FISHQuant Module 1.12 User's Guide June 11, 2009
Contents
1. Zoom factor glide Zooms in out on the objects in the right panel 3DHISTECH Ltd 21 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 4 Working with Measurement Visualization Toggle mode You can select objects with the help of your mouse in the right panel You can rescore ob jects using right click Field Parameters Shows the field specific parameters Tooltip Moving cursor over an object shows the basic in formation of the given object View You can select among normal horizontal or ver tical view of the objects in the right panel June 19 2009 3DHISTECH Ltd 22 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 4 Working with Measurement Visualization Related documents MIRAX Viewer 1 12 User s Guide ImmunoScreener Module for MIRAX Viewer 1 12 User s Guide MIRAX SCAN User s Guide http books google com books id kvWKgG6iPXMC amp dq June 19 2009 3DHISTECH Ltd 23 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 4 Working with Measurement Visualization Index C MISP e 5 computation time cesse 9 S L Segmentation essseseeeeene 5 We 5 Segmentation Profile sususuee 5 M June 19 2009 3DHISTECH Ltd 24 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 4 Working with Measurement Visualization Appendix A FISH Analysis A 1 Object specific parameters Parameter Descript2. e 3DHISTECH FISHQuant Module 1 12 User s Guide June 11 2009 FISHQuant for MIRAX Viewer 1 12 User s Guide Contents Peine UPS 3 Font types and symbols ssssessessessseseee nennen nnn nnne nnn nnns ann nnn 4 Terms and abbreviatloris ecrini en RR ERERERRR EAR GARY AK RR A E IRLRKEXRPRRREPRRX TRA ARA E a 5 1 About FISH Analy SiS ir nennen nennen messes nnns nnn nnne nn nnn nnn nnn nnn nnn nnn nnn 6 1 1 FISH Analysis in the MIRAX product family cccceccccecee cece eee eens eee mmm 6 1 2 Overview of FISH Analysis ccce tek exe CER Aa R vide NER CREER AYXE TERT RE 7 1 2 1 FISHQuant algorithms 2 irit teen pee ee da aeo ANEN a EE 7 12 2 MISP MIB icit ob LE reti ebat d en tics Le ob M Lr eu COPIER MU FCU MEN DIERUM Ue opa EA 7 1 2 3 Using a MISP file on other SIiG S cece e cece e eee eee ee m mmn 7 2 Installing MIRAX Viewer and FISHQUAN1 cccee eee eee eee eee eee ee eee e tena ee teen ee teeta eae 9 3 Working With FISH Analy Z hiscvi cvs cena tondscuilevatons cone o Ou Rag REDE conde QUAM REOR APER PR EY PAAR ga Pad EX Ra da 10 3 1 Before you start uiis ed ecd ea ea Deni e aee ne ade ag E a Ra E A Dea E FAR ERE Era De TTE cua ERR 10 3 2 Creating an annotation for FISHQuant sssssssssessssessese ems seems nennen 10 3 3 Running the Algorithm on a Single Slide sseesesssseesememmeee 11 3 4 Running Batch Process in FISHQUANL 0 2 eceee eee e eee e eee ee
3. that stems from or is associated with use of Product digitalized slides quality of staining quality of stained slides quality of used method of staining Certain legal systems do not allow the limitation or exclusion of accidental damage This restriction therefore may not apply in your case 3DHISTECH Ltd assumes no responsibility for the functionality and fault free condition of your application programs Workflows VBA macros Commander scripts CAUTION For research and education uses only not for use in diagnostic procedures This product has not been approved or cleared as a medical device by the U S Food and Drug Administration The data and images obtained or viewed using this product are not intended for clinical or diagnostic use Third party disclaimer LibTIFF TIFF Library and Utilities 3DHISTECH Ltd is not liable for damage of whatever nature including but not limited to general or specific damage indirect damage consequential damage or incidental damage including damage resulting from lost profits interruption of business loss of business information pecuniary loss or similar damage that stems from or is associated with the incorporated part of this Product that is made by Silicon Graphics Inc THE SOFTWARE IS PROVIDED AS IS AND WITHOUT WARRANTY OF ANY KIND EXPRESSED IMPLIED OR OTHERWISE INCLUDING WITHOUT LIMITATION ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT SHAL
4. from the roll down list 3 If it s not automatical choose the adequate channel name for the colors 4 Select the annotation s you want to analyze in the Available window and move them to the Selected window Also the whole slide can be selected to work with 5 Select Profile Settings to define the parameters of the algorithm f MISP Execution D stides FISH huh 7 FISH Settings Probe Selection Profile Settings HER 2 neu CEP17 Dual Color Probe iv Channel Settings Blue channel E DAPI Blue iv Red channel i Rhodamine orange Green channel E FITC green v Annotations Selection Process Annotation Area Process whole Slide Available Selected Caption Freehand Annotation Caption Rectangle Annotation Save Region measurements Export Settings v Save Cumulative measurements O Save to single CSV MISP Execution D slides FISH huh 7 June 19 2009 3DHISTECH Ltd 12 26 FISHQuant for MIRAX Viewer 1 12 User s Guide FISH Settings Setting or changing Profile Setup of the FISH algorithm Channel Settings Specifying BRG color attributes Annotation Selection Selecting annotation s for the measuring process Process Annotation Area The algorithm will be executed only on the selected annotations Process Whole Slide The algorithm will be executed on the whole digital slide area Export settings The m
5. L SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR ANY SPECIAL INCIDENTAL INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE DATA OR PROFITS WHETHER OR NOT ADVISED OF THE POSSIBILITY OF DAMAGE AND ON ANY THEORY OF LIABILITY ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE Further information For the latest information on 3DHISTECH products and services visit http www 3dhistech com June 19 2009 3DHISTECH Ltd 3 26 FISHQuant for MIRAX Viewer 1 12 User s Guide Font types and symbols Example Abbreviation or term that is explained in the section Terms and Abbrevi ations Example Words or characters that appear on the screen These include field names screen titles pushbuttons and menu names paths or options Keys on the keyboard For example function keys such as F11 or the Ctrl O key combination Example Cross references to other documents Indicates that you need an additional module to use the feature or that Warning there are prerequisites for the task or that special care should be taken arning when using certain feature of the device An important piece of information or a recommendation The application i will work if you choose not to follow the recommendation but its perform Important ance might be less than optimal A suggestion about using the application in some other way or to some in G teresting pur
6. channels Nucleus filtering Nuclei can be filtered based on their shape factor and size Spots filtering Spots can be filtered by size Nuclei setup Setting the number of nuclei to measure and the average nucleus area for segmentation Score Color Score specific labelling can be defined 7 Click OK to save settings and the form will be closed Save Region measurements The measurements will be exported to a CSV file that can be opened and edited further in Microsoft Excel Save Cumulative measure ments The measurements will be exported to CSV files A cumulative file will be created for each detected ayer Save to single CSV The measurements will be exported to a single CSV file This file will contain all the parameters of the ayers 8 Launch the FISH Analysis algorithm by clicking Start The process is fully automated you only need to click Close when FISH Analysis has finished FISH Analysis leaves open the slide If more than one slide is open when you start FISHQuant FISHQuant starts using the active one ES Local huh 7 Progress 200 um June 19 2009 Un EN 00 IES 3 A ix m Background color d wiles Caption Freehand Annotation Caption Rectangle Annotation 3DHISTECH Ltd 3 Working with FISH Analyzer FISHQuant for MIRAX Viewer 1 12 User s Guide 3 Working with FISH Analyzer Tip To view the existing annotati
7. e Gate Histogram CSV file export v O Scatter Plot O Galery Color 3DHISTECH Ltd 18 26 FISHQuant for MIRAX Viewer 1 12 User s Guide Auto Refresh Automatically updates the histogram when you change the settings for the parent form Statistics Overall it shows the quantitative data of the objects X Axis Offers various parameters for the X axis Y Axis Offers various parameters for the Y axis Gate Chooses an interval within the examined range on X axis You can position the scatter plot gates by clicking on the arrow Mode By using Gate function the program either creates new histogram new scatter plot shows gallery or opens a new form where the user can save CSV files but only in the selec ted interval By not using Gate function the program uses all the above mentioned features but for the whole data range 7 optional To create a snapshot of the scatterplot click Save 4 3 Creating a Gallery 1 Click a on the slide toolbar in the MIRAX Viewer 4 Working with Measurement Visualization 2 Select the name of the measurement from the drop down menu that has been previously saved to the slide 3 Select the annotations that you want to analyze 4 Select the object layer that you want to display 5 Select Gallery and the press the Show button 6 Set the parameters 3DHISTECH Ltd June 19 2009 19 26 FISHQuant fo
8. easurements will be exported to a CSV file that can be opened and edited further in Microsoft Excel Important FISHQuant is able to work with slides scanned in appropriate channel order B G R and with adequate channel name blue DAPI Aqua green FITC red orange rhodamine only 6 Click ProfileSetup and set the following attributes fo Profile Setup Nucleus Threshold Settings vi g Emboss radius 10 Shape smooth iterations 7 Spot threshol v Red e v Green 20 Filter Nuclei By Size v FilterNuclei By Shape v Min 50000 Sle win 080 S Max 200000 ue wa 100 Filter Spots By Size L1 Nuclei Setup Min Number of Nulcei to Detect 200 Average Nucleus Area 800 2 umt Score Color Normal G 2 v E Restore OK Cancel Separation Seed distance 3 v Extended segmentation 25 DET gt 4 gt Maximal parts to merge 8 iding 3 Working with FISH Analyzer Nucleus Threshold settings Specifying the limit values in DAPI channel enabling Hole Filling with the DAPI mask if necessary Extended Segmentation Especially for tissue samples Emboss radius 1 100 Shape smooth iteration 1 100 and Maximal parts to merge 2 16 can be defined June 19 2009 3DHISTECH Ltd 13 26 FISHQuant for MIRAX Viewer 1 12 User s Guide Spot Thresholding Specifying the limit values in FITC and Rhodamine
9. ect all option 4 Select the object layer that you want to display from the Layer drop down me nu 5 Select Histogram and the press Show button 6 Set the parameters If you enter new values into the text fie ds press Enter to refresh the diagram June 19 2009 3DHISTECH Ltd 16 26 FISHQuant for MIRAX Viewer 1 12 User s Guide GH 3 Piece oA 50 100 Copy To Clipboard Statistics Overall 12 X Axis Parameter Area Min Value Max Value Mode 9 Histogram Scatter Plot C Gallery Gated 0 Ratio 150 200 250 300 350 400 450 Area um 2 Auto Refresh AVG 278 41 STD 108 43 Cv 383 0 AVG 0 STD 0 cv 0 x Number Of Classes 25 v AutoScale Linea Logarithmic Gate CSV file export Lower Value Use Gate Upper Value Go l lt Back Save Close Auto Refresh Automatically updates the histogram when you change the settings for the parent form Statistics Overall shows the quantitative data of the ob jects X Axis Offers various parameters for the X axis When you export the results into a CSV file there is an explanation for the abbreviations of the parameter names Gate Chooses an interval within the examined range on X axis Mode By using Gate function the program either creates new histogram new scatter plot shows gallery or opens a n
10. ew form where the user can save CSV files but only in the selec ted interval By not using Gate function the program uses all the above mentioned features but for the whole data range 4 Working with Measurement Visualization As the measurements run on digital slides the perimeter and area sizes of the very small objects appropriating the pixel size can show some inaccuracy 7 June 19 2009 optional To create a snapshot of the histogram click Save 3DHISTECH Ltd 17 26 June 19 2009 FISHQuant for MIRAX Viewer 1 12 User s Guide 4 2 Creating a Scatterplot Click ko in the slide toolbar in the MIRAX Viewer 4 Working with Measurement Visualization Select the name of measurement from the drop down menu that has been previously saved to the slide Select the annotations that you want to analyze Select the object layer that you want to display Select Scatter Plot and the press the Show button Set the parameters If you enter new values into the text fields press Enter to refresh the diagram bs SF 0 l 60 Q g S 0 50 100 150 200 250 300 350 400 450 500 550 600 650 Area um 2 Statistics Overal 90 Selection count 19 Percent 21 1 Copy To Clipboard Auto Refresh X Axis Y Axis Parameter Area Iw Parameter SF vl Min Value Min Value AutoScale AutoScale Max Value Max Value Linear Logarithmic Linear Logarithmic Mod
11. ion name Area Area of the detected object in um BInt B intensity of the detected object GInt G intensity of the detected object GrayInt Gray intensity of the detected object IF C1 Integrated fluorescence in channel 1 IF C2 Integrated fluorescence in channel 2 IF C3 Integrated fluorescence in channel 3 LDia Longest diameter of the detected object in uum Peri Perimeter of the detected object in um RInt R intensity of the detected object SDi Shortest diameter of the detected object in um SF Shape factor of the detected object A 2 Summing parameters for an area Parameter Description name AvgPosO Average positivity of negative Nuclei AvgPos 1 Average positivity of 1 Nuclei AvgPos 2 Average positivity of 2 Nuclei AvgPos 3 Average positivity of 3 Nuclei FA Overall annotation area in mm fNO NO FA frequency of detected objects per um HSCORE MA Overall mask area in mm Total area of all detected objects in each ayer MAO Mask area of negative Nuclei MA 1 Mask area of 1 Nuclei MA 2 Mask area of 2 Nuclei MA 3 Mask area of 3 Nuclei NO Number of detected objects Total number of each detected object in each layer NOO Number of negative Nuclei NO 1 Number of 1 Nuclei NO 2 Number of 2 Nuclei June 19 2009 3DHISTECH Ltd 25 26 FISHQuant for MIRAX Viewer 1 12 User s Guide NO 3 Number of 3 Nuclei rMA MA FA 100 re
12. lative mask object area in rMAPos CMAO 1 MAO 2 MA 3 MA 100 rNOPos CNO 1 NO 2 NO 3 NO 100 June 19 2009 3DHISTECH Ltd 4 Working with Measurement Visualization 26 26
13. meters Toggle mode V Tooltip Horizontalview v Normal G 2 2 6 14 16 1 Nu Nm w a u a 40 42 56 62 64 65 72 78 87 88 X m wj xj 24 27 28 31 38 38 18 20 2 Area 176 2126 Peri 50 4724 soi 13 8825 Di 21 761 SF 0 8692 PresCellCount 2 Score Polysome G gt 2 SSpotnum Green 5 5potnum HER2 Green 5 Spotpercent Green 0 7143 SpotPerArea Green 0 0284 SpotnumberPCC Green 2 Spotnum Red 2 Spotnum HER2 Red 2 Spotpercent Red 0 2857 SpotPerArea Red 0 0113 SpotnumberPCC Red 1 FusionNum 0 TranslocNum 2 PoliFusionPercent 0 TranslocPercent 1 ArtefactNum 3 or 17 22 E EE 8 7830E 3 88 6 4107E 0 6 4229E 2 CNO Normal G 2 Noo CNO Monosome G 1 NO 1 CNO Polysome G gt 2 N0 2 CNO Artefact Artefact 4 12 15 18 23 25 Dee ee 75 8 sae NO 3 Avg AvgR AvgRpG 1 85227272727273 1 38636363636364 0 748466257668712 Slideview Shows the selected slide Outline Shows the group specific outline Boundary Shows the number of the detected objects Export CSV Exports the measurements to a CSV file Save to slide Saves the changes to the slides Auto save Automatically saves all changes Note that it de celerates the program Border size glide Increases decreases the size of object borders in the right panel
14. n eee eee eee nennen 15 4 Working with Measurement Visualization cece eee e cece eee eee eee ee mm mmm 16 4 1 Creating a HIStOgrFatm reor citer nee cane aaa au epe y ek xke E Rd PERO 16 4 2 Creating a Scatterplot iiu eene rene prex cea c dne c a a rk er e Re M 18 453 Creating A Gallery ErE M m 19 4 4 Creating a Classification Gallery cccceeeeee cece eee eee eee emen enne 21 Related documents eiie cix i a E AE a N ESSERI Y YMO A ERRORS 23 Index iei nete roS GU a EUG bt hd REA a Dhak Reed rex ELE pat EE AKE 24 Appendix A FISH Analysis eiiceeu euusu a ruo ro ERR ER RETE EAEEKRFIRIAR KXDARIERERETRIREERRRRINIKRIAARX Y4ls Riga 26 A 1 Object specific parameters sssssssssesseeseeeennn nnne 26 A 2 Summing parameters for an AFa sce cece eee eee eee eee eee ee eee mense nnne 26 June 19 2009 3DHISTECH Ltd 2 26 FISHQuant for MIRAX Viewer 1 12 User s Guide Disclaimer Copyright 2001 2008 3DHISTECH Ltd All rights reserved The following patents are pending for 3DHISTECH products WO 2006 030326 P0700409 and 11 826 752 3DHISTECH Ltd is not liable for damage of whatever nature including but not limited to general or specific damage indirect damage consequential damage or incidental damage including the results of the analysis of the digitized slides for example change of health status related to erroneous diagnosis from the digitalized slide s
15. nnotation as small as possible The annotated areas should not be larger than 300x300 um 1 1 magnification e When you are creating a free hand annotation follow the outline of the area as closely as possible Membrane Analysis only works on slides to which you have write access You may have only read permission to a slide if you access it through Teleconsultation and the host only gave you read permission or if you access a slide stored on a net work drive and you only have read but not write permission to the drive 9 Tip If you need measurements on the entire specimen put an annotation on the slide to cover the entire specimen 3 2 Creating an annotation for FISHQuant 1 Open the slide in MIRAX Viewer For more information on how to open slides in MIRAX Viewer see section Working with slides in MIRAX Viewer in the MIRAX Viewer 1 12 User s Guide 2 Create the annotation on the area of your interest Select the annotation type rectangle or free hand and cover the area with the annotation June 19 2009 3DHISTECH Ltd 10 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 3 Working with FISH Analyzer For information on navigating and zooming on the slide see section Viewing slides in document Mirax Viewer 1 12 User s Manual In the Create or Edit Annotation window add a title to the annotation enter a comment and determine the background color of the title and the outline color of the annotation You can either
16. ons and existing measurements on the slide click INFO in the slide toolbar and then select Show Annotations or Show HQ Measurements from the shortcut menu 3 4 Running Batch Process in FISHQuant In Image Analysis Modules menu you have the option to work with batch files Select the slides you want FISHQuant to work with and specify the parameters for which they should be analyzed Every slide needs to have the correct channel name and order as mentioned above June 19 2009 3DHISTECH Ltd 15 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 4 Working with Measurement Visualization 4 Working with Measurement Visualization The Measurement Visualization module for MIRAX Viewer creates a scatter plot or a histo gram from the FISHQuant measurements 4 1 Creating a Histogram 1 Click ka in the slide toolbar in the MIRAX Viewer L Data Visualisation Data Selection Misp names E FISH_Detection 1633_24 02 2009 Mi Annotations C IC Caption Rectangle Annotation Ar C Caption Area C FISHQuant_Area Caption Rectangle Annotation_Ar C Caption Freehand Annotation_Are C Caption Area v Layers Nuclei v Mode Histogram Scatter Plot Gallery Classification Gallery Close Show 2 Select the name of measurement from the drop down menu that has been pre viously saved to the slide 3 Select the annotations that you want to analyze You can select all by checking the Sel
17. pose Tip June 19 2009 3DHISTECH Ltd 4 26 FISHQuant for MIRAX Viewer 1 12 User s Guide Terms and abbreviations Annotation A particular detail of a digitized slide FISHQuant can perform measurements on annotations CSV format Comma separated value Digital slide Slide digitized with a MIRAX scanner microscope for example MIRAX SCAN Consists of an MRXS file and a folder with the same name as the MRXS file Field In image analysis module an annotation In ImmunoScreener a grid cell Layer A group of cell compartments matching the same stain and size criteria Measurement FISHQuant can perform two types of measurements field specific related to the annotation object specific MISP MIRAX Imaging Segmentation Profile An image analysis segmentation and measuring algorithm is stored in a MISP file MRXS MIRAX Slide File extension of a digitized MIRAX slide Object A cell compartment for example the FISH cell or tissue that is relevant for the immunohistochemical analysis Segmentation Identification of cells or cell compartments based on their different reaction to immunohistochemical staining June 19 2009 3DHISTECH Ltd 5 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 1 About FISH Analysis 1 About FISH Analysis FISHQuant is an optional module for MIRAX Viewer It allows you to detect and separate FISH spots on the virtual slides and digitali
18. r MIRAX Viewer 1 12 User s Guide 4 Working with Measurement Visualization S561 BAX Copy To Clipboard Auto Refresh Border size t Zoom Factor J 0 66 Auto Refresh Automatically updates the histogram when you change the settings for the parent form Border size Sets the size of the image border Zoom factor Sets the zooming rate of the images You can determine the zooming value by entering the exact rate in the text field Moving the cursor over an image an info box appears conveying all the neces sary data regarding that image 7 optional To export the gallery as an image click Save 5 E v Tip If you select an image in the gallery it will be highlighted in the Scatter Plot as well June 19 2009 3DHISTECH Ltd 20 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 4 Working with Measurement Visualization 4 4 Creating a Classification Gallery You can group your objects in accordance with their score values the probe used on the objects You can revalidate and rescore your object On the right side panel you can move cell nuclei from one group to the other On the left panel you can view the selected cell nuclei 4 Classification Gallery v Slideview v Outline Export CSV Save to side Close Boundary June 19 2009 Auto save Border size order size v Zoom factor 9 v Field para
19. ram or a gallery 6 Digital slides including slides that store FISHQuant measurements can be shared via PathoNet They can also be used in E School training and exam material 1 2 Overview of FISH Analysis You can perform three types of tasks in FISHQuant create algorithms based on your parameters and then run them on a slide or a set of slides view the measurement results with the Measurement Visualization module save the measurement annotations with the slide or export the measurement re sults to CSV file s create a report based your saved measurements 1 2 1 FISHQuant algorithms FISHQuant allows you a FISH analysis setup application which has a segmentation and a thresholding setup section You can also change the score outlining color The informa tion needed for the algorithm is not saved on the slide but in a MIRAX Image Segmenta tion Profile MISP file which can be used later to evaluate other annotations on the same slide or on other slides 1 2 2 MISP files FISHQuant algorithms are saved in MISP files that store the following information about the algorithm segmentation algorithm filters for noise reduction segmentation and object separation Classifications June 19 2009 3DHISTECH Ltd 7 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 1 About FISH Analysis 1 2 3 Using a MISP file on other slides You can reuse the MISP on other slides from the same batch on slides that are from the
20. same specimen without modifications You can also use the same algorithm on slides from other specimens with the same staining You might need to adjust the profile to ensure that differences in the specimen or stain quality do not affect the result June 19 2009 3DHISTECH Ltd 8 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 2 Installing MIRAX Viewer and FISHQuant 2 Installing MIRAX Viewer and FISHQuant 1 June 19 2009 Start the MIRAX Viewer setup exe file that you received on a MIRAX Viewer DVD or downloaded in a compressed file Follow the instructions in the installation wizard Start the application setup exe file that you received on the application DVD or downloaded in a compressed file Follow the instructions in the installation wizard 3DHISTECH Ltd 9 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 3 Working with FISH Analyzer 3 Working with FISH Analyzer 3 1 Before you start FISHQuant works on selected annotations You will be able to run other algorithms on several annotations by selecting all the annotations that you need when you start the al gorithm H Important FISH Analysis algorithms require a significant amount of computer re sources The resource need and the speed of the Membrane Analysis eval uation depends on the size and the number of the measured annotations and the quantity of detected objects To ensure accurate results and to reduce computation time e Make the training a
21. select from predetermined colors or you can define custom colors Only captions are exported to the CSV output file Annotation descriptions are vis ible only in MIRAX Viewer ES Local huh 7 oE fo SOP e 7 A DO m E 8 O a ne EC GE EE 10x EET E Maoniication 10 28 Progress 200 um Caption Freehand Annotation Caption Rectangle Annotation Bon EN oe ERES 39 A x m Background color gn 3 Repeat step 2 for each area on which you want to run the algorithm 3 3 Running the Algorithm on a Single Slide Open the slide in MIRAX Viewer 1 In the main toolbar click Eg and select FISHQuant from the Image Analysis Mo dules June 19 2009 3DHISTECH Ltd 11 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 3 Working with FISH Analyzer Ef image analysis modules P o Slide D slides FISH huh General applications HistoQuant is an image segmentation solution for general purposes based on color brightfield or wavelength fluorescent information IHC applications NuclearQuant detects and separates nuclei on immunolabeled slides i e ER PR Ki6 MembraneQuant analyses cellmembrane positivity on immunolabeled slides i e HER 2 EGFR dd Fluorescent applications FISHQuant analyses FISH slides by detecting fluorescent spots and counter stained nuclei Evaluates the results based on the applied probes 5 Batch Processing Delete Measurements 2 Select a FISH probe
22. zed with MIRAX microscopes FISH Analysis performs segmentation and measurements on MIRAX digital slides based on the colors of the spots Based on the applied FISH probe it can classify the cell nuclei 1 1 FISH Analysis in the MIRAX product family The following picture shows how FISH and Measurement Visualization extend MIRAX Viewer and how they fit into the MIRAX product family Slides j XU MIRAX Server Fluorescent slides a MIRAX Scan Local file system PathoNet ly En Lex FD ImmunoScrener eur Teleconsultation co PET ev A im d q of mage analizis modules 4 zl 19 Measurement Visualization E School MIRAX Viewer 1 Slides are digitized with MIRAX microscopes A digitized slide consists of an MRXS file and a folder with the same name as the MRXS file 2 Digitized slides are stored on a computer You can also use a dedicated server MIRAX Server for storing the MIRAX slides June 19 2009 3DHISTECH Ltd 6 26 FISHQuant for MIRAX Viewer 1 12 User s Guide 1 About FISH Analysis 3 Slides digitized with a MIRAX microscope can be viewed in MIRAX Viewer If the slide is stored on a MIRAX Server it is opened through the Teleconsultation module Local slides are opened directly with MIRAX Viewer 4 FISHQuant allows you to perform measurements on digital slides and to export the measurements in CSV format 5 Measurement Visualization displays the FISHQuant data as a scatterplot a histog
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