Times below one hour are displayed as minutes seconds and milliseconds e Longer times are displayed as hours minutes and seconds By default the slowest five processes are displayed Under the Options tab you can change the profiling settings Process Profiler slowest 5 process C processes longer than 1 sec C processes takemorethan 30 Show long process name IV Always do profiling gt Report Options Figure 8 4 The Options tab of the Process Profiler window You can also inactivate process profiling in Tools gt Options which removes the time display before the process name 8 5 Snippets A process snippet is part of a rule set consisting of one or more processes You can organize and save process snippets for reuse in other rule sets You can drag and drop processes between the Process Tree window and the Snippets window To reuse snippets in other rule sets export them and save them to a snippets library Open the Snippets window using View gt Windows gt Snippets or Process gt Snippets from the main menu By default the Snippets window displays frequently used algorithms that you can drag into the Process Tree window Drag a process from the Process Tree window into the Snippets window you can drag any portion of the Process Tree along with its child 27 September 2012 User Guide Additional D
242. n be selected whenever layers can be selected for example in features domains and algorithms They can be passed as parameters in customized algorithms Map Variables Map Variables have maps as their values They can be selected wherever a map is selected for example in features domains and algorithm parameters They can be passed as parameters in customized algorithms Feature List Variables Feature List lets you select which features are exported as statistics Image Object List Variables The Image Object List lets you organize image objects into lists and apply functions to these lists 7 3 2 Creating a Variable To open the Manage Variables box go to the main menu and select Process gt Manage Variables or click the Manage Variables icon on the Tools toolbar Manage Variables Scene Object Chats Fosse Levei Image Layer ThemsicLayer Regen Map FestreLit image Otject List Nore v Figure 7 11 Manage Variables dialog box 27 September 2012 User Guide Advanced Rule Set Concepts 131 Select the tab for the type of variable you want to create then click Add A Create Variable dialog box opens with particular fields depending on which variable is selected Creating a Scene or Object Variable Selecting scene or object variables launches the same Create Variable dialog box Create Scene Variable Name new vanai Figure 7 12 Create Scene Variable dialog box The Name and Val
243. n3 dep Server http focalhost 8 186 Package XD 2 0 last M Advanced Analyze Top scenes Figure 9 10 Start Analysis General setting however you can address a specific package if it is available on the Grid e g XD 2 0 4 2073 6 Selecting Advanced offers two further options 6 1 The Analyze drop down lets you restrict analysis to Tiles Top Scenes or All Scenes 6 2 Use Time Out will cancel a job if the server is not responding after a defined time period NOTE If you want to repeat an automated image analysis for example when testing you can rollback all changes of the analyzed projects to re store the original version To determine which projects have been analyzed go to the Workspace window and sort the State column Select the ones marked processed for rollback Changing the Configuration of the Analysis Engine These settings are designed for advanced users Do not alter them unless you are aware of a specific need to change the default values and you understand the effects of the changes The Export tab figure 9 11 lets you change the destination folder of your exported re sults The Configuration tab figure 9 12 enables you to review and alter the configuration information of a job before it is sent to the server The configuration information for a job User Guide 27 September 2012 200 Developer XD 2 0 4 describes the required software and licenses needed to process the job This
244. nates If you select Execute in the Image Object Domain drop down box the given PIXEL co ordinates of the source scene are used e Based on classified image objects If you select an image object level in the Image Object Domain drop down list you can select classes of image objects For each image object of the selected classes a subset is created based on a rectangular cutout around the image object Neighboring image objects of the selected classes which are located inside the cutout rectangle are also copied to the scene subset You can choose to exclude them from further processing by giving the parameter Exclude Other Image Objects a value of Yes If Exclude Other Image Objects is set to Yes any segmentation in the scene subset will only happen within the area of the image object used for defining the subset Results are not transferred to scene subsets The scene subset is created as a sub scene below the project in the workspace Scene subsets can be created from any data set for example 2D or 3D data sets Creating a subset from a 3D 2D T or 4D data set will reverse the slice order for the created sub scene Scene Tiles Sometimes a complete map needs to be analyzed but its large file size makes a straight forward segmentation very time consuming or processor intensive In this case creating scene tiles is a useful strategy The absolute size limit for an image to be segmented in Definiens Developer XD 2 0 4 is 231 46 340
245. nce segmentation e Multiresolution segmentation region grow 2 In the Algorithm parameters area expand the Thematic Layer usage list and select the thematic layers to be considered in the segmentation You can use the following methods e Select an thematic layer and click the drop down arrow button placed inside the value field Define for each the usage by selecting Yes or No e Select Thematic Layer usage and click the ellipsis button placed inside the value field to set weights for image layers Edit Process Aigne ae etes LA Por ameter 5 Levei Name t 2 E insp Lager wagi relsens seperi yar 1 addaw 9 ltdiv Image Otci Doman poai vei Passera ddew T a tet no condon Mamam anbe Of maage decti Looge amp Cycles Loop whe cometheng change Number of ccie Figure 7 10 Define the Thematic layer usage in the Edit Process dialog box 27 September 2012 User Guide Advanced Rule Set Concepts 129 7 3 Variables in Rule Sets Within rule sets you can use variables in different ways Some common uses of variables are e Constants e Fixed and dynamic thresholds e Receptacles for measurements e Counters e Containers for storing temporary or final results e Abstract placeholders that stand for a class feature or image object level While developing rule sets you commonly use scene and object variables for storing your dedicated fine tuning tools for reuse within similar projects
246. nearest neighbor te Nearest neighbor Object features Customized Shape 3 Textue Variables ds Hierarchy Thematic attributes Class Related features e Relations to neighbor objects A Relations to sub objects Retations to super objects Relations to Classification Scene features Variables ClassReloted SceneRelated Process felated features Customized Srrdanitty to classes Logical terms t t t t t Ca J coe Figure 6 5 Insert Expression dialog box het with and mn rhen wth and min Cortsmed Contaned EEE symmetiy and reer wot Clase D SS gt n 3 alm s not Class D N Asymmetry or max Y Rel Border to Class C Neighbor Objects Y Rel Bordes to Class C Neighbor Objects _ Ratio Amm_ihv_o bmp L Ratio Amm_thy_o bap Figure 6 6 Moving expressions using drag and drop operations e Select Operator for Expression Allows you to choose a logical operator from the list e Edit Standard Nearest Neighbor Feature Space Selects or deselects features for the standard nearest neighbor feature space e Edit Nearest Neighbor Feature Space Selects or deselects features for the nearest neighbor feature space Evaluating Undefined Image Objects Image objects retain the status undefined when they do not meet the criteria of a feature If you want to use these image objects anyway for example for further processing you mu
247. need to be in the Workspace window which is displayed by default in views and 3 on the main toolbar or can be launched using View gt Windows gt Workspace You can select a single project to tile its scenes or select a folder with projects within it To open the Create Tiles dialog box choose Analysis gt Create Tiles or select it by right clicking in the Workspace window The Create Tiles box allows you to enter the horizon tal and vertical size of the tiles based on the display unit of the project For each scene to be tiled a new tiles folder will be created containing the created tile projects named tilenumber You can analyze tile projects in the same way as regular projects by selecting single or multiple tiles or folders that contain tiles Stitching Tiling Results Together Only the main map of a tile project can be stitched together In the Workspace window select a project with a scene from which you created tiles These tiles must have already been analyzed and be in the processed state To open the Stitch Tile Results dialog box select Analysis gt Stitch Projects from the main menu or right click in the Workspace window The Job Scheduler field lets you specify the computer that is performing the analysis It is set to http localhost 8184 by default which is the local machine However if you are running Definiens Developer XD 2 0 4 over a network you may need change this field to the address of another comp
248. ning class related features Only classes at the bottom level of the inheritance class hierarchy can use class related features in a nearest neighbor e It is impossible to use class related features that refer to classes in the same group including the group class itself User Guide 27 September 2012 7 Advanced Rule Set Concepts 7 1 Units Scales and Co ordinate Systems Life science images do not typically carry co ordinate information therefore units scales and pixel sizes of projects can be set manually in two ways e When you create a project you can define the units in the Create Project dialog box File gt Create Project When you specify a unit in your image analysis Developer XD will always reference this value For example if you have an image of a land area with a scale of 15 pixels km enter 15 in the Pixel Size Unit box and select kilometer from the drop down box below it You can also change the unit of an existing project by going to File gt Modify Open Project e During rule set execution with the Scene Properties algorithm See the Reference Book for more details The default unit of a project with no resolution information is a pixel For these projects the pixel size cannot be altered Once a unit is defined in a project any number or features within a rule set can be used with a defined unit Here the following rules apply e A feature can only have one unit within a rule set The unit of the feature
249. nnot delete an extension If you have altered the initial configuration return to the initial state by using the context menu or clicking the Reset Configuration Info button In the initial state the plug ins displayed are those associated with the rule set that has been loaded Click the Load Client Config Info button or use the context menu to load the plug in configuration of the client For example if you are using a rule set developed with an earlier version of the client you can use this button to display all plug ins associated with the client you are currently using 9 2 2 Tiling and Stitching Tiling and stitching is a Definiens method for handling large images When images are so large that they begin to degrade performance we recommend that they are cut into smaller pieces which are then treated individually Afterwards the tile results are stitched together The absolute size limit for an image in Developer XD is 2 46 340 x 46 340 pixels User Guide 27 September 2012 202 Developer XD 2 0 4 Creating tiles splits a scene into multiple tiles of the same size and each is represented as a new map in a new project of the workspace Projects are analyzed separately and the results stitched together although we recommend a post processing step Creating Tiles Creating tiles is only suitable for 2D images The tiles you create do not include results such as image objects classes or variables To create a tile you
250. ns cascading loops based on a number you define the feature can also run loops while a feature changes for example growing 4 2 4 Executing a Process To execute a single process select the process in the Process Tree and press F5 Alterna tively right click on the process and select Execute If you have child processes below your process these will also be executed You can also execute a process from the Edit Process dialog box by pressing Execute instead of OK which adds the process to the Process Tree window without executing it 4 2 5 Executing a Process on a Selected Object To execute a process on an image object that as already been defined by a segmentation process select the object then select the process in the Process Tree To execute the process right click and select Execute on Selected Object or press F6 User Guide 27 September 2012 40 Developer XD 2 0 4 4 2 6 Parent and Child Processes The introductory tutorial p 29 will have introduced you to the concept of parent and child processes Using this hierarchy allows you to organize your processes in a more logical way grouping processes together to carry out a specific task Go to the Process Tree and right click in the window From the context menu choose Append New the Edit Process dialog figure 4 2 will appear This is the one time it is recommended that you deselect automatic naming and give the process a logical name as you are essentially making
251. ntation to calculate a threshold dividing the selected set of pixels into two subsets Spectral Difference Segmentation Spectral difference segmentation lets you merge neighboring image objects if the dif ference between their layer mean intensities is below the value given by the maximum spectral difference It is designed to refine existing segmentation results by merging spectrally similar image objects produced by previous segmentations and therefore is a bottom up segmentation The algorithm cannot be used to create new image object levels based on the pixel level 4 3 3 Segmentation by Reshaping Algorithms All algorithms listed under the Reshaping Algorithms group technically belong to the segmentation strategies Reshaping algorithms cannot be used to identify undefined im age objects because these algorithms require pre existing image objects However they are useful for getting closer to regions and image objects of interest The Multiresolution Segmentation algorithm criteria Smoothness and Compactness are not related to the fea tures of the same name Sometimes reshaping algorithms are referred to as classification based segmentation algorithms because they commonly use information about the class of the image objects to be merged or cut Although this is not always true Definiens Developer XD 2 0 4 uses this terminology User Guide 27 September 2012 46 Developer XD 2 0 4 NOTE Sometimes reshaping a
252. ntent of the image layers 1 To create a general settings definition go to the upper pane of the Analysis Builder window select and right click any item or the background and choose Add General Settings The General Settings definition item is added at the top of the window 2 For editing select a General Settings definition item and edit the widgets in the same way as for action definitions Editing Action Library Properties Edit Action Library Cell Based Assay Library GUIO CO0E235E C086 4858 AC30 2A87A7CD3F3A Generate Location D Module _6_BulldanarchitectSolution 2 Acton Library location D Module_6 BulldAnarchitectSolution CelBasedAssayLibrary Figure 10 3 Edit Action Library dialog box Selecting Library gt Action Library Properties brings up the Edit Action Library dialog box figure 10 3 The dialog has fields which allow you to edit the name and version of your action library To create a globally unique identifier GUID press the Generate button Generating a new GUID when an action library is amended is a useful way for a developer to notify 27 September 2012 User Guide en Rule Sets for Definiens Architect XD 215 an action library user of changes as the software will tell the user that the identifier is different Editing Action Groups Every action is part of a certain action group If the appropriate action group does not yet exist you have to create it Edit Group F
253. nterest and create a scene subset of the regions of interest at a higher scale e In order to allow faster and concurrent processing create tiles e Stitch the tiles back together and copy the results to the scene subsets e Stitch the scene subsets with their results back together Workflow Subroutine Key Algorithm 1 Create a scene copy at lower Main Create Scene Copy magnification 2 Find regions of interest ROIs Create rescaled subsets of Common image analysis ROIs algorithms User Guide 27 September 2012 170 Developer XD 2 0 4 Workflow Subroutine Key Algorithm 3 Create subsets of ROIs at Create rescaled subsets of Create Scene Subset higher magnification ROIs 4 Tile subsets Tiling and stitching of Create Scene Tiles subsets 5 Detailed analysis of tiles Detailed analysis of tiles Several 6 Stitch tile results to subset Detailed analysis of tiles Submit Scenes for results Analysis 7 Merge subsets results back to Create rescaled subsets of Submit Scenes for main scene ROIs Analysis 8 Export results of main scene Export results of main Export Classification View scene This workflow could act as a prototype of an analysis automation of an image at different magnifications or resolutions However when developing rule sets with subroutines you must create a specific sequence tailored to your image analysis problem Multi Scale 1 Rescale a Scene Copy Create a rescaled scene copy at a lower magnifica ti
254. o array can contain any number of cores which can be automatically detected and matched to a de fault or user defined grid before being analyzed The results of automatic core detection and matching can be manually edited The actions described in this section are performed in the TMA Grid View which opens by default when you select the TMA portal at startup 11 3 1 Defining the Grid Layout A default grid layout is supplied with Definiens Developer XD 2 0 4 It is automatically displayed when you start the application and can be used to match all available slides However depending on the analysis you wish to perform it might be necessary to edit an existing layout or to create a new layout 1 Open a workspace containing the slides of the tissue micro array you want to ana lyze In the TMA Grid View select the Layout tab 2 To edit an existing layout select the layout name from the dropdown list under Grid Layout Templates and then click Edit To create a new layout click New 3 Under Grid Parameters define the following settings e Enter a name for the new or amended grid layout in the Name field e If necessary change the number and order of the grid s rows and columns User Guide 27 September 2012 234 Developer XD 2 0 4 Figure 11 9 TMA Grid View in Layout mode e To set the new or amended layout as the default layout check the Default checkbox 4 Under Core Type define arrays as positive or negative contro
255. o substan tial over stretching on many normal images It can be helpful in cases where you want to display dark areas with more contrast Manual Image Layer Equalization enables you to control equalization in detail For each image layer you can set the equalization method In addition you can define the input range by setting minimum and maximum values Compare the following displays of the same scene Figure 2 16 Left Three layer mix red green blue with Gamma correction 0 50 Right One layer mix with linear equalizing 1 00 2 5 7 Adding Text to an Image In some instances it is desirable to display text over an image for example patients names on MRI and CT scans In addition text can be incorporated into a digital image if it is exported as part of a rule set 27 September 2012 User Guide Starting Developer 21 E Pret A inked TER Bris sired Figure 2 17 Left Three layer mix red green blue without equalizing Right Six layer mix with Histogram equalization Image data courtesy of the Ministry of Environmental Affairs of Sachsen Anhalt Germany Figure 2 18 MRI scan with text display To add text double click on the image in the corner of Map View not the image itself where you want to add the text which causes the appropriate Edit Text Settings window to launch figure 2 19 The buttons on the right allow you to insert the fields for map name slice position and any values you wis
256. ocess or to update a variable Update Variable Combined with threshold if Combined with map on map Threshold Loop While Change while Threshold condition Map Pixel level Applies the algorithm to the pixel level Typically used for initial segmentations and filters Map Threshold condition Image object level Applies the algorithm to image objects on an image object level Typically used for object processing Level Class filter Threshold condition Map Region Max number of image objects Current image object Applies the algorithm to the current internally selected image object of the parent process Class filter Threshold condition Max number of image objects Neighbor image object Applies the algorithm to all neighbors of the current internally selected image object of the parent process The size of the neighborhood is defined by the Distance parameter Class filter Threshold condition Max number of image objects Distance Continues User Guide 27 September 2012 38 Developer XD 2 0 4 Basic Domain Usage Parameters Super object Applies the algorithm to the superobject of Class filter Threshold the current internally selected image object condition Level distance of the parent process The number of levels Max number of image up the image objects level hierarchy is objects defined by the Level Distance parameter Sub objects Applies the al
257. of the tissue micro array you want to ana lyze In the TMA Grid View select the Matching tab Select the slide whose cores you want to match You can switch between all avail able slides using Slide Navigation or selecting a slide from the workspace list If necessary select another than the default grid layout from the dropdown list and click Assign to assign the selected layout to the current slide Under Core Detection define a spectral threshold as well as a minimum size for the detected cores The background threshold is defined as the maximum percentage of a defined spectral background value that is taken into account for core detection in other words only cores with a value below this threshold are accepted The minimum size is defined as the minimum percentage of a complete core that is taken into account for core detection therefore only cores with a size above this threshold are accepted The higher the background threshold and the lower the minimum size threshold the more cores are detected 1 Click Detect Cores The application determines all the cores that match your core detection settings and inserts them into the assigned grid A subset is created for each core You can display the individual subsets by double clicking them in the slide To switch back to the display of the complete slide select Show Slide Check whether all relevant cores have been detected You can manually add or delete cores or change th
258. of workspace automation subroutines enable you to automate and accelerate the processing especially the processing of large scenes Removing Projects and Deleting Folders When a project is removed the related image data is not deleted To remove one or more projects select them in the right pane of the Workspace window Either right click the item and select Remove or press Del on the keyboard To remove folders along with their contained projects right click a folder in the left hand pane of the Workspace window and choose Remove from the context menu If you removed a project by mistake just close the workspace without saving After reopening the workspace the deleted projects are restored to the last saved version Saving a Workspace List to File To save the currently displayed project list in the right hand pane of the Workspace window to a csv file 1 Go to the right pane of the Workspace window Right click a project and choose Save list to file from the context menu User Guide 27 September 2012 196 Developer XD 2 0 4 2 The list can be opened and analyzed in applications such as Microsoft Excel In the Options dialog box under the Output Format group you can define the decimal separator and the column delimiter according to your needs Copying the Workspace Window The current display of both panes of the Workspace can be copied the clipboard It can then be pasted into a document or image editing program for exa
259. ogic Double clicking on a class in the Class Hierarchy window launches the Class Description dialog box To open the Membership Function dialog right click on an expression the default expression in an empty box is and min to insert a new one select Insert New Expression You can edit an existing one by right clicking and selecting Edit Expression Membership Function mH 68 8281044 097 Figure 6 9 The Membership Function dialog box The selected feature is displayed at the top of the box alongside an icon that allows you to insert a comment The Initialize area contains predefined functions these are listed in the next section It is possible to drag points on the graph to edit the curve although this is usually not necessary we recommend you use membership functions that are as broad as possible Maximum Value and Minimum Value allow you to set the upper and lower limits of the membership function It is also possible to use variables as limits Left Border and Right Border values allow you to set the upper and lower limits of a feature value In this example the fuzzy value is between 100 and 1 000 so anything below 100 has a membership value of zero and anything above 1 000 has a membership value of one Entire Range of Values displays the possible value range for the selected feature For certain features you can edit the Display Unit User Guide 27 September 2012 94 Developer XD 2 0 4 e The name of
260. om one subroutine to another subroutine using copy and paste commands Subroutines are saved together with the rule set right click in the Process Tree window and select Save Rule Set from the context menu 7 10 5 Multi Scale Workflows The strategy behind analyzing large images using workspace automation depends on the properties of your image and the goal of your image analysis Most likely you will have one of the following use cases e Complete analysis of a large image for example finding all the houses in a satellite image In this case an approach that creates tiles of the complete image and stitches them back together is the most appropriate e A large image that contains small regions of interest requiring a detailed analysis such as a tissue slide containing samples In this use case we recommend you create a small scale copy and derive full scale subsets of the regions of interests only To give you practical illustrations of structuring a rule set into subroutines refer to the use cases in the next section which include samples of rule set code For detailed instructions see the related instructional sections and the algorithm settings in the Developer XD Reference Book Tiling and Stitching Tiling an image is useful when an analysis of the complete image is problematic Tiling creates small copies of the image in sub scenes below the original image For an example of a tiled top scene see figure 7 43 on the following pa
261. on image objects of the class no_background in order to analyze ROIs only The subsets created must be sent to a subroutine for analysis Add a process with the algorithm Submit Scenes for Analysis to the end of the main process tree this executes a subroutine that defines the detailed image analysis processing on a separate tab Use Cases Multi Scale Image Analysis 1 3 Creating scene copies and scene subsets is useful if working on a large image data set with only a small region of interest Scene copies are used to downscale the image data Scene subsets are created from the region of interest at a preferred magnification or resolution Reducing the resolution of an image can improve performance when analyzing large projects In Developer XD you can start an image analysis on a low resolution copy of a map to identify structures and regions of interest All further image analyses can then be done on higher resolution scenes For each region of interest a new subset project of the scene is created at high resolution The final detailed image analysis takes place on those subset scenes This multi scale workflow can follow the following scheme e Create a downsampled copy of the scene at a lower resolution to perform an overview analysis This scene copy will become a new map in a new project of the workspace e Analyze the downsampled scene copy to find regions of interest To allow a faster detailed image analysis select regions of i
262. on in the Value field to open the Select Single Feature dialog box and select a feature as a value After you confirm the variable with OK the new variable displays in the Manage Vari ables dialog box and under Feature Variables in the feature tree in several locations for example the Feature View window and the Select Displayed Features dialog box Creating a Region Variable Region Variables have regions as their values and can be created in the Create Region Variable dialog box You can enter up to three spatial dimensions and a time dimension The left hand column lets you specify a region s origin in space and the right hand column its size The new variable displays in the Manage Variables dialog box and wherever it can be used for example as an image object domain parameter in the Edit Process dialog box Creating Other Types of Variables Create Level Variable allows the creation of variables for image object levels image layers thematic layers maps or regions Create Level Variable Figure 7 15 Create Level Variable dialog box The Value drop down box allows you to select an existing level or leave the level variable unassigned If it is unassigned you can use the drop down arrow in the Value field of the Manage Variables dialog box to create one or more new names 27 September 2012 User Guide Advanced Rule Set Concepts 133 7 3 3 Saving Variables as Parameter Sets Parameter sets are storage containers for
263. on or resolution and submit for processing to find regions of interest In this use case you use a subroutine to rescale the image at a lower magnification or resolution before finding regions of interest ROIs In this way you reduce the amount of image data that needs to be processed and your process consumes less time and perfor mance For the first process use the Create Scene Copy algorithm With the second process based on the Submit Scenes for Analysis algorithm you submit the newly created scene copy to a new subroutine for finding ROIs at a lower scale NOTE When working with subroutines you can merge back selected re sults to the main scene This enables you to reintegrate results into the complete image and export them together To fulfill a prerequisite to merg ing results back to the main scene set the Stitch Subscenes parameter to Yes in the Submit Scenes Analysis algorithm Figure 7 45 Subroutines are assembled on tabs in the Process Tree window 27 September 2012 User Guide Advanced Rule Set Concepts 171 Multi Scale 2 Create Rescaled Subset Copies of Regions of Interest In this step you use a subroutine to find regions of interest ROIs and classify them in this example as ROD Based on the image objects representing the ROIs you create scene subsets of the ROIs Using the Create Scene Subset algorithm you can rescale them to a higher magnification or resolution This scale wil
264. ontains the class ID color coding RGB values and class name by default However with this export type adjacent image objects belonging to the same class can no longer be distinguished 3 From the Format drop down list select the file format for the export file Supported formats are asc img tif jpg jp2 png bmp pix tif and png 4 Under Level select the image object level for which you want to export results 5 Change the default file name in the Export File Name text box if desired 6 Click the Select classes button to open the Select Classes for Shape Export dialog box where you can add or remove classes to be exported 7 Click the Select features button to open the Select Features for Export as Attributes dialog box where you can add or remove features to be exported 6 The thematic raster layer is saved as a 32 bit image file But not all image viewers can open these files To view the file in Definiens Developer XD 2 0 4 add the 32 bit image file to a current map or create a new project and import the file 27 September 2012 User Guide Automating Data Analysis 205 Export Results Expeet Type Raster file Brghiness Mean Layes_Cell_Stan Content Type Image objects v Foemat 8 bit png png Levet Figure 9 13 Exporting image objects with the Export Results dialog box 8 To save the file press Export An attribute table in csvq file format is automatically created 9 To view
265. or Each Layer checkbox Select one or more image layers Enter a value for those pixels that are not to be analyzed Click Assign For exam ple in the dialog box above the no data value of Layer 1 is 0 000000 This implies that all pixels of the image layer Layer 1 with a value of zero i e the darkest pix els are excluded from the analysis The no data value of Layer 2 is set to 255 in the Value field Select Intersection to include those overlapping no data areas only that all image layers have in common Select Union to include the no data areas of all individual image layers for the whole scene that is if a no data value is found in one image layer this area is treated as no data in all other image layers too 5 2 5 Importing Image Layers of Different Scales You can insert image layers and thematic layers with different resolutions scales into amap They need not have the same number of columns and rows To combine image layers of different resolutions scales the images with the lower resolution having a larger pixel size are resampled to the size of the smallest pixel size If the layers have exactly the same size and geographical position then geocoding is not necessary for the resampling of images Figure 5 7 Left Higher resolution small pixel size Right Lower resolution image is resampled to be imported 5 2 6 Geocoding Geocoding is the assignment of positioning marks in images by co ordinates In earth
266. ou select image layers and optional data sources like thematic layers or metadata for loading to a new project You can rearrange the image layers select a subset of the image or modify the project default settings In addition you can add metadata An image file contains one or more image layers For example an RGB image file con tains three image layers which are displayed through the Red Green and Blue channels layers Open the Create Project dialog box by going to File gt New Project for more detailed information on creating a project refer to The Create Project Dialog Box The Import Image Layers dialog box opens Select the image data you wish to import then press the Open button to display the Create Project dialog box 5 2 1 File Formats Opening certain file formats or structures requires you to select the correct driver in the Files of Type drop down list Then select from the main file in the files area If you select a repository file archive file another Import Image Layers dialog box opens where you can select from the contained files Press Open to display the Create Project dialog box figure 5 4 27 September 2012 User Guide Projects and Workspaces 67 File pame Files of type All Files Go to folder Evotec Flex Files Hex Mirax ShdelO Files inil Figure 5 3 The Import Image Layers dialog box 5 2 2 The Create Project Dialog Box The Create Project dialog box figure 5 4 giv
267. out actually changing them You can also choose to hide layers which can be very helpful when investigating image data and results NOTE Changing the image layer mixing only changes the visual display of the image but not the underlying image data it has no impact on the process of image analysis 27 September 2012 User Guide Starting Developer 17 When creating a new project the first three image layers are displayed in red green and blue 1 To change the layer mixing open the Edit Image Layer Mixing dialog box fig ure 2 10 e Choose View gt Image Layer Mixing from the main menu e Double click in the right pane of the View Settings window Define the display color of each image layer For each image layer you can set the weighting of the red green and blue channels Your choices can be displayed together as additive colors in the map view Any layer without a dot or a value in at least one column will not display Choose a layer mixing preset see figure 2 11 e Clear All assignments and weighting are removed from the Image Layer table One Layer Gray displays one image layer in grayscale mode with the red green and blue together False Color Hot Metal is recommended for single image layers with large intensity ranges to display in a color range from black over red to white Use this preset for image data created with positron emission tomography PET False Color Rainbow is recomm
268. pplications workspaces reference the values of exported results and hold processing information such as import and export templates the required ruleware processing states and the required software configuration A workspace is saved as a set of files that are referenced by a dpj file Creating Saving and Loading Workspaces The Workspace window lets you view and manage all the projects in your workspace along with other relevant data You can open it by selecting View gt Windows gt Workspace from the main menu The Workspace window is split in two panes e The left hand pane contains the Workspace tree view It represents the hierarchical structure of the folders that contain the projects e In the right hand pane the contents of a selected folder are displayed You can choose between List View Folder View Child Scene View and two Thumbnail views In List View and Folder View information is displayed about a selected project its state scale the time of the last processing and any available comments The Scale column displays the scale of the scene Depending on the processed analysis there are additional columns providing exported result values Opening and Creating New Workspaces To create a new workspace select File gt New Workspace from the main menu or use the Create New Workspace button on the default toolbar The Create New Workspace dialog box lets you name your workspace and define its file location it will
269. r mangar ol ho cumert imago tinct fio ace at deckiog lt unclarsted ol Mean Layer 24 Adgertten p arreter Parameter Vole B Candidate Settings Cradle conch stes classes Yes Candidates caase unclacubed B Fitton Furcton Feng mode ater Farg heron Presid Mean Layer 2 Git PPO M gt 40 Use sbeokse iing vake Weighted sum Taget value factor Seed vakse factor Candidate vave lector B Merge Settings Funan super otsects Use Thematic Layers Compatitdity mode B Clasmhcation Settings Acteve eases Crave oid clanuhicahon there a no new clasihication Use class descnphon Figure 7 27 Process settings to perform an image object fusion using the difference from the parent process object PPO Figure 7 28 Result after doing an image object fusion using the difference to the PPO 0 if Mean Lae 2 oF PFO Wl eae Lae 3 at PPO IT ul Mean OF waaga abe hgoy iaasa wp to VEO Layer 1 at FFD 1 eo Moan Lape a FO D Figure 7 29 Process Related features can be used for parent process objects PPO 27 September 2012 User Guide Advanced Rule Set Concepts 145 7 7 1 Creating Customized Features The Manage Customized Features dialog box allows you to add edit copy and delete customized features and to create new arithmetic and relational features based on the existing ones To open the dialog box click on Tools gt Manage Customized Features from the main menu or click the icon on the Tools toolbar Manage Customized Fe
270. r map parameters including name and scale e Use the Next process to set the new map as image object domain e Using child processes below the process on map temp Modify the image object and synchronize the results User Guide 27 September 2012 162 Developer XD 2 0 4 7 is i g Figure 7 37 Example of a one map per object ruleset 7 10 Workspace Automation 7 10 1 Overview Detailed processing of high resolution images can be time consuming and sometimes im practical due to memory limitations In addition often only part of an image needs to be analyzed Therefore workspace automation enables you to automate user operations such as the manual selection of subsets that represent regions of interest More importantly multi scale workflows which integrate analysis of images at different magnifications and resolutions can also be automated Within workspace automation different kinds of scene copies also referred to as sub scenes are available e Scene copy e Scene subset e Scene tiles Sub scenes let you work on parts of images or rescaled copies of scenes Most use cases require nested approaches such as creating tiles of a number of subsets After processing the sub scenes you can stitch the results back into the source scene to obtain a statistical summary of your scene In contrast to working with maps workspace automation allows you to analyze sub scenes concurrently as each sub scene is handled
271. r the names of any contributors may be used to endorse or promote products derived from this software without specific prior written permission THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CON TRIBUTORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES INCLUD ING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABIL ITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED IN NO EVENT SHALL THE AUTHORS OR CONTRIBUTORS BE LIABLE FOR ANY DI RECT INDIRECT INCIDENTAL SPECIAL EXEMPLARY OR CONSEQUENTIAL DAMAGES INCLUDING BUT NOT LIMITED TO PROCUREMENT OF SUBSTI TUTE GOODS OR SERVICES LOSS OF USE DATA OR PROFITS OR BUSINESS INTERRUPTION HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY WHETHER IN CONTRACT STRICT LIABILITY OR TORT INCLUDING NEGLI GENCE OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE ITK Copyright Copyright 1999 2003 Insight Software Consortium All rights reserved 255 256 Developer XD 2 0 4 Redistribution and use in source and binary forms with or without modification are permitted provided that the following conditions are met e Redistributions of source code must retain the above copyright notice this list of conditions and the following disclaimer e Redistributions in binary form must reproduce the above copyright notice this list of conditions and the following disclaimer in the documentation and or other
272. re saved to one file Generic All files that are found in a All Yes Yes Yes one scene folder will be loaded to one per folder scene Generic import templates may support additional instruments or image readers not listed here For more information about unlisted import templates contact Definiens via www definiens com support About Generic Import Templates Image files are scanned into a workspace with a specific method using import templates and in a specific order according to folder hierarchy This section lists principles of basic import templates used for importing scenes within the Import Scenes dialog box e Generic one file per scene Creates one scene per file The number of image layers per scene is dependent on the image file For example if the single image file contains three image layers the scene is created with three image layers Matching Pattern anyname For the scene name the file name without extension is used Geocoded one file per scene Reads the geoco ordinates separately from each readable image file e Generic one scene per folder All image layers are taken from all image files Creates a scene for each subfolder Takes all image files from the subfolder to create a scene If no subfolder is available the import will fail The name of the subfolder is used for the scene name Geocoded one file per scene Reads the geoco ordinates separately from each readable image file
273. ree archaeal claonsticaborn 7 Actrve ciatte Bachgound Cell Nuckeus Une chars eloted fester Yes jmage Object Doman mage obyect bevel Parameter Level Claes Me Threshold condition Map Regon Man rember of mage hy Loops amp Cycies Humber of cycles 5 Figure 4 2 The Edit Process dialog box 4 1 3 Image Object Domain This defines the image objects p 2 on which algorithms operate 4 1 4 Algorithm Parameters This defines the individual settings of the algorithm in the Algorithms Parameters group box We recommend you do this after selecting the image object domain 4 2 Adding a Process 4 2 1 Selecting and Configuring an Image Object Domain An algorithm can be applied to several objects of interest in Definiens software these are called image object domains This allows you to narrow down the objects of interest and therefore the number of objects on which algorithms act For many algorithms you can define the image object domain by selecting a level within the image object hierarchy Typical targets may be the pixel level an image object level or specified image objects When using the pixel level the process creates a new image object level Depending on the algorithm you can choose among different basic domains and specify your choice by setting execution parameters Common parameters are 27 September 2012 User Guide Basic Rule Set Editing 37 e Level If you choose image object l
274. reference values called ground truth in geographic and satellite imaging based on pixels The Error Matrix Based on Samples dialog box displays a statistic type used for accuracy assessment Error Matrix based on Samples Figure 11 5 Output of the Error Matrix based on Samples statistics This is similar to Error Matrix Based on TTA Mask but considers samples not pixels derived from manual sample inputs The match between the sample objects and the classification is expressed in terms of parts of class samples User Guide 27 September 2012 230 Developer XD 2 0 4 11 2 Tissue 11 2 1 The Heat Map A heat map is a method of displaying data where variables are represented as colors A typical application is in the comparison of gene expression across multiple samples The Heat Map is only available when you select the Tissue or Life portals on startup Viewing Thumbnails in the Heat Map Window Thumbnails show the main map of a corresponding project and display by default when a workspace scene or tiles are opened and the Heat Map window is open To display Heat Map choose View gt Windows gt Heat Map from the main menu If thumbnails are not already displayed in the Heat Map window click on a folder in the Workspace to open it and view the corresponding map in the Heat Map window The folder name displays in the Heat Map window along with the number of groups and the number of total projects within them The subfolder
275. relationship exists between dependencies of rule set items used in customized algo rithms and their scope If for example a process uses class A with a customized feature Arithmeticl which is defined as local within the customized algorithm then class A should also be defined as local Defining class A as global or parameter can result in an inconsistent situation for example a global class using a local feature of the customized algorithm Scope dependencies of rule set items used in customized algorithms are handled automat ically according to the following consistency rules e Ifa rule set item is defined as global all its references and dependent must also be defined as global If at least one dependent or referencing rule set item cannot be defined as global this scope should not be used An exception exists for features without dependents such as area and other features without editable parameters If these are defined as global their references are not affected e If a rule set item is defined as local or as parameter references and dependents also have to be defined as local If at least one dependent or referencing rule set item cannot be defined as local this scope should not be used Again features without dependents such as area and other features without editable parameters are excepted These remain global as it makes no sense to create a local copy of them 7 8 2 Handling of References to Local Items During Runtime
276. resampling uses the pixel value of the pixel closest to the center of the source matrix to be resampled In case the image has internal zoom pyramids such as Mirax then the pyramid image is used Image layers copied with this method can be renamed e Smooth resampling creates the new pixel value from the mean value of the source matrix starting with the upper left corner of the image layer The time consumed by this algorithm is directly proportional to the size of the image data and the scale difference 7 9 4 Editing Map Properties In most use cases Developer XD images are available as image file stack which means one image file per slice or frame Usually this image data has slice and frame resolution information In case this information is not provided with the data it can be entered using the 3D 4D Settings algorithm The 3D 4D Settings algorithm provides three different modes e Non Invasive should be used for MRI and CT images It assumes a square image size and you can set the slice distance and time frame settings e 2D extend allows you to convert a 2D image into an Developer XD image This is useful for images that resemble film strips Enter the slice and frame sizes and resolution to virtually break up the image e 4D layout can be used to edit the slice distance and time frame settings of your image data Ensure the correct number of slices and frames are entered The 3D 4D Settings algorithm was created for very specific use
277. roduces simple square objects it is often used to subdivide images and image objects The following are some typical uses e Refining small image objects Relatively small image objects which have already been identified can be segmented with a small square size parameter for more detailed analysis However we recommend that pixel based object resizing should be used for this task 27 September 2012 User Guide Basic Rule Set Editing 43 e Applying a new segmentation Let us say you have an image object that you want to cut into multiresolution like image object primitives You can first apply chess board segmentation with a small square size such as one then use those square image objects as starting image objects for a multiresolution segmentation You can use the Edit Process dialog box to define the size of squares e Object Size Use an object size of one to generate pixel sized image objects The effect is that for each pixel you can investigate all information available from fea tures e Medium Square Size In cases where the image scale resolution or magnification is higher than necessary to find regions or objects of interest you can use a square size of two or four to reduce the scale Use a square size of about one twentieth to one fiftieth of the scene width for a rough detection of large objects or regions of interest You can perform such a detection at the beginning of an image analysis procedure Quadtree Based S
278. roperties 225 10 1 10 Exporting Action Definition to File 226 11 Advanced Data Visualizations 227 11 1 Accuracy ASSessment o c ioa ek Gos wa pod es OE a oa Be 227 11 1 1 Classification Stability oaa 228 Hle Enor Mates ore y e e kee ek a a ES e e es 229 ME E E E E eee eRe Ee ee YHA 230 IEZA TSRS NaP coe rae y ed Bae lee e a E Bee A 230 113 TMA Gd VIEW cc ace bh oe a ah E Sew e a Pee a 233 TL31 Defining the Gad Layout c aa pan e 20854 24 840 233 11 3 2 Matching Cores tothe Grid 2 056 65 ea eee eyt 234 11 3 3 Changing the Grid After Matching 236 11 34 Editng Cores lt o cas ca eR Seed ew SRS apt ee 237 ILA Celeng o coos A a a AE ee Ba eee eS 238 114 1 Plate VIEW oc eck eng ks ce i eR eS ao Bo a ee 238 11 4 2 Creating Dose Response Curves 2 242 11 Acceptand Reject Results ee i o eta Sede eee Ga ed de wes 246 12 Options 247 13 Aperio Spectrum Database Integration 253 13 1 Creating a Developer XD Workspace from the Aperio Spectrum Database 253 User Guide 27 September 2012 viii Developer XD 2 0 4 Acknowledgments 255 27 September 2012 User Guide 1 Key Concepts This chapter will introduce some terminology that you will encounter 1 1 Image Layer In Definiens Developer XD 2 0 4 an image layer is the most basic level of information contained in a raster image All images contain at least one image layer A grayscale image is an exa
279. rs the morphology of existing image objects according to specific criteria This means a segmentation can be a subdividing operation a merging operation or a reshaping operation There are two basic segmentation principles e Cutting something big into smaller pieces which is a top down strategy e Merging small pieces to get something bigger which is a bottom up strategy An analysis of which segmentation method to use with which type of image is beyond the scope of this guide all the built in segmentation algorithms have their pros and cons and a rule set developer must judge which methods are most appropriate for a particular image analysis 4 3 1 Top down Segmentation Top down segmentation means cutting objects into smaller objects It can but does not have to originate from the entire image as one object Definiens Developer XD 2 0 4 offers three top down segmentation methods chessboard segmentation quadtree based segmentation and multi threshold segmentation Multi threshold segmentation is the most widely used chessboard and quadtree based segmentation are generally useful for tiling and dividing objects into equal regions Chessboard Segmeniation Chessboard segmentation is the simplest segmentation algorithm It cuts the scene or in more complicated rule sets the dedicated image objects into equal squares of a given size Figure 4 5 Chessboard segmentation Because the Chessboard Segmentation algorithm p
280. s E freme loywi p0 Maem nbe of mage cbacha Loops amp Oces Looe whale someting changes tember of goes Figure 6 36 Process to import samples from shapefile NOTE The Sample Brush will select up to one hundred image objects at a time so you may need to increase magnification if you have a large number of image objects 6 4 7 Setting the Nearest Neighbor Function Slope The Nearest Neighbor Function Slope defines the distance an object may have from the nearest sample in the feature space while still being classified Enter values between 0 and 1 Higher values result in a larger number of classified objects 1 To set the function slope choose Classification gt Nearest Neighbor gt Set NN Func tion Slope from the main menu bar 2 Enter a value and click OK Set Nearest Neighbor Function Slope PR Membership value at standard deviation a _ ce Figure 6 37 The Set Nearest Neighbor Function Slope dialog box 6 4 8 Using Class Related Features in a Nearest Neighbor Feature Space To prevent non deterministic classification results when using class related features in a nearest neighbor feature space several constraints have to be mentioned 27 September 2012 User Guide About Classification 117 e It is not possible to use the feature Similarity To with a class that is described by a nearest neighbor with class related features e Classes cannot inherit from classes that use nearest neighbor contai
281. s are left after execution Using this approach you will cre ate customized algorithms with a much better performance compared to algorithms that relying on the automatic clean up capability 7 8 3 Domain Handling in Customized Algorithms When a customized algorithm is called the selected image object domain needs to be handled correctly There are two options If the Invoke Algorithm for Each Object option is selected the customized algo rithm is called separately for each image object in the selected image object domain This option is most useful if the customized algorithm is only called once using the Execute domain You can also use the current image object domain within the customized algorithm to process the current image object of the calling process However in this case we recommend to pass the image object domain as a param eter The Pass Domain from Calling Process as a Parameter option offers two possibili ties If Object Set is selected a list of objects is handed over to the customized al gorithm and the objects can be reclassified or object variables can be changed if a segmentation is performed on the objects the list is destroyed since the objects are destroyed with new segmentation If Domain Definition is selected filter settings for objects are handed over to the customized algorithm Whenever a process segmentation fusion or classification is performed all objects are checked to see if the
282. s are possi ble Polygon smoothed with auto abstraction The exported shapefile describes the border of the image objects along abstracted and simplified outlines Line skeleton is based on all lines of a skeleton of each image object Line main line is based on the main line only of the skeleton of each image object Point center of gravity is the result of the calculation of the center of gravity for each image object Point center of main line is the result of the calculation of the center of the main line for each image object The format must be shapefile shp Select the image object level for which you want to export results 5 Select the Write Shape Attributes to csv File check box to store the shape attributes as Statistics Change the default file name in the Export File Name text field if necessary 7 Click the Select Classes button to open the Select Classes for Shape Export dialog box where you can add or remove classes to be exported 8 Click the Select features button to open the Select Features for Export as Attributes dialog box where you can add or remove features to be exported 9 To save the shapefile to disk press Export 10 To view a preview of the attribute table that will be exported press the Preview button The export results in a dbf file an shp file and an shx file The dbf file supports string int and double formats and the columns are formatted automatically according to the data type The column width is adj
283. s description like any other expression 6 3 4 Evaluation Classes The combination of fuzzy logic and class descriptions is a powerful classification tool However it has some major drawbacks e Internal class descriptions are not the most transparent way to classify objects e It does not allow you to use a given class several times in a variety of ways e Changing a class description after a classification step deletes the original class description User Guide 27 September 2012 98 Developer XD 2 0 4 e Classification will always occur when the Class Evaluation Value is greater than 0 only one active class e Classification will always occur according to the highest Class Evaluation Value several active classes There are two ways to avoid these problems stagger several process containing the re quired conditions using the Parent Process Object concept PPO or use evaluation classes Evaluation classes are as crucial for efficient development of auto adaptive rule sets as variables and temporary classes Creating Evaluation Classes To clarify evaluation classes are not a specific feature and are created in exactly the same way as normal classes The idea is that evaluation classes will not appear in the classification result they are better considered as customized features than real classes Like temporary classes we suggest you prefix their names with _Eval and label them all with the same color to distinguis
284. s display as separate groups The thumbnails displayed depend on whether Folder View or List View is selected in the Workspace window Thumbnails of tiles are displayed only if the Show Tiles button is selected in the Heat Map window If the images have been analyzed statistics can be viewed in the form of a heat map If they have not been analyzed the heat map will be gray 1 To change the display of the thumbnails select Thumbnail Settings in the context menu or choose View gt Thumbnail Settings from the main menu 2 Click a thumbnail to display identifying information in the Selected Image field at the bottom of the window or move the cursor over a thumbnail to view an identi fying tooltip The corresponding project will be highlighted in the right hand pane of the Workspace window Double click a thumbnail to open it in the map view 4 To change the size of the thumbnails use the drop down list at the bottom of the Heat Map window to select small medium or large squares 5 To save an image of the thumbnails as a file click the Export button at the bottom of the Heat Map window select a file format and location and click Save 6 If a scene includes tiles you can select it in the Heat Map window and click the Show Tiles button to display all tiles in the selected scene in the Heat Map window The Show Tiles button is not available if there are no tiles in the selected scene e Click a tile thumbnail to display the tile name in the Select
285. s in the Display group box on the Curve Data tab to adjust the way data displays e Use the Points drop down list to select Single Wells or Combined Wells e Use the Controls drop down list to activate or inactivate controls When inac tive they are ignored and when active they are treated as normal wells e Use the X axis drop down to toggle between logarithmic and non logarithmic displays A concentration of 0 will not be displayed in the Logarithmic view 8 There may be data points in the graph that represent invalid values These data points can be inactivated unless two data points are overlapping so they do not influence the curve 27 September 2012 User Guide Advanced Data Visualizations 245 e To inactivate points click them in the graph The inactive points will become gray e To reactivate the points click them again 9 You can use the context menu to copy an image of the dose response curve to the clipboard 10 Click the Result button to display results of the fitting These include the same fields as the Start tab but they cannot be edited see step six 11 To export data e Click the Export button to export the values of the currently active curve as a csv file e Click the Export Saved button to export all saved curves for the plate into a csv file e Data exported includes the parameters discussed in step six and also Pearson s correlation coefficient r and the sum of the squared error SSE e Multiple compounds o
286. s project which has a dpr extension A dpr file is separate to the image and although they are linked objects does not alter it What can be slightly confusing in the beginning is that Developer XD creates another hierarchical level between a scene and a project a map Creating a project will always create a single map by default called the main map visually what is referred to as the main map is identical to the original image and cannot be deleted Maps only really become useful when there are more than one of them because a single project can contain several maps A practical example is a second map that contains a portion of the original image at a lower resolution When the image within that map is analyzed the analysis and information from that scene can be applied to the more detailed original 1 5 3 Workspaces Workspaces are at the top of the hierarchical tree and are essentially containers for projects allowing you to bundle several of them together They are especially useful for handling complex image analysis tasks where information needs to be shared The Definiens hierarchy is represented in figure 1 3 on the facing page 27 September 2012 User Guide Key Concepts 5 Figure 1 3 Data structure of a Definiens workspace User Guide 27 September 2012 2 Starting Developer Definiens clients share portals with predefined user interfaces A portal provides a se lection of tools and user interface ele
287. sasa soree he ee Se eee 82 6 About Classification 83 6 1 Key Classification Concepts 0000 4 83 GLI CASSIGMING Classes con ie Re RAR Eee BO 83 6 1 2 Class Descriptions and Hierarchies 83 6 1 3 The Edit Classification Filter so e coni see peg ee eee 88 6 2 Classification Algorithms gt 2 ee a ew es 89 6 2 1 The Assign Class Algorithm 89 6 2 2 The Classification Algorithm 89 6 2 3 The Hierarchical Classification Algorithm 90 6 2 4 Advanced Classification Algorithms 91 OS Thesholdss c 2 ti be Gh bade cheese BAe eS SAS 92 6 3 1 Using Thresholds with Class Descriptions 92 6 3 2 About theClass Description lt s s ec s ween Seo we YES 92 6 3 3 Using Membership Functions for Classification 93 6 3 4 Evaluation Classes 5 bee eu Oe eed Se eS ees 97 6 4 Supervised Classification 0 02 55000 99 6 4 1 Nearest Neighbor Classification 99 6 4 2 Working with the Sample Editor 0 106 6 4 3 Training and Test Area Masks 111 6 4 4 The Edit Conversion Table 0 113 6 4 5 Creating Samples Based ona Shapefile 114 6 4 6 Selecting Samples with the Sample Brush 115 6 4 7 Setting the Nearest Neighbor Function Slope 116 6 4 8 Using Class Related Features in a Neares
288. se for the same feature because now the object has the first object as a My Class neighbor 10 To summarize in the first example one list with 64 objects that fitted the condition is created at once in the second example one list of 64 is created in the upper process line but then 64 lists of 1 or 0 image objects each are created in the 64 run times of the child process 11 In other words the result with the usage of the parent process object PPO is totally different than without using it The case is that using the parent process ob ject PPO will process each image object in the image in succession That means the algorithm checks for the first unclassified image object complying with the set condition which is Existence of My Class 0 0 The image object identifies that there is no My Class neighbor so it classifies itself to My Class Then the algorithm goes to the second unclassified image object and finds a neighbor which means the condition does not fit Then it goes to the third there is no neighbor so it classifies itself and so on 12 For verification we generated an object variable to give each object a number with the parent process called counting and numbering of each image object Select the variables to be loaded to the Image Object Information window and select an image object in your image figure 7 23 oo 1 Algorithms that are referring to a parent process object PPO must be executed
289. select Append New which will create a process at the same level Call this process Define and isolate circles To add the rule right click the new process and select Insert Child In the Algorithm drop down box select Assign Class Click on Threshold Condition to navigate towards the Elliptic Fit algorithm using the path describe earlier To allow for a bit of image 27 September 2012 User Guide An Introductory Tutorial 33 degradation we re going to define a circle as anything with a value of over 0 95 click on the greater than symbol and enter the value 0 95 Press OK Back in the Edit Process window we will give our classification a name Replace the unclassified value in Use Class with Circle press enter and assign it a color of your choosing Press OK Finally in the Edit Process window press Execute to run the process There is now a Circle classification in the class hierarchy and placing your cursor over the circle shape will display the new classification Isolating the Squares There is also a convenient algorithm we can use to identify squares the Rectangular Fit value which for a square is of course one The method is the same as the one for the circle create a new parent class and call it Define and isolate squares When you create the child you will be able to find the algorithm by going to Object Features gt Geometry gt Shape gt Rectangular Set the range to
290. ses Image Layers Thematic Layers B Added Classes Levels Image Layers Thematic Layers Removed Classes Levels Image Layers Thematic Layers Levels Levels required to execute the action Figure 10 6 Edit Action Dependencies dialog box 2 You can now save the solution again and thereby update it to changes in the rule set files 10 1 8 Building an Analysis Solution Before you can analyze your data you must build an analysis solution in the Analysis Builder window To construct your analysis solution you can choose from a set of predefined actions for object detection classification and export By testing them on an open project you can configure actions to meet your needs With the Analysis Builder you assemble and configure these actions all together to form a solution which you can then run or save to file The Analysis Builder Window Image analysis solutions are built in the Analysis Builder Window To open it go to either View gt Windows gt Analysis Builder or Analysis gt Analysis Builder from the main menu You can use View gt Analysis Builder View to select preset layouts When the Analysis Builder window opens ensure that the name of the desired action library is displayed in the title bar of the Analysis Builder window 27 September 2012 User Guide Rule Sets for Definiens Architect XD 219 The Analysis Builder window consists of two panes In the upper pane you assemble actions to build
291. sification tab of the Image Object Information window The refinement of the classification result is an iterative process e First assess the quality of your selected samples e Then remove samples that do not represent the selected class well and add samples that are a better match or have previously been misclassified e Classify the scene again e Repeat this step until you are satisfied with your classification result When you have finished collecting samples remember to turn off the Select Sam ples input mode As long as the sample input mode is active the viewing mode will automatically switch back to the sample viewing mode whenever an image object is selected This is to prevent you from accidentally adding samples without taking notice Figure 6 28 Map view with selected samples in View Samples mode Image data courtesy of Ministry of Environmental Affairs of Sachsen Anhalt Germany User Guide 27 September 2012 110 Developer XD 2 0 4 Assessing the Quality of Samples Once a class has at least one sample the quality of a new sample can be assessed in the Sample Selection Information window It can help you to decide if an image object contains new information for a class or if it should belong to another class Sample Selection Information E Membertho MrenesDet MeanDet Cica Sampie Number of Sample om 02 7527 ova 120 615 o0 14278 ues ou 14788 2 Figure 6 29 The Sample Selection Information window
292. sified If two or more class descriptions share the highest membership value the assignment of an object to one of these classes is random To change the default value of 0 1 open the Edit Minimum Membership Value dialog box by selecting Classification gt Advanced Settings gt Edit Minimum Membership Value from the main menu Edit Minimum Membership Value PR Minimum membership value om _ ows Figure 6 13 The Edit Minimum Membership Value dialog box Adding Weightings to Membership Functions The following expressions support weighting e Mean arithm e Mean geom e Mean geom weighted Weighting can be added to any expression by right clicking on it and selecting Edit Weight The weighting can be a positive number or a scene or object variable Infor mation on weighting is also displayed in the Class Evaluation tab in the Image Object Information window Weights are integrated into the class evaluation value using the following formulas where w weight and m membership value wy xm WnX mn Mean arithm gt eg ees ae 27 September 2012 User Guide About Classification 97 Class Description Name Display r gt Bigard m M Away Lal Parert chavs lor duphey Modifiers Background Stared Abstract inactive F Use parent class color Ad Cotai irhatod Cortened mas ignom weated TAN y rhoed Edt Expression Irrgert Expressen v CUxpresson Is ate Quie
293. solutions in the lower properties pane you can configure them by cus tomizing specific settings Depending on the selected action the lower properties pane shows which associated settings to define The Description area displays information to assist you with the configuration Analysis Builde TissueMap 3 Name of the action libra EE General Settings Small Images FN Calibrate Stans Sequencing pane Assemble actions to build solutions Properties pane Configure the selected action by customizing specific settings Description eshold for the minimum size in pores Stained regions with an area smsler Help text concerning configuration settings n class ed as nuclei Figure 10 7 Analysis Builder window with sample actions from Cellenger action library Opening and Closing Action Libraries To open an existing action library go to Library gt Open Action Library in the main menu The name of the loaded action library is displayed in the title bar of the Analysis Builder window The action groups of the library are loaded in the upper pane of the Analysis Builder window If you open an action library after opening a project all rule set data will be deleted A warning message will display To restore the rule set data close the project without saving changes and then reopen it If you are using a solution built with a older action library browse to that folder and open the library before opening your solution You c
294. splay the Analysis Runs dialog Make a run active or delete a run using the Activate and Delete buttons Reverting to a Previous Version Besides the Roll Back button in the Project History dia log box you can manually revert to a previous version 1 Do one of the following e Select a project in the right pane of the Workspace window and select Analy sis gt Rollback All on the main menu e Right click a folder in the left pane of the Workspace window and select Rollback All on the context menu Alternatively you can select Analysis gt Rollback All on the main menu The Rollback All Changes dialog box opens 2 Select Keep the Current State in the History if you want to keep the history when going back to the first version of the projects The intermediate versions are not lost Select Destroy the History and All Results if you want to restart with a new version history after removing all intermediate versions including the results In the Project History dialog box the new version one displays Rollback in the Operations column Importing an Existing Project into a Workspace Processed and unprocessed projects can be imported into a workspace Go to the left hand pane of the Workspace window and select a folder Right click it and choose Import Existing Project from the context menu Alternatively Choose File gt New Project from the main menu The Open Project dialog box will open Select one project file extension dpr and cli
295. splays the number of selected wells You cannot select wells with missing data 27 September 2012 User Guide Projects and Workspaces 61 5 4 2 Selecting a Single Well Select a single well for display in the map view 1 Click on a well to select it The main map of the selected well is displayed in the Map View window The corresponding entry in the right Workspace pane is also selected 2 To change the plate select the plate number or name from the plate list 3 To browse through different fields of the selected image click the up or down arrow of the Site list or enter the number of the desired image directly The map in the Map View window changes as you browse through the layers When selecting All you can select from the Result Statistics list what to display mean value minimal or maximal value or sum 4 To deselect all selected wells click on the plate between the wells 5 4 3 Select Multiple Wells Select multiple wells to analyze the corresponding scenes 1 To select multiple wells do one of the following e To select a row click the row header character on the left side of the plate e To select a column click the column header number on top of the plate e To select all wells click in the upper left corner of the plate e To select a number of adjacent wells drag over them Each well you touch with the mouse will be selected The corresponding entries in the right Workspace pane are also selected The Wells sele
296. sses should begin the initial growth cycle with isolated seed image objects defined in the image object domain Otherwise if any candidate image objects border more than one seed image objects ambiguity will result as to which seed image object each candidate image object will merge with 27 September 2012 User Guide Basic Rule Set Editing 47 Figure 4 8 Red seed image objects grow stepwise into green candidate image objects 4 4 Object Levels and Segmentation Although you can perform some image analysis on a single image object level the full power of the Definiens object oriented image analysis unfolds when using multiple levels On each of these levels objects are defined by the objects on the level below them that are considered their sub objects In the same manner the lowest level image objects are defined by the pixels of the image that belong to them This concept has already been introduced in Image Object Hierarchy 4 4 1 About Hierarchical Image Object Levels The levels of an image object hierarchy range from a fine resolution of image objects on the lowest level to the coarse resolution on the highest On its superlevel every image object has only one image object the superobject On the other hand an image object may have but is not required to have multiple sub objects To better understand the concept of the image object hierarchy imagine a hierarchy of image object levels each representing a meaningf
297. sses that can be assigned to the image objects Select Use Class Related Features if necessary 6 2 4 Advanced Classification Algorithms Advanced classification algorithms are designed to perform specific classification tasks All advanced classification settings allow you to define the same classification settings as the classification algorithm in addition algorithm specific settings must be set The following algorithms are available Find domain extrema allows identifying areas that fulfill a maximum or minimum condition within the defined image object domain Find local extrema allows identifying areas that fulfill a local maximum or mini mum condition within the defined image object domain and within a defined search range around the object Find enclosed by class finds objects that are completely enclosed by a certain class Find enclosed by object finds objects that are completely enclosed by an image object Connector classifies image objects that represent the shortest connection between objects of a defined class User Guide 27 September 2012 92 Developer XD 2 0 4 6 3 Thresholds 6 3 1 Using Thresholds with Class Descriptions A threshold condition determines whether an image object matches a condition or not Typically you use thresholds in class descriptions if classes can be clearly separated by a feature It is possible to assign image objects to a class based on only one condition however the advantage o
298. st put them in a defined state The function Evaluate Undefined assigns the value 0 for a specified feature 1 In the Class Description dialog box right click an operator 2 From the context menu select Evaluate Undefined The expression below this operator is now marked User Guide 27 September 2012 88 Developer XD 2 0 4 Deleting an Expression To delete an expression either e Select the expression and press the Del button on your keyboard e Right click the expression and choose Delete Expression from the context menu Using Samples for Nearest Neighbor Classification The Nearest Neighbor classifier is recommended when you need to make use of a complex combination of object features or your image analysis approach has to follow a set of defined sample image objects The principle is simple first the software needs samples that are typical representatives for each class Based on these samples the algorithm searches for the closest sample image object in the feature space of each image object If an image object s closest sample object belongs to a certain class the image object will be assigned to it For advanced users the Feature Space Optimization function offers a method to math ematically calculate the best combination of features in the feature space To classify image objects using the Nearest Neighbor classifier follow the recommended workflow 1 Load or create classes 2 Define the feature space3Define sample i
299. st use unique names for parameter sets We recommend developing adjustable variables of a more general nature such as low contrast which have influence on multiple features instead of having one control per feature Additionally in rule sets to be used for actions avoid identically named parent processes This is especially important for proper execution if a Definiens action refers to inactive parts of a rule set 211 212 Developer XD 2 0 4 10 1 2 Creating a Quick Test Button When creating a Quick Test button in an action you need to implement a kind of internal communication to synchronize actions with the underlying rule sets This is realized by integration of specific algorithms to the rule sets that organize the updating of parameter sets variables and actions Synchronizing Actions with Rule Sets by Using Specific Algorithms Algorithm Algorithm Update parameter Apply parameter set from action set Action Parameter Rule Set Set widget 1 parameter 1 variable 1 widget 2 f parameter 2 alaorithm variable 2 widget3 parameter 3 goram variable3 Update action from Update parameter parameter set set Figure 10 1 The communication between action and rule set is organized by algorithms arrows These four specific algorithms are e Update Parameter Set From Action e Update Action From Parameter Set e Update Parameter Set e Apply Parameter Set The first two transfer values between the action
300. system recognizes a suspicious fit and displays the curve in red if the slope is greater than or equal to 3 or less than or equal to 3 or if the r2 value is below 0 97 5 If desired click Save Fit to save one fit per compound with the Workspace e You can select a compound and click Restore Fit to use a saved fit e You can also export a saved fit using the Export Saved button on the Result tab User Guide 27 September 2012 244 Developer XD 2 0 4 Dose Response N K Cuve Data Stat Result Compound Compound A Seq 01 2 Model Logistic 4 parameters v Figure 11 16 Dose Response Curve window Curve Data tab 6 To view or change the start parameters go to the Start tab of the Dose Response window You can change the following values by entering them in their respective fields ECs0 ICs0 Edit the concentration that produces the median response Slope Enter a value to change the degree of slope The default value is 1 00 or 1 00 depending on the value selected in the Type field In general the default should be used for the first curve fitting The slope should be in the range of 5 00 to 5 00 Max Edit the highest Y value You can enter a value to change it Min Edit the lowest Y value You can enter a value to change it After changing values you can click the Curve Data button and click Fit again to refit the curve To restore the default values click the Reset button on the Curve Data tab 7 Use the control
301. t Image Object Information Figure 4 12 Image Object Information window User Guide 27 September 2012 52 Developer XD 2 0 4 The selected feature values are now displayed in the map view To compare single image objects click another image object in the map view and the displayed feature values are updated a New Level of 1 Objects R Figure 4 13 Map view of selected image object values Image data courtesy of EMBL Hei delberg Double click a feature to display it in the map view to deselect a selected image object click it in the map view a second time If the processing for image object information takes too long or if you want to cancel the processing for any reason you can use the Cancel button in the status bar 4 5 2 The Feature View Window Image objects have spectral shape and hierarchical characteristics and these features are used as sources of information to define the inclusion or exclusion parameters used to classify image objects There are two major types of features e Object features which are attributes of image objects for example the area of an image object e Global features which are not connected to an individual image object for exam ple the number of image objects of a certain class Available features are sorted in the feature tree which is displayed in the Feature View window figure 4 14 It is open by default but can be also selected via Tools gt Feature View or View
302. t Develop Rule Set view The menu item Window gt Enable Docking facilitates this feature When you deselect this item the windows will display independently of each other al lowing you to position and resize them as you wish This feature may be useful if you are working across multiple monitors Another option to undock windows is to drag a window while pressing the Ctrl key You can restore the window layouts to their default positions by selecting View gt Restore Default Selecting View gt Save Current View also allows you to save any changes to the workspace view you make 2 5 5 Developer XD Views View Layer To view your original image pixels you will need to click the View Layer button on the toolbar Depending on the stage of your analysis you may also need to select Pixel View by clicking the Pixel View or Object Mean View button In the View Layer view figure 2 4 you can also switch between the grayscale and RGB layers using the buttons to the right of the View Settings toolbar To view an image in its original format if it is RGB you may need to press the Mix Three Layers RGB button View Classification Used on its own View Classification will overlay the colors you manually assign when classifying objects these are the classifications visible in the Class Hierarchy window figure 2 5 on the next page shows the same object when displayed in pixel view with all 27 September 2012 User Guide Starting Dev
303. t Membership Functions gt Delete You 27 September 2012 User Guide About Classification 95 Meas Lover 100 PO2 3 1 S Dew 6 87 Cosplay Randard iearest Neighbor Features Mess tare ou DEJ 47 G1 S04 Dew 077 essan e sa 7aniera72549 sho sh Left border Fight bender CK _ cores Figure 6 11 Automatically generated membership function can switch the display of generated membership functions on or off by right clicking in the Sample Editor window and activating or deactivating Display Membership Functions Editing Membership Function Parameters You can edit parameters of a membership func tion computed from sample objects 1 Oe In the Sample Editor select Membership Functions gt Parameters from the context menu The Membership Function Parameters dialog box opens Edit the absolute Height of the membership function Modify the Indent of membership function Choose the Height of the linear part of the membership function Edit the Extrapolation width of the membership function User Guide 27 September 2012 96 Developer XD 2 0 4 Membership Function Para PR Figure 6 12 The Membership Function Parameters dialog box Editing the Minimum Membership Value The minimum membership value defines the value an image object must reach to be considered a member of the class If the membership value of an image object is lower than a predefined minimum the image object remains unclas
304. t Neighbor Feature Space 116 7 Advanced Rule Set Concepts 119 7 1 Units Scales and Co ordinate Systems 119 7 2 Thematic Layers and Thematic Objects 120 7 2 1 Importing Editing and Deleting Thematic Layers 120 7 2 2 Displaying a Thematic Layer gt e e s o esse cese ter 121 7 2 3 The Thematic Layer Attribute Table ce es s accese a a e A 121 7 2 4 Manually Editing Thematic Vector Objects 122 7 2 5 Using a Thematic Layer for Segmentation 128 TL3 Variables m Rule Sets ce a a e A a Se ee eS A 129 hal About Variables 24 5 ehh eh bles eS EE SSS e A 129 Tide Creatine a Variable o oe ok Ge ea we AG a ORA 130 7 3 3 Saving Variables as Parameter Sets 133 Foe ATAY Cogs ok Me eo gt oe So E Pe ee e ea we a 135 TALL ARB AtING ATIYS o e our oe e a E E a 135 TA2 Orderot Array Items e we ok A ke 136 7 4 3 Using Arrays in Rule Sets 136 7 5 Image Objects and Their Relationships 136 7 5 1 Implementing Child Domains via the Execute Child Process Al COn 6 Ya ek eo te RGR ee HIS Bara Ree amp amp ee 136 7 5 2 Child Domains and Parent Processes 137 User Guide 27 September 2012 vi Developer XD 2 0 4 7 6 Tutorial Using Process Related Features for Advanced Local Processing 141 va Customized Features lt o ccp acneea ee ee ee E ed eS 143 7 7 1 Creating Customized Features
305. t and are especially useful for cus tomized algorithms that are always used in the same environment or that change the current status of variables of the main rule set We do not recommend using global rule set items in a customized algorithm if the algorithm is going to be used in different rule sets e Parameter scope Parameter rule set items are locally scoped variables in a cus tomized algorithm They are used like function parameters in programming lan guages When you add a process including a customized algorithm to the Main tab of the Process Tree window you can select the values for whatever parameters you have defined During execution of this process the selected values are assigned to the parameters The process then executes the child processes of the customized algorithm using the selected parameter values 7 8 1 Dependencies and Scope Consistency Rules Rule set items can be grouped as follows in terms of dependencies User Guide 27 September 2012 152 Developer XD 2 0 4 e Dependent Dependent rule set items are used by other rule set items For example if class A uses the feature Area and the customized feature Arithmetic in its class description it has two dependencies Area and Arithmetic 1 e Reference Reference rule set items use other rule set items For example if the Area feature is used by class A and the customized feature by Arithmeticl classA is its reference and and Arithmetic is a dependent A
306. t from the drop down box Confirm with OK and the Export Image Layer dialog box opens Enter a file name and select the file format from the drop down box Note that not all formats are available for export Click Save to confirm The current view settings are used however the zoom settings are ignored Copying the Current View to the Clipboard e Exporting the current view to clipboard is an easy way to create screenshots that can then be inserted into other applications Choose Export gt Copy Current View to Clipboard from the main menu Right click the map view and choose Copy Current View to Clipboard on the context menu 9 3 3 Exporting the Contents of a Window e Many windows contain lists or tables which can be saved to file or to the clipboard Others contain diagrams or images which you can copy to the clipboard Right click to display the context menu and choose 27 September 2012 User Guide Automating Data Analysis 209 e Save to File allows you to save the table contents as csv or transposed csv tcsv file The data can then be further analyzed in applications such as Microsoft Ex cel In the Options dialog box not available in Definiens Viewer under the Output Format group you can define the decimal separator and the column delimiter ac cording to your needs e Copy to Clipboard saves the current view of the window to clipboard It can then be inserted as a picture into other program for example
307. t hand pane the contents of a selected folder are displayed You can choose between List View Folder View Child Scene View and two Thumbnail views In List View and Folder View information is displayed about a selected project its state scale the time of the last processing and any available comments The Scale column displays the scale of the scene Depending on the processed analysis there are additional columns providing exported result values 5 3 1 Opening and Creating New Workspaces To open a workspace go to File gt Open Workspace in the main menu Workspaces have the dpj extension This function uses the same customized dialog as described for loading an image file on page 65 Open Workspace a Ee TestWorkspace Name a P TestWorkspace de _ Go to folder File Type dj Definiens Workspace v Clopen asRead Only _ Open as Edit Only Vcox64 installInput XD _ 16 Input Products eCognition Image Proxy Server Examples TestWorkspace TestWorkspace dpj kaal Figure 5 11 The Open Workspace dialog box To create a new workspace select File gt New Workspace from the main menu or use the Create New Workspace button on the default toolbar The Create New Workspace dialog box lets you name your workspace and define its file location it will then be displayed as the root folder in the Workspace window If you need to define another output root folder it is preferable to do so before you load scenes into the wor
308. ta Visualizations 241 Plate View 20050707 U205 ps 1883 GS CI 1G11 1A9_0 333333338899 2 EE N 00002066066 Soot ei Le 0000 299999 Ce O00000 ool hamna x 000000 AEA Sequence Seq 08 7 Edt New Delete Direction Assign to Selection Unassign Compound Selected wells 13456292 BP YY 5851502 F Compound C 3 moti Figure 11 14 Plate View Dose tab 2 Click the Dose button on the Plate View window 3 To create a compound click the New button in the Compound group box to open the New Compound dialog e You can change the default name and assign a color e Each time you click New a new compound is added with a default name e The drop down list displays all compounds that have been created or added 4 To edit the compound selected in the Compound dropdown click the Edit button to open the Edit Compound dialog box for the selected Customizing Dilution Sequences To customize the dilution sequences on the Dose tab of the Plate View click New in the Dilution Sequence group box to open the New Dilution Sequence dialog box Use the default name or enter your own 1 Select an available unit in the Unit drop down list and choose the Number of con centrations if you want to generate a sequence In the Series field choose loga rithms of the displayed values for concentration steps if you select No Default you will need to enter the steps Click Generate to create the new sequence 2 C
309. te Expression Figure 6 14 Adding a weight to an expression my 1X Xmp I e Mean geom weighted gt Using Similarities for Classification Similarities work like the inheritance of class descriptions Basically adding a similarity to a class description is equivalent to inheriting from this class However since similari ties are part of the class description they can be used with much more flexibility than an inherited feature This is particularly obvious when they are combined by logical terms A very useful method is the application of inverted similarities as a sort of negative inher itance consider a class bright if it is defined by high layer mean values You can define a class dark by inserting a similarity feature to bright and inverting it thus yielding the meaning dark is not bright It is important to notice that this formulation of dark is not bright refers to similarities and not to classification An object with a membership value of 0 25 to the class bright would be correctly classified as bright If in the next cycle a new class dark is added containing an inverted similarity to bright the same object would be classified as dark since the inverted similarity produces a membership value of 0 75 If you want to specify that dark is everything which is not classified as bright you should use the feature Classified As Similarities are inserted into the clas
310. ted without reconfirma tion 7 8 9 Using a Customized Algorithm in Another Rule Set You can save a customized algorithm like any regular process and then load it into another tule set 1 Right click on an instance process of your customized algorithm and choose Save As from the context menu The parameters of the exported process serve as default parameters for the customized algorithm 2 You may then load this algorithm to any rule set by selecting Load Rule Set from the context menu in the Process Tree window An process using the customized algorithm appears at the end of your process tree The customized algorithm itself is available in the Customized Algorithms tab figure 7 36 User Guide 27 September 2012 158 Developer XD 2 0 4 3 To add another process using the imported customized algorithm you can to select it from the Algorithm drop down list in the Edit Process dialog box Process Tree BB Pen background with Aethnetc Feature 0 at Hew Level quadtree Prn_my Var ar using Aree with Border index ot New Lowel 2 merge regen a 4 h Man Customized Algorithms Figure 7 36 Instance of a customized algorithm loaded to a process tree above 7 9 Maps 7 9 1 The Maps Concept As explained in chapter one a project can contain multiple maps A map can e Contain image data independent of the image data in other project maps a multi project map e Contain a copy or subsets from another map
311. ter from left to right adjusts window leveling on page 18 To zoom in and out either Use the mouse wheel Hold down the Ctrl key and the right mouse button then move the mouse up and down 2 5 9 3D and 4D Viewing The map features of Definiens Developer XD 2 0 4 also let you investigate e Three dimensional images made up of slices of 2D images e Four dimensional images where a sequence of 3D frames changes over time e Time series data sets which corresponds to a continuous film image There are several options for viewing and analyzing image data represented by Definiens maps You can view three dimensional four dimensional and time series data using specialized visualization tools Using the map view you can also explore three or four dimensional data in several perspectives at once and also compare the features of two maps Viewing Image Data in 3D and Over Time The 3D image objects display and the planar projections allow you to view objects in 3D while simultaneously investigating them in 2D slices You can select from among six different split screen views figure 2 21 of the image data and use the 3D Settings toolbar to navigate through slices synchronize settings in one projection with others and change the data range To display the 3D toolbar go to View gt Toolbars gt 3D User Guide 27 September 2012 24 Developer XD 2 0 4 Layer Lirear LOO 75 Figure 2 21 Map view with three planar pro
312. text menu of the Class Description dialog box e To insert an expression right click the operator in the Class Description dialog and select Insert New Expression Alternatively double click on the operator The Insert Expression dialog box opens displaying all available features e Navigate through the hierarchy to find a feature of interest e Right click the selected feature it to list more options Insert Threshold In the Edit Threshold Condition dialog box set a condi tion for the selected feature for example Area lt 100 Click OK to add the condition to the class description then close the dialog box Insert Membership Function In the Membership Function dialog box edit the settings for the selected feature NOTE Although operators and similarities can be inserted into a class as they are the nearest neighbor and the membership functions require further definition Moving an Expression To move an expression drag it to the desired location figure 6 6 Editing an Expression To edit an expression double click the expression or right click it and choose Edit Expression from the context menu Depending on the type of expression one of the following dialog boxes opens e Edit Threshold Condition Modifies the threshold condition for a feature e Membership Function Modifies the membership function for a feature 27 September 2012 User Guide About Classification 87 Insert Expression te Standard
313. th of an image object shared with the parent process object PPO to its total border length Region Features Region features return properties referring to a given region They are global because they are not related to individual image objects They are grouped as follows 27 September 2012 User Guide Basic Rule Set Editing 55 e Region related features provide information on a given region e Layer related region features evaluate the first and second statistical moment mean standard deviation of a region s pixel value e Class related region features provide information on all image objects of a given class per region Metadata Metadata items can be used as a feature in rule set development To do so you have to provide external metadata in the feature tree If you are not using data import proce dures to convert external source metadata to internal metadata definitions you can create individual features from a single metadata item Feature Variables Feature variables have features as their values Once a feature is assigned to a feature variable the variable can be used in the same way returning the same value and the assigned value It is possible to create a feature variable without a feature assigned but the calculation value would be invalid Creating a New Feature Most features with parameters must first be created before they are used and require values to be set beforehand Before a feature of image obje
314. th the new grid settings click Confirm Changes To discard your changes click Discard Changes Clicking the Discard button resets the grid to its last confirmed state You can therefore use this function to reset single or multiple steps if you confirm frequently in the course of your edits If you want to display the initial state of the grid click Reset 6 Deactivate the manual adaptation mode by clicking the Matching button 11 3 4 Editing Cores E Activate core addition and deletion mode Le Move or resize core Ly Mark core Lx Delete core Editing the cores on a slide allows you to manually correct the results of automatic core detection or to manually determine the cores you want to include in the matching process gt O N Defining and adjusting ROIs is only possible if the complete slide is open in the map view If necessary use the zoom buttons to zoom into the slide You can add or delete cores as well as adjust their frames and define their regions of interest ROI 1 Select the Editing tab 2 To edit the number of cores on the slide or to adjust their frames proceed as fol lows e Click the Cores button e If necessary activate core addition and deletion mode 1 e To define new cores mark the cores in the map view by drawing a rectangle frame around them Each frame represents a subset comprising a core with one or more ROIs The results of later analyses will be displayed per core e To adjust the size
315. the appropriate folder ws Dvfiniens Dwevlopey XD 7 amp feo be pe Qm gt amp Pw Dru T Pong ee aires Cedom Reuters Figure 2 20 Location of default_image_view xml file Open the xml file using Notepad or your preferred editor and look for the following code lt TopLeft gt lt TopLeft gt lt TopRight gt lt TopRight gt lt BottomLeft gt lt BottomLeft gt lt BottomRight gt lt BottomRight gt Enter the text you want to appear by placing it between the relevant containers for exam ple lt TopLeft gt Sample_Text lt TopLeft gt You will need to restart Definiens Developer XD 2 0 4 to view your changes 27 September 2012 User Guide Starting Developer 23 Inserting a Field In the same way as described in the previous section you can also insert the feature codes that are used in the Edit Text Settings box into the xml For example changing the xml container to lt TopLeft gt Active pixel x value Active pixel x Name Active pixel x value Active pixel x Value lt TopLeft gt will display the name and x value of the selected pixel Inserting the code APP_DEFAULT into a container will display the default values map number and slice number 2 5 8 Navigating in 2D The following mouse functions are available when navigating 2D images e The left mouse button is used for normal functions such as moving and selecting objects e Holding down the right mouse button and moving the poin
316. the class you are currently editing is displayed at the bottom of the dialog box e To display the comparable graphical output go to the View Settings window and select Mode gt Classification Membership Membership Function Type For assigning membership the following predefined functions are available os pax z 5 i g 5 eI 5 s 5 Larger than Smaller than Larger than Boolean crisp Smaller than Boolean crisp Larger than linear Smaller than linear Linear range triangle Linear range triangle inverted Singleton exactly one value Approximate Gaussian About range BDEEKEZNEEEE Full range Generating Membership Functions Automatically In some cases especially when classes can be clearly distinguished it is convenient to automatically generate membership functions This can be done within the Sample Ed itor window for more details on this function see Working with the Sample Editor on page 106 To generate a membership function right click the respective feature in the Sample Editor window and select Membership Functions gt Compute Membership functions can also be inserted and defined manually in the Sample Editor window To do this right click a feature and select Membership Functions gt Edit Insert which opens the Membership Function dialog box This also allows you to edit an auto matically generated function To delete a generated membership function selec
317. the drop down list such as current image object When you use local processing the routine goes to the first random image object de scribed in the parent domain and processes all child processes defined under the parent process where the PPO is always that same image object The routine then moves through every image object in the parent domain The routine does not update the parent domain after each processing step it will continue to process those image objects found to fit the parent process s image object domain criteria no matter if they still fit them when they are to be executed User Guide 27 September 2012 138 Developer XD 2 0 4 A special case of a PPO is the Oth order PPO also referred to as PPO 0 Here the PPO is the image object defined in the image object domain in the same line 0 lines above For better understanding of child domains subdomains and PPOs see the tutorial on page 141 Using Parent Process Objects for Local Processing This example demonstrates how local processing is used to change the order in which class or feature filters are applied During execution of each process line Definiens soft ware first creates a list of image objects that are defined in the image object domain Then the desired routine is executed for all image objects on the list Try out PPO e simple use a segmentation H counting and numbering of each object a paint chessboard using a kind of PPO e t
318. the rule set and are deleted when the Generate button is pressed However they are preserved if you Save to File or Copy to Clipboard Save to File saves the documentation to ASCII text or rich text format 8 3 Process Paths A Process Path is simply a pathway to a process in the Process Tree window It can be used to locate a process in a rule set and is useful for collaborative work Right click on a process of interest and select Go To or use the keyboard shortcut Ctrl G The pathway to the process is displayed you can use the Copy button to copy the path or the Paste button to add another pathway from the clipboard Go To Process Process Path Figure 8 2 Go To Process dialog box 8 4 Improving Performance with the Process Profiler The time taken to execute a process is displayed before the process name in the Process Tree window This allows you to identify the processes that slow down the execution of your rule set You can use the Process Profiler to identify processes so you can replace them with less time consuming ones eliminating performance bottlenecks To open the Process Profiler go to View gt Windows gt Process Profiler or Process gt Process Profiler in the main menu Execute a process and view the profiling results under the Report tab e Times below one minute are displayed as seconds and milliseconds User Guide 27 September 2012 182 Developer XD 2 0 4 Process Prof er 07 0108 14 00 4 thomso
319. the slider to change the transparency A value of O indicates an opaque object Navigating the Planar Projections There are several ways to navigate slices in the planar projections The slice number and orientation are displayed in the bottom right hand corner of the map view If there is more than one map the map name is also displayed e Reposition the cursor and crosshairs in three dimensions by clicking inside one of the planar projections e Turn crosshairs off or on with the Crosshairs button e To move through slices Select a planar projection and click the green arrows in the 3D Settings tool bar Use the mouse wheel holding down the mouse wheel and moving the mouse up and down will move through the slices more quickly Click the Navigation button in the 3D Settings toolbar to open Slice Position sliders that display the current slice and the total slices in each dimension 1 Any image object with transparency setting greater than zero is ignored when selected the image object is not simultaneously selected in the planar projections At very low transparency settings some image objects may flip 180 degrees Raise the transparency to a higher setting to resolve this issue 27 September 2012 User Guide Starting Developer 27 Use PgUp or PgDn buttons on the keyboard You can move an object in the window using the keyboard arrow keys If you hold down the Ctrl key at the same time you can move down the vertic
320. the window into four horizontally and vertically to a size of your choosing Alternatively you can select Window gt Split Horizontally or Window gt Split Vertically to split the window into two There are two more options that give you the choice of synchronizing the displays Inde pendent View allows you to make changes to the size and position of individual windows such as zooming or dragging images without affecting other windows Alternatively User Guide 27 September 2012 12 Developer XD 2 0 4 selecting Side by Side View will apply any changes made in one window to any other windows A final option Swipe View displays the entire image into across multiple sections while still allowing you to change the view of an individual section 2 5 3 Magnifier The Magnifier feature lets you view a magnified area of a region of interest in a separate window It offers a zoom factor five times greater than the one available in the normal map view To open the Magnifier window select View gt Windows gt Magnifier from the main men Holding the cursor over any point of the map centers the magnified view in the Magnifier window You can release the Magnifier window by dragging it while holding down the Ctrl key 2 5 4 Docking By default the four commonly used windows Process Tree Class Hierarchy Image Object Information and Feature View are displayed on the right hand side of the workspace in the defaul
321. they are not parent classes themselves are meaningfully applied to the classification of image objects The above logic is following the concept that child classes are used to further divide a more general class Therefore when defining subclasses for one class always keep in mind that not all image objects defined by the parent class are automatically defined by the subclasses If there are objects that would be assigned to the parent class but none of the descriptions of the subclasses fit those image objects they will be assigned to neither the parent nor the child classes 2 Classes are only applied to a classification of image objects if all contained classi fiers are applicable The second rule applies mainly to classes containing class related features The reason for this is that you might generate a class that describes objects of a certain spectral value in addition to certain contextual information given by a class related feature The spectral value taken by itself without considering the context would cover far too many image objects so that only a combination of the two would lead to satisfying results As a consequence when classifying without class related fea tures not only the expression referring to another class but the whole class is not used in this classification process Contained and inherited expressions in the class description produce membership values for each object and according to the highest membership value each
322. thms for analyzing selected sub scenes Workspace automation can only be done on a Definiens Server Rule sets that include subroutines cannot be run in Developer XD in one go For each subroutine the according sub scene must be opened A subroutine is a separate part of the rule set cut off from the main process tree and applied to sub scenes such as scene tiles They are arranged in tabs of the Process Tree window Subroutines organize processing steps of sub scenes for automated processing Structuring a rule set into subroutines allows you to focus or limit analysis tasks to regions of interest The general workflow of workspace automation is as follows 1 Create sub scenes using one of the Create Scene algorithms User Guide 27 September 2012 166 Developer XD 2 0 4 Figure 7 40 Subroutines are assembled on tabs in the Process Tree window 2 Hand over the created sub scenes to a subroutine using the Submit Scenes for Anal ysis algorithm All sub scenes are processed with the rule set part in the subroutine Once all sub scenes have been processed post processing steps such as stitch back are executed as defined in the Submit Scenes for Analysis algorithm 3 The rule set execution is continued with the next process following the Submit Scenes for Analysis algorithm A rule set with subroutines can be executed only on data loaded in a workspace Process ing a rule set containing workspace automation on a Definiens
323. tiled you can click the Show Tiles button to display a tiled view all tiles and also view result values for tiles in the Heat Map W User Guide 27 September 2012 232 Developer XD 2 0 4 Heat Map Figure 11 7 Heat Map window with scene statistics Comparing Tile Statistics This function allows you to view tiles in the Heat Map window and compare result statistics among tiles 1 Click the Show Tiles button to open tiles in the Heat Map window If there are no tiles in the project the Show Tiles button is not available The folder name displays in the Heat Map window along with the number of tiles and the Show Tiles button becomes the Show Group button 2 Use the Display drop down list to select a result to display in the heat map across the entire tile display 3 To adjust the distribution of the colors enter the desired values for minimum or maximum at either side of the scale or use the arrow buttons to count up or down 4 Click the Show Group button to return display scenes in groups 27 September 2012 User Guide Advanced Data Visualizations 233 colon Rat BE 10016 14 Coe 12 x stm r om F a Co Figure 11 8 Heat Map window with heat map displayed across tiles with the correspond ing map view and workspace list view Image data courtesy Novartis Pharma AG Pathol ogy Toxicology EU E Persohn 11 3 TMA Grid View The TMA application is used to analyze tissue micro arrays A tissue micr
324. tion choose Library gt Load Calibration from the main menu The Load Calibration Parameter Set dialog box opens Browse for a Definiens Parameter Set file with the extension psf Common cal ibrations are stored in the Calibration folder within the corresponding application folder The default path is C Program Files Definiens Developer XD 2 0 4 bin applications Cell Calibration You can check the loaded General Settings properties in the lower properties pane of the Analysis Builder window Although some image formats are saved as 16 bit they don t use the full range of 65 536 gray values In case you are using image data with a range of approximately 8 000 gray values we generally recommend using the 12 bit setting Loading a calibration deletes the currently displayed general settings and substitutes the loaded calibrated gen eral settings 27 September 2012 User Guide Rule Sets for Definiens Architect XD 223 Saving and Loading Analysis Solutions e You can save analysis settings in the Analysis Builder as solution files extension dax and load them again for example to analyze slides e To save the analysis settings click the Save Solution to a File button on the Archi tect toolbar or Library gt Save Solution on the main menu e Alternatively you can encrypt the solution by selecting Save Solution Read Only on the Architect toolbar or Library gt Save Solution Read Only from the main menu To lo
325. tion the Sample Editor window allows you to generate membership functions The following options are available e To insert a membership function to a class description select Display Membership Function gt Compute from the context menu e To display membership functions graphs in the histogram of a class select Display Membership Functions from the context menu User Guide 27 September 2012 108 Developer XD 2 0 4 e To insert a membership function or to edit an existing one for a feature select the feature histogram and select Membership Function gt Insert Edit from the context menu e To delete a membership function for a feature select the feature histogram and select Membership Function gt Delete from the context menu e To edit the parameters of a membership function select the feature histogram and select Membership Function gt Parameters from the context menu Selecting Samples A Nearest Neighbor classification needs training areas Therefore representative samples of image objects need to be collected 1 To assign sample objects activate the input mode Choose Classification gt Samples gt Select Samples from the main menu bar The map view changes to the View Samples mode To open the Sample Editor window which helps to gather adequate sample image objects do one of the following e Choose Classification gt Samples gt Sample Editor from the main menu e Choose View gt Sample Editor
326. ton G The main line of a skeleton is represented by the longest possible connection of branch points Beginning with the main line the connected lines then are ordered according to their types of connecting points The branch order is comparable to the stream order of a river network Each branch obtains an appropriate order value the main line always holds a value of 0 while the outmost branches have the highest values depending on the objects complexity The right image shows a skeleton with the following branch order e 4 Branch order 2 e 5 Branch order 1 e 6 Branch order 0 main line User Guide 27 September 2012 178 Developer XD 2 0 4 l y 3 5 PX Ee W a a Rit l BS bas SFB SD 7 P4 A b LA f Oe e7 Ey Figure 7 51 Skeleton creation based on a Delauney triangulation 7 13 Encrypting and Decrypting Rule Sets Encrypting rule sets prevents others from reading and modifying them To encrypt a rule set first load it into the Process Tree window Open the Process menu in the main menu and select Encrypt Rule Set to open the Encrypt Data dialog box Enter the password that you will use to decrypt the rule set and confirm it The rule set will display only the parent process with a padlock icon next to it If you have more than one parent process at the top level each of them will have a lock next to it You will not be able to open the rule set to read or modify it but you can append
327. toxin administered to an organism and the response of the organism to that drug A dose response curve DRC or concentration response curve describes the relationship between the amount or concentration of a drug or toxin administered to an organism and the response of the organism to that drug Many biological systems in which a univariate one parameter of interest response can be measured show a typical relationship between concentration of the agonist or antagonist and the magnitude of the response This concentration response or dose response relationship derives from the law of mass action At sufficiently low concentration no effect is seen As the concentration is in creased above a threshold concentration an increasing effect is observed Finally at high concentrations orders of magnitude higher than the threshold concentration the response saturates it does not increase any further When the response is plotted on a lin ear vertical scale versus the concentration on a logarithmic horizontal scale a sigmoidal S shaped relationship is apparent The characteristic value of a sigmoidal relationship is the half maximal response in other words the point at which the sigmoidal curve is halfway from the lowest value to the high est value This also corresponds to the inflection point of the curve For concentration response curves this point corresponds to the concentration at which the response is halfway between baseline and
328. tton to open the Edit Classification Filter dialog box and check the boxes beside the classes you want to display Click OK to display your choices Navigating in 3D Several options are available to manipulate the image objects in the 3D image objects display The descriptions use the analogy of a camera to represent the user s point of view e Hold down the left mouse button to freely rotate the image in three dimensions by dragging the mouse Ctrl left mouse button rotates the image in x and y dimensions Shift left mouse button moves the image around the window e To zoom in and out Holding down the right mouse button and moving the mouse up and down zooms in and out with a high zoom factor Holding down the right mouse button and moving the mouse left and right zooms in and out with a low zoom factor To enhance performance you can click the 3D Visualization Options button in the 3D Settings toolbar and use the slider to lower the detail of the 3D image objects When you select a 3D connected image object it will automatically be selected in the planar projections Setting Transparency for 3D Image Objects Changing the transparency of image objects allows better visualization 1 Open the Classification menu from the main menu bar and select Class Legend If you are using Developer XD you can also access the Class Hierarchy window 2 Right click on a class and click Transparency 3D Image Objects to open the slider 3 Move
329. tween surrounding objects 2 As with class related features the relations refer to the group hierarchy This means if a relation refers to one class it automatically refers to all its subclasses in the group hierarchy User Guide 27 September 2012 148 Developer XD 2 0 4 Table 7 1 Relations between surrounding objects Object Description Neighbors Related image objects on the same level If the distance of the image objects is set to 0 then only the direct neighbors are considered When the distance is greater than 0 then the relation of the objects is computed using their centers of gravity Only those neighbors whose center of gravity is closer than the distance specified from the starting image object are considered The distance is calculated either in metric units or pixels Sub objects Image objects that exist below other image objects whose position in the hierarchy is higher superobjects The distance is calculated in levels Superobject Contains other image objects sub objects on lower levels in the hierarchy The distance is calculated in levels Sub objects of superobject Only the image objects that exist below a specific superobject are considered in this case The distance is calculated in levels Level Specifies the level on which an image object will be compared to all other image objects existing at this level The distance is calculated in levels An overview of a
330. two features of selected image ob jects If two features correlate highly you may wish to deselect one of them from the Image Object Information or Feature View windows As with the Feature View window not only spectral information maybe displayed but all available features e To open 2D Feature Space Plot go to Tools gt 2D Feature Space Plot via the main menu e The fields on the left hand side allow you to select the levels and classes you wish to investigate and assign features to the x and y axes The Correlation display shows the Pearson s correlation coefficient between the values of the selected features and the selected image objects or classes 25 Feature Space Plot P x Figure 4 21 2D Feature Space Plot dialog box User Guide 27 September 2012 62 Developer XD 2 0 4 4 5 7 Using Metadata and Features Many image data formats include metadata or come with separate metadata files which provide additional image information To use this metadata information in your image analysis you can convert it into features The available metadata depends on the image reader or camera used the industry specific environment and the original settings Industry specific examples are e Satellite image data that may contain metadata providing cloudiness information e Microscopy image data that may contain metadata providing information about the magnification used The metadata provided can be displayed in the Image Object
331. u can view the difference from the green highlighted image object in the Image Object Information window fig ure 7 27 Refer to figure 7 28 on page 144 to see the result of the image object fusion 4 Typically you create the process related features you need for your specific rule set For features that set an image object in relation to the parent object only an integer number has to be specified the process distance Dist It refers to the distance in the process hierarchy the number of hierarchy levels in the Process Tree window above the current editing line in which you find the definition of the parent object This is true for the following features e Same super object as PPO e Elliptic Distance from PPO e Rel border to PPO e Border to PPO For the following process related features comparing an image object to the parent object the process distance Dist has to be specified as well e Ratio PPO e Diff PPO In addition you have to select the feature that you want to be compared For example if you create a new ratio PPO select Distance 2 and the feature Area the created feature will be Area ratio PPO 2 The number it returns will be the area of the object in question divided by the area of the parent process object of order 2 that is the image object whose identity was handed down from two lines above in the process tree A special case are process related features with process Distance 0 called PPO 0 features They on
332. ue fields allow you to create a name and an initial value for the vari able In addition you can choose whether the new variable is numeric double or textual string The Insert Text drop down box lets you add patterns for ruleset objects allowing you to assign more meaningful names to variables which reflect the names of the classes and layers involved The following feature values are available class name image layer name thematic layer name variable value variable name level name feature value The Type field is unavailable for both variables The Shared check box allows you to share the new variable among different rule sets Creating a Class Variable Edit Class Variable Figure 7 13 Create Class Variable dialog box The Name field and comments button are both editable and you can also manually assign a color To give the new variable a value click the ellipsis button to select one of the existing classes as the value for the class variable Click OK to save the changes and return to the Manage Variables dialog box The new class variable will now be visible in the Feature Tree and the Class Hierarchy as well as the Manage Variables box User Guide 27 September 2012 132 Developer XD 2 0 4 Creating a Feature Variable Create Feature Variable Value Set value of lestve vanable Cel am Figure 7 14 Create Feature Variable dialog box After assigning a name to your variable click the ellipsis butt
333. ul structure in an image These levels are related to the various coarse medium fine resolutions of the image objects The hierarchy arranges subordinate image structures such as a cell below generic image structures such as tissue figure 4 9 on the following page shows some biological and geographical examples The lowest and highest members of the hierarchy are unchanging at the bottom is the digital image itself made up of pixels while at the top is a level containing a single object such as an organ or a forest 4 4 2 Creating an Image Object Level There are two ways to create an image object level e Applying a segmentation algorithm using the pixel level domain will create a new level Image object levels are usually added above an existing ones although some algorithms let you specify whether new layers are created above or below existing ones e Using the Copy Image Object Level algorithm User Guide 27 September 2012 48 Developer XD 2 0 4 Examples of Meaningful Hierarchical Entire Image Object Levels ntire Image Biology Geography Coarse Tree Type Medium Cell Tree Fine Pixel Level fk oe pf go Figure 4 9 Meaningful image object levels within an image object hierarchy The shapes of image objects on these super and sublevels will constrain the shape of the objects in the new level The hierarchical network of an image object hierarchy is topologically definite In other words the
334. ustable up to 255 characters Kw e fon Exporting the Current View Exporting the current view is an easy way to save the map view at the current scene scale to file which can be opened and analyzed in other applications This export type does 8 The class names and class colors are not exported automatically Therefore if you want to export shapes for more than one class and you want to distinguish the exported features by class you should also export the feature Class name You can use the Class Color feature to export the RGB values for the colors you have assigned to your classes User Guide 27 September 2012 208 Developer XD 2 0 4 not include additional information such as geo referencing features or class assignments To reduce the image size you can rescale it before exporting Select Scale Figure 9 15 Select Scale dialog box To export a current active map choose Export gt Current View from the main menu bar The Select Scale dialog box opens To export the map with the displayed scale click OK If you want to keep the original scale of the map select the Keep Current Scene Scale check box You can select a different scale compared to the current scene scale which allows you to export the current map at a different magnification or resolution If you enter an invalid scale factor it will be changed to the closest valid scale as displayed in the table To change the current scale mode selec
335. utation Mean Skies Select Master Fie OOG HE Skdedat re Select Seach ring looct Incorm Stdedal ra neverse Scere Name Come Create wodkspace fokder bom ach sting f Create moh ipace fodder bom Me puter Customized import Workapace lage Layers Thematic Layers Metadata Soene ee Nave Metadata Seach Sang lewr wrgl Ore ORA Mea Scan dae v30 Correon setri irei ator Figure 4 24 Metadata options in Customized Import the metadata use the default search string expression If the metadata file is external this link must be defined e Select a format driver to use for importing e Convert metadata to include it in the feature tree A master file must be defined in the Workspace tab if it is not you cannot access the Metadata tab The Metadata tab lists the metadata to be imported in groups and can be modified using the Add Metadata and Remove Metadata buttons Populating the Metadata List You may want to use metadata in your analysis or in writing rule sets Once the metadata conversion box has been generated click Load this will send the metadata values to the Feature View window creating a new list under Metadata Right click on a feature and select Display in Image Object Information to view their values in the Image Object Information window 27 September 2012 User Guide 5 Projects and Workspaces 5 1 Creating a Simple Project To create a simple project one without thematic l
336. uter Click Load to load a ruleware file for image analysis this can be a process dcp or solution dax file The Edit feature allows you to configure the exported results and the export paths of the image analysis job in an export template Clicking Save allows you to store the export template with the process file Select the type of scene to analyze in the Analyze drop down list e All Scenes applies the rule set to all selected scenes in the Workspace window e Top Scenes refers to the original scenes which have been used to create scene copies subsets or tiles e If you have created tiles you can select Tiles Only to filter out everything else Select the Use Time Out check box to set automatic cancellation of image analysis after a period of time that you can define This may be helpful for batch processing in cases of unexpected image aberrations When testing rule sets you can cancel endless loops automatically and the state of projects will marked as canceled 27 September 2012 User Guide mn Automating Data Analysis 203 In rare cases it may be necessary to edit the configuration For more details see the Developer XD reference book 9 2 3 Interactive Workflows The principle of an interactive workflow is to enable a user to navigate through a pre defined pathway For instance a user can select an object or region on a virtual slide prompting the software to analyse the region and display relevant data
337. utomatically reload last project No Start with a blank map view when opening Definiens Developer XD 2 0 4 Yes Useful if working with the same project over several sessions Use standard Windows file selection dialog No Display the default multi pane selection dialog Yes Use classic Windows selection dialog Predefined import connectors folder If necessary enter a different folder in which to store the predefined import connectors Store temporary layers with project Display In Developer XD this setting is available in the Set Rule Set options algorithm Image position Choose whether an opened image is displayed at the top left or center of a window Annotation always available No The Annotation feature is not available for all image objects Yes The Annotation feature is available for all image objects 247 248 Developer XD 2 0 4 Default image equalization Select the equalization method of the scene display in the map view The Options dialog box allows several optional settings concerning Linear None Standard deviation Gamma correction Histogram Manual The default value automatic applies no equalization for 8 bit RGB images and linear equalization for all other images Display default features in image object information If set to yes a small number of default features will display in Image Object Information Display scale with
338. v 0 00 56 0 6F MS 93 1 1055 1179 103 1426 1550 707 Figure 6 27 The Sample Editor window The first graph shows the Active Class and Compare Class histograms The second is a histogram for all image object levels The third graph displays an arrow indicating the feature value of a selected image object Comparing Features To compare samples or layer histograms of two classes select the classes or the levels you want to compare in the Active Class and Compare Class lists Values of the active class are displayed in black in the diagram the values of the compared class in blue The value range and standard deviation of the samples are displayed on the right hand side Viewing the Value of an Image Object When you select an image object the feature value is highlighted with a red pointer This enables you to compare different objects with regard to their feature values The following functions help you to work with the Sample Editor e The feature range displayed for each feature is limited to the currently detected feature range To display the whole feature range select Display Entire Feature Range from the context menu e To hide the display of the axis labels deselect Display Axis Labels from the context menu e To display the feature value of samples from inherited classes select Display Sam ples from Inherited Classes e To navigate to a sample image object in the map view click on the red arrow in the Sample Editor In addi
339. ve a particular view e Use the buttons to add or delete views e Selecting Add launches the Add New View dialog box Enter the name of your custom view and select the view on which you wish to base it in the Copy Columns From field 5 4 Managing Data in Plate View Plates are commonly used for automated image analysis in cell biology To open the Plate View window figure 5 17 go to View gt Windows gt Plate View on the main menu User Guide 27 September 2012 80 Developer XD 2 0 4 Edit Views List View default New View Layout Add new view lt Name of new view gt fust View dafauit eme Figure 5 16 Edit Views Dialog Box selecting Add launches Add New View 5 4 1 Navigating Through a Plate To navigate through a plate and specify wells to display in the map view or select them for analysis press the Navigation button Plate View Plate2 HT29 00000000 00000000 5251005 B WY 13504552 39 wet selected Figure 5 17 Plate View window displaying the Navigation tab In this view the plate is displayed in gray with all active wells circled When you select one or more wells the selected wells appear light gray the rest of the plate is shaded Inactive wells are always marked dark gray While holding the mouse pointer over a well its co ordinates and if already processed the value for the selected parameter are displayed in the Selected Wells area otherwise this area just di
340. vely you can remove already tested actions delete them from the Analysis Builder window and add them later again You can also save the actions and the settings as solution to a dax file When removing single actions you must make sure that the analysis job remains complete For instance you must first detect nuclei before you can classify them or you must first detect cells or simulate cell bodies before you can classify cells e To execute a configured solution not locally but on the Definiens Server select a project in the workspace window Click the Run Solution on Server button on the Architect toolbar This option is needed if the solution contains actions with workspace automation algorithms 5 When you open a solution file extension dax the actions are compared with those of the current action library If the current action library contains an action with the same name as the solution file the action in the current Action Library is loaded to the Analysis Builder window This does not apply when using a solution file for automated image analysis User Guide 27 September 2012 224 Developer XD 2 0 4 Importing Action Definitions To get access to new customized or special actions you have to load action definitions which are simply unconfigured actions If not yet available in the Add Actions dialog box you can load additional action definitions from a file to an action library This can be used to update action libraries
341. ving distance or direction of an object in time 2 Link distributed cancer indications 3 Linking a bridge to a street and a river at the same time The concept of creating and working with image object links is similar to analyzing hierar chical image objects where an image object has virtual links to its sub or superobjects Creating these object links allows you to virtually connect objects in different maps and areas of the image In addition object links are created with direction information that can distinguish between incoming and outgoing links which is an important feature for object tracking 27 September 2012 User Guide Advanced Rule Set Concepts 173 7 11 2 Image Objects and their Relationships Implementing Child Domains via the Execute Child Process Algorithm Through the tutorials in earlier chapters you will already have some familiarity with the idea of parent and child domains which were used to organize processes in the Process Tree In that example a parent object was created which utilized the Execute Child Processes algorithm on the child processes beneath it The child processes within these parents typically defined algorithms at the image object level However depending on your selection Developer XD can apply algorithms to other objects selected from the Image Object Domain Current image object The parent image object itself Neighbor obj The distance of neighbor objects to the parent image ob
342. vsis test 006 w37E6EF 788 2 M Folder 1 841 analysis test D06 w4596AC748 R Folder 1 841 snalysis test 007 w183S30374 4 File Name Filter See Date Modified 18 08 2006 21 45 18 08 2006 21 46 18 08 2006 21 47 18 08 2006 21 48 18 08 2006 21 49 18 08 2006 21 50 18 08 2006 21 51 18 08 2006 21 52 18 08 2006 21 53 18 08 2006 21 54 18 08 2006 21 56 18 08 2006 21 57 18 08 2006 21 58 18 08 2006 21 59 18 08 2006 22 00 18 08 2006 22 01 18 08 2006 22 02 18 08 2006 22 03 18 08 2006 22 04 18 08 2006 22 05 18 08 2006 22 06 18 08 2006 22 07 18 08 2006 22 08 18 08 2006 22 09 v Figure 5 1 Load Image File dialog box for a simple project with recursive file display selected Load Image File along with Open Project Open Workspace and Load Ruleset uses a customized dialog box Selecting a drive displays sub folders in the adjacent pane the dialog will display the parent folder and the subfolder Clicking on a sub folder then displays all the recognized file types within it this is the default en In Windows there is a 260 character limit on filenames and filepaths http msdn microsoft com en us library windows desktop aa365247 28v vs 85 29 aspx Definiens software does not have this restriction and can export paths and create workspaces beyond this limitation For examples of this feature refer to the FAQs in the Windows installation guide 2 You can revert to the standard dialog if you prefer s
343. window with context menu for viewing polygons Click on Polygons in the left pane and select one of the following polygon display modes e Raster Draws outlines along the pixel borders e Smoothed Draws generalized polygons with smoothed outlines e Scale Parameter Analysis Displays the result of a scale parameter analysis in grad uated colors Scale Parameter is a legacy function from previous versions and not available in Definiens Developer XD 2 0 4 User Guide 27 September 2012 176 Developer XD 2 0 4 CK Gplevel 2 ef 2 Objects inked Figure 7 48 Different polygon displays in the map view Left raster outline mode Right smoothed outline mode pects Linked Figure 7 49 Different polygon display methods in the map view Bottom left Result of scale parameter analysis Bottom right Selected image object Image data courtesy of Ministry of Environmental Affairs of Sachsen Anhalt Germany NOTE If the polygons cannot be clearly distinguished due to a low zoom value they are automatically deactivated in the display In that case choose a higher zoom value If the polygon view is activated any time you select an image object it will be rendered along with its characterizing polygon This polygon is more generalized than the poly gons shown by the outlines and is independent of the topological structure of the image object level Its purpose is to describe the selected image object by its shape
344. wing Press Ctrl F on the keyboard Choose Process gt Find and Replace or View gt Window gt Find and Replace from the main menu Right click a class within the Class Hierarchy window and choose Find Class from the context menu Right click a feature in the Image Object Information or Feature View windows and choose Find from the context menu The Find What drop down list lets you select the category of rule set items you want to find To search on text occurring in any category select the Text field The Name field lets you specify a rule set item within the category When you press Find the corresponding processes are highlighted in the Process Tree window Use View Next to browse the found items To edit a rule set item double click it or select the item and click the Edit button The appropriate editing dialog will open for example the Edit Process dialog box for a found process Replace and Replace All functions are available To copy the path of a process select the appropriate result and press Copy Path 179 180 Developer XD 2 0 4 Find and Replace Fe oh CMM Name Teton z r Replace wath zj Find ureniuakoed varsbies Pan Cytopissm Goby Anaras Prd Background and Cytoplasn Goy acabes Prd Background and Cytoplemn Sepe ate Colt Preps Goig Acabem Find Background and Cytoplamn Separ ate Colt Prep Gop Acabyas Pind Background and Cytoplacny Sepa ate Colt Prope Goy techy Find Background and C
345. with externally defined action definitions Action definitions can be created with the Definiens Developer XD 2 0 4 Alternatively Definiens offers consulting services to improve your analysis solutions You can order special task actions for your individual image analysis needs To use an additional action definition you have import it Beside the xml file describing the action definition you need a rule set file dcp file providing a rule set that is related to a specific part of the solution The rule set has to include a parameter set providing variables to be adjusted by the user of the action library 1 Copy the action definition files to the system folder of your installation 2 Choose Library gt Import Action on the main menu Select an xml file to load 3 Now the new unconfigured action can be selected in the Add Actions dialog box Hiding Layers and Maps Definiens Developer XD 2 0 4 users have the option of chang ing the visibility settings for hidden layers and hidden maps see Tools gt Options p 247 This is a global setting and applies to all portals the setting is stored in the UserSet tings cfg file The default value in the Options dialog is No and all hidden layers are hidden Saving Configured Actions with a Project To facilitate the development of ruleware you can save your configured action with single projects and come back to them later A saved project includes all actions and their configurations which
346. x 46 340 pixels Creating scene tiles cuts the selected scene into equally sized pieces To create a scene tile you can e Use the Create Tiles dialog described in the next section for manual creation e Use the Create Scene Tiles algorithm within a rule set for more details see the Developer XD Reference Book Define the tile size for x and y the minimum size is 100 pixels Scene tiles cannot be rescaled and are created in the magnification or resolution of the selected scene Each scene tile will be a sub scene of the parent project in the workspace Results are not included in the created tiles Scene tiles can be created from any data set 2D or 3D for example When tiling z stacks or time series each slice or frame is tiled individually User Guide 27 September 2012 164 Developer XD 2 0 4 7 10 2 Manually Creating Copies and Tiles Creating a Copy with Scale Manually created scene copies are added to the workspace as sub scenes of the originat ing project Image objects or other results are not copied into these scene copies 1 To create a copy of a scene at the same scale or at another scale select a project in the right hand pane of the Workspace window 2 Right click it and select Create Copy with Scale from the context menu The Create Scene Copy with Scale dialog box opens see figure 7 38 3 Edit the name of the subset The default name is the same as the selected project name 4 You can select a different sc
347. y incoming links entering directly e Out Only outgoing links entering directly e All All links coming into and out of the selected object including paths that change direction The length of a path is described by a distance Linked object features use the max distance parameter as a condition Using the example in the figure below distances are counted as follows e TO to T1 Distance is 0 e TO to T2 Distance is 1 e TO to T4 Distance is 3 to both objects User Guide 27 September 2012 174 Developer XD 2 0 4 An object link is stored in a class called the link class These classes appear as normal classes in the class hierarchy and groups of links can be distinguished by their link classes When creating links the image object domain defines the source object and the candidate object parameters define the target objects The target area is set with the Overlap Settings parameters Existing links are handled in this way e Splitting an object with m links into n fragments creates n objects each linking in the same way as the original object This will cause the generation of m x n 1 new links which are clones of the old ones e Copying an image object level will also copy the links e Deleting an object deletes all links to or from this object e Links are saved with the project When linking objects in different maps it may be necessary to apply transformation parameters an example is where two images of th
348. y of image objects You can also define image object domains by their relations to image objects of parent processes for example sub objects or neighboring image objects 1 5 Scenes Maps Projects and Workspaces The organizational hierarchy in Definiens software is in ascending order scenes maps projects and workspaces As this terminology is used extensively in this guide it is important to familiarize yourself with it 1 5 1 Scenes On a practical level a scene is the most basic level in the Definiens hierarchy A scene is essentially a digital image along with some associated information For ex ample in its most basic form a scene could be a JPEG image from a digital camera with the associated metadata such as size resolution camera model and date that the camera software adds to the image At the other end of the spectrum it could be a four dimensional medical image set with an associated file containing a thematic layer containing histological data User Guide 27 September 2012 4 Developer XD 2 0 4 i i e Figure 1 2 Different image object domains of a process sequence 1 5 2 Maps and Projects The image file and the associated data within a scene can be independent of Definiens software although this is not always true However Developer XD will import all of this information and associated files which you can then save to a Definiens format the most basic one being aa Definien
349. y still suit the filter settings If the Pass Domain from Calling Process as a Parameter option is selected the customized algorithm is called only once regardless of the selected image object in the calling process The image object domain selected by the calling process is available as an additional domain within the customized algorithm When this option is selected you can select the From Calling Process domain in the child processes of the customized algorithm to access the image object that is specified by the calling process 7 8 4 Creating a Customized Algorithm 1 To create a customized algorithm go to the Process Tree window and select the par ent process of the process sequence that you want to use as customized algorithm Do one of the following e Right click the parent process and select Create Customized Algorithm from the context menu e Select Process gt Process Commands gt Create Customized Algorithm from the main menu The Customized Algorithms Properties dialog box opens Assign a name to the customized algorithm The Used Rule Set Items are arranged in groups To investigate their dependencies select the Show Reference Tree checkbox You can modify the scope of the used rule set items Select an item from the list then click the dropdown arrow button The following options are available e Global The item is used globally It is also available for other processes User Guide 27 September 2012
350. yer trom calling process dark lt odi trih lt bright on lever tom c airu pr Figure 7 34 Original process sequence above and customized algorithm displayed on a separate tab The local features and feature parameters are displayed in the feature tree of the Feature View window using the name of the customized algorithm for example MyCustomizedAlgorithm ArithmeticFeaturel The local variables and variable parameters can be checked in the Manage Variables dialog box They use the name of the customized algorithm as a prefix of their name for User Guide 27 September 2012 156 Developer XD 2 0 4 Class Hierarchy global classes 22y m x tgr ar auto threshold segmertation using domarsy classes new css who threshold segret aon using domarsy varieties beige a dork Figure 7 35 Local classes displayed in the Class Hierarchy window example MyCustomizedAlgorithm Pm_myVar The image object levels can be checked by in Edit Level Names dialog box They use the name of the customized algorithm as a prefix of their name for example MyCustomizedAlgorithm New Level 7 8 5 Using Customized Algorithms Once you have created a customized algorithm it displays in the Customized Algorithms tab of the Edit Process Tree window The rule set items you specified as Parameter are displayed in parentheses following the algorithm s name Customized algorithms are lik
351. ysis Automated analysis is running Automated analysis has failed See Remarks column for details Automated analysis could not be completed due to a timeout Automated analysis has crashed and could not be completed Inspecting the History of a Project Inspecting older versions helps with testing and opti mizing solutions This is especially helpful when performing a complex analysis where the user may need to locate and revert to an earlier version Figure 9 7 The Project History dialog box 1 To inspect the history of older project versions go to the right hand pane of the Workspace window that lists projects Right click a project and choose History from the context menu The Project History dialog box opens 2 All project versions Ver are listed with related Time User Operations State and Remarks 3 Click OK to close the dialog box Clicking a column header lets you sort by column To open a project version in the map view select a project version and click View or double click a project version To restore an older version choose the version you want to bring back and click the Roll Back button in the Project History dialog box The restored project version does not replace the current version but adds it to the project version list The intermediate versions are not lost User Guide 27 September 2012 194 Developer XD 2 0 4 Managing Analysis Runs Right click on a workspace and select Manage Runs to di
352. ytophaseny Seper ate Goby Analyses Find Background and Cytoplasmd Sepa ate C C Gop Anahyss Find Background and Cytaphasn Sepa ate Cols iC Golp Analyse Find Background and Cytaplasw Sepa ate Cells O Goby Anaras Find Background and Cytophasny Detect Golgy Cytopder Goby araras Pind Background and CytockasnyPinaioe Cytoclane at Goby seaby we Pied badigard and Cytoplasn ncleenhed amp Steel Figure 8 1 Find and Replace window with a sample search of the class Background 8 1 1 Find and Replace Modifiers There are two checkboxes in the Find and Replace window Delete After Replace All and Find Uninitialized Variables Selecting Delete After Replace All deletes any unused features and variables that result from the find and replace process For instance imagine a project has two classes dark and bright With class selected in the Find What drop down box a user replaces all instances of dark with bright If the box is unchecked the dark class remains in the Class Hierarchy window if it is selected the class is deleted Find Uninitialized Variables simply lets you search variables that do not have an explicit initialization 8 2 Rule Set Documentation 8 2 1 Adding Comments It is good practice to include comments in your rule sets if your work will be shared with other developers To add a comment select the rule set item for example a process class or expression in a window where
353. zed scene tiles together in the top scene e Setting Request Post Processing to No will prevent further analysis of the stitched tiles as an extra step after stitching Each tile is now processed with the rule set part from Subroutine 1 After all tiles have been processed stitching takes place and the complete image hierarchy including object variables is copied to the top scene 3 In case you want to remove the created tiles after stitching use the Delete Scenes algorithm and select Type of Sub Scenes Tiles For a more detailed explanation consult the Reference Book 4 Finally in this example project statistics are exported based on the image objects of the top scene Only the main map of tile projects can be stitched together 27 September 2012 User Guide Advanced Rule Set Concepts 169 Create a Scene Subset In this basic use case a subroutine limits detailed analysis to subsets representing ROIs this leads to faster processing Commonly such subroutines are used at the beginning of rule sets and are part of the main process tree on the Main tab Within the main process tree you sequence processes in order to find ROIs against a background Let us say that the intermediate results are multiple image objects of a class no_background representing the regions of interest of your image analysis task While still editing in the main process tree you can add a process applying the Create Scene Subset algorithm

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