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Insight: Measurement Tool User Guide
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1. Future additio nse sale A addi dis 20 Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 4 October 2007 1 Introduction to the Measurement Tool This document complements the OMERO Client User Guide by focusing on the Measurement Tool a new feature to the OMERO Insight Beta 2 2 release which significantly extends the image measurement and analysis functionalities These include e Defining Regions of Interest ROIs on the image and on each z section or timepoint of multi dimensional images e Annotating ROIs with textual annotations e Assigning stroke and fill colours to shapes e Getting measurements of the ROI shapes including area length and angle e Plotting intensity values e Loading existing ROIs and saving ROIs to file and e Managing ROIs editing shapes viewing deleting and adding DMSOHigh_001 dv 3 OC Measurement Tool DMSOHigh_001 dv Controls View Zoom Window Help Controls Options EJS aja A 14 80 BH save settings on close aga MM ojolelxis n a a Em view Annotation Split 4 Inspector a Manager E Results gt Field Value Loading LLLE Z 2 4 T 0 0 Figure 1 Image Viewer with Measurement Tool 1 1 Accessing the Measurement Tool Assuming the image on which you wish to perform measurement is currently open in the Image Viewer you can open the Measurement Tool by one of two ways e Click
2. OMERO Beta v2 2 Measurement Tool User Guide 7 October 2007 4 Release the mouse button the line is now created The length of the line will be shown along with the angle of the line to the horizontal see Figure 5 To draw a connecting line between two ROI shapes N Click inside or on the first ROI shape you wish to connect Select the Line Connection toolbar button O Ns Click inside or on the second ROI shape you wish to connect 4 A connecting line will be drawn between the two ROI shapes see Figure 6 To draw a freehand line scribble 1 Select the Scribble toolbar button Mn 2 Move the mouse pointer to the area of the image at which you want to start drawing the line 3 Hold down the mouse button and drag the mouse pointer to form the line 4 Release the mouse button the line is now created To draw a polygon t 2 Move the mouse pointer to a point on the image at which you want to start drawing the polygon 1 Select the Polygon toolbar button 3 Hold down the mouse button and drag the mouse pointer to create the polygon shape 4 Release the mouse button the polygon is now created Figure 4 point ROI Figure 5 line ROI Figure 6 elliptical ROI shapes shape showing length shapes and connector and angle detail line 2 3 Adding multiple ROI shapes on one plane There is an option to allow to quickly add many ROI shapes of the same kind on the same image plane To move to multiple
3. In the Image Viewer window move the mouse pointer to a point inside the ROI shape you wish to move Hold down the mouse button the mouse pointer will change to the drag cursor Drag the shape to the desired location Release the mouse button 4 3 2 Resizing a single ROI shape To adjust the shape of an ROI shape 1 2 4 5 Select the Selection toolbar button In the Image Viewer window move the mouse pointer to the border of the ROI shape you wish to move Hold down the mouse button the mouse pointer will change to the resize cursor Adjust the ROI shape to the desired appearance Release the mouse button NB For ROI shapes propagated across multiple z sections or timepoints resizing an ROI shape will only change the shape on the one plane not all z sections or timepoints 4 4 Changing the appearance of an ROI shape Various changes to the visual display of a selected ROI shape can be made through the ROI Shape Inspector see Figure 10 Measurement Tool DMSOHigh_001 dv Controls Options apa PB ojoje xix mio a Inspector Manager Results gt Field Value Text Text Show Text Y Show Measurements a Line Width 1 0 Font Size 10 0 Line Colour Measurement Text Colour ke Loading Figure 10 ROI shape Inspector view To bring up the Inspector view adjust the appearance of an ROI shape Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2
4. Measurement Tool User Guide 14 October 2007 1 Select the ROI shape either by clicking on it in the Image Viewer window or by selecting it in the ROI Manager or ROI Results view Select the Inspector tab Current display settings for the ROI shape will be displayed 4 4 1 Adjusting display of annotation text The following adjustments can be made to the ROI shape s annotation text e Click the Show Text checkbox to turn on off annotation text e Click the Show Measurements checkbox to turn on off measurement text e Change the size of the annotation text by selecting the Font Size menu and selecting the appropriate value 4 4 2 Adjusting display of the ROI shape The following adjustments can be made to the appearance of the ROI shape itself e Change the width of the ROI shape s line by selecting the Line Width menu and selecting the appropriate value e Change the colour of o the ROI shape s text o the ROI shape s fill for polygonal ROI shapes o the ROI shape s boundary line o the ROI shape s measurement text To change a colour 1 Double click the appropriate coloured area in the Inspector window 2 In the colour picker window that appears select the appropriate colour from the options displayed 3 Adjustments can be made to the Alpha value by using the slider 4 Select Accept to make the change Annotation text is also shown here but cannot be edited 4 4 3 Hiding ROI shapes To hide sele
5. shape to be copied Selected timepoints or z sections will be highlighted see Figure 8 Make sure the Add ROI radio button is selected Select the Close button The ROI shape and any accompanying information including annotations see Section 3 will now be propagated across the selected z sections or timepoints The ROI Assistant can also be used to remove ROI shapes from selected z sections or timepoints by following the instructions above but selecting the Remove ROI radio button Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 9 October 2007 Users dave Desktop usable image Test Images Img_R3D dv ID 5850 gt Measurement Tool Els 217 a o 9 B View ROI Assistant _ The ROI Assistant allows you to create an RO which extends R d A through time and z sections f Sr J Ao Add RO 4 8 Remove ROI 3 O 2 1 1 Shape Type X Coord Width Description Y Coord Height Close 2 3 4 T 0 0 x1 0 Figure 7 Propagating ROI shapes e g an elliptical ROI shape with the ROI Assistant Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 10 October 2007 ROI Assistant The ROI Assistant allows you to create an ROI which extends R through time and z sections N _0 Add ROI 4 gt Remove ROI 310 210 110 Shape Type Ellipse X Co
6. 0 Max 1708 00 253 0 313 0 377 0 439 0 528 0 286 0 330 0 429 0 495 0 602 0 Mean 976 68 272 0 316 0 367 0 466 0 588 0 707 0 286 0 329 0 427 0 524 0 671 0 761 0 E e A Ready Figure 14 Intensity view of pixel intensities The Intensity View window shows intensity values for a selected channel The selected channel can be changed using the menu towards the top right of the window It also shows summary intensity data to the right of the tabular display of intensities including e Minimum intensity value e Maximum intensity value e Mean intensity value e Sum of all intensity values e Standard deviation Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 20 October 2007 e X and Y co ordinates of the ROI shape e Width and height of the ROI and e X and Y co ordinates of the centre of the ROI shape If the ROI shape is moved or resized or another ROI shape is chosen the values will be automatically updated in the Intensity View window If the selected ROI shape is part of a multidimensional ROI menus will be provided to allow you to move through each timepoint and or z section In the example shown in Figure 14 the menu to the left of the figure allows you to change the z section for which the intensity data should be shown Results shown in the Intensity View can be saved in a similar way to the Results view by selecting the Save button at the botto
7. 3 Moving or resizing a single ROl oooonnicinnnncncoconcccccnnnccnnnnnnnnos 4 3 1 Moving a single ROI shape oooooicccnccncnncccccccccnnnnccnnnnonono 4 3 2 Resizing a single ROI ShaP8 oooccccccncccnococcccccnnnnccnnnnnnnno 4 4 Changing the appearance of an ROI shape 608 4 4 1 Adjusting display of annotation teXt ooooooniccnnnnncnnnccnnns 4 4 2 Adjusting display of the ROI shape ooooooooiccccnccccccccnccns 4 4 3 Hiding ROI Shapes ccccccccccooococnccccnnnncononnnnnnnccnnnnnnnnnnnnnnos 4 5 Deleting a single ROI Shape ooooooooocccccnnncccnncnocccccnnnnncnnnnnnanos 4 6 Editing multiple ROI shapes and ROIS ooooooconncccccnnccccccncnnns 5 Viewing ROI information oooocconooocnnccccnnnncnnnonnnnncnnnnnnnnnnonanannnnnnos 5 1 Viewing summary ROI information 5 2 Measurement results ooocoooccccccnnccccconocccnncnnancnnconnncnnnnnnnacnnnns 5 2 1 Showing summary resultS ooooicccnnnccococccccccnnnnncnnnnnnnnos 5 2 2 Refreshing summary data ooooooocccccccccccncnncocccnnnnncnnnnnnnno 5 2 3 Saving summary data ooooooooooooccccccncnccononnnonccnnnncnnnnnnnanos 5 3 Viewing pixel intensity values oooooconnccccccoccccncnnncccnconnnccnncns 5 3 1 Graphical VieW oooooooooonnncccnnncccnnnnnnnncnnnnnnnnnonnnnncnnnnnncnnnns it 5 Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 3 October 2007 Diaz lntensity VIS WA eta a 19 O
8. O Beta v2 2 Measurement Tool User Guide 18 October 2007 5 3 Viewing pixel intensity values Pixel intensity values for an individual ROI shape can be viewed graphically or as figures in tabular format 5 3 1 Graphical view Selecting the Graph Pane tab shows intensity values as a histogram Additionally a line profile will be shown for line ROI shapes see Figure 13 Measurement Tool Users dave Desktop usable image Test Images Img_R3D dv BS ojo x 5 m 6 a 2 Manager Inspector Results Graph Pane 7 Intensity View t Line Profile z3 1 500 TRIIR t ns gt PS a Sore i A 1 000 S 750 AA A AI STA lid fennen A ae a xX soo 250 7 gi nmm so a 0 o S 10 13 2 25 0 3 40 43 50 355 00 65 20 73 w 85 MU oo Pixel 457 528 617 2 A Histogram 3 s 0 3 o gas a bul LIII 1 miT wu NE nn M1 o 250 500 750 1 000 1 250 1 500 1 Intensity 7 1457 1528 1617 Ready Figure 13 Graph pane view of pixel intensities If the ROI shape is moved or resized or another ROI shape is chosen the histogram and line profile if shown will be automatically updated to reflect these changes 5 3 1 1 Configuring the Graph view To change the magnification of the Graph view right click on the histogram or line profile This brings up a menu that allows you to e Apply a zoom in or zoom out effect to the data by changing the visible values of the x and or y axes increas
9. OMERO Beta v2 2 Measurement Tool User Guide 1 October 2007 Insight Measurement Tool User Guide AT ne tes open microscopy environment OMERO insight OMERO is developed under the GPL For more information visit www openmicroscopy org Open Microscopy Environment http www openmicroscopy org Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 2 October 2007 Table of Contents Introduction to the Measurement Tool ooooocccccoccccccccnnccnncnnnccnncnnnnnn 1 1 Accessing the Measurement Tool 0cceeeeeeeeeeeeeeeeeees 1 2 The Measurement Tool interface ccccceeeeeeeeeeeeeteeeeeees 2 RAIN ROIS ak ot a iia ica 2 1 What isan ROI iio e dicta 2 2 Creating a single Shape ooocccccncccnoncoonccccnnnncnnnonnnanccinnnnnnnnns 2 3 Adding multiple ROI shapes on one plaNe oooooooonccccnnccccc 2 4 Creating an ROI across z sections and timepoints 3 Saving and loading ROIS ccccceceeeeeceeeeeeeeeeeeeeeeaaaeeeeeeeeeeees SIN Saving ROIS A 3 2 Loading ROIS ntre r a Eee reae eE EE HAREE ke aheri As Editing ROIS ii e R EE 4 1 Selecting ROIS sirier ainn e i 4 2 Annotation and labellidg ooooocin nnnnnnnnniconncnnnccnnccnnnccnncnnnns 4 2 1 Annotating an existing ROI Shape ooooooooicccccnnnccnncncccns 4 2 2 Labelling IMages oooocccnnncccccccnnccnnconaccnnconnncnnncnnancnnnnnnns 4
10. Propagating ROI shapes to create multi dimensional ROls is discussed more in Section 2 4 Viewing and managing ROIs and ROI shapes is discussed more in Sections 4 and 5 2 2 Creating a single shape To create a single ROI shape on a single plane z section or timepoint on an image select the appropriate toolbar shape option and draw the shape To draw a rectangle 1 Select the Rectangle toolbar button O 2 Hold down the mouse button on one corner of the area you wish to form the ROI and drag to the opposite corner 3 Release the mouse button the rectangle is now created To draw an ellipse O 2 Click on the edge of the area you wish to form the ROI and drag the mouse pointer until the circular shape approximates the ROI you wish to produce 1 Select the Ellipse toolbar button 3 Release the mouse button the elliptic ROI is now created To draw a circular point for example for counting spots Q 2 Click on the area of the image you wish to mark 1 Select the Point toolbar button 3 The point is now created see Figure 4 for an example of multiple points drawn on an image To draw a straight line N 1 Select the Line toolbar button 2 Move the mouse pointer to the area of the image at which you want to start drawing the line 3 Hold down the mouse button and drag the mouse pointer to the point you wish to finish the line Copyright C 2006 2007 University of Dundee All rights reserved
11. Type the annotation the annotation will appear as you type in the Annotation column iv The annotation will appear within the ROI shape 3 Use the ROI Inspector i Select the shape to be annotated the selected ROI shape will be highlighted ii Open the ROI Inspector iii Double click on the Annotation field iv Edit the existing text or add new texts See details of adjustments that can be made to the appearance of the annotation text in Section 4 4 1 4 2 2 Labelling Images To add a text label ROI shape A Select the Text toolbar button Click on the area of the image in which the label is to be added A text box with the word text will appear Double click on the text box to add the desired label text Or Po NS The label is now shown resizing the area of the text label will adjust the size of the text Note that the text label will exist as an ROI with a single shape and appear as such in the ROI Manager Inspector and Results views Double clicking on the text ROI in the ROI Manager and Inspector allows you to edit the text 4 3 Moving or resizing a single ROI Once an ROI shape has been created it is possible to move or resize it as required 4 3 1 Moving a single ROI shape To adjust the position of an ROI shape i 1 Select the Selection toolbar button Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 13 October 2007
12. addition mode open the Options menu select ROI Creation and then select Create Multiple ROIs which allows you to add many ROI shapes Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 8 October 2007 When you have finished adding shapes click the Selection button h to select an ROI shape To return to single addition mode open the Options menu select ROI Creation and then select Create Single ROI Alternatively you can toggle between single and multiple addition mode by right clicking on the ROI shape format button before adding a shape of that format This will allow you to add multiple ROI shapes of the selected format To move from multiple addition mode to Selection mode you will have to click the Selection button as above 2 4 Creating an ROI across z sections and timepoints ROI shapes once drawn on a single plane can be propagated copied across multiple z sections or timepoints to create a multi dimensional ROI To propagate an ROI shape 1 ON oOo Select the ROI shape to be propagated A The ROI Assistant shows the timepoints and z sections in which the selected ROI shape currently appears with the symbol of the ROI shape s type see Figure 7 which shows an elliptical ROI shape Open the ROI Assistant by selecting the ROI Assistant button Click on ROI shape symbol and drag it across the z sections or timepoints into which you wish the
13. cted ROI shapes from display 1 Open the ROI Manager see Figure 9 2 For the ROI shapes to be hidden uncheck the Visible checkbox Repeating the above actions will make currently hidden ROI shapes visible again 4 5 Deleting a single ROI shape To delete an individual ROI shape Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 15 October 2007 1 Select the shape to be deleted by clicking on the shape in the Image Viewer window for rectangles ellipses and polygons clicking inside the shape will select it 2 Then e Either press the Delete key on your keyboard to delete the selected shape e Or open the ROI Manager right click on the selected ROI shape select ROI Management Options and then Delete 4 6 Editing multiple ROI shapes and ROIs You can select whole ROIs including all constituent ROI shapes or selected ROI shapes for editing 1 Right click on the ROI Manager 2 Select ROI Management Options This gives access a menu that allows you a number of options e Duplicate the selected ROI or ROI shape A copy of the selected ROI or ROI shape will appear in the ROI Manager as a new ROI e Merge two selected ROIs with constituent ROI shapes into a single ROI e Split removing selected ROI shapes from their parent ROI and putting them into a new ROI e Propagate propagating the selected ROI or ROI shape as described in e Delete th
14. e selected ROI or ROI shapes 5 Viewing ROI information A range of information relating to the ROI shapes present in the selected image can be viewed 5 1 Viewing summary ROI information A summary information for all ROIs of an image can be revealed by clicking on the Manager tab All ROIs and constituent ROI shapes are listed see Figure 9 indicates an ROI indicates an ROI shape For each ROI ROI shape the following essential information is shown e For ROIs all constituent ROI shapes this will be the case where an ROI shape has been propagated across z and or t to create a multi dimensional ROI e The unique ID number of the ROI ROI shape e For ROIs the timepoints and or z sections across which it exists Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 16 October 2007 e The type of ROI shape one of Rectangle Ellipse Point Line Connector Polygon or Text is indicated by the appropriate symbol e Annotation text Whether or not the ROI ROI shape is currently visible To adjust the amount of data shown in the ROI Manager the display can be adjusted in the following ways e ROls can be expanded to show constituent ROI shapes by clicking on the grey Expand arrow to the left of the ROI gt e To collapse an expanded ROI select the grey Collapse arrow 5 2 Measurement results The ROI Results View shows su
15. f the perimeter of the ROI if a rectangle ellipse or polygon e x y values for the start co ordinates of the ROI e x y values for the end co ordinates of the ROI e x y values for all constituent co ordinates of the ROI The specific data values displayed in the Results view can be configured by selecting the Results Wizard button see Figure 12 It may be necessary to use the scrollbar to reveal all columns of data alternatively the window can be resized to show all data Results Wizard Select the measurements you wish to record Unused Measurements Selected Measurements Perimeter Annotation Coord List X gt Centre X Coord List Y Centre Y StartCoord X Area StartCoord Y Length EndCoord X Width EndCoord Y Height gt Angle Reset Accept Cancel Figure 12 The Results Wizard 5 2 2 Refreshing summary data If any changes are made to the image s ROls for example by resizing them adding new ROI shapes or deleting existing ROI shapes the data shown in the Results view will not be displayed unless being refreshed through the Refresh button 5 2 3 Saving summary data To save the currently displayed data e Select the Save button e Specify the location of the file to be saved e Choose the format for the saved data At present this is limited to Comma Separated Variable CSV format e Select Save Copyright C 2006 2007 University of Dundee All rights reserved OMER
16. ing or reducing the range of values shown in the graph Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 19 October 2007 e Apply an automatic scaling effect so that the ranges of the x and y axes accommodate exactly the maximum and minimum values of the intensity data of the ROI shape in question If the selected ROI shape is part of a multidimensional ROI slider bars will be provided to allow you to move through each timepoint and or z section in a similar way to the Image View window In the example shown in Figure 13 the vertical slider bar to the left of the figure allows you to change the z section for which the intensity data should be shown 5 3 1 2 Saving graphical views The graphs shown can be saved as images e Right click on the graph to be saved e Select the Save as option in the menu that appears e Choose the location of the image file to be saved e Select the Save button 5 3 2 Intensity View Selecting the Intensity View tab shows intensity data for the selected ROI shape as a table of values Figure 14 Measurement Tool Users dave Desktop usable image Test Images Img_R3D dv Ams BM O O O N N mlala Manager Inspector Results Graph Pane Intensity View 3 0 1 2 3 4 5 Lad Oo 457 247 0 271 0 307 0 254 0 281 0 335 0 r 240 0 263 0 297 0 365 0 Min 200 00 254 0 301 0 366 0 428 0 244 0 282 0 313 0 376 0 451
17. it the appearance of an individual ROI shape including colour of line fill and any text associated with the image e Results view shows a summary of key measurement data for all ROI shapes present It allows you to select an individual ROI shape for further detailed analysis e Graph Pane generates graphical representations histogram and for line ROI shapes line plots of intensity values by channel for the selected ROI shape These can be saved as images e Intensity View provides numerical data of individual pixel intensity values plus values such as mean maximum and minimum values plus an option to export this data for viewing in spreadsheet applications such as Excel as a CSV file 2 Creating ROIs You can create Regions of Interest ROIs of varying types on a single plane which can then be expanded to become multi dimensional 2 1 What is an ROI In OMERO we use the following definitions Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 6 October 2007 e ROI a multi dimensional object consisting of one or more ROI shapes gt indicated by the icon e ROI shape a two dimensional object that appears on one plane only indicated by the icon An ROI shape also automatically exists as an ROI An ROI across multiple dimensions z sections or timepoints will be created when an individual ROI shape is selected and propagated
18. m right of the Intensity View window 6 Future additions A number of additional features are planned to be added to the Measurement Tool These include the following e The ability to treat ROIs as volumes for measurement Enhanced management of annotations multiple text annotation for ROI shapes e The ability to assign relationships between ROIs e The ability to assign categories to ROIs other than text annotation e Automatic creation of ROIs around cells and objects e Lineage management and e Enhanced measurement Copyright C 2006 2007 University of Dundee All rights reserved
19. mmary measurement results for all ROIs and ROI shapes see Figure 11 It also allows you to configure which data should be included in a results data file to be saved for exporting to other applications Measurement Tool Users dave Desktop usable image Test Images Img_R3D dv aus BGIOIoI lt Nteter a Manager Inspector E Results Graph Pane A Intensity View ID T 2 Type Annotatioi Centre X Centre Y Area Length Width Height Angle 1 1 3 Text Some te 2 E 1 Ellipse 87 432 2843 93 51 71 2 i 2 Ellipse 87 432 2843 93 51 71 2 1 3 Ellipse 99 432 4238 01 76 71 Results Wizard Refresh Save Ready Figure 11 Results view 5 2 1 Showing summary results The data displayed by default in the Results view includes e Unique ID of the ROI shape e The T section in which the ROI appears e The z section in which the ROI appears Type of ROI shape e Annotation text e x and y co ordinates of the centre of the ROI e The area of the ROI if a rectangle ellipse or polygon in square microns or pixels depending on the units specified in the Options menu e The length of the ROI if a line Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 17 October 2007 e The width and height of the ROI if a rectangle ellipse or polygon e The angle of the ROI from the horizontal if a line In addition it is possible to view The length o
20. on one ROI shapes and select Select All from the menu that appears e To select only ROI shapes of the same type right click on one ROI shapes and select Select Same from the menu that appears Using the ROI Manager Open the Manager view see Figure 9 and select an ROI shape by clicking on it e To select multiple ROI shapes hold down the Shift key while clicking Measurement Tool Users dave Desktop usable image Test Images Img_R3D dv ana PR OOlO NIN mG A a Manager Inspector Results H Graph Pane 7 Intensity View ROI ID F Z Type Annotation Visible E ME 1 0 0 3 3 T Y 1 0 3 T Some text here Y ve 2 0 0 1 3 O e 2 0 1 O M O 2 0 2 Y 2 0 3 Y Ready Figure 9 ROI Manager window For more on editing ROIs groups of ROI shapes see Section 4 6 4 2 Annotation and labelling You can add a text annotation to an existing ROI shape or label an area of the image directly by adding a text ROI Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 12 October 2007 4 2 1 Annotating an existing ROI shape Separate to text ROIs an existing ROI shape can be annotated in one of three ways 1 Double click on the shape you can either edit the current annotation text or add new ones 2 Use the ROI Manager i Open the ROI Manager ii Select the shape to be annotated the selected ROI shape will be highlighted iii
21. on the measurement tool icon 7 in the main Image Viewer toolbar above the image or e Open the Controls menu select Measurement Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 5 October 2007 This will launch the Measurement Tool see Figure 1 1 2 The Measurement Tool interface It is worth familiarising yourself with the Measurement Tool user interface shown in Figure 1 It consists of two key areas a series of buttons identified by icons and below that a series of tabbed navigation options Additionally there are menu options available at the top of the application window and in specific situations available by right clicking the mouse The Measurement Tool has a toolbar giving access to the key features of the tool shown in Figure 2 As OJOS xs m t A Figure 2 Measurement Tool toolbar Below this are a series of tabs giving access to key views of data relating to ROIs present in the selected image see Figure 3 a Manager Inspector Results Graph Pane Intensity View Figure 3 Measurement Tool s tab navigation In turn these tabs give access to the following features of the Measurement Tool Manager shows a hierarchical view of all ROIs and constituent shapes present in the image This allows you to select an individual ROI shape or ROI a collection of shapes for analysis or editing e Inspector allows you to ed
22. ord 100 0 Width 44 0 Description Text Y Coord 230 0 Height 79 0 Close Figure 8 Propagating ROI shapes selecting z sections as propagation destinations 3 Saving and loading ROIs ROI data need to be saved manually in order to be able to recall it in future This is because ROls and associated date are saved separately to the image itself and ROI information is currently not saved automatically in OMERO 3 1 Saving ROIs To save all ROI information for an image 2 Choose the location for the saved ROI file using the file browser window that appears 1 Select the Save button 3 Select Save NB If you try to close the Measurement Tool or Image Viewer with unsaved ROI information a prompt will ask you whether or not you wish to save this information 3 2 Loading ROIs To view ROls associated with an image e Open the image in Insight s Image Viewer Copyright C 2006 2007 University of Dundee All rights reserved OMERO Beta v2 2 Measurement Tool User Guide 11 October 2007 e ROls associated with the image will be automatically loaded so long as they were created on the same computer used to view them 4 Editing ROIs 4 1 Selecting ROIs There are a number of ways to select one or more ROI shapes for editing Using the Image Viewer window e To select a single ROI shape on a single plane click on the ROI shape in the Image Viewer window e To select multiple ROI shapes on a single plane right click
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