Aperio Image Analysis User`s Guide
Contents
1. requirements Display Type CRT minimum LCD flat panel recommended Screen Resolution 1024 h x 768 v pixels minimum 1920 x 1050 or larger recommended Screen Size 15 minimum 19 or larger recommended Color Depth 24 bit Brightness 300 cd m2 minimum 500 or higher recommended Contrast Ratio 500 1 minimum 1000 1 or higher recommended FDA Cleared Image Analysis Algorithms Several Aperio algorithms have been cleared by the FDA for clinical use when used on ScanScope models that are labeled as approved medical devices and are intended for research use for other applications These algorithms have their own user guides Please see the Intended Use section of the user guides for the specific cleared applications you wish to use for details on in vitro diagnostic use 2 Aperio Image Analysis User s Guide Chapter 1 Introduction Intended Use Algorithms are intended to be used by trained pathologists who have an understanding of the conditions they are testing for in running the algorithm analysis Each algorithm has input parameters that must be adjusted by an expert user who understands the goal of running the analysis and can evaluate the algorithm performance in meeting that goal You will adjust tune the parameters until the algorithm results are sufficiently accurate for the purpose for which you intend to use the algorithm You will want to test the algorithm on a variety of images so its2. 222 33 4444 Unetele 1981 12 03 Female St Barnabes E 555 1212 Stage ll Sent 49 Lisa Dr John Breast Cancer Report Project o m2 111 22 3333 Svensson 19591231 Female Ciy Hospital Hanley 555 1212 Stage I ee iz Janet _ Mercy General Dr Beth Stage II Breast Project o jij 3 1332 888 5987 Hopwood 1955 01 23 Female Caucasian Hospital E 555 346 7890 Tie 2008 03 12 Approved 49 O E 4 6878 444 5698 MingHo 1960 07 04 Female Asian Mercy General Dr Beth 3467899 Stage I Breast 2008 03 12 Approved Proiect Hospital Edwards Cancer 4 Os 6578 454 3987 Maria Rossi 1952 05 06 Female Caucasian Mercy General Dr Beth 555 346 7890 Stage Breast 2008 03 12 Approved Project Hospital Edwards Cancer 49 Display 25 Customer Name XYZ Hospital HealthCare Inc Records Per Page You now see the case or project information page that contains details about that case or project 6 On the detail page move down to the Digital Slides area of the page and open a digital slide in ImageScope by clicking its thumbnail in the digital slide list Case Digital Slides 4 View Images Open Data Analyze Delete Unassign Move Copy Export Data Annotations 4 Thumbnail Slide Barcode ID Block ID Comment Status 1D 1 ois 1 Angeique Unetele 1 A 100 3 Le O il SE 2 Angelique Unetelle 12 A See Microscopic 2 m T y map S 2 Angelique Unetele 17 A 100 1
3. Layer Attributes lt gt ES Date StartTime EndTime Status Algorithm S StatusDescription Algorithm Version Nwp Number of Weak Positive Positive Pixel Count 2004 08 11 Tuesday March 11 2008 2 47 59 PM 2 47 59 PM 0 Positive Pixel Count 2004 08 11 8 100 49135 To export the text of the Layer Regions pane to a text file On the Layer Regions pane click al You will be asked to specify the name and location of the text file to be created This text file is a tab delimited file that can be imported into a spreadsheet program Text Nwp Numbi ss Exporting Results to a Spreadsheet To export the text of the Layer Attributes pane to a Microsoft Excel spreadsheet On the Layer Attributes pane click E You will be asked to specify the name and location of the spreadsheet xls file to be created StatusDescription Algorithm Version E Nwp Number of Weak Positive Layer Attributes gt 2 B Algorithm Positive Pixel Count 2004 08 11 Date Tuesday March 11 2008 StartTime 2 47 59 PM EndTime 2 47 59 PM Status 0 Positive Pixel Count 2004 08 11 8 100 49135 To export the text of the Regions Attributes pane to a Microsoft Excel spreadsheet On the Regions Attributes pane click E You will be asked to specify the name and location of the spreadsheet xls file to be created Region Length um Area u Text Nwp Numbi 38 Aperio Ima
4. Select the Create markup image s check box if desired 34 Aperio Image Analysis User s Guide O pero Chapter 6 Running the Analysis 7 Click Analyze The slides chosen for analysis will be added to the Analysis Job Queue ses Specimens Digital Slides TMA Blocks Analysis Administrative Help Font Size Case User Dr Beth Edwards Role Pathologist Log off 3 Pending Analysis Jobs Cancel Hi JobID Submitted Date Submitted By Image ID Image Of Macro Create Markup Processing Host Status Details Tasks D 4 2008 11 06 16 46 57 Dr Beth Edwards 3 Digital Slide 3 PPC Dr Beth Edwards true Submitted Cancel 3 2008 11 06 16 46 57 Dr Beth Edwards 2 Digital Slide 2 PPC Dr Beth Edwards true Submitted Cancel Fl 2 2008 11 06 16 46 57 Dr Beth Edwards 1 Digital Slide 1 PPC Dr Beth Edwards true Spectrum In Progress Cancel See the Spectrum Spectrum Plus Operator s Guide for information on m Checking the progress of the analyses E Canceling analysis jobs m Viewing the analysis history for specific digital slides For More Information For details on using Aperio algorithms to analyze digital slides see E Spectrum Spectrum Plus Operator s Guide for information on using algorithms to analyze individual digital slides or batches of digital slides E ImageScope User s Guide for information on using algorithms to analyze local digital slides on your workstation or local network or to analyze remote digita
5. View Height 1000 Overlap Size 0 Image Zoom 1 Markup Compression T 0 Same as processe Compression Quality 30 Classifier Neighborhood 0 Classifier 35 View Width Width of processing box outs _ Outputs Region of Analysis Current Screen Entire Image Selected Annotation Layer 2 Generate aro mage 5 On the algorithm parameter window click Tune On the ImageScope main window you see a new Algorithm Tuning window with the mark up image from the analysis using the current parameters Aperio Image Analysis User s Guide 29 O pero Chapter 5 Registering the Algorithm on Spectrum 30 You see the numeric results of the analysis in the Annotations window Annotations Detailed View Layer Regions X E ES a Region Length um Area um2 Layer Attributes gt Nwp Number of Weak Positive Np Number of Positive Text Result 2 1 3149 8175 Nsp Number of Strong Pasitive lwp Total Intensity of Weak Positive Ip Total Intensity of Positive Isp Total Intensity of Strong Positive lavg 91 0777 lwp p sp Nwp Np Nsr 0 659307 Nso INwo No Nsol 6 To adjust the size of the Algorithm Tuning window grab a corner until you see the double headed arrow and pull the window to change the size 7 To see the analysis of another area of the digital slide drag the Algorithm Tuning window to another area or move the digital
6. aperio Chapter 3 Opening a Digital Slide for Analysis Opening a Remote Digital Slide To open a remote digital slide directly from within ImageScope without going through the Spectrum user interface 1 14 Go to the ImageScope File menu and select Access Remote Server to connect to Spectrum Enter the name of the server containing the digital slides usually the server on which Spectrum resides Access Remote Server Server Connection Information Server spectrum server Port 82 Connect Cancel Set the Port value to 82 Click Connect When asked for your user name and password enter your Spectrum user name and password Aperio Image Analysis User s Guide O pero Chapter 3 Opening a Digital Slide for Analysis 5 Now you see a page of digital slides on the Spectrum site You can choose between two views List and Thumbnail by selecting the view you want from the drop down list at the upper right Spectrum L Ar a ta e i py amp Ng P SE 1225387887 1339 3003ER svs 1225387890 1342 3003HE svs 1225387891 1340 3003PR svs 4000 x 3000 20X 4000 x 3000 O 20X 4000 x 3000 20X 4000 x 3000 20X view ImageScope WebScope view ImageScope WebScope view ImageScope WebScope view ImageScope WebScope 1225387893 Breast Cancer Infiltrating Ductal jpg 281x 175 4000 x 3000 20X 4000 x 3000 20X view ImageScope WebScope st ImageSco
7. 5 Select the algorithm you want to create a macro for by clicking it in the list and then clicking Select If you don t see the algorithm you want to use listed you will need to install that algorithm on the Spectrum server and on your workstation The Create button creates a new macro based on the selected algorithm This loads the algorithm macro with its default parameters so you can see its unmodified parameters The Analysis window now appears Macro on server spectrum Positive Pixel Count v9 Parameters View Width 1000 a View Height 1000 Overlap Size 0 Image Zoom 1 Markup Compression T 0 Same as processe Compression Quality 30 Classifier Neighborhood 0 Classifier View Width Width of processing box Inputs Outputs Region of Analysis Current Screen Entire Image Selected Annotation Layer 2 Generate at age Ready 4 6 If not already selected click Inputs and modify the parameters referring to the user guide for particular algorithm you are using for guidelines If Aperio Image Analysis User s Guide 23 O pero Chapter 5 Registering the Algorithm on Spectrum the algorithm you are using does not have any inputs skip to the next step 7 Click Outputs and select the output results you want to display in Spectrum clearing the check boxes next to the results you don t want to display Macro on server spectrum Select Algor Positive Pixel Coun
8. Annotations Thumbnail Slide Barcode ID Block ID Comment The Analysis page appears depends on the digital slides you have selected to batch analyze Analyze 3 Images Select Analysis Macro PPC Dr Beth Edwards x The number of Select Input Annotation Layer L Most Recent annotation layers all a the selected slides Da have in common are El Wwnole mage listed in this section Create markup image s This is because Spectrum does not allow you to select an annotation layer 4 Select the analysis macro of your choice If you don t see the algorithm that does not exist for all the selected digital slides In this example all slides have three or more annotation layers you want to use see Chapter 5 Registering an Algorithm on Spectrum on page 21 for instructions on creating and saving an algorithm macro 5 Ifyou want to analyze only a portion of the image select a specific annotation layer in the Select Input Annotation Layer section or click Most Recent to select the annotations in the most recently created If one of the digital gt slides selected has annotation layer If you want to analyze the entire digital slide select AO annatetior Whole Image layers you will only see Most Recent or See Chapter 4 Selecting Areas to Analyze on page 17 for information Whole Image as on drawing annotations to select areas to analyze selecions 6
9. User s Guide O pero Chapter 4 Selecting Areas to Analyze Each of the three annotations we drew is listed in the Layer Regions panel with area and length measurements in microns To select a specific annotation for example if you want to delete it or move it click it in the ImageScope image or click it in the Layer Regions panel of the Annotations window and you see it highlighted on the ImageScope main window For example below we clicked on annotation 1 the rectangular annotation and see that its boundary contains a dark line showing it is selected i Aperio ImageScope v10 0 35 1790 Barcode Angelique Unetelle 12 3 1981 S08 03003 A HER2 Breast HER2 080215 1 3 MBR E Fie Edit Image View Tools Window Help C Images 1225387891_1 341_3003HER2 svs ion Length um 1 336 2 3 Layer Regions Regi E To delete the selected annotation press the Delete key on your keyboard or click the red X in the Layer Regions pane To move it hold down the Control key and drag it on the ImageScope main window Aperio Image Analysis User s Guide 19 O pero Chapter 4 Selecting Areas to Analyze 20 Aperio Image Analysis User s Guide 5 Registering the Algorithm on Spectrum An algorithm macro is an algorithm and its settings Before you can use an algorithm on Spectrum you must create an algorithm macro and save it on Spectrum To analyze a digital sli
10. all Cases View all Cases as Folders Search all Cases Add new Cases Specimens List all Specimens View all Specimens as Folders Search all Specimens Add new Specimens Digital Slides List all Digital Slides View all Digital Slides as Folders List ScanScope Slides List ScanScope Slides Past Day List ScanScope Slides Past Week List ScanScope Slides Past Month Search all Digital Slides Add new Digital Slides g TMA Blocks List all TMA Blocks View all TMA Blocks as Folders Search all TMA Blocks Add new TMA Blocks o Image Analysis Analysis Jobs The exact categories of data you see depend on your Spectrum configuration and options For the purposes of this guide we will assume Spectrum Plus is configured for clinical or research use 4 Navigate to the list of cases by clicking List all Cases or to the list of projects by clicking List all Projects Aperio Image Analysis User s Guide 71 O pero Chapter 3 Opening a Digital Slide for Analysis 5 Open the case or project you want to review by clicking the open data icon for the case or project User Dr Beth Edwards Role Pathologist Specimens Digital Slides TMA Blocks Analysis Administrative Cases Open Data Delete New Export Data Patient ID Gender Ethnicity Hospital Physician Physician Final Comment Date Status ID Name Phone I Reported Angelique Dr Bob Breast Cancer Report Project lid
11. cscssssscsctscscesessssssssssessssssessssseseasssesessees 12 Opening a Remote Digital Slide sessossosesssessssorsososssessoscesosessseorosorsososssessosessose 14 For Mor Information sessccsesissssetssccsesccsissvssscccesctassecatessssssaastesevessanseevescsenstessstestostees 15 CHAPTER 4 SELECTING AREAS TO ANALYZE 0cececeecececuecececeeaecucueesaucusesarsrees 17 CHAPTER 5 REGISTERING THE ALGORITHM ON SPECTRUM scececsececesaececesenerees 21 Opening the Digital Slide isiccsssesscesssecssssseesesossecssensseessvoasessasesesesenossessvenssoscosess 21 Creating a New Macro ssscisssssnccssasesssecoasecsssnssssedoaseccesnssnssssesbectosedsnetssssbeosensuetonsseenss 22 Saving and Registering the Macro on Spectrum cssesssssssessesssesesssceseseseees 26 Testing and Modifying an Existing Macro ce ss ananasas senas aa 27 Using the Tuning Window to Test Algorithm Parameters 28 CHAPTER 6 RUNNING THE ANALYSIS 00cccecescececesaucueesaeceseeueaveueueevaususenanaeses 31 Analyzing in ImageScOpe ssssscsscssssssssscssscsssssssssssssssssssassssssessssssessssasssessesess 31 Spectrum Analysis Batch JODS cssssssscscsssssssssscscessssssssssssssessssssesssseseessenes 33 For Mor Information sensicisscsssscscscessdvceascacsacsaseasseseesseacsscuaanceieveceasebenacesancaseusseteosieee 35 CHAPTER 7 EXPORTING RESULTS eccecceccecceeceeceacenceeceneeeneneeeneeaceneeneeneenaee
12. of the macros listed in the window 3 Inthe Region of Analysis section click one of the following selections a Entire Image When analyzing the image testing an existing macro or creating a new macro the entire image will be used b Selected Annotation When analyzing the image testing an existing macro or creating a new macro only the portion of the image defined by the active annotation will be used If no annotations exist for the image Entire Image is automatically selected 22 Aperio Image Analysis User s Guide Chapter 5 Registering the Algorithm on Spectrum O pero 4 Click the Create button to make a new macro The Select an Algorithm window appears Select an Algorithm Filename 2 Positive Pixel Count 2004 08 11 8 100 Counts itive Pixels into Three Intensity CM es ScanS cope A Positive Pixel Count v9 91 Counts Positive Pixels into Three Intensity C Program Files ScanScope ss A IHC ER Breast Dako Clone1D 1 0 IHC ER Image Analysis for Breast Tissue C Program FilestScanScopel s A IHC PR Breast Dako ClonePg 1 0 IHC PR Image Analysis for Breast Tissue C Program FilestScanScopel s A IHC HER2 Breast Dako Herc 1 0 IHC HER2 Image Analysis for Breast Tiss C Program Files ScanScope A4 A IHC HER2 Breast v1 1 0 IHC HER2 Image Analysis for Breast Tiss C Program FilestScanScopelds A Colocalization v9 91 Measures Colocalization of Multiple Stains C Program FilestScanScopetds 2
13. or on a non Spectrum remote server see Opening a Local Digital Slide on page 12 and Opening a Remote Digital Slide on page 14 For example in this case we have selected areas to analyze as discussed in the previous section WO ROM Cimapen t225907 00383 244 _2003MERZ0v8 Aperio Image Analysis User s Guide 31 O pero 32 Chapter 6 Running the Analysis 2 Go to the View menu and select Analysis The Algorithm Server window appears Algorithm Server Job Server spectrum Select Algorithm Macro Macro Name PPC Dr Beth Edwards IHC HER2 Breast Dako Colocalization Version 9 Aperio Positive Pixel Count Sample Macro Generate Markup Image Incremental Processing Region of Analysis Selected Annotation O Entire Image 3 Click an algorithm macro to select it If the algorithm you want to use doesn t appear in this window a macro for the algorithm has to be created and saved on Spectrum See the previous chapter for details 4 Click the appropriate radio button to select the area of the digital slide to analyze a Entire Image The part of the image shown in the ImageScope main window b Selected Annotation Analyze only the areas selected by drawn annotations in the current annotation layer If you have more than one layer of annotations go to the Annotations window and select the annotation layer in the Layers pane that contains the drawings that select the areas to
14. or project to see the digital slides associated with that case project m You may list all slides by going to the Digital Slides menu and selecting All Digital Slides As List E Or you may want to search within the slides for a specific stain or status See the Spectrum Spectrum Plus Operator s Guide for more information Aperio Image Analysis User s Guide 33 Duero Chapter 6 Running the Analysis 2 Select the box to the left of each slide to be batch analyzed E Case Digital Slides View Images Open Data Analyze Delete Unassign Move Copy Export Data Annotations a Thumbnail Slide Barcode ID Block ID Comment Status Image Captured File Locatior ID Date E 1 CAlmages e Z B 1 Angelique Unetele 17 A 100 3 1 V225387867 Ag 7 2 Angelique Unetele 17 A See Microscopic 2 1225987800 1 p a K pa CNmages ivi ad S o Gomme tom 112253878911 3 4 Angelique Unetete 1q A 30 1 4 cAlmages IZ M225387891 10 Cilmages 122538789 i V MM ee DP Ma ae ea 2 ge Gg Pa S r 5 Angelique Unetelle 12 A 100 2 3 5 3 Click Analyze E Case Digital Slides He fd The list of annotation layers you see in the Select Input Annotation Layer section of the Analysis page View Images Open Data Analyze Delete Unassign Move Copy Export Data
15. performance can be evaluated across the full spectrum of expected imaging conditions To be successful it is usually necessary to limit the field of application to a particular tissue type and a specific histological preparation A more narrowly defined application and consistency in slide preparation generally equates to a higher probability of success in obtaining satisfactory algorithm results If you get algorithm analysis results that are not what you expected please see Appendix A Troubleshooting on page 39 for assistance IHC Quick Analysis The examples in this guide show the use of the ImageScope detailed Annotations window which provides a general solution for image analysis However a more streamlined version of image analysis is also available that uses the ImageScope Annotations summary view The Annotations summary view was specifically developed for analyzing IHC digital slides and make the process quicker and simpler by fitting into a pathologist s or researcher s normal activities For details on using the Digital IHC features on setup steps for Spectrum and for guidelines on creating validation studies for the specific IHC application you want to use see m Digital IHC User s Guide m Digital IHC Guide to Spectrum Setup m The user s guide for the specific IHC application you are using Slide Specific Processing The key to the Digital IHC workflow is slide specific processing which defines how a digital sli
16. 3 3 og 4 Angeique Unetele 17 A 30 1 4 F 10 DB Angeique unetetie 12 A 100 2 3 5 W Although you usually will want to find a digital slide by going to its parent case project or specimen you can also use Spectrum s search functions to find a specific digital slide or you can go to the digital slide table on the main page to browse all digital slides Opening a Local Digital Slide To open a digital slide that resides on your workstation or local area network 1 Start ImageScope by clicking Start pointing to All Programs gt ScanScope and then selecting ImageScope 2 Go to the File menu and select Open Image or click E on the ImageScope toolbar 12 Aperio Image Analysis User s Guide O pero Chapter 3 Opening a Digital Slide for Analysis 3 On the Open Image window navigate to the location that contains the image you want to view 4 Click the name of the digital slide you want to open and click Open You may need to change the file type in the Open Image window to see the type of image you want to view For example to view a CWS image click the file type drop down list and select Composite WebSlides SlideScan ini Composite Webslides SlideScan ini EEE ScanScope Virtual Slides svs jp2 gt gt 2 e pro RES Sets sis n DEA Files po Composite Webslides Slide Scan ini Aperio Image Analysis User s Guide 13 d
17. Aperio Image Analysis User s Guide O pero Duero Copyright O 2008 Aperio Technologies Inc Part Number Revision MAN 0013 Revision C Date September 4 2009 This document applies to software versions Release 10 1 and later All rights reserved This document may not be copied in whole or in part or reproduced in any other media without the express written permission of Aperio Technologies Inc Please note that under copyright law copying includes translation into another language User Resources For the latest information on Aperio Technologies products and services please visit the Aperio Technologies website at http www aperio com Disclaimers Use normal care in maintaining and using the Spectrum servers Interrupting network connections or turning off the Spectrum and DSR servers while they are processing data such as when they are analyzing digital slides or generating an audit report can result in data loss This manual is not a substitute for the detailed operator training provided by Aperio Technologies Inc or for other advanced instruction Aperio Technologies Field Representatives should be contacted immediately for assistance in the event of any instrument malfunction Installation of hardware should only be performed by a certified Aperio Technologies Service Engineer ImageServer is intended for use with the SVS file format the native format for digital slides created by scanning glass slides with
18. Compression T 0 Same as processe Compression Quality 30 Classifier Neighborhood 0 Classifier View Width Width of processing box Inputs Outputs Region of Analysis Current Screen Entire image Selected Annotation Layer 2 Generate ar age Ready 4 2 You are asked to enter a name for the macro Save macro on server spectrum Enter a name for the macro 50 characters or less then press OK to save the macro or press Cancel to cancel the save Type a name that will help you identify the macro in the future and click OK You now see a message letting you know that the macro is saved It is now registered on Spectrum Now when you bring up the Analysis window you will be able to select your macro by clicking Select Algorithm because your macro will appear in the list 26 Aperio Image Analysis User s Guide Chapter 5 Registering the Algorithm on Spectrum Duero 17 gt 2 The Test and Create buttons are disabled if you are not logged in as a Spectrum administrator as only administrators can create and modify algorithm macros The Analyze button is disabled if your user permissions are not set to Full Control for the data group containing the digital slide image or if your user role does not permit image analysis Testing and Modifying an Existing Macro After opening an image from Spectrum when you sele
19. analyze 5 Select the Generate Markup Image check box to create a pseudo color markup image Aperio Image Analysis User s Guide Chapter 6 Running the Analysis O pero 7 Click Analyze to start the analysis If you have selected the Generate Markup Image check box the image in the ImageScope window shows the visual results of the analysis The Annotations window shows the analysis result data You can export the analysis results in an Excel spreadsheet or as text using the icons in the Annotations window see Chapter 7 Exporting Results on page 37 for details i Aj Annotations Detailed View Layer 3 PPC Dr Beth Edward StartTime EndTime Status StatusDescription Nwp Number of __ Weak Positive Np Number of Positive Nsp Number of Strong Positive lwp Total Intensity of Weak Positive Ip Total Intensity of Positive E Positive Pixel Count vg 2008 11 06 04 39 44 PM 04 39 45 PM Spectrum Analysis Batch Jobs Spectrum provides a convenient tool for batch analysis of slides Before you can batch analyze selected slide images in Spectrum the Spectrum administrator must first create a macro for each image analysis algorithm you want to use for analysis Analysis can be taking place while you continue to work within Spectrum organizing data and annotating images 1 Display the desired list of digital slides E Open a specific case
20. cope or by first going through Spectrum In most cases we expect you to open a digital slide in Spectrum Other methods of access are discussed at the end of this chapter About ImageScope In most cases you will be using ImageScope to view and analyze digital slides In addition to the basic features shown in this guide ImageScope also contains many advanced features that will help you view and assess digital slides m Image Quality IQ the IO feature is available when your site is licensed for Spectrum Plus and when you open a digital slide in ImageScope from Spectrum IQ contains a variety of tools that help you to better assess a digital slide based on its stain In addition to allowing you to view stain channels separately IQ also remaps stain colors accentuates cellular detail and recombines stains For details see the IQ Image Quality User s Guide m Scale Axes and Grid You can optionally overlay the digital slide image with measurement axes and axes grid m ImageScope Ruler The ImageScope ruler tool allows you to measure an object on the digital slide by drawing on the slide For more information see the ImageScope User s Guide Aperio Image Analysis User s Guide 9 O pero Chapter 3 Opening a Digital Slide for Analysis Accessing a Digital Slide in Spectrum Cases or projects specimens and digital slides are managed using Aperio s p Spectrum A pathologist who wants to access a digital slide firs
21. ct Analysis from the View menu you see the Algorithm Server Job window Algorithm Server Job Server spectrum Select Algorithm Macro Macro Name IHC HER2 Breast Dako Colocalization Version 9 Aperio Positive Pixel Count Sample Macro 4 Generate Markup Image Region of Analysis Selected Annotation Entire Image The Test button modifies an existing macro for the algorithm you have selected and tests it before saving it to Spectrum Using the Test button loads the algorithm macro with its existing parameters Macro on server spectrum Positive Pixel Count v9 Parameters View Width 1000 7 View Height 1000 Overlap Size 0 Image Zoom 1 Markup Compression T 0 Same as processe Compression Quality 30 Classifier Neighborhood 0 Classifier View Width Width of processing box inputs _ Outputs Region of Analysis Current Screen Entire image Selected Annotation Layer Z Generate ato age Ready 4 Aperio Image Analysis User s Guide O pe Chapter 5 Registering the Algorithm on Spectrum Modify the parameters and click Run to test it on the digital slide Or click the Tune button to test the algorithm parameters as discussed in the next section When you are satisfied with the results click the Save Macro button as discussed in the previous section to save the modified macro Using the Tuning Window to Test Algorithm Parameters The algorithm t
22. de on Spectrum you will need to create an algorithm macro and register it on Spectrum Creating a macro is a simple matter of adjusting the parameters of the algorithm and saving those settings In order to create an algorithm macro you need to install the algorithm on both your local workstation and on Spectrum This consists of simply running the algorithm installer on both computers Note that creating and registering a macro requires that you log into Spectrum as an administrator Opening the Digital Slide You can either open a remote digital slide in Spectrum or open the remote digital slide directly in ImageScope See Chapter 3 Opening a Digital Slide for Analysis on page 9 for details Open a digital slide you will use to create an algorithm macro Aperio Image Analysis User s Guide 21 O pero Chapter 5 Registering the Algorithm on Spectrum Creating a New Macro 1 Log into Spectrum as an administrator 2 From Spectrum after opening a digital slide in ImageScope go to the ImageScope View menu and select Analysis You see the Algorithm Server Job window Algorithm Server Job Server spectrum Select Algorithm Macro Macro Name IHC HER2 Breast Dako Colocalization Version 9 perio Positive Pixel Count Sample Macro Generate Markup Image Incremental Processing Region of Analysis Selected Annotation Entire Image Because you are going to create a new algorithm macro you won t select one
23. de will be processed based on its stain and type of tissue body site The slide specific processing can define what algorithm will be used to analyze that type of slide how analysis results will be display and how to interpret those results alternatively manual scoring can be set up for the slide and what comments will be available to be used by the pathologist or researcher viewing the slide Aperio Image Analysis User s Guide gt O pero Chapter 1 Introduction The slide specific configuration for each stain body site combination is defined by the Spectrum administrator See the Digital IHC Guide to Spectrum Setup for details Once slide specific processing is set up viewing annotating and analyzing a digital slide becomes a quick process that takes just a few mouse clicks The summary view of the Annotations window is designed specifically for working with IHC digital slides to provide a quick way to mark tumor regions and analyze them in one simple step To open the Annotations window in summary view 1 Identify a digital slide in Spectrum for which stain body site slide specific processing has been defined 2 From the Spectrum page open the digital slide in ImageScope by clicking its thumbnail The Annotations window in summary view appears If the window does not look like this click the Summary button to return the Annotations window to the summary view ae ee E EEE i PE G SE IHC HER2 Breast Da
24. ge Analysis User s Guide A Troubleshooting This appendix provides tips on identifying problems with glass slides that may contribute to unsatisfactory analysis results In Intended Use on page 2 we discussed the importance of understanding algorithm parameters so that you can fine tune them so the analysis provides the results you expect and want Even after adjusting algorithm parameters a number of factors can arise that may cause the algorithm to yield unsatisfactory results for your application Detection of these conditions must be done by a trained expert user who can identify these situations and take the appropriate corrective action In some cases the appropriate action may be to mark the glass slide as defective In other cases it may be that new tuning of the algorithm input parameters is required or the staining preparation process must be repeated This appendix contains a partial list of conditions that may result in unsatisfactory analysis results Problem Cause Effect Corrective Action Defective Broken slide Blurry image and or You should reject the slide artifacts at crack slide Air pockets under Image very blurry objects You can exclude these coverslip too light and not easily areas from analysis by identifiable The algorithm using the ImageScope will likely miss information negative pen in this area annotation tools Pen marks Areas will be dark and will You can exclude these obscure
25. ko TT Caras O Selected Annotation Current Screen Result Slide Region gt 3 2 1 0 Cells The algorithm appropriate for this type of slide is listed in the drop down box You can select another algorithm if you wish from that box From this window you can draw annotations to identify areas to analyze and run the analysis all in one easy step For details on using the Annotations summary view window see the Digital IHC User s Guide Other Options m To navigate between annotations you have drawn use the numbered buttons or arrow keys As you draw annotations the buttons at the top of the window display a number for each annotation When you select an annotation in this way that annotation is centered in the ImageScope window 4 Aperio Image Analysis User s Guide Chapter 1 Introduction O pero m Tosee a report image you have selected select Report Image from the drop down list m To create an annotation that will not be used for analysis for example a ruler or arrow select Annotations from the drop down list before drawing Aperio Image Analysis User s Guide 5 O pero Chapter 1 Introduction 6 Aperio Image Analysis User s Guide 2 Algorithm Installation The instructions in this section apply to all Aperio algorithms If you purchased an algorithm when you purchased a ScanScope the algorithm may already be installed on your ScanScope server In this case
26. l 44 0 1934 733679 Email Email europesupport aperio com EXE Tel 81 3 3259 5255 Fax 81 3 3259 5256 Customer Service Email asiainfo aperio com Technical Support Email asiasupport aperio com ii Aperio Image Analysis User s Guide Contents CHAPTER 1 INTRODUCTION cccececcececeececeececeeeeceaceceneeceaeesueeeseaeaeeeeaseaeaneneaes 1 Aperio AlgorithiMS L ssisasaiasn ksnsasoasssstssas k sskss sasas os k ke se k e k i ki 1 PreregUISit S si uiuieis esi aaa asa eks a i ai k k o k i k iii 2 FDA Cleared Image Analysis Algorithms seeseesesesesesresesseseseseeseseeseseseseeeeseseseeses 2 Init nid d WS ese casscscesccncccssanecacasestegsnsceccesctaaceaceessacccesencesaceesbet Aa aaa kak ai a ii ossis 3 IHC Quick Atal ysis Lsssaksiniasakssisskss iki s sss k sksksks asaks i ks as ae a i ss e k vesion 3 Slide Specific PrOCeSSING RR 3 Other Opt Ons sikna i k i i a E NEE 4 CHAPTER 2 ALGORITHM INSTALLATION ccecececcucvecececescecuscecveceeneuavecuneansneess 7 Where to Install the Algorithm sesesseseesesesesessereeseseseseeseseesesesesnesereeseseseseesesesesseses 7 CHAPTER 3 OPENING A DIGITAL SLIDE FOR ANALYSIS 2cscesceceeeseececeeaeeeseeeearees 9 About ImageScope ci cccsicsissicccssccssccsccatsscsssocassccasseosvascansesvnsensosddvseacseusse sab i cotnas tia 9 Accessing a Digital Slide in Spectrum ssssseeseresesrererceresesrseeserreseseseeseseeeeresesnssee 10 Opening a Local Digital Slide
27. l slides on an ImageServer Aperio Image Analysis User s Guide 35 O pero Chapter 6 Running the Analysis 36 Aperio Image Analysis User s Guide Exporting Results This chapter discusses how to export analysis results as text or Excel spreadsheet files Algorithm analysis results are stored in an annotation layer so you may want to export that information into a text file to include it in a report or to chart the information in a spreadsheet program To see the numerical results of the analysis 1 Go to the ImageScope View menu and select Annotations The Annotations window appears with the results displayed Annotations Detailed View E3 FIRE B Bl Layer 2 gt Algorithm Positive Pixel Count Region Length um Area um2 Text N PPC Dr Beth Edward 8 1 EES a _ Date 2008 11 06 StartTime 04 39 44 PM EndTime 04 39 45 PM Status StatusDescription Nwp Number of Weak Positive Np Number of Positive Nsp Number of Strong Positive lwp Total Intensity of Weak Positive Ip Total Intensity of Positive Aperio Image Analysis User s Guide 37 O pero Cc Chapter 7 Exporting Results Exporting Results as Text To export the text of the Layer Attributes pane to a text file On the Layer Attributes pane click al You will be asked to specify the name and location of the text file to be created This text file is a tab delimited file that can be imported into a spreadsheet program
28. lide cell Staining is not For nuclear analysis Prepare new slide specific to the significant cytoplasmic features being staining may cause cells to analyzed be misidentified 40 Aperio Image Analysis User s Guide algorithm installation 7 algorithm macro 21 algorithm tuning window 28 analysis 31 creating new macro 22 saving macro 26 testing modifying macros 27 annotations exporting 38 measuring 19 viewing 19 Annotations window detailed view 3 summary view 3 Aperio release requirements 2 batch analysis 33 Colocalization algorithm 2 Color Deconvolution algorithm 2 creating new algorithm macro 22 digital slide 1 analyzing 31 opening in Spectrum 10 opening local 12 opening remote 14 exporting results 38 Aperio Image Analysis User s Guide Index as spreadsheet 38 as text 38 FDA clearance 2 THC analysis 3 ImageScope 1 advanced features 9 drawing tools 18 installation 7 intended use 3 introduction 1 IO 9 macro 21 creating new 22 saving 26 monitor reguirements 2 opening digital slides 12 14 opening remote digital slide 14 Positive Pixel Count algorithm 1 prereguisites 2 Rare Event Detection algorithm 2 registering macros on Spectrum 26 running the algorithm 31 selecting areas to analyze 18 slide specific processing 3 troubleshooting 39 4 d perio Aperio Image Analysis User s Guide MAN 0013 Revision C
29. n ImageScope viewing window C Images 1225387891_1 341 3003HER2 svs Aperio Image Analysis User s Guide 17 Papero Chapter 4 Selecting Areas to Analyze 18 2 Now you can use the ImageScope drawing tools to select or exclude areas to analyze For example in the image below we used the following tools on the ImageScope toolbar 4 Freehand pen Use to draw a free form area of interest Negative freehand pen Use to draw an area to exc ude from the 6 analysis Note that you can use this in combination with the other drawing tools to first select an area of interest and then exclude areas within the selected area that you do not want to analyze Rectangle tool Draws a rectangular area If you want to select a P square hold down the Shift key while drawing If you have defined a fixed size for annotations hold down the Control key while you use the drawing tool to draw an annotation of that predefined size See the ImageScope User s Guide for details on this feature Freehand negative pen Freehand negative pen mai 3 To see information about the annotations you have drawn go to the ImageScope View menu and select Annotations Annotations Detailed View Cammer JIE E Layer Attributes E E Layer Regions X 6 J Description Region Length um Area um2 Text 1 336 1 7059 2 157 8 us Aperio Image Analysis
30. nd the documentation for the algorithm you are using To see the numerical results of the analysis 1 Go to the ImageScope View menu and select Annotations Annotations Detailed View Result 3 Nsr La Nsp Nwp Np Nsp gt Nwp Number of a Weak Positive Np Number of Positive Nsp Number of Strong Positive wp Total Intensity of Weak Positive p Total Intensity of Positive sp Total Intensity of EE Strong Positive avg 109 332 Iwp lp lsp Nwp Ne 0 435087 wavg 135 961 lwp p Nwp Np Nn Number of Negative n Total Intensity of E Negative NTotal Total 22942 amp C summary m B Layer Regions gt 2 ES Region Length um Area um2 Test MESES Note the color shown next to each parameter that is the color for that result shown in the mark up image Keep adjusting the algorithm parameters until you are satisfied with the results Then save the macro see the next section Aperio Image Analysis User s Guide 25 O pero Chapter 5 Registering the Algorithm on Spectrum Saving and Registering the Macro on Spectrum After you have created the macro save it to register it on Spectrum 1 Onthe Analysis window click Save Macro to save the macro and register it on Spectrum Macro on server spectrum Positive Pixel Count v9 Parameters View Width 1000 a View Height 1000 Overlap Size 0 Image Zoom 1 Markup
31. pe oo Ss WebScope view ImageScope WebScope 7 ae 1225387893_1481_3003Ki67 svs 225387894 1368 3005ER svs 1225387895 1371 3005HE svs 4000 x 3000 20X Bs es EA a 1225387903 rat liver tox jpg 1225387897 1370 3005HER2 svs 1225387903 1369 3005PR svs 385 x 227 1225387912 muret 001 svs 4000 x 3000 20X 4000 x 3000 20X view ImageScope WebScope 4000 x 3000 20X view ImageScope WebScope view ImageScope WebScope view ImageScope WebScope 6 Select a digital slide by clicking ImageScope beneath an image suman ON For More Information For more information on opening a digital slide in ImageScope see the ImageScope User s Guide Aperio Image Analysis User s Guide 15 O pero Chapter 3 Opening a Digital Slide for Analysis 16 Aperio Image Analysis User s Guide 4 Selecting Areas to Analyze You can analyze an entire digital slide or just selected areas This chapter discusses how to select areas of the digital slide to analyze Whether you decide to use an algorithm directly in ImageScope or wish to use Spectrum s batch analysis feature you may want to first use ImageScope to select areas of interest in the digital slide to analyze 1 Open a digital slide in ImageScope See Chapter 3 Opening a Digital Slide for Analysis on page 9 for instructions on opening a digital slide in ImageScope After opening the digital slide you see the mai
32. s the analysis results are stored on your workstation not in the Spectrum database m Analyzing remote digital slides If you will be using the algorithm to analyze remote digital slides that is digital slides that are located on your Aperio ImageServer by opening the digital slide directly on the Aperio Image Analysis User s Guide Z O pero Chapter 2 Algorithm Installation ImageServer install the algorithm on the DSR the server or computers connected to the server on which A AFClient is installed m Creating analysis macros No matter where you are going to analyze digital slides if you are going to create an algorithm macro you need to install the algorithm on your local workstation as well as on the locations discussed above You will need to create and save an algorithm macro to analyze digital slides on Spectrum 8 Aperio Image Analysis User s Guide 3 Opening a Digital Slide for Analysis Before you can analyze a digital slide you will open it for viewing in ImageScope You can either open the slide in Spectrum or directly from ImageScope There are several different ways to open a digital slide for viewing depending on whether the digital slide is local or remote m Local digital slides reside on your workstation or on your local network where you can access them in ImageScope using Microsoft file sharing m Remote digital slides reside on a remote server where you can access them directly in ImageS
33. s 37 Exporting Results aS Text sccicssssssscnsstscsesasescssvdenssssessessaseasnssssssesosassscesssssssosssonascsensess 38 Exporting Results to a Spreadsheet csssesssscsssssssssssssssscsssssessssssessssssesssesseeess 38 APPENDIX A TROUBLESHOOTING c cececseeeeaeacacecececucncucncuceceratatatansceeeseeaes 39 INDEX 2555 is aa is nro a E Ss 41 Aperio Image Analysis User s Guide iii O pero Contents iv Aperio Image Analysis User s Guide Ses This user guide discusses using Aperio image analysis algorithms to analyze digital slides Aperio s image analysis algorithms are FDA cleared for specific clinical applications and are intended for research use for other applications Please see the Intended Use section of the user guides for the specific cleared applications you wish to use for details on in vitro diagnostic use 1 Introduction This chapter introduces Aperio image analysis algorithms The process of analyzing digital images begins with the digital slide a digital image created by scanning glass slides Using Aperio image analysis algorithms to analyze digital slides provides several benefits Increases productivity Image analysis automates repetitive tasks Improves healthcare Analyzing digital slides helps you to examine slide staining to find patterns that will tell you more about the slide Using an algorithm to look for these patterns provides precise guantitative data that i
34. s accurate and repeatable Development of new computer based methods Image analysis helps you answer questions that are beyond the capabilities of manual microscopy such as What is the significance of multiple stains at the cell level and colocalization of stains Workflow integration The Spectrum digital pathology information management software suite integrates image analysis seamlessly into your digital pathology workflow requiring no additional work by the lab or pathologist With the click of a button the algorithm is executed while you review the digital slide Aperio Algorithms Analyzing a digital slide is done by applying algorithms directly to the digital slide or selected regions of the digital slide after opening the digital slide in ImageScope Using image analysis algorithms can answer such questions as Where and how much staining is there Where and how many objects for example tumor cells are there How much staining is there on different objects for example cell nuclei Several algorithms developed for specific applications are available including Positive Pixel Count This algorithm quantifies the area and intensities of two stains based on user defined values for color and intensity thresholds Aperio Image Analysis User s Guide Chapter 1 Introduction m Color Deconvolution The professional version of the positive pixel count algorithm Color Deconvolution accurately separate
35. s stains resolving multi stain colocalization problems This algorithm separates the image into three channels corresponding to the actual colors of the stains used This allows the pathologist to accurately measure the area for each stain separately even when the stains are superimposed at the same location m Colocalization The Colocalization algorithm is an extension of the Color Deconvolution algorithm quantifying the area and intensities of colocalized markers m Rare Event Detection The rare event detection algorithm is often used to detect micrometastasis of tumor cells found in circulating blood The Positive Pixel Count algorithm is provided for free with Aperio software Other algorithms are available from Aperio for a fee Algorithms have also been developed by third parties and tools are available from Aperio for creating your own algorithms contact Aperio for details These algorithms all have control parameters for example intensity and hue settings that allow the algorithm to be tailored to your specific needs Prerequisites The examples in this guide assume you are using Aperio Release 10 or later Because Aperio digital slides are by design high resolution and information rich for best results you should use a high quality monitor to view them Make sure the monitor is at the proper viewing height and in a room with appropriate lighting We recommend any high quality LCD monitor meeting the following
36. slide under the window 8 To see the results of the analysis when you change the parameters simply change the parameters in the algorithm parameters window and the Algorithm Tuning window updates to show the analysis using the new parameters Every time the Algorithm Tuning window updates the analysis a new mark up image appears in the window and the numeric data in the Annotations window changes to reflect the new analysis Aperio Image Analysis User s Guide 6 Running the Analysis This chapter discusses how to use an algorithm in Spectrum to analyze a digital slide This is a general discussion which applies to all algorithms For details on using a specific algorithm refer to the user guide for that algorithm Once you have identified the digital slide or slides you want to analyze you can analyze them together in a Spectrum batch analysis or you can open each one in ImageScope and analyze the digital slides one at a time Analyzing in ImageScope You can either analyze the entire digital slide or only selected portions of it see the previous section for information on selected areas of analysis To analyze a digital slide directly in ImageScope 1 Open a digital slide in ImageScope See Accessing a Digital Slide in Spectrum on page 10 for instructions on opening a digital slide in ImageScope from within Spectrum For details on opening a digital slide that resides on your workstation
37. t needs to log into To analyze digital slides and to create Spectrum and navigate to the case and the specimen that shows the list of its and change associated digital slides algorithm macros the user role you log Please ask your Spectrum administrator for the Spectrum web address your in with must have logon name and a password the following command permissions 1 Open Microsoft Internet Explorer or another web viewer like Firefox enabled and enter the Spectrum web address You see a login page Analysis Macros m Add Edi Login Required Images Analyze Contact the Username Spectrum I administrator if you are not sure if your user role allows these actions Password 2 Log onto Spectrum by entering your user name and password The password is case sensitive 3 If more than one user role is assigned to your login you are asked to choose which user role you want to log in with Please Choose a Role Lab Supervisor Lab supervisor with administrative privileges Pathologist Pathologist 10 Aperio Image Analysis User s Guide O pero Chapter 3 Opening a Digital Slide for Analysis After logging in you see the Spectrum main page Spectrum Papero User Dr Beth Edwards Role Pathologist Cases Specimens Digital Slides TMA Blocks Analysis Administrative Help Font Size Log off Last Login Time 2008 11 06 15 54 17 E Cases List
38. t v9 Parameters ECA Np Number of Weak Positive Np Number of Positive Nsp Number of Strong Positive lwp Total Intensity of Weak Positive Ip Total Intensity of Positive Isp Total Intensity of Strong Positive lav Iwp lp lsp Nwp Np Nsp Nsr Nsp Nwp Np Nsp Iwavg Iwp lp Nwp Np Nn Number of Negative In Total Intensity of Negative v Inputs Outputs Region of Analysis Current Screen Entire image Selected Annotation Layer Z Generate aro mage Ready 8 Click Run to test the macro on the digital slide p Instead of clicking When the analysis is complete the markup image in the main ImageScope Run you can click window shows the results the Tune button to open a tuning window in which you can see instant feedback on parameter changes See Using the Tuning Window to Test Algorithm Parameters at the end of this chapter for details In this example we drew a rectangle to select the area we wanted to analyze but also used the negative freeform pen to exclude areas within the rectangle from analysis See Chapter 4 Selecting Areas to Analyze on page 17 for information on using the ImageScope drawing tools 24 Aperio Image Analysis User s Guide Chapter 5 Registering the Algorithm on Spectrum O pero For information on the meaning of the colors shown in the mark up image see the numerical results displayed in the Annotations window a
39. the ScanScope scanner Educators will use Aperio software to view and modify digital slides in Composite WebSlide CWS format Aperio products are FDA cleared for specific clinical applications and are intended for research use for other applications For clearance updates visit www aperio com Trademarks and Patents ScanScope is a registered trademark and ImageServer TMALab ImageScope and Spectrum are trademarks of Aperio Technologies Inc All other trade names and trademarks are the property of their respective holders Aperio products are protected by U S Patents 6 711 283 6 917 696 7 035 478 7 116 440 7 428 324 7 457 446 7 463 761 7 502 519 7 518 652 and licensed under one or more of the following U S Patents 6 101 265 6 272 235 6 522 774 6 775 402 6 396 941 6 674 881 6 226 392 6 404 906 6 674 884 and 6 466 690 Contact Information Headquarters Europe Office Asia Office Aperio Technologies Inc Aperio UK Ltd Aperio Technologies KK 1360 Park Center Drive The Vineyard UZ Building 5F Vista CA 92081 Axbridge 3 3 17 Surugadai United States Somerset BS26 2AN UK Kanda Chiyoda ku Tokyo Japan 101 0062 United States of America Tel 866 478 4111 toll free Fax 760 539 1116 Customer Service Tel 866 478 4111 toll free Technical Support Tel 866 478 3999 toll free Email Email support aperio com Europe Tel 44 0 1934 733679 Fax 44 0 1934 733660 Customer Service amp Technical Support Te
40. the algorithm installer program will also be located on your ScanScope server in C AperioInstall Or you may have received information from Tech Support on where to download the algorithm installer so you can install the algorithm yourself Installing an algorithm is a simple matter of using Windows Explorer to navigate to the location of the algorithm installer file and double clicking the file name Follow the instructions of the algorithm installer clicking Next when instructed to do so Where to Install the Algorithm Where you install the algorithm depends on how you are going to be analyzing digital slides m Analyzing digital slides through Spectrum If you are going to be using Spectrum to analyze a single digital slide or a batch of digital slides you will need to install the algorithm on both your local workstation and on DSR Digital Slide Repository which is the server or computers connected to the server on which AAFClient is installed You will also need to register the algorithm macro on Spectrum See Chapter 5 Registering the Algorithm on Spectrum on page 21 for details m Analyzing local digital slides If you will be using the algorithm to analyze local digital slides that is digital slides that are located on your workstation or on your network where they can be accessed by Microsoft file sharing install the algorithm on your workstation However be aware that when analyzing local digital slide
41. underlying areas from analysis by information using the ImageScope negative pen annotation tool Wrong Algorithm tuned The algorithm analysis will Choose a different tissue type for one type of still give results but the algorithm or input tissue for results will likely be parameter set example breast meaningless cancer and operator runs it on another type of tissue for example liver Aperio Image Analysis User s Guide 39 O pero Appendix A Troubleshooting Problem Cause Effect Corrective Action Wrong For nuclear Nuclear counts will be too Operator must regions analysis stromal large recognize these areas designated and lymphocytes and annotate them to for analysis were included in exclude them from the designated analysis regions Bad Tissue sections Image will be blurry all Prepare new slide histology too thick over preparation Folds in tissue Blurry areas and cells that are superimposed on each other Prepare new slide or annotate these areas to exclude them from analysis Variations Staining is too Cells are not solidly Adjust input in staining light stained and the algorithm parameters if possible process may over count by or prepare a new slide subdividing single cells into multiple cells Staining is too Cells which are close Adjust input dark together become merged parameters if possible and counted as a single or prepare a new s
42. uning window gives you a way to guickly see the results of p analyzing a different area of an image or to test changes you make to the Tinese insirucions discuss using the tuning window when opening an image from Spectrum algorithm parameters To use the algorithm tuning window 1 In Spectrum open a digital slide in ImageScope You can also use the algorithm tuning window when you 2 In ImageScope go to the View menu and select Annotations to open the Annotations window This window is where your numeric algorithm open a local image analysis results appear just remeraben thar in this case analysis 3 Go to the View menu and select Analysis reculits wil ge sevet locally not in the You see the Algorithm Server Job window where you can select the SEL For details on analyzing local images see the ImageScope User s Guide algorithm macro you want to use Algorithm Server Job Server spectrum Select Algorithm Macro Macro Name Rare Event Detection Colocalization Version 9 PPC Dr Beth Edwards IHC HER2 Breast Dako Generate Markup Image Incremental Processing Region of Analysis Selected Annotation O Entire Image 28 Aperio Image Analysis User s Guide Chapter 5 Registering the Algorithm on Spectrum Oper 4 Select the macro you want to use and click Test You see the algorithm parameter window Macro on server spectrum Positive Pixel Count v9 Parameters View Width 1000 A
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