User Manual - DITABIS AG
Contents
1. 21 CM IMPOR ILO NEN L E EEEERR 21 GEE Pn Sec NUN 21 GN Ue 0 3 00 RERO MONTRE 21 OPUS LC 22 9 2 9 ODUOLIS eae ee ee ea ee ene ee ee on emt mendicus eto ERU eee ene eee 22 CHCNEE IURIS ER 26 3 3 1 OVOIVIOW s cce ruorcaei bote turenstemutpesacuzedasanun beste tus nEbenslbekt e vsdososuus basta sictasbg oet cB 26 3 3 2 CS Navigator RR REO EROR ERE 27 3 3 9 Al ed NAVIGAION sosoran eosi ekan reino EEn eai En KEAK OANE NI ENERE EaR RERS 28 SAC E e Ee ES UN NITET 28 Or Os OPO VIG Me E caus eeeeees 29 3 3 6 Ribbon View FUNCTIONS cccccececececcececececcccecuccccccececucuaececscecetauaenerass 29 3 3 7 Ribbon Lookup Table Functions eseeeeesseeeeseeeeeeeeeeee 30 3 4 Menu Protocol sesseseseeeenem emm Rene nm he menter meter re rere eire reser e trans 31 CP M NER Ua ne A EAE EE 31 3 4 2 Protocol FIOW P RTT danari AA A aAa KAAKAA KAKAA a 32 3 4 3 Section Save OPTIONS ccccccccccecsssseeeeeecceeeassseceeeeeseeeasseeeeeesseseaaaseeeeeess 33 3 4 4 Define New Session ccccceccececcececcececcccuccccuccceccececueaeceuaceucaeaucauaecuuaeceuaeees 35 344 5 Load PFIOLOGOIS 1o eta a oe aen orci AE E utis taxa s cute anta rs bexuwe ce veu aA 35 3 4 6 Start Stop the Processing of the Protocol2. seseeeeeeseseeeeees 37 re Bo Pm Vn Relecin M EE E EEE EE EE AE E EE E EAE AA EE 38 Be 1 OV 0 E E E EEE AE E 38 392 Vey PUO ONO re ee ee 39 353 SC mU eie 9 ERE NEN ITE 39 3 5 4 Section Scan Settings ccccccccccccssseeeeeeeeeeeaeeseeeceeeeeseeaeesseeeeeeeessaaaeeseeeess 40 3 Software Version 1 0 Soot Scout Content 2 5 5 SECON Grid SIMICUING ccoiuccc iron toit iE EE i aa 41 3 6 Menu Evaluation only SpotScout Pro cccccececceeeeeeeeeeeeeeeeeeeeeeeesaansseeeeeees 43 3 6 1 Tab Finding Settings ccccccccsssscceeceeeeceeecseeeceesseeaeeeeseeseaeeeeessaaaeeeessseaees 44 3 6 2 Tab Quality Settings eeeeeeesssseseeeeeeseesseeeeeennn nnns 45 3 6 9 Grid Finding ODIIOFIS suasit orbita 3 epa eot n5 Iba aa taie ER inina diniinan 47 3 6 4 Evaluation Options ssseeeeesessssssseeeeeeennnnennnnnnnnn nennen nnns 48 3 6 5 Flags Visibility Options eeesssesseeseeeeeeeeeeeennn nmn 48 26 6 Tab IIS LO QM aN PTT TTE TEM 49 Cay gales la elec gt PO NER nner ne ne ee ne nnn eee eee 50 3 6 9 Tab Evaluation Table orien orant pin San Fern tu eder kx ca endatecdeedatentsedexs 51 4 P lejor ipo p dem 53 LE cieME eRLT R 53 4 2 License Information cccceeececceeseeecceeeeecceuseeeseuueeecsauseessagseeeseseessseeesens 54 4 Software Version 1 0 DIGITAL BIOMEDICAL IMAGIN
3. Information By clicking on Informations the program version of SpotScout or SpotScout Pro is displayed 3 2 6 Recent By clicking on Recent the documents column Recent Documents and directories column Recent Places opened recently are displayed see Fig 5 Q If you click on a document in the column Recent Document the relevant image file is opened and displayed in the menu Viewer Q If you click on a directory in the column Recent Places here the relevant directory with the files included therein is displayed Here you can select and load a file The file is displayed in the menu Viewer Permanent Display The ico files and directories are provided with one pin each displayed as loose pin By clicking on a pin the file or the folder are displayed permanently even if it has not been opened for a long time This is marked symbolically by an inserted pin a see Fig 5 3 2 7 LabBook In the LabBook all processes of SpotScout are protocolled and saved 21 Software Version 1 0 3 Software Documentation So dt Scout Lab Book After the selection of this option the protocol is displayed with date time and 22 process No process can be deleted or modified SpotScout Pro2 25 01 2011 13 55 57 Load Scan Settings Slot 25 01 2011 13 55 57 Load Grid Definition Slot 25 01 2011 13 55 57 Load Quality Settings Slot0 25 01 2011 13 55 57 Load Grid Finding Settings Slot 25 01 2011
4. Linear Automatic Noe HLLAAELLLLLLLLLLLUTI Red Channel Green Channel Overlayed r g ursor Cursor Cursor Spot Spot Spot Background Background Background ame Fig 12 Menu Viewer setting slide total view 3 3 1 Overview Via the Slide Navigator and the Area Navigator desired image details for the Slide View can be selected and enlarged or reduced Likewise the Slide View itself can be zoomed see chapter 3 1 3 These settings mirror themselves in the navigator windows and show you the image detail with surroundings Area Navigator within the total view of the slide Slide Navigator The Histogram shows the brightness distribution of the total image as well as the number of counts at the cursor position in the image or in the section you have highlighted in the histogram with the cursor The Spot Viewer indicates the spot and background values for the spots on which the cursor is placed A setting of the size of the indicated spots can be made in the menu File Options General 3 2 9 d IMAGING SYSTEMS AG Software Version 1 0 KD NOREDICAL So dt Scout Blue Rectangle Zoom range Blue Rectangle Zoom range with surrounding 3 3 2 Slide Navigator 3 Software Documentation The Slide Navigator shows the total view of the slide the grey frame shows a block on the slide Q Clicking on the block sets the zoom on the block in such a way tha
5. Submenu Device General Device Information Here the Firmware Version the FPGA Version and the Serial Number of the scanner are displayed if the MArS Scanner is connected and switched on Preview scan Here the scanner resolution for the Preview Scan can be selected spot size Submenu Device Laser Filter Combination 23 Software Version 1 0 3 Software Documentation 24 Sot Seeut Red Setial red a RR E Sena gen Green 8 S aser Filter combinations me Co oo oo y so ms 20 uz Cancel Fig 10 The four preset laser filter combinations The four preset laser and filter combinations see Fig 10 are displayed Meaning of the individual columns Name Laser Filter CalCor Calibration Name of the laser filter combination The possible values Red Green depend on the desired laser Red 635 nm or Green 532 nm Filter position on the filter wheel in MArS see Fig 11 Possible values are 1 8 Calibration correction value At the delivery of the device it is 0 no correction For user defined filter settings a deviating value can be entered here which affects the value in the column Calibration Please note that the top value is 255 counts there This is the calibration value individually identified for your device It can be between 0 and 255 E a DIGI L BIOMEDICAL IMAGING SYSTEMS AG Software Version 1 0 Sod Scout 3 Software Documentation Add
6. protocol is loaded for the active slot Quick Load Function Via the button Quick Load a quick load function for protocols is available to provide several slots with protocols subsequently Procedure Q Click on Quick Load The quick load function is activated Q Click on the desired protocol in the ribbon Then the selected protocol for the active slot is loaded At the same time the program jumps to the next slot and activates it Q Click on the protocol that you want to assign to this slot It is loaded and the program jumps to the next slot LJ In this way you can provide all slots one after the other with different or identical protocols Software Version 1 0 Sob Seat 3 Software Documentation 3 4 6 Start Stop the Processing of the Protocol The protocol can be started if the protocol steps and the saving parameters are defined Start the Processing of the Protocol Procedure Q To scan all slots click on lt Start gt Q To scan only the displayed slot click on the drop down menu of lt Start gt and select the option Current Slot Q Then all steps of the Protocol Flow are processed automatically and if defined in the Protocol Flow saved The data are saved per slot in a ses file Stop the Processing of the Protocol Procedure Q Click on the button Stop The processing of the protocol is stopped LI To proceed with the processing click on Start again or select the opti
7. test3 ses Eigene Dateien CADokumente und Einstellungen jens Eigene Dateien MArS Scanlmages a C Dokumente und Einstellungen jens Eigene Dateien test2 ses Information C Dokumente und Einstellungen jens Eia C Dokumente und Einstellungen je Lab Book SpotScoutExample tif c ADokumente und Einstellungen je Help test tif c ADokumente und Einstellung j Options EJ Exit test tif Dokumente und Einstellungen jens Eigene Dateien Fig 5 Menu File with options and default setting Recent 3 2 1 Save A click on Save saves the session or image file active in the menu Viewer If a tif file is active the selection window Save as always appears at the function Save to define the name and to select the file format Loaded tif files can also be saved as ses files In this case they also include the additional information of the session If the opened file is a ses file the available file is overwritten with the changes Default setting for the saving of file images is My Files MArS Scanlmages 19 Software Version 1 0 3 Software Documentation Sot Scout 3 2 2 Save As This option saves the session or image file active in the menu Viewer under a new name to be entered The following settings have to be considered and made d d Enter the desired File Name Set the desired File Type tif or ses Please observe the explanations on the file types in chapter 3 1
8. 13 55 57 Create Session Slott 25 01 2011 13 55 58 Load Scan Settings Slot1 25 01 2011 13 55 58 Load Grid Definition Slot1 25 01 2011 13 55 58 Load Quality Settings Slot1 25 01 2011 13 55 58 Load Grid Finding Settings Slot1 25 01 2011 13 55 58 Create Session Slot2 25 01 2011 13 55 58 Load Scan Settings Slot2 25 01 2011 13 55 58 Load Grid Definition Slot2 25 01 2011 13 55 58 Load Quality Settings Slot2 25 01 2011 13 55 58 Load Grid Finding Settings Slot2 25 01 2011 13 55 58 Create Session Slot3 25 01 2011 13 55 58 Load Scan Settings Slot3 25 01 2011 13 55 58 Load Grid Definition Slot3 25 01 2011 13 55 59 Load Quality Settings Slot3 25 01 2011 13 55 58 Load Grid Finding Settings Slot3 25 01 2011 13 55 58 Create Session Slot4 25 01 2011 14 32 28 Open Session CGH Full Slide grid finding done Information Recent Lab Book Help tj Options J Exit ES ES ES ES ES ES ES ES S ES ESI ES ES ESI ES S ESI ESI ESI ES EI Fig 7 Display of a laboratory protocol 3 2 8 Help After the selection of Help a window with several options is opened eo SpotScout Pro Viewer Protocol Scan Evaluation Information Recent Lab Book tj Options Exit S SpotScout short description Quick help about DITAGIS SpotScout DITABIS Homepage Get more information about DITABIS products A Contact Us Let us know if you need help or how we can make Scot
9. 4 Set the desired memory mode Single TIFF Every scan image e g per ScanSetting per area is saved as individual tif file Multi TIFF All images are saved in a tif file Multi TIFF per Area All images per area are saved in a tif file Enter the desired Orientation of the image For that click on the arrow button next to Orientation A selection list opens where the orientation of the sample carrier is pictorially represented Speichern unter verwendete Dok Netzwerkumgebu Eigene Dateien Arbeitsplatz Q 2 gt Hiv Speichern in Scanlmages II Zuletzt Desktop gt 2 Abbrechen ng Dateiname example green Dateityp TIFF tit iff Multi Tiff ingle Tiff Multi Tif Multi Tiff per Area kinde Orientatinn Fig 6 Dialogue window Save as 20 Software Version 1 0 StS 3 Software Documentation 3 2 3 Open The default path for the opening of image files is My Documents MArS Scanlmages This path can be modified like in the Windows Explorer Open file Q Select the desired path LI Select the desired file type ses tif or Q Select the desired file name and click on lt Open gt 3 2 4 Close By clicking on Close the file currently active in the menu Viewer is closed If the data have not yet been saved or if you have made modifications you are asked whether you want to save the data 3 2 5
10. icon on your desktop Software Version 1 0 2 Software Installation and Connection with MArS1 Overview Soot Scout Activation of the Software with a License Key Procedure Select GetSpotScoutlD in the start menu Then the file HardwarelD txt is created on your desktop Send the file HardwarelD txt per email to sales ditabis de After having paid the license fee we will send you the license file immediately Otherwise you get information on payment options Copy the license file in the SpotScout program directory and start SpotScout V m md P V A Software Version 1 0 Sod Scout 3 Software Documentation 3 Software Documentation Quick Access Bar with user defined tools Ribbon tools corresponding to the selected menu Display Bar for slots and loaded files Setting and Evaluation Section 3 1 Program Structure and Operation 3 1 1 Structure of the Program Window After the program start click on the program icon on the desktop SpotScout or SpotScout Pro is loaded and the program with the start window is displayed This is the window of the menu Viewer with the display fields for the images still being empty If MArS is not connected and switched on all functions are deactivated can be moved randomly o IQ a SpotScout Pro File Viewer Protoco Scan Evaluation JI amp Le Scan Qi d cked T J JERBE e eret Overla des Auto Linked 9 6553
11. in the Area Navigator Accordingly the display in Slide View changes Q To draw a range within the blue frame push the button lt Strg gt and draw the desired rectangle with the button lt Strg gt being pushed LY The dragging on one side of the frame enlarges or reduces the detail in the main window LI To move the zoom range click on the blue rectangle and drag the rectangle in the desired direction with the mouse button being pushed 3 3 4 Histogram The histogram illustrates the distribution of the color values of the complete image In order to visualize the distribution the Y axis is displayed logarithmically default You can also change to linear illustration Depending on the setting either the red or the green or both channels see chapter 3 3 7 are displayed at the same time see Fig 14 For the relevant cursor position the corresponding values Level Red count Green count are displayed numerically A random range can be dragged with the mouse Thereby the values for this range Level from to Red count Green count are shown The selected range is displayed in orange If you push and hold the button Strg the percent values instead of the absolute values for the red and or green channel are displayed see Fig 14 Green count 14 855 08 Linear Fig 14 Histogram illustration with selected range The histogram also shows whether the scanned image is overexposed or underexposed If the values
12. 007 Free Software Foundation Inc http fsf org Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License supplemented by the additional permissions listed below 0 Additional Definitions As used herein this License refers to version 3 of the GNU Lesser General Public License and the GNU GPL refers to version 3 of the GNU General Public License The Library refers to a covered work governed by this License other than an Application or a Combined Work as defined below An Application is any work that makes use of an interface provided by the Library but which is not otherwise based on the Library Defining a subclass of a class defined by the Library is deemed a mode of using an interface provided by the Library A Combined Work is a work produced by combining or linking an Application with the Library The particular version of the Library with which the Combined Work was made is also called the LinkedVersion The Minimal Corresponding Source for a Combined Work means the Corresponding Source for the Combined Work excluding any source code for portions of the Combined Work that considered in isolation are based on the Application and not on the Linked Version The Corresponding Application Code for a Combined Work mea
13. 51 Linked Channel Slide View display of the loaded scanned imade Level T queer nea Automatuc Green count E E Red Channel Green Channel Overlayed r g Cursor Cursor Spot Background Cursor Spot Background Background Spot Block Instrument ready unloaded Status Display Progress Bar for the Loading Global Progress selected Slot Status Bar Fig 1 Structure of the Program Window In all program parts the program window is structured similarly Only in the menu File there is no Slide View Software Version 1 0 3 Software Documentation Soot Seat 3 1 2 Operation Quick Access You can copy buttons and tools which you use frequently from the Ribbon into the tool bar Quick Access Then they are additionally available in every menu The quick access can be configured pursuant to your individual needs For that the Context Menu of the individual Buttons or Functional Groups e g View or Lookup Table is available The options of the Context Menu are related to the clicked on object The buttons can be removed from the Quick Access again by opening the Context Menu of the Button or the Functional Group in Quick Access and selecting the relevant option e g Remove The options of the context menu Add to Quick Access Toolbar Copies the clicked on function or function group i
14. FXXX Mean mean feature pixel intensity FXXX SD standard deviation of the feature pixel intensity FXXX CV Coefficient of variation is calculated by FXXX SD F XXX Median BXXX median feature background intensity BXXX Median median feature background intensity BXXX Mean mean feature background intensity BXXX SD standard deviation of the feature background intensity BXXX CV Coefficient of variation is calculated by BXXX SD B XXX Median gt BXXX 1SD percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity gt BXXX 2SD percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity FXXX Sat Percentage of feature pixels which intensity equals the maximum intensity FXXX Median the median feature pixel intensity at wavelength with the median BXXX background subtracted FXXX Mean BXXX the mean feature pixel intensity at wavelength with the median background subtracted FXXX Total the sum of spot pixel intensities at wavelength Index number of the spot as Intensity it occurs on the array SNR XXX the signal to noise ratio at wavelength defined by Mean Foreground 1 Mean Background 1 Standard deviation of Background 1 Bum FbEC ndi tm 93 Software Version 1 0 4 Appendix 54 Sot Scout 4 2 License Information ZedGraph is published under LGPL GNU LESSER GENERAL PUBLIC LICENSE Version 3 29 June 2007 Copyright C 2
15. G SYSTEMS AG ee s Content Dear customer We are delighted that have chosen SpotScout or SpotScout Pro a Scan Software to control the Microarray Scanner MArS of Ditabis and to qualify and evaluate biochip image data The Software has been developed with utmost care involving the use of newest tools and high performance algorithms to allow routine operation as well as individual research tasks The intuitive user navigation makes working with the SpotScout Pro very simple The operator s manual includes all that you need for operating the software and for using all implemented functions We wish you every success in solving your tasks with SpotScout Pro If you have any questions or if a problem occurs please do not hesitate to contact us Your Ditabis AG Development Team Freiburger StraBe 3 75179 Pforzheim www ditabis de Software Version 1 0 2 Software Installation and Connection with MArS1 Overview 1 Overview re 1 1 What is SpotScout and SpotScout Pro SpotScout is the basic module of the scanner software to control the MArS Microarray Scanner and to display biochip image data for analysis It is also possible to load and display image data of other devices if they are available as 16 bit grey scale images in TIF format Besides it is possible to import all GAL files SpotScout Pro additionally includes the complete evaluation module to evaluate image data automatically or pursuant to individual
16. Individual Laser Filter Settings You can add any individual settings according to the arrangement of the filters in the filter wheel of MArS Procedure d d d d Click on the lt gt button A new line is added to the available table Enter the parameters of the additional filter pursuant to the above description Confirm the entry by clicking on Apply For more filters repeat this process accordingly To save the modifications click on lt Ok gt 5 4 Fig 11 Filter wheel with the position numbers for the individual filters Be careful when handling the setting of the calibration correction factors Even minor modifications of e g 1 can increase the measured fluorescence measuring signal by 6 to 10 95 25 Software Version 1 0 3 Software Documentation Display Bar for loaded files and slots Setting and Evaluation Section 26 So dt Scout 3 3 Menu Viewer The menu Viewer is the start page of the program as well as the display page for a loaded file or a scanned slide The menu window is subdivided into the following sections e Ribbon with all tools for image setting and navigation e Display bar for loaded files and slots e Setting and evaluation section with navigators histogram and Spot Viewer e Slide View with display of the scanned or loaded image SpotScout Pro2 BH E Low Hy High Linked Channel Level Level Red count Green count Loo
17. Scan 3 Software Documentation Progress Bar of the Selected Slot It displays the progress of the current action like e g scanning in the active slot in Loading Status Unloaded The MArS loading table is moved out Empty The MArS loading table is in scan position and contains no slides sample carriers Loaded The MArS loading table is in scan position and includes one slide in the displayed slot sample carrier Barcode If the barcode is read it replaces the loading status Global Progress Bar Displays the progress of the processing of a protocol in of the total time see menu Protocol Context Menu of the Slide View Main Window A click with the right mouse button on the Slide View opens the Context Menu with the following functions Navigate Back The program returns to the last navigation setting e g zoom setting Navigate Forward Proceeds by one navigation setting Zoom Activates the zoom function Hand Activates the hand function Zoom to Slide Zooms to the complete slide Zoom to Scan Zooms to the complete scanned image Keyboard Control The program can also be controlled via the keyboard Pushing the lt Alt gt button indicates the letter to perform a function For the options of the drop down menu the letter which performs the option is underlined Default Protocol Software Version 1 0 3 Software Documentation Save Store as Default Restore Default Organize Import
18. Scout even better Fig 8 Menu File SpotScout Help Displays the available manual SpotScout Help MArS Displays the MArS manual SpotScout short description Opens the short description of SpotScout Ditabis Homepage The web browser is started and the DITABIS homepage is opened The web browser is started and the contact page of the DITABIS homepage is opened 3 2 9 Options A EUMAA REC PE E FADED Software Version 1 0 DIGITAL BIOMEDICAL IMAGING SYSTEMS AG Soot Stout 3 Software Documentation After the selection of lt Options gt a dialogue window with two submenus is opened Options E Options Appearance General Color scheme Blue B Device General Show brightness near cursor Laser Filter combinations Cancel Service mode Fig 9 Menu Options submenu Options General Submenu Options General In this submenu the general appearance Appearance of SpotScout and the size of the spots in the Spot Viewer Menu Viewer and in the menu Evaluation tab Scatter Plot and Evaluation Table can be modified Appearance Color scheme Here the color scheme can be selected blue black silver Show brightness f the control box is activated the brightness values are near cursor displayed in the menu Viewer next to the cursor Spot Viewer Zoom With the slider control the spot size displayed in the Spot Viewer can be modified See chapter 3 3 5 By clicking on Olc the settings are saved
19. Sod Scu User Manual Software Version 1 0 Soo dio Content Content 1 OV GF V GW RRE M 6 1 1 What is SpotScout and SpotScout Pro sess 6 1 2 System Requirements ccccceeeeccccceeeseceeeeeeeeeeeeesaeeeceeesseaeeeseeseaeeeeeessaseeees 6 du9 Wr VOONANT NV CUSIOMN erea detienen hir paient vatis idis 7 1 4 Content and Structure of the Manual 0 ccc eee ceceecceceececceceeceeceeeeeeeeeeeeees 7 Jo Witing RUGS ecirar ronne ar arar ERE QE eR Y vU pa VaUR GU xu S 7 1 6 License Information 0 cc cc ececececececcccccccccecececeneceuecececeuececececacacacacanacanananas 7 2 Software Installation and Connection with MATS 9 3 Software Documentation eese nenne nenne nena nene 11 3 1 Program Structure and Operation seeeesseeeeseeseeereeene 11 3 1 1 Structure of the Program Window cccccccssesseececeeeeseeeeeeeeeeeeesesuaeseeeeeeees 11 SwIEcWe cue Re 12 So Progam eli E CUS ERROR ETE 17 3 1 4 File FOTelS esten poe rta seo Ert paezrtinre i rtebPre rvtr Sa Isid resrrcUtielbrtetiqerrEtabpol rM PPbds 18 ac Nen Oh ca gt ee uide em tucdu scu c de E E M eM c IR EU E E 19 cU NEST m 19 XC NE Oi NRI 20 SES GU LONE UT Tm 21 CAN P I NDTP
20. The tab of the active menu is highlighted brightly The tab of the menu File is always highlighted in orange Wiewer Protocol Scan Evaluation Fig 4 Menu Bar Ribbon Depending on the menu the required functions and tools in the form of buttons are arranged and subdivided into functional groups here You can also move functions which you use frequently to Quick Access See above Setting and Evaluation Section Depending on the menu the parameters are entered or the displayed image can be analyzed and evaluated here Display Bar for Slots and Loaded Files slot 1 Slot 2 Slot3 stot 4 example 1 1 02 22 14 40 05 SpotScoutSession 14 40 05 SpotScoutSession vx Here the four slot tabs as well as all loaded files are displayed A ses file always only includes the files of one slot The active slot or the active file is highlighted By clicking on a slot or a file name the relevant slot or file is activated A scan can only be performed in a slot tab These tabs are always available if a MArS is connected and identified Software Version 1 0 So dt Scout 3 Software Documentation The files can also be selected via the drop down menu of the Display Bar lt Y gt The active file is closed via x in the Display Bar Slide Display In this section the scanned or loaded image is a The following scroll and zoom functions are available if the zoom function is active Scroll vertically Moving the mouse wh
21. Time Uses the current time for the file name Barcode Uses the barcode for the file name The barcode is read before the Slide Scan Prompt Uses a Prompt for the file name The Prompt can then be specified before the processing of the protocol in a pop up window Fixed Text You can add a fixed text which e g characterizes the sample E Moves the element highlighted in the box Order forward by one position Moves the element highlighted in the box Order backward by one position x Deletes the highlighted element 34 V at P amp YA Software Version 1 0 Sob Seat New Scan Sessions New Scan Sessions Current slot All slots 3 Software Documentation 3 4 4 Define New Session A new session for all slots is defined via the button New Scan Sessions LI Click on New Scan Sessions A possibly opened session is closed and a new protocol for all slots is opened Q If information of an old session which is not yet saved is available a save prompt is performed If applicable save the data of the last session Only then a new protocol for all slots is opened A new session for the active slot is defined via the drop down menu of the button New Scan Sessions gt Q Click on the drop down menu of New Scan Sessions and then the option Current Slot A possibly opened session for the active slot is closed and a new protocol for this slot is opened 3 4 5 Load Protocols In the ribbon th
22. button Spot or Block By that you can move a spot or a spot block or all spots with the mouse button being pushed If you select a range with the button lt Strg gt being pushed the spots in this range are highlighted and the spots in this range which have already been highlighted remain highlighted Tool to move a spot The tool Move Spots must be activated Tool to move a spot block The tool Move Spots must be activated Tool to move all spots together The tool Move Spots must be activated Resets the last soot movement Repeats the last soot movement 47 Software Version 1 0 CoU cuu 3 Software Documentation 3 6 4 Evaluation Options In this section of the ribbon the evaluation options are summarized Analyzes the spots within a grid structure Cancels the grid analysis To be able to evaluate the data with other programs the analyzing result can be exported as gpr file gene pix results Creates a HTML Report which describes the quality of the grid analysis The report is filed together with the session file of the same name Tool to highlight spots Individual spots are highlighted by clicking A spot group is highlighted by selecting the relevant range with the mouse If you push the button lt Strg gt during that spots already highlighted in this range remain highlighted 3 6 5 Flags Visibility Options In this section of the ribbon the options are summarized with whi
23. ch the flags defined by the evaluation parameters can be displayed Display of the highlighting symbols for the spots highlighted by the user See tab Quality Settings parameter User tagged Display of the highlighting symbols for the spots classified as bad See tab Quality Settings parameter Poorly sized Spots Display of the highlighting symbols for the spots classified as no signal spots See tab Quality Settings parameter No Signal Spots Display of the highlighting symbols for the spots classified as saturated See tab Quality Settings parameter Saturated Spots 48 E Software Version 1 0 Sob Scout 3 6 6 Tab Histogram SpotScout Pro2 Evaluation cH PS Cd Undo Redo Analyse Cancel Export Create Tag GPR Report Spots Select All Grid Finding Evaluation m Histogram 3 Software Documentation Red count Green count Level Level Log Linear Automatic Display the histogram in loga ithmic p esel tation Fig 27 Evaluation Ribbon Histogram Please read description in chapter 3 3 4 DIGITAL BIOMEDICAL IMAGING SYSTEMS AG Software Version 1 0 49 3 Software Documentation 50 3 6 7 Tab Scatter Plot After the analysis of the spots two new tabs are displayed in the left section Scatter Plot and EvaluationTable Grid Finding Slot 1 Slot 2 Slot3 Slot4 SpotScoutExample a Evaluation ca oe ca B Bee R
24. cludes an overview over the software explains the writing rules and provides license information describes the installation of the software and the connection with the Microarray Scanner MArS as well as the activation of the Software with the license key represents the Software documentation Here the individual functions and their meaning are described is the appendix with further explanations about the program 1 5 Writing Rules In the available manual we use the following writing rules for better orientation The names of Menus Options Register File Viewer Protocol Tabs etc are written in bold letters The Selection of an Option in a Menu is File Options written as a command sequence separated by a vertical line Buttons if not depicted are written in bold Save Open Close letters and set in angle brackets Enumerations Action steps 1 6 License Information ZedGraph is published under LGPL GNU LESSER GENERAL PUBLIC LICENSE Version 3 29 June 2007 Software Version 1 0 Sob Seuut 2 Software Installation and Connection with MArS1 Overview Copyright C 2007 Free Software Foundation Inc http fsf org Please read the license information completely and observe it It is included in the appendix in chapter 4 2 DITABIS Software Version 1 0 o IGITAL BIOMEDICAL IMAGING SYSTEMS AG Sot Steu 2 Software Installation and Connection with MArS 2 Software Installatio
25. e protocol files already saved are displayed At the first program start only placeholders for the protocols are displayed Fig 19 After the protocol has been saved the placeholder is replaced as well as the name of the saved protocol is displayed Fig 19 Display of the placeholders for protocols in the ribbon Recent Common 100 100 Save Store as default Organize Fig 20 Saved protocol Save Delete Protocol Procedure 35 Software Version 1 0 3 Software Documentation 36 God cuu Q Click on the arrow button in the protocol display see red arrow in Fig 19 The drop down menu with the available protocols as well as the options is displayed LJ For saving select the option Save and then enter the desired file name in the dialogue window LJ You can also save a protocol as default protocol Option Save as Default Since there is only one default file Default you are asked whether you want to overwrite the previous settings in the default file If you confirm this the old default file is overwritten with the new files see also the details on default files page 15 Q To delete a protocol file select the option Organize The window Organize Protocols opens in which all protocols are listed Highlight the protocols to be deleted and click on the button lt Delete gt Load Protocol Procedure Q To load a protocol click on the desired protocol in the ribbon The highlighted
26. edo Analyze Cancel Export Create GPR Report l Evaluation Flags Visibility Spot Scout Example X Axis B635 Median Y Axis F635 Median Values on the x axis Spot Viewer Red Channel Cursor Spot Background x Green Channel Cursor Spot Background Spot Block Sot Seeut SpotScout Pro Default Scale Overlayed r g Cursor Spot Background Instrument ready Fig 28 Tab Scatter Plot with an example evaluation In Scatter Plot all features of the spots like e g background intensity of the relevant wavelength can be plotted against each other on the X axis and on the Y axis The blue line in the plot is a Regression Line which is calculated depending on the selected value pairs The symbol size of the displayed spots can be set in the box Symbol Size below the Scatter Plot By clicking on lt Default Scale gt the original size is restored When you move the mouse over a spot the ID of the spot is faded in via Tooltip and the relevant spot is displayed in the Spot Viewer Software Version 1 0 gt Lei ata OH E OED ED GITAL BIOMEDICAL IMAGING SYSTEMS AG Soot Scout 3 Software Documentation 3 6 8 Tab Evaluation Table Q SpotScout Pro Viewer Protocol Scan Evaluation mz PS Spat Block Ed 4 t E ks Ur ncel Export Create Select All GPR Report Grid Finding Evaluatio
27. eel Scroll horizontally Moving the mouse wheel with pushed lt Shift gt button Enlarge Moving the mouse wheel with pushed Ctrl button reduce image Select and zoom Draw a rectangle with the mouse The selected detail is detail zoomed to the size of the slide display Splitter Bar The splitter bar between Slide Display and the Setting and Evaluation Section can be moved randomly For that purpose the splitter bar is provided with a marking in the middle to be dragged with the mouse or to be clicked on Move Click on the marking of the splitter bar and move the splitter bar in the desired direction with the mouse button being pushed Maximize A click on the marking of the splitter bar enlarges the image display to the total width of the program window Restore Double clicking the marking of the splitter bar restores the original division between the two sections In the maximized state the splitter bar is on the far left at the edge of the program window On the tabs Histogram and Scatter Plot in the menu Evaluation only SpotScout Pro clicking on the Splitter Bar has the effect that the image display is faded out in favor of the result display Status Display Status display for the scanner as well as for the analyzing processes like Find Grid and Analyze Software Version 1 0 Dt INONEDICAL wake ie ST TENS Ke Sod Sau Navigate Back Navigate Forward E zoom Hand zoom To Slide Zoom To
28. er controls Option Brightness Contrast Via the slider control Brightness and Contrast of the image can be set The option Ramp is the default setting At Low the lowest and at High the highest intensity value for the desired illustration is entered Between those two values the illustration from black to bright color takes place Values below the low value are illustrated black values above the high value are illustrated bright Option False color The intensity values are shown on the color scale See explanations for the option Ramp T Automatic setting of the LookUp Table If this function is active the Lookup Table settings for all sessions are taken over If this option is active the red and the green channel are set via joint slider controls Otherwise different slider controls are displayed for the two channels 30 V a amp Wi Software Version 1 0 Sod Scout 3 Software Documentation 3 4 Menu Protocol SpotScout Pro Protocol Flow n Description Read Barcode Find Grid Multi Tiff Stitched Areas Orientation i M Folder C Dokumente und Einstellungen jens Eigene Dateien Filename Fig 16 Menu Protocol Protocol Flow in the left section above file name 3 4 1 Overview Display of the defined steps in a Protocol Flow and Start In the Protocol Flow the steps to be processed are defined The steps include the settings w
29. eter defines the lower intensity limit lt defines how much background is to be deducted of each spot in percent This parameter defines whether the grid finding is to be performed with a fix or variable radius This parameter defines the range for the spots radii which is acceptable 100 corresponds to the radius of the spot Here the possible eccentricity of the expected spots i e the deviation from an exact circle is set A value of 096 means that only perfect circles are accepted as spots A value of 1096 means that also slightly oval spots are accepted At the maximum input of 100 even a linear spot is accepted Here the angle is entered by which the grid can be maximally rotated The smaller the angle entered here the smaller the searching range of the grid finding function This parameter influences the depth of focus for lower image signals High image signals lead to an exact analysis while lower values consume storage space and evaluation time in favor of a high grade detection of lower spot signals Via the drop down menu Grid Finding parameters can be saved or saved parameters can be loaded See details on Presets on page 16 Sob beaut 3 Software Documentation 3 6 2 Tab Quality Settings Viewer Protocol Scan Evaluation 00000 00000 Em JX Spot Block Select All Grid Finding Evaluation Settings Good Shaped Spot Radius Interval Saturated Spot Area Threshold Array Qualit
30. from Session Impart GAL E ample Sod out A default protocol for all parameter settings is implemented in the program which the user can define according to his needs It must only be observed that there is only one single default file There are two basic possibilities for a modification of the default protocol e Modification of individual parameter groups Every parameter group in the menus Scan and Evaluation has a drop down menu Presets Here the relevant parameter group can be saved in the default file Thus only the relevant parameters are overwritten the remaining data remain unaffected e Modification of the complete default protocol is performed if you save a protocol in the menu Protocol as default file since then the associated settings are saved together with the protocol steps As standard the default file is loaded if a new session is opened New Scan Sessions gt Drop Down Menus Presets In the drop down menus Presets there is the possibility to save the current settings of the associated parameter group and to load or to delete settings already saved Save Save as Default Load Default Organize Import from Session Import GAL XXX Software Version 1 0 Saves the parameter group under a user defined name Saves the parameter group in the available default file see above If you have overwritten a default file you can restore the previous state of the default file with this comma
31. hich are made in the menus Scan and Evaluation only SpotScout Pro for the active slot The steps highlighted in yellow are active and are performed The individual steps of the Protocol Flow are displayed as buttons which can be activated or deactivated by clicking Next to the step switches the scan surface and the settings of the active slot are displayed like they are defined by the selected protocol Define New Session Via the button New Sessions new sessions in the four slots can be defined Then the parameters for the new session can be entered by loading available protocols or by entering the parameters for the currently active slot in the menus Scan and Evaluation only SpotScout Pro 31 Software Version 1 0 3 Software Documentation 32 Sot Sea Saving the Session In the section Save Options the saving parameters for the session can be defined Starting the Scan Process With the defined settings the scan process either for the active or for all occupied and defined slots can be started via the button lt Start gt 3 4 2 Protocol Flow The meaning of the individual steps Read Barcode Scan Slide Find Grid Evaluate Spots Save Session Export Results Create Report Software Version 1 0 Scans the barcode Scans the loaded slots Searches the grid structure pursuant to the preset parameters only for SpotScout Pro Performs the evaluation pursuant to the preset evaluation
32. ined library with a copy of the same work based on the Library uncombined with any other library facilities conveyed under the terms of this License b Give prominent notice with the combined library that part of it is a work based on the Library and explaining where to find the accompanying uncombined form of the same work 6 Revised Versions of the GNU Lesser General Public License The Free Software Foundation may publish revised and or new versions of the GNU Lesser General Public License from time to time Such new versions will be similar in spirit to the present version but may differ in detail to address new problems or concerns Each version is given a distinguishing version number If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License or any later version applies to it you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation If the Library as you received it does not specify a version number of the GNU Lesser General Public License you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply that proxy s public statement of acceptance of any version is permanent authorizatio
33. istance between the individual blocks Indicates the scan excess i e how far does the scanner scan beyond the block borders Tolerances of spotter and insertion tolerances are evened out Naming of the blocks You can select numerical or alphabetical for each the X or Y coordinate Number of spots within a blocks in X and Y direction Indication of the size of the barcode Indication of the position of the barcode Selection of barcode type and orientation Loading saving of the grid structure settings see details on Presets on page 16 Hints for the Setting of the Grid Structure BIOMEDICAL IMAG 41 Software Version 1 0 Soot Scout 3 Software Documentation Q First define the top left block L For that measure the size of this block and enter the values in the line Block Size Q Then measure the position of this block on the slide and enter the values in the line First Block Location L Measure the distance between the blocks and enter the value in the line Block Spacing L Enter the number of blocks in X and Y direction in the line Number of Blocks 42 Software Version 1 0 Sod Scout 3 Software Documentation 3 6 Menu Evaluation only SpotScout Pro eQ SpotScout Pro2 File Viewer Protocol Scan Evaluation Grid Finding Grid Finding Settings Auto Shift Limit Spot Cutting Fraction Radius Detection Variable Radiu
34. lowing parameters a weight for flowing into the total evaluation and the definition as exclusion criteria can be made The exclusion criteria say if the parameter concerned delivers a red evaluation the chip must be evaluated as being red Average Signal Limits for the average intensity of all spots Signal Variance Limits for the variance of the intensity of all spots Limits for the percentage of the pixels above the Image Saturation E overexposure limit Average Background Limits for the average background intensity of all spots Limits for the percentage of overexposed spots within the Saturated Spots relevant spot range Poorly Sized Limits for the percentage of badly positioned spots within the Spots spot range Limits for the percentage of no signal spots within the spot No Signal o Signal Spots eG Limits for the percentage of user defined spots within the User tagged 99 spot range Loading or saving of parameters See details on Presets on Presets page 16 46 EUM D ECE owe L Software Version 1 0 iei Na 3 Software Documentation 3 6 3 Grid Finding Options In this section of the ribbon the options for Grid Finding are summarized Starts the Grid Finding For that at least 5 spots must be defined By another click on this button the function is reset By yet another click the grid finding is started again Cancels the Grid Finding Activates the tool Move Spot Then click on the
35. lt setting is My Files MArS Scanlmages Specification of the file name By clicking on the arrow button the dialogue window Auto Filename for the input of the parameters for the file name opens Fig 18 After the saving of the entries the file name is displayed Barcode Prompt Fixed Text Fixed Text tes Separator Underscore Order lt Date gt lt Time gt lt Barcode gt lt Prompt gt Fig 18 Dialogue window Auto Filename 33 Software Version 1 0 Soot eut 3 Software Documentation For the automatic scan process with the Protocol Flow please note that the file names are generated automatically For the automatic naming a selection of the following elements in random order can be used lt Date gt lt Time gt lt Barcode gt lt Prompt gt and lt Fixed text gt As separator you can use either an underline or a blank Procedure Q Define the Separator Q If you want to use a specified text in the file name enter it in the box Fixed Text L Then click on the element buttons in the desired order The selected elements are then displayed in the box Order Q To change the order you can use the arrow buttons below the box Order explanation see below Li To delete an element click on JX gt Q By clicking on OK you save the parameters for the file name The Elements of the automatic file naming in detail Date Uses the current date for the file name
36. n Flags Visibility SpotScoutExample 9Wejuogenje jojjJeneo5 weiboysiy sumas feng sBumes Bupu Spot Viewer Red Channel Green Channel Overlayed r g Cur 847 Cur 750 Cur 1 13 Spot Spot Spot Background Background Background x y 11 507 25 656mm Spot Block Name Fig 29 Evaluation Table In the Evaluation Table all results of the analysis of the slide are summarized Q A double click on a spot in Slide View lets the table jump directly to this spot e g in Fig 29 spot 5396 has been clicked on Q A double click on a spot in the table positions the spot in Slide View in the middle of the image Q A double click on the splitter bar between Slide View and Table see page 14 maximizes the table Next to the vertical splitter bar there are two other splitter bars above and below the table Q A double click on the lower splitter bar hides shows the Spot Viewer Q A double click on the top splitter bar opens closes the section where columns displayed in the evaluation table can be selected Selected columns are highlighted by ticks Clicking on a checkbox deactivates activates the relevant column in the table see Fig 30 51 Software Version 1 0 A 3 Software Documentation In Fig 30 the columns ID X and Y are faded out Likewise the column Name of spot 5396 has been changed into an example text In the Evaluation Table the columns Name ID can be indi
37. n and Connection with MArS This chapter describes the installation of SpotScout or SpotScout Pro on your PC and the connection of the PC with the Microarray Scanner MArS and the activation of the Software You get the Software either on CD ROM or by download After the Installation of the Software the Software is activated by receiving a license key from Ditabis AG Installation Procedure d d d You get the Setup file on the enclosed CD ROM or have downloaded it otart the file setup exe When asked for the target drive enter the desired path e g C Programme Ditabis SpotScoun If Net Framework 4 0 is not installed on your computer it will be automatically installed during the setup If you connect the Microarray Scanner MArS with the PC for the first time you have to install the corresponding USB driver For that switch on MArS wait a few seconds and connect the instrument with your PC with an USB cable The PC now detects a new USB device and Windows requesis you to search a corresponding driver in a directory Select the setup directory or the directory you have downloaded After that the USB driver is installed automatically As last installation step click on lt Next gt or lt Continue gt Finally Windows indicates that the installation has been successful The setup routine creates a file in the Start menu and the icon on your desktop For starting SpotScout or SpotScout Pro double click the program
38. n for you to choose that version for the Library V at P amp YA Software Version 1 0
39. n the manner specified by section 6 of the GNU GPL for conveying Corresponding Source 1 Use a suitable shared library mechanism for linking with the Library A suitable mechanism is one that a uses at run time a copy of the Library already present on the user s computer system and b will operate properly with a modified version of the Library that is interface compatible with the Linked Version e Provide Installation Information but only if you would otherwise be required to provide such information under section 6 of the GNU GPL and only to the extent that such information is necessary to install and execute a modified version of the Combined Work produced by recombining or relinking the Application with a modified version of the Linked Version If you use option 4d0 the Installation Information must accompany the Minimal Corresponding Source and Corresponding Application Code If you use option 4d1 you must provide the Installation Information in the manner specified by section 6 of the GNU GPL for conveying Corresponding Source 55 Software Version 1 0 4 Appendix 56 Sot Scout 5 Combined Libraries You may place library facilities that are a work based on the Library side by side in a single library together with other library facilities that are not Applications and are not covered by this License and convey such a combined library under terms of your choice if you do both of the following a Accompany the comb
40. nd Lists the available parameter files in this parameter group Here you can delete files Here you can read in parameters of a session file For that the available ses files are displayed This option is only available for grid settings Here a GAL file with a grid structure can be loaded In the lower part of the window the available presets of the relevant parameter group are displayed V 2 D E YA Soot Scout 3 Software Documentation 3 1 3 Program Structure The program is subdivided into several menus which refer to special program functions Menu File It includes e Functions for loading and saving of files e Function for modifying program settings as well as e Information and documentation functions Menu Viewer In the menu Viewer the loaded or scanned images are displayed in which you can navigate zoom and analyze spots with the different functions A histogram shows the color value distribution of the complete image Menu Protocol In the menu Protocol the steps for a session from the parameter input to scanning and evaluation are defined as a Protocol Flow and the complete process is started The parameter input itself is done in the menus Scan and Evaluation only SpotScout Pro or by loading saved protocols in the menu protocol For routine analyses protocols saved by means of Quick Function can be loaded with corresponding scan and grid parameters and the scan and evaluation pr
41. ne position Moves the selected wavelength in the scan sequence up by one position Setting possibility of the Defocus in um Loading saving of the settings for the scan process See page 16 40 wi EN DIEC Pi iFa DED Software Version 1 0 StSt 3 Software Documentation 3 5 5 Section Grid Structure Here the grid structure and the distances between the blocks are defined Grid Structure Number of Blocks Block Size First Block Location Block Spacing Scan Overrun Block Naming Number of Spots Barcode Settings Size Location Type Orientation X Y 1 I 23000m A O00 urn 1000um c 3 pum c m 3 2pm Ayr 31k AE MEI ae 1000um ALP ALH ape ayy yay Numerical 4 Alphabetical I Lil 18 00pm 500 500m BOOOOur P y E fun Codel 28 Horizontal me Presets Instrument ready Fig 23 Grid Structure and Barcode Settings The Parameters in Detail Number of Blocks Block Size First Block Location Block Spacing Scan Overrun Block Naming Number of Spots Barcode Settings Size Location Type Orientation Presets Number of blocks in X or Y direction Size of blocks X and Y position of the first block D
42. ns the object code and or source code for the Application including any data and utility programs needed for reproducing the Combined Work from the Application but excluding the System Libraries of the Combined Work 1 Exception to Section 3 of the GNU GPL You may convey a covered work under sections 3 and 4 of this License without being bound by section 3 of the GNU GPL 2 Conveying Modified Versions If you modify a copy of the Library and in your modifications a facility refers to a function or data to be supplied by an Application that uses the facility other than as an argument passed when the facility is invoked then you may convey a copy of the modified version a under this License provided that you make a good faith effort to ensure that in the event an Application does not supply the function or data the facility still operates and performs whatever part of its purpose remains meaningful or IFA DIC Software Version 1 0 Soot Scout BIOMED A c ja 4 Appendix b under the GNU GPL with none of the additional permissions of this License applicable to that copy 3 Object Code Incorporating Material from Library Header Files The object code form of an Application may incorporate material from a header file that is part of the Library You may convey such object code under terms of your choice provided that if the incorporated material is not limited to numerical parameters data structure layout
43. nto the Quick Access Bar Remove from Quick Reversing Right mouse click on the function or Access Toolbar the functional group in the Quick Access Bar and select Remove Customize Quick Access Via a dialogue window selected functions of all Toolbar menus can be selected and copied in Quick Access or removed from Quick Access Place Quick Access Toolbar Relocates Quick Access into the bar below or below above the Ribbon above the Ribbon Minimize the Ribbon Fades the ribbon out Maximize the Ribbon Reversing Right mouse click on a function in Quick Access opens the Context Menu with the option Maximize the Ribbon Addto Quick Access Toolbar Customize Quick Access Toolbar Place Quick Access Toolbar below the Ribbon Minimize the Ribbon Fig 2 Context Menu of the functions on the ribbon V 2 D E YA Software Version 1 0 Sod S t 3 Software Documentation Procedure Extend Quick Access Option Quick Access Toolbar Copied into Quick Access F ea e EE Viewer Protocol Scan Evaluation Kam FW X gm Orientation LookUpTable Fig 3 Quick Access and Ribbon Q Click with the right mouse button on the desired function on the Ribbon The relating Context Menu Fig 2 is opened Q Click on Add to Quick Access Toolbar The relevant function is copied into the Quick Access Fig 3 Menu Bar Here are the menus of the program A click on the menu name activates the menu
44. ocess can be started Menu Scan Here the Scan Parameters as well as the Grid Structure for the slide sample carrier are defined A single slot can be scanned with the parameters defined here or be tested with a Preview Function Menu Evaluation only SpotScout Pro Before scanning the Evaluation Parameters are defined in the evaluation menu After scanning the image is analyzed and evaluated here The results are available as Result Table GPR format The values of the result table can be directly assigned to every spot in the slide view Besides Regression Analyses with random value pairs can be performed and displayed as Scatter Plot Additionally a report on the quality of the evaluation can be created Software Version 1 0 3 Software Documentation Soot Scout 3 1 4 File Formats SES Files Files with the ending ses are created by SpotScout Here all information program and scan settings as well as evaluation settings and results only for SpotScout Pro are saved per slot Additionally the image files are saved as TIF files corresponding to the number of images and used filters They have file names which correspond to the associated ses file When loading a ses file the associated TIF files are also loaded To prevent the destruction of the relationship of these files you should not modify the names of the files and copy all related files when copying TIF Files The scanned images are saved a
45. on Start Current Slot again in the drop down menu of the button Start 37 Software Version 1 0 Sot Seeut 3 Software Documentation 3 5 Menu Scan Grid structure and spacings Number of Blocks Block Size 4150ym gt 4150um First Block Location 3500ym 10000um Block Spacing 500um 500um Scan Overrun 100m 100m Block Naming Numerical Alphabetical Number of Spots 20 5 20 Barcode settings Size 18000um 2000um Location 3500um 60250pm Type Orientation Code128 Horizontal Presets Fig 21 Menu Scan 3 5 1 Overview Parameter Input and Grid Definition In the left section the parameters for the scanning and the grid structure of the active slot are entered The parameters can be saved via the corresponding drop down menus Presets and saved parameters can be loaded In the slide view the settings are displayed Scanning The active slot can be scanned according to the entered settings As preview with lower resolution or as optimal scan The barcode can also be scanned Please note that these scanning functions only refer to the active slot In the menu Protocol all slots can be scanned one after the other automatically 38 E Software Version 1 0 DIGITAL BIOMEDICAL IMAGING SYSTEMS AG iie Na 3 5 2 View Function
46. on the left side of the histogram are too high the image is underexposed if peaks appear on the right side of the histogram the image is overexposed 28 A Software Version 1 0 iie Ns O O gt ru w 3 Software Documentation 3 3 5 Spot Viewer The Spot Viewer shows the extreme enlargement of the spot which is in Slide View below the cursor At the same time the intensity value is displayed at the cursor position After evaluation the brightness of the spot and the background for every channel Red Channel Green Channel Overlayed is displayed Below there are the values for the X Y position of the cursor on the slide Red Channel Green Channel Ovenayed rg Cur 4 320 Cur 29412 Cur 1 61 Spat Spot Spot Background Background Background x y 6 553 18 490mm Spot Block Abb 15 Spot Viewer 3 3 6 Ribbon View Functions Goes to the previous or next view In this drop down menu there are preset zoom factors Next to these values a random zoom factor up to 10000 can be entered The input must be confirmed with lt Enter gt Those three functions are related to the scanned image d F The loaded image is enlarged until the width or the height of the scan exactly fills in the main window The loaded image is enlarged until the scanned part is completely visible in the main window Those three functions are related to the slide 4 The slide i
47. parameters only for SpotScout Pro Saves the session under the file name specified in Save Options Exports the evaluation results as GPR file GenePix Results It is filed together with the session file under the same name The files only differ from each other in the ending Creates a HTML report about the quality of the evaluated grid structure The report is filed together with the session file under the same name The files only differ from each other in the ending StSt 3 Software Documentation 3 4 3 Section Save Options Save Options Mode Multi Tiff Stitched Areas Orientation 4 Folder eFC Filename Fig 17 Section Save Options Here it is specified how the scanned image is to be saved Please note that a ses file only includes the data of one slot each Mode Stitched Areas Orientation Folder File Name Auto filename Elements Date Time Selection of the file format in which the image not the session is to be saved Multi TIFF Single TIFF and Multi TIFF per area can be selected See chapter 3 1 4 If the checkbox is activated the section between the areas is filled black intensity 0 and one single image is created per Scan Setting By clicking on the arrow button the drop down menu is opened in which it is defined with which orientation the image is to be saved Specification of the folder in which the file is to be filed Defau
48. s transparent image in the Slide View ay SES THO current 3 5 3 Scan Functions Lood If MArS is closed the loading table is retracted IES The barcode is scanned in the active slot selected via the related drop down menu Scans the active slot with current settings Stops the current scan process Software Version 1 0 If this button is active the defined block structure is faded in as half The range which is scanned at the moment is displayed The preview image of the current slide is generated in one or all wavelengths for the active slot with low resolution The selection can be 3 Software Documentation 39 3 Software Documentation Presets Soot Scout 3 5 4 Section Scan Settings Presets Fig 22 Scan Settings The scan parameters for the active slot are displayed In our example it is Slot 3 These parameters can be saved via the button lt Presets gt or available parameters can be loaded The Parameters in Detail Displays the resolution spot size in um with which the slide is scanned Selection of the laser and filter for the scan process Intensity of the laser with which the slide is scanned Data transfer via the standard channel Data transfer via the high channel Data transfer in Dual Mode St and Hi Allows adding more wavelengths Removes the currently selected wavelength Moves the selected wavelength in the scan sequence down by o
49. s ses files and associated TIF files It is also possible to load individual TIF files 16 bit grey scale images even if they originate from other scanners In this case SpotScout Pro only needs the information included in the TIF file You can also save a session as TIF file In this case only image data are saved all other data get lost GAL Files GAL files GenePix format include grid definitions for slides They can be directly loaded in the menu Scan and replace a manual creation of the grid structure GPR Files The results are given in GPR file format GenePix Format They include image data and analysis data In this format the evaluation results of SpotScout Pro are given SEP and SLT Files In this format protocols are saved HTML Format The reports of SpotScout Pro are saved in HTML format BAK Files in case of Computer Crash In case of a computer software crash you are prompted to save the current session In case of an inconsistency of the new file the previous session is saved as backup file extension bak Software Version 1 0 Soot Scout 3 Software Documentation 3 2 Menu File After the selection of the menu File the menu window with the menu options on the left and the option Recent last used files and directories is displayed see Fig 5 eo SpotScout Pro Viewer Protocol Scan Evaluation Recent Documents test tif C Dokumente und Einstellungen jens ma
50. s Interval Spot Eccentricity Maximum Rotation Angle Maximum Low Signal Enhancement 100 lt ueiGojsiH sSumes enp sSumes Guipuly Presets Fig 24 Evaluation Ribbon Finding Settings The menu Evaluation is provided with two different functionalities e Parameter input for evaluation For that 2 tabs in the left section are available Finding Settings Quality Settings e Evaluation after the scan process Display of the used parameters and display of the evaluation results For that more tabs are available in the left section Histogram Scatter Plot and Evaluation Table After evaluation the parameters for the Grid Finding can be changed as well as specific evaluation and analyzing functions can be performed which are available in the form of buttons in the ribbon 5 EUR A ERE COMPE B AED 43 GITAL BIOMEDICAL IMAGING SYSTEMS AG Software Version 1 0 3 Software Documentation 44 Soin 3 6 1 Tab Finding Settings Parameters for the Finding of the Grid Structure see Fig 24 Auto Shift Limit Spot Cutting Fraction Radius Detection Radius Interval Spot Eccentricity Maximum Rotation Angle Maximum Low Signal Enhancement Presets Software Version 1 0 Here the maximum distance of the ideal grid structure is defined within which spots are still searched 10096 corresponds to half the spot distance This param
51. s and accessories or small macros inline functions and templates ten or fewer lines in length you do both of the following a Give prominent notice with each copy of the object code that the Library is used in it and that the Library and its use are covered by this License b Accompany the object code with a copy of the GNU GPL and this license document 4 Combined Works You may convey a Combined Work under terms of your choice that taken together effectively do not restrict modification of the portions of the Library contained in the Combined Work and reverse engineering for debugging such modifications if you also do each of the following a Give prominent notice with each copy of the Combined Work that the Library is used in it and that the Library and its use are covered by this License b Accompany the Combined Work with a copy of the GNU GPL and this license document c For a Combined Work that displays copyright notices during execution include the copyright notice for the Library among these notices as well as a reference directing the user to the copies of the GNU GPL and this license document d Do one of the following 0 Convey the Minimal Corresponding Source under the terms of this License and the Corresponding Application Code in a form suitable for and under terms that permit the user to recombine or relink the Application with a modified version of the Linked Version to produce a modified Combined Work i
52. s displayed in full width or in full height In the main window the zoom factor is set so that the slide is entirely visible Zoom tool If this tool is activated a section can be selected in the Slide View with the mouse which then is enlarged accordingly see chapter 3 1 2 Hand tool If this tool is active the image can be moved in the Slide View so that m another image detail is displayed For that you have to click on the image and drag it I In the drop down menu Orientation the orientation of the slide can be changed 3 in steps of 90 HUM JA DEC ere E WD 45 N sys Software Version 1 0 Soot Scout 3 Software Documentation With the option As saved the image is displayed in the saved original position i LJ As saved 3 3 7 Ribbon Lookup Table Functions Selection of the displayed channel red or green In case of more than one scan image the desired image can be selected via a drop down menu lt Y gt The selected images are overlaid red and green channel In this drop down menu the type of the lookup table can be selected Brightness Contrast Ramp and False color Via the slider control on the right the parameters can be set The relevant setting is displayed on the screen As long as the slider control is hold with the mouse the image is displayed in the preview mode If the function Linked is active red and green are set via one slider control otherwise via separate slid
53. specifications e Automatic grid finding e Quantification of image data e Reliable and efficient quality control spot position evaluation artifact identification saturation check with report e Export of the results in GPR format With the evaluation module of SpotScout Pro you can also evaluate TIF image files Definition of Terms To simplify matters we talk about the software system SpotScout in this operator s manual if functions are concerned which exist in both systems SpotScout Pro is used if functions are concerned existing only in this system 1 2 System Requirements Hardware Processor 2GHz multi core recommended Main Memory at least 2GB 4GB recommended USB 1 0 Software Operating System Windows XP Win7 only 32bit Acrobat 6 0 or higher MArS with firmware 1 0 32 or higher During a scan no other software besides SpotScout may be running Software Version 1 0 Cod en gy Chapter 1 Chapter 2 Chapter 3 Chapter 4 BIOMED A Ts Soe 1 Overview 1 3 Program Version Version 1 1 4 Content and Structure of the Manual The available manual is the operating manual and software documentation for SpotScout and SpotScout Pro Since SpotScout is a subset of SpotScout Pro it is indicated which software functions surpass the basis module SpotScout Basically it is the menu Evaluation The manual is structured in such a way that every user can immediately find his parts in
54. t only the block is indicated in the Slide View Slide Navigator Level Red count Spot Viewer Red Channel Cursor Spot Background Level Green count Green Channel Cursor Spot Background Area Navigator Los Linear X y Spot Block Overlayed r g Cursor Spot Background Name Slide View zoomed detail image Fig 13 Selection in Slide Navigator and display in Slide View Set and Move Zoom Range The blue rectangle is the range which is currently displayed in the main window You can define a random blue rectangle in the Slide Navigator and with that define the zoom range for the main window and move it afterwards At the same time the selected range is displayed in the Area Navigator together with the surrounding Q Drag a rectangle in Slide Navigator with the mouse with the button lt Strg gt being pushed According to the drawn rectangle the corresponding range is zoomed in Slide View Q To move the zoom range click on the blue rectangle and drag the rectangle in the desired direction with the mouse button being pushed Software Version 1 0 2 re 3 Software Documentation 3 3 3 Area Navigator In addition to the selected image detail the Area Navigator shows a range around the displayed image detail see Fig 13 Set and Move Zoom Range Q A random rectangle can be drawn with the mouse
55. vidually labeled The columns User Tag No Signal Poor Size and Saturated can also be changed via drop down menu E a Spot Information Mean Quantification Z Median Quantification Z F635 Median Z B635 Median LI rmm Ra Diameter Gene description 5394 140 Gene description 5395 140 Gene description 5396 140 Gene description 5398 Gene description 5399 Gene description 5400 Gene description 5401 Gene description 5402 Gene description 5403 Gene description 5404 Fig 30 Evaluation Table with edited names If you move over the lines with the cursor in the table the relevant spot is displayed in the Spot Viewer mic 52 P E BA EPE Software Version 1 0 GITAL BIOMEDICAL IMAGING SYSTEMS AG ESSA Sot Steu 4 Appendix 4 Appendix 4 1 Evaluation Table Columns created by the evaluation algorithms Block Block number of the feature Column Column number of the feature in block Row Row of the feature in block Name Description field for spot ID Description field for spot X X coordinate in um of the center of the feature indicator associated with the feature where 0 0 is the top left of the image Y Y coordinate in uim of the center of the feature indicator associated with the feature where 0 0 is the top left of the image Dia Diameter in um of the feature indicator For each analyzed channel XXX marks channels wavelength FXXX Median median feature pixel intensity
56. y Settings Average Signal Signal Variance Image Saturation Average Backgr 4 Q E a e a amp a a a Sg a a a Saturated Spots Poorly Sized Spots No Signal Spots User tagged Total Array Quality SpotScout Pro2 Tag Spots Evaluation Flags Visibility Presets Fig 25 Tab Quality Settings Section Evaluation Settings Good Shaped Spot Radius Interval Saturated Spot Area Threshold With these parameters the upper and lower limit for the deviation of a spot position from the defined position is set The distance is entered as percentage of the spot radius median Values of more than 10096 are possible This parameter defines the limit from which a spot is considered to be overexposed Here the percentage of spot pixel is entered which has an intensity value of more than 9896 of the maximum intensity AL BIOMEDICAL IMAGING SYSTEMS AG Software Version 1 0 45 Sot Soa 3 Software Documentation Section Array Quality Settings Here the limits for the evaluation ranges are defined They are the basis for the Report In the medium range values are accepted as OK Green This range is followed at both ends by ranges with the evaluation yellow Outside those ranges the evaluation is red Average Signal 1000 5 2000 5 50000 eoooo if 125 Fig 26 Scheme Quality Parameter For the levels as well as for the fol
Download Pdf Manuals
Related Search