ImmunoScreener Module 1.12 User's Guide March 03, 2009
Contents
1. 10301 07 _ER_ 7 10301 07_HER2_ 10301 07_HE_ 1 10301 07_Ki 67_ 10301 07 _PR7 4 40 ER 4 40 Her2 4 40 HE 4 40 Ki67 f 4 40 PRi i 5 N 9 5 gt avs 4 i a gt x gt 44 x AJ HistoQuant a i t S SA J O is O cs March 4 2009 3DHISTECH Ltd 29 36 6 Scoring Slides in an ImmunoScreener Project ImmunoScreener Module 1 12 User s Guide 6 Scoring Slides in an ImmunoScreener Project 6 1 Scoring Options e From the gallery e Sequential scoring e Per slide 6 1 1 Scoring in the ImmunoScreener Gallery 1 Open the ImmunoScreener project 2 Click Gallery in the project menu and display the thumbnails 3 Score the grid fields 2 Gallery Order by Primary Field Filters Secondary Disabled E 00A 10301 07_ER_I 1 1 OFERI 7 10301 07_HER2_ 1 1 0fHer2 10301 07 _HE 1 141 OfHEI s 10301 07 _Ki 67_ 7 141 Of Ki67 7 1 10301 07_PR_1 11 OFPRI T Slide a o 10301 07_ER_ 10301 07_HER2_ 10301 07 _HE 1 1 M anm nr vien Grid O cs Mo H1 M2 ma Field Moo Mio M20 ian Stain a ER HE M Her2 a vior Score HistoQuant O Mik tee e ee e ee e e gasa 10301 07_ER1 2 20 ERI T a 10301 07_ER_ S SOFERI s 10301 07_ER_I 4 40 ERI 7 ah 3 ae2. Pseudo Color Show Grid Definition Slide Alignment Reference Slide 10301 07 _ER_I Actual Slide 10301 07 _HER2_ Slide Operation B Progress v 10301 07_HE_I 1 10301 07 _Ki 67_ 10301 07 _PR_I Next Slide Finish Save grid s to slide s Tor amp Grid Fitting Slide Zoom 44 W o _ Grid Show Color Iii m Opacity 33 y Pseudo Color Show Grid Definition Slide Alignment Reference Slide 10301 07_ER_ Actual Slide 10301 07_HER2_ Slide Operation Progress 10301 07_HER2_ 10301 07_HE_I 1 10301 07_Ki 67_I 10301 07_PR_I Next Slide Finish Save grid s to slide s 3 10 Grid fitting Go through all slides pairwise and align them onto each other Move left mouse button or rotate right mouse button the slides so that the grids cover exactly the same area on the other March 4 2009 3DHISTECH Ltd 20 36 ImmunoScreener Module 1 12 User s Guide 3 10 Grid fitting Using Pseudo Color option helps you to better adjust slides m Grid Fitting Slide Zoom Grid Show Color E E Opacity 61 G Pseudo Color Show Grid Definition Slide Alignment Reference Slide Actual Slide Slide Operation Next Slide Finish
3. 4 2009 3DHISTECH Ltd 31 36 ImmunoScreener Module 1 12 User s Guide 6 1 Scoring Options amp ImmunoScreener Project User1 Manage a Grid Fitting Gallery E Export Marked Stain Definition positive 1 Open Slide negative 1 Grid Fitting Reset Score 10301 10301 07_HE 10301 07 Ki Renovasi 07_HER2 1 671 10301 07 _ER estrogen Her2 HeMa ki 67 HistoQuant 6 2 Marking Slides You can flag slides in ImmunoScreener projects for example to mark the ones that you have already scored 1 Start the ImmunoScreener project 2 Right click the slide that you want to flag and select Marked from the shortcut menu March 4 2009 3DHISTECH Ltd 32 36 ImmunoScreener Module 1 12 User s Guide 7 Exporting Information from an ImmunoScreener Project 7 Exporting Information from an ImmunoScreener Project 7 1 Exporting Data from an ImmunoScreener Project to a CSV File In the export menu you can export your added values and scores to a CSV comma sep arated value file that you can open in a spreadsheet or import into a database You can export individual grid field values data about this project or you can export the data from this project into a long term CSV file a cumulative data file e Open the ImmunoScreener project e From the menu select Export and select the data you want to export from the ImmunoScreener project o Full export data from the ImmunoSc
4. HistoQuant annotations inside fields Section 3 11 Score fields in ImmunoScreener Gallery Section 6 1 1 Consolidate scores Section 8 Export picture Gallery Export data to CSV Section 7 3 Section 7 1 For instructions on how to consolidate scores see section 8 March 4 2009 3DHISTECH Ltd 8 36 ImmunoScreener Module 1 12 User s Guide 1 2 2 Grids 1 2 Overview of the ImmunoScreener Module 1 12 In routine pathology an ImmunoScreener project contains slides from the same speci men In such cases grids are typically put on the same area on each slide for example on a group of cancer cells Typically used grid setups n x m grid You can put a grid on the area of interest and obtain data about smaller areas grid fields You can fit grids on the same area on several slides ImmunoScreener helps you rotate and align the grid throughout several cuts from the same specimen This allows you to obtain a report at object level for example about the nuclei found in the field and also at the level of the field for example the number of pos itive cells compared to the number of negative cells You can also knock out fields which are not interesting or not needed for the evaluation for example no tumor cells in it 1 x 1 grid For better sampling from the specimen if one n x m grid is too large Several grids You can
5. module note that only captions are ex ported to the CSV output file Annotation descriptions are for internal use in MIRAX Viewer and HistoQuant 3 Repeat step 2 for each area you want to run the algorithm on You will be able to run other algorithms on these annotations March 4 2009 3DHISTECH Ltd 22 36 ImmunoScreener Module 1 12 User s Guide 4 Handling an ImmunoScreener Project 4 Handling an ImmunoScreener Project 4 1 Options in the ImmunoScreener Project You can manage slides and stains perform grid fitting open gallery and export options from ImmunoScreener Toolbar or by directly choosing from the options by right click ing on the slide You can also mark slides give a final score or open the slide or the HistoQuant module B ImmunoScreener Project User1 Manage Fa Grid Fitting EJ Gallery D Export l Marked Stain Definition estrogen Final Score gt HeMa Her2 ki 67 p53 Open Slide 10301 10301 07 _HE J yews 10301 07_ER_ O7_HER2_ Grid Fitting Remove Silde estrogen Her2 HeMa en ee o progesteron HistoQuant 4 2 Modifying an ImmunoScreener Project i Important If you modify an ImmunoScreener project the scores related to the slide stain or grid are lost for all users who have already submitted scores to the project March 4 2009 3DHISTECH Ltd 23 36 ImmunoScreener Module 1 12 User s Guide 4 2 Modifying an ImmunoScreener Project Most of the
6. settings of an ImmunoScreener project can be modified In Single user mode the user can modify the project but in Multi user mode only the Consolidator user can modify ImmunoScreener projects e slides that are included in the project add or delete slides e stains that are used in the project add or delete stains e number of grids that are used in the project add or delete grids e grid layout modify the size of a grid change the number of rows or columns knock out fields or put fields back into the grid 4 3 Adding or Removing Slides The way of adding or removing slides from the ImmunoScreener project 1 Start the ImmunoScreener project 2 Select Manage gt Add Remove Slide s 3 Add or remove slides as needed a Browse for slides to add b Clear the checkbox of the slide s that you want to remove 4 Click OK to update the ImmunoScreener project The way of removing a slide quickly 1 Start the ImmunoScreener project 2 Right click the slide to be removed and select Remove Slide 4 4 Adding or Removing Stains 1 Start the ImmunoScreener project 2 Select Manage gt Stain Manager 3 Add or remove stains as needed and click OK March 4 2009 3DHISTECH Ltd 24 36 ImmunoScreener Module 1 12 User s Guide 4 5 Changing the Grid 4 5 Changing the Grid i Important In multi user projects only the Consolidator user can fit or modify grids 1 Start the ImmunoScreener project 2 Star
7. AN AARNEN AENEA AD ARAE ERN EEES 11 2 3 Installing the Application Bundle ssssssssssssrssssssrrrrsssrrrrrrnsnrrrrnnnnnnnnrnrnrrrrrrrrrrnenne 11 3 Creating an Immu noScreener PrOjeCt cece ninda i paiia 12 3 1 Create New ImmunoScreener PrOjeCt c cece ee nee eee 12 3 2 Name the New ImmunoScreener Project ccceee eee ee ee eee ee eases eens eats eee ee eee eee eae 13 3 3 Define at Least One User on User Management SCreen eceeeee eect ee eee eee eee eaeees 13 3 4 Project Dal ieiecritgeeraierc ere peveteved weg chet E R E Ai 13 3 5 Slide Selections nrasane aa eka cea nee Beene 2d ea eens be ee aa Vea ea re 14 320 Stain EISU scassuccetaie tice E E EE E ede E E E EE eas E E 15 3 7 SCOPING SETUD snis ne tiecnie abcde ia dy waitin ce eda csi bia baad eds davies Ab teie de i einds edb cane de dweweteawend es 16 3 8 Stalin DEFMITON esis icc dinates ia E Eh dea deeded sods AEE shee de es Aad ees 17 3 9 Grid DEFINITION sdssaisenatsiinendcetasenssoneneydcs eE EIn Eri DETE DEDEN EED E AARETE Tiii h NOSED 18 310 Grid PCN sits iini a aaee oao a 20 3 11 Creating Annotations Inside an ImmunoScreener Grid ssssssssssrrrrrrrsserrrrrrrrrrrssns 22 4 Handling an ImmunoScreener Project ss sssssssrrsssrrnerrnnurrnnsrrnnurrnnurnnnurnnnunnnnunnnnunn nunne 23 4 1 Options in the ImmunoScreener Project ccceee cece eee e eee eee eee e teens eee ee teeta eee eae 23 4 2 Modifying an ImmunoScreener Project cccceee
8. E_l 1 10301 07_Ki 67_1 Secondary 2120 Her21 1 2 20 HE f 21201K67 1 1 Filters Slide mj 10301 07 ER Z 10301 07 _HER2 I 10301 07 _HE 1 annm nT vie 1 cs O 6 amp 9 ewe e e lx l e os Alcs a 0 ics 10301 07_ER1 10301 07_HER21 10301 07_HEJ 17 10301 07 _Ki 67_17 10301 07_PRI SIS O ER f 3430 Her2i SISOFHE 3130 1KIB7 7 1 SIZ OIPRI 7 0 1 2 4 HRS 8 1 10301 07 HER2I 10301 07 HEJM 10301 07 K671 10301 07 PR ste 41401Her2i 1 41401HEF 1 41401KB71 7 4 40 PRI 7 cs TERA i March 4 2009 3DHISTECH Ltd 27 36 ImmunoScreener Module 1 12 User s Guide 5 2 Display Options of ImmunoScreener Gallery You can also enlarge the preview objects within their frames by using Cell Fitting but the size of the gallery and the zoom will not change March 4 2009 Zoom T B Order by Primary Field Filters Slide Z 10301 07_HER2_ 10301 07_HE 1 10301 07_Ki 67_ 10301 07_PR_I Secondary Disabled Z 10301 07 ERI HistoQuant es ese 40301 07_ER_1 0 of 10301 07_ER1 1 o A 10301 07 _HER2 7 odt 10301 07 _HER2_ 107 10301 07 _HE 1 7 007 10301 07 _HE 1 7 107 10301 07 _Ki 67 17 007 10301 07_E
9. Keh 10301 07 _HER2_ 2 20 sHer2i 7 i 10301 07_HER2_ 3 30 Her2s A 10301 O07_HER2_ 4 40 Her2 f 10301 07 _HE 1 1 2420 E 4 10301 07_HE_l 1 7 SI3OfHE s 10301 07 _HE 1 4140i EF t 10301 07 _Ki 67_1 7 2 20 Ki67 7 7 negative 0 10301 07 PR 2 20 PRi T positive 1 Reset Score Open Slide Save Image 10301 07 _Ki 67_ 4 40 fKIB7 i i DN As 10301 07 _PR 4i40IPRI T e To change the order of the display before you start scoring change the grouping settings in the Order by frame March 4 2009 3DHISTECH Ltd 30 36 ImmunoScreener Module 1 12 User s Guide 6 1 Scoring Options e To score the annotations in the order they are displayed in the gallery start se quential scoring e To score the annotations one by one right click each thumbnail and select the score from the shortcut menu 6 1 2 Sequential Scoring Sequential scoring is a comfortable way to go through and score each field of the grids You can launch this option by clicking in the Gallery Only one field appears in the window for evaluation and by clicking the score at the bottom toolbar the next field appears au tomatically 10301 07_ER_ 10 Key 2 negative 6 1 3 Scoring a Single Slide 1 Open the ImmunoScreener project 2 Right click the slide that you want to score select Final Score from the short cut menu and select the score March
10. LnmunoScreener project wizard a User Management Slide Selection Project Data Path 0 Slide Selection 10301 07_ER_I i 10301 07 _HER2_l Scoring Setup 10301 07_HE_I 1 Stain Definition 10301 07_Ki 67_I 10301 07_PR_I Stain List lt Previous Next gt Finish allows you to view the thumbnails of the slides allows you to view the list of the slides March 4 2009 3DHISTECH Ltd 14 36 ImmunoScreener Module 1 12 User s Guide 3 6 Stain List 3 6 Stain List Specify which markers are used in the actual project Use checkboxes to add markers to the marker list You can also add new stains here ImmunoScreener Project Wizard Welcome to the ImmunoScreener project wizard a User Management Stain List Project Data Stored stain list Slide Selection estrogen estrogen Stain List HeMa HeMa Her2 Scoring Setup me ki 67 Stain Definition p53 pas progesteron Active stain list New stain Remove stain March 4 2009 3DHISTECH Ltd 15 36 ImmunoScreener Module 1 12 User s Guide 3 7 Scoring Setup 3 7 Scoring Setup Create a scoring scheme for the stains You can assign a different scheme numeric value and color to each stain You can also speed up scheme generation by cloning or reusing existing schemes You can also use the available scoring schemes If you modify them for a stain the scor ing scheme is saved with the changes for this
11. R1 2 0t 10301 07 _HER2_ 207 Fa 10301 07_HER2_1 307 10301 07_HER21 407 10301 07 _HE 1 1 207 a 10301 07 _HE 1 307 e 10301 07 _HE 1 1 407 3DHISTECH Ltd 10301 07 _PR170 E 10301 07 _PR71 0r 40301 07_PR_ 2 0t 10301 07 PR 1 3 o 10301 07 _PR174 0t 28 36 ImmunoScreener Module 1 12 User s Guide 5 3 Setting Which Labels Are Visible in the HTML Export 5 3 Setting Which Labels Are Visible in the HTML Export You can change the content of the captions visible above the fields in the Immuno Screener Gallery For example you might want to show the slide number and the grid field number in the caption of the thumbnails if you plan to export an HTML gallery from your ImmunoScreener project because this is the only way to show the scores in the output 10301 07_ERI 10301 07_HER21 10301 07 HE 14 10301 07_Ki 67_I 11 OFERI 7 111 Of Her2 7 11 OFHES f 1 10 67 7 Order by Primary Field vif Secondary Disabled 10301 07_ERI 10301 07_HER21 10301 07_HEI4 10301 07 _Ki 67_ 2 20 ER 7 2 20 Her2s 7 2 20 HEs f 2 20 Ki67 7 Tag Filters Slide m E 10301 07_ERI Z 10301 07_HER2_ Z 10301 07_HE_I 1 M anm nr vien t Grid oD mo m1 iG 10301 07_HER2_ 10301 07_HE_ 1 7 10301 07_Ki 67_ 3 30 Her2 f S SO HEI s 3 30 Ki67 f s reer O k Dee e eA e Ee e ol
12. Save grid s to slides Grid Fitting Slide Zoom Gid Show X Color E Opacity 61 9 Pseudo Color Show Grid Definition Slide Alignment Reference Slide 1 07_ER Actual Slide Slide Operation Progress C 10301 07 _Ki67_ E 10301 07_PR_ Next Slide Finish Save grid s to slide s March 4 2009 3DHISTECH Ltd 21 36 ImmunoScreener Module 1 12 User s Guide 3 10 Grid fitting Repeat these steps for each slide that you want to use in this ImmunoScreener project Save the grid to the slide if you want to further analyze annotations with HistoQuant Click Finish to create the ImmunoScreener project 3 11 Creating Annotations Inside an ImmunoScreener Grid ImmunoScreener grids are annotations that you create when you create the Immuno Screener project You can nevertheless use further annotations on the slides There might already be annotations on a slide or you might want to create HistoQuant anno tations that are smaller than the grid field If you have the optional HistoQuant module you can perform measurements on the HistoQuant annotations 1 Open the slide in MIRAX Viewer 2 Create the annotation on the area of your interest a Select the annotation type rectangle free hand or point and cover the area with the annotation b Add a caption to the annotation and enter a description If you are using the HistoQuant
13. Y Wie Measurement Visualization E School MIRAX Viewer With the ImmunoScreener module you can perform an immunohistochemical analysis on a slide set digitized with MIRAX scanners and stored on a local file system or on a MI RAX Slide Server March 4 2009 3DHISTECH Ltd 7 36 ImmunoScreener Module 1 12 User s Guide 1 2 Overview of the ImmunoScreener Module 1 12 1 2 Overview of the ImmunoScreener Module 1 12 ImmunoScreener supports decision making in targeted therapy or in marker validation It also makes your evaluations more reliable With ImmunoScreener you make subjec tive slide scoring more accurate and you make it measurable because you compare ar eas and scores on digitized MIRAX slides which is a more reliable method than analyzing the actual slides empirically under traditional microscopes 1 2 1 Workflow The following figure summarizes your workflow Create Immunoscreener project Section 3 1 Fit Grids Section 3 10 Create HistoQuant a annotations inside fields Section 3 11 J Y Score fields in ImmunoScreener Gallery Section 6 1 1 Export picture Gallery Export data to csv Section 7 3 Section 7 1 You can also use ImmunoScreener together with your colleagues In this case each team member scores the slides and then one team member consolidates the scores Create Immunoscreener project Fit Grids Section 3 1 Section 3 10 Create
14. cece eee eee eee eee eee eee eee eee eee eee 23 4 3 Adding or Removing SIideS cece vrenr eee rane rete Na eae 24 4 4 Adding or REMOVING StainS 0 cece eee ene eee eee EENE EEEN 24 455 Changing the Grids irera csea ra ie vada sens eves teed sda EEANN REEDENI ANE ENNEA NEE 25 5 Working with ImmunoScreener Gallery cccecece eee e eee eee eee eee eee eee eee ee 26 5 1 Enlarging the Preview WiNdOW cceee eect eee eee een een eee ene eee eee ents 26 March 4 2009 3DHISTECH Ltd 2 36 ImmunoScreener Module 1 12 User s Guide 5 2 Display Options of ImmunoScreener Gallery cceeeee cece eee eee eee ee eee eee ee eee eee eeaeas 26 5 3 Setting Which Labels Are Visible in the HTML Export ccceceeeeeeeeeeee teens teens teenies 29 6 Scoring Slides in an ImmunoScreener Project ceeceee eect e eee eee eee eee eee eee ee eeaee 30 6 1 SCOFMGOPUlONS acson serinin inann AE E E E EEE deri sake nantes 30 6 1 1 Scoring in the ImmunoScreener Gallery sssssssssssrrserrrssrrrnsnsrrrrrrrnnnununrnrnrnnnnn 30 6 1 2 Sequential SCOriNG issenensis nanara hee ENE 31 6 1 3 Scoring a Single Slide u csescceacsedesesereienssdsvsaaees weseab hans denthu TE 31 6 2 Marking Slide Sienai anaa tence aaa E tetera neduees sabes A E i 32 7 Exporting Information from an ImmunoScreener Project sssssssrrssrrrsrrrnsrnrrnrrrnnrrrrerrrns 33 7 1 Exporting Data from an ImmunoScreener Project to a CSV File assesecer
15. d 12 36 ImmunoScreener Module 1 12 User s Guide 3 2 Name the New ImmunoScreener Project 3 2 Name the New ImmunoScreener Project As it cannot be modified later be sure to incorporate all the necessary information into the name of the new project The ImmunoScreener Project will be located within the folder of its slides which can be visualized after pressing Update Tree in the Mirax Viewer screen 3 3 Define at Least One User on User Management Screen Enter a user name and ID who will score the slides If you need a multi user project you can add further users later on when the project has been created and you first start the project 3 4 Project Data You may add parameters and values to the project for example patient name s and the corresponding IDs or registry numbers if it is needed You may skip this option March 4 2009 3DHISTECH Ltd 13 36 ImmunoScreener Module 1 12 User s Guide 3 5 Slide Selection 3 5 Slide Selection You can see all slides in the actual folder Select or clear checkboxes to create the slide set that you need for this ImmunoScreener project For multiple selection you can select several slides at the same time with Shift Click and or Ctri Click This option is also valid for the further steps in the Wizard The slides that you leave out are not removed from the file system You can also add them or new ones to the project later ImmunoScreener Project Wizard i ay Welcome to the
16. eerrrrrrr 33 7 2 EXPOrting an ATMEL Fils isis ccssaiessentvauscadaaeasecesnans egbsveaaueabalesdeghtackteesateciesseasha n 33 723 EXPOMING an IMAQCssccccccsscarssseadexce ces ecveseve dees seus geve sens AAN ONEEN ANDER EA TA tees caverta 33 7 4 Exporting One Annotation as a Picture from an ImmunoScreener Gallery 055 34 8 Working with ImmunoScreener in Multi User Mode cceeeeeee eects eee ceases teens ee eeeeaeeeeaes 35 9 Using HistoQuant and ImmunoScreener Together cccceceeeeeeee eee eee eee e eee eee eee eae taeeees 36 March 4 2009 3DHISTECH Ltd 3 36 ImmunoScreener Module 1 12 User s Guide Disclaimer Disclaimer Copyright 2001 2008 3DHISTECH Ltd All rights reserved The following patents are pending for 3DHISTECH products W0O 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 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 3DHISTECH Ltd assumes no responsibility for the functionality and fault free condition of your application programs Workflows VBA macros C
17. ield in each grid on each slide and assigns it a score In a multi user ImmunoScreener project evaluators do not see each other s scores Field A cell of the grid that is fitted onto an area of interest on the virtual slide If you put a grid on slides from the same speci men you can analyze the marker expression of the same fragment immunostained for different antigens Immuno Screener projects allow you to correlate the different antigens and perform measurements for example with a separately available MIRAX Viewer module HistoQuant Grid A set of annotations used in ImmunoScreener They are inde pendent of other annotations for example HistoQuant annota tions that might be smaller than a grid field Unlike plain MIRAX annotations or HistoQuant annotations grids are not saved with the slides by default Grid informa tion is stored with the ImmunoScreener project where you created or modified them but you can also save them on the slides ImmunoScreener Gallery An ImmunoScreener gallery contains all fields from all grids from all slides in the project For example if you used a 2x3 grid and marked an area with the grid on 3 slides the gallery for this stain on this specimen contains 2x3x3 18 images In gallery mode you can magnify small parts the grid fields to score them and to export them for reporting or in an image gallery ImmunoScreener project An ImmunoScreener project is a set of slide
18. itive negative parameter and run the al gorithm on all fields in the ImmunoScreener project Compare the results from the manual scoring and from the HistoQuant algo rithm and adjust the manual scores or refine the HistoQuant algorithm as nec essary If you first run the HistoQuant algorithm on the grid fields or annotations inside the fields the HistoQuant measurements make it is easier for the Evaluators to score the ImmunoScreener Gallery March 4 2009 Create Immunoscreener project Fit Grids Section 3 1 Section 3 10 Create HistoQuant annotations inside fields Section 3 11 Score fields in ImmunoScreener Gallery Section 6 1 1 Export picture Gallery Section 7 3 Consolidate scores Section 8 Export data to CSV Section 7 1 3DHISTECH Ltd 36 36
19. iz os 3DHISTECH ImmunoScreener Module 1 12 User s Guide March 03 2009 ImmunoScreener Module 1 12 User s Guide Contents DISCLAIMERS visa esis sccidheecnnaidar dares oedseseh E ee furs nedeaw a N a a aa ED OS 4 Font Types and SYMbOlSi ii icsanicirdacesiin colar tran ade catiuntenad le catharteeelid aaenia one daaeiden ali 5 Terms and ADDreVIationS sic isevoccravvervvas yenyi aa vas Va Yena YRAN a Wien vias yy eves KANAE Wee et evens ss 6 1 About the ImmunoScreener Module 1 12 ce cceee eee eee eee eee eee ened 7 1 1 ImmunoScreener Module in the MIRAX Product Family c ceceeee eee eee eee sees eeeeeeeeas 7 1 2 Overview of the ImmunoScreener Module 1 12 ccccceeeee eee e eee eee eee eset esta eee eeeeaas 8 12 1 WOrKHOW vsissi cede tisenede ater nrvecsanusersae E E EO EEEN EEA AS 8 1 22 GrIAS orraa aa EE A OANE ET E EE AE EE area waned N NE 9 1 2 3 Scoring Sheme Sisenen Era a EAE AE ATAA AAE 10 1 2 4 Reusing Stain Definitions and Scoring SChemesS ssssssssssrrssrrrssrrresrrnesrrnreerrrns 10 1 2 5 Multi User Mode and Score Consolidation cceeeee eee ee eee eee ee eee eee eaeeaeeees 10 1 3 ImmunoScreener and HistoQuant Measurement Visualization cccccceeeeeeeeeeeeees 10 2 Installing the ImmunoScreener module for MIRAX ViQWEL c cece e eee e tees eee ee eee eae eee eeeee 11 2 1 Licensing of MIRAX ProdUCtS siriisin nine riian U E AEA E A ERE ETN aaa 11 244 PFELEQUISILES iniri EAE
20. n If you want to check your consistency in scoring order the thumbnails by Score CL aa U aA EAN Label ca 40301 07 _HER2 1 10301 07 HE 1 10301 07_Ki 671 10301 07_PR1 1 107 107 107 of Order by Primary Field v We Secondary Disabled v i Fae P Filters H 4 gr 44 e e be 7 10301 07_ER_ ae Ba amp Z 10801 07_HER2_ Z 10301 07_HE_I 1 v v 10301 TRI 42 10301 07_HER21 10301 07_HE_ 1 07 rii J 10301 07 _PR1 2 20 20 07 10301 07 _Ki 67_I 10301 07_PR_ eke Ai A bebe A 10301 DRI 13 O7 a 10301 07_HE_l 47 10301 ge 10301 07 _PR 73 307 307 of eee meral a yer Pas 4 ECEE ts RN DE 10501 07 ER 144 40301 07 _HER2 I 10301 07 _HE 1 10301 07 KST ay 40t 407 oF paN y HistoQuant 006 Rek i gt is March 4 2009 3DHISTECH Ltd 26 36 JAKKAR ImmunoScreener Module 1 12 User s Guide 5 2 Display Options of ImmunoScreener Gallery You can zoom in out on the selected field previews by left clicking on the window hold ing down the button and moving the glide 5 Gallery 10301 07_ER_ 10301 07 _HE 1 7 TI 07ER1 1 ole 11 OFHEL s V Score Value Primary Oo amp AES 10301 07_HER21 10301 07_H
21. olidator user for each multi user report to facilitate score consolida tion 1 3 ImmunoScreener and HistoQuant Measurement Visualization You can also use ImmunoScreener with other MIRAX Viewer modules A Warning Each MIRAX Viewer module is licensed separately e With HistoQuant the module that allows you to define and run measurement algorithms on MIRAX annotations you can perform the measurements on the en tire slide set in an ImmunoScreener project e With Measurement Visualization you can display the HistoQuant measure ments as a scatterplot a histogram or as a gallery of pictures You can also ex port your results into a CSV file or as an HTML picture gallery March 4 2009 3DHISTECH Ltd 10 36 ImmunoScreener Module 1 12 User s Guide 2 Installing the ImmunoScreener module for MIRAX Viewer 2 Installing the ImmunoScreener module for MIRAX Viewer 2 1 Licensing of MIRAX Products Mirax software is purchased with a valid license file MView lic which the software needs to exploit its all options Without this file the Mirax Viewer offers only limited options as a free Mirax Viewer 2 2 Prerequisites ImmunoScreener is not a standalone application you need MIRAX Viewer to run it Therefore it is installed together with MIRAX Viewer bundled into one executable MIRAX Viewer 1 12 version Running on Microsoft Windows XP Hardware minimum Pentium P4 3GHz 1GB RAM recommended Pentium C2D DualC
22. ommander 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 SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR ANY SPECIAL INCIDENTAL INDIRECT OR CONSEQUENTIAL DAMAGES OF ANY KIND OR FOR 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 service
23. ore 2 GHz 2GB RAM Disk space MIRAX Viewer bundled with the ImmunoScreener mod ule minimum 88 MB 2 3 Installing the Application Bundle 1 Start the MIRAX Viewer setup exe file that you received on a MIRAX Viewer DVD or downloaded in a compressed file 2 Follow the instructions in the installation wizard 3 Start the application setup exe file that you received on the application DVD or downloaded in a compressed file 4 Follow the instructions in the installation wizard 5 For more information see MIRAX Viewer 1 12 Installation Guide March 4 2009 3DHISTECH Ltd 11 36 ImmunoScreener Module 1 12 User s Guide 3 Creating an ImmunoScreener Project 3 Creating an ImmunoScreener Project Before You Start Make sure that the slides that you want to add to the ImmunoScreener project are all in one folder at a location that you can access from MIRAX Viewer 3 1 Create New ImmunoScreener Project ImmunoScreener projects are handled and created within Mirax Viewer In the Project Tree right click the folder where you want to create the ImmunoScreener project se lect Create New ImmunoScreener Project from the menu and enter a name for the new project DEK CRORE O DPP Kicsi_meretuek IHHIBASLIDE IH_Project hiba_parameter hq param t aaa E oO ImmunoScreener Project Wizard is launched and helps you go through all the neces sary steps March 4 2009 3DHISTECH Lt
24. put several grids on the slides scoring is done per annotation that is per grid field ImmunoScreener calcu lates the final score per slide Grid internal annotations You can also create annotations that are smaller than the grid fields You can use grid annotations and non Immuno Screener annotations on the same slide without any prob lem If you want to use HistoQuant you can run Histo Quant algorithms on either type of the annotations Grids on several slides in the project You can analyze several slides in a project and get a better overview of a specimen Furthermore you can export the data into one report March 4 2009 3DHISTECH Ltd 9 36 ImmunoScreener Module 1 12 User s Guide 1 2 Overview of the ImmunoScreener Module 1 12 1 2 3 Scoring Schemes You can define a separate scoring scheme for each stain and several users can evaluate the slides A Consolidator user reviews the scores and ImmunoScreener computes the final score for each annotation each field in each grid on each slide 1 2 4 Reusing Stain Definitions and Scoring Schemes You can reuse stains and scoring schemes defined in other ImmunoScreener projects The definitions are saved in a file IHLabConfig xml and you can copy them to the ma chine of other MIRAX Viewer users 1 2 5 Multi User Mode and Score Consolidation ImmunoScreener can handle scores from several eva uators and average their results It also creates a Cons
25. reener Module 1 12 User s Guide 8 Working with ImmunoScreener in Multi User Mode 8 Working with ImmunoScreener in Multi User Mode If several users are assigned to an ImmunoScreener project the application automati cally creates a Consolidator user who can see the scores entered by all other users and can finalize the score into one consolidated report Consolidator s Scoring offers the following options to consolidators e The Consolidator can see and score only those fields grid cells that received the same score from all users e The Consolidator can decide whether to take the lower or the upper median if there are even numbered users assigned to the project March 4 2009 3DHISTECH Ltd 35 36 ImmunoScreener Module 1 12 User s Guide 9 Using HistoQuant and ImmunoScreener Together Using HistoQuant and ImmunoScreener Together You can use ImmunoScreener and HistoQuant together to perform measurements re garding the markers used on the slides If you first score a slide set with Immuno Screener you can create and run a HistoQuant algorithm on the grid annotations to cross check the manual scores or to support the Consolidator s decisions in hard to de cide cases For example 1 Evaluate the cuts from the specimen with possibly cancerous cells and score them manually as positive negative in ImmunoScreener Create an algorithm on an annotation with easy to decide positive negative stains in HistoQuant for the same pos
26. reener project including a summary line exported into its own CSV file o Cumulative export summary line appended to an existing CSV file where you compile longitudinal or otherwise cumulative data 7 2 Exporting an HTML File Tip ImmunoScreener does not export the scores to the HTML file Add the scores to the annotation label before you export the ImmunoScreener Gallery and the score will be visible above each annotation 1 Open the ImmunoScreener gallery 2 Click A on the top panel and select Save to HTML from the shortcut menu 7 3 Exporting an image Listed images can be exported at arbitrary magnification into a HTML file You can also save all listed pictures as image files BMP JPEG or PNG 1 Open the ImmunoScreener gallery March 4 2009 3DHISTECH Ltd 33 36 ImmunoScreener Module 1 12 User s Guide 7 3 Exporting an image 2 Click iA on the panel and select Save to Picture s from the shortcut menu 3 Set the magnification level and the format and then save the pictures 7 4 Exporting One Annotation as a Picture from an ImmunoScreener Gallery Listed annotations can be exported at arbitrary magnification into a HTML file or you can save all listed annotations as image files BMP JPEG or PNG 1 Open the ImmunoScreener gallery 2 Right click the annotation that you want to export 3 Set the magnification level and the format and save the picture March 4 2009 3DHISTECH Ltd 34 36 ImmunoSc
27. s please visit http www 3DHISTECH com March 4 2009 3DHISTECH Ltd 4 36 ImmunoScreener Module 1 12 User s Guide Font Types and Symbols Example Abbreviation or term that is explained in the section Terms and Abbrevia tions 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 Ctri O key combination Example Cross references to other documents Warning Indicates that you need an additional module to use the feature or that there are prerequisites for the task or that special care should be taken when using certain feature of the device Important An important piece of information or a recommendation The application will work if you choose not to follow the recommendation but its perfor mance might be less than optimal Q Tip A suggestion about using the application in some other way or to some in teresting purpose March 4 2009 3DHISTECH Ltd Font Types and Symbols 5 36 ImmunoScreener Module 1 12 User s Guide Terms and Abbreviations Annotation Area of interest on the digitized slide Consolidator An additional user in a multi user ImmunoScreener project who can see the scores given by all the other users and who can consolidate them Evaluator A user who checks each f
28. s that you want to evaluate with each other In multi user ImmunoScreener projects only the Consolidator can modify the project add or remove slides add or remove stains IHC Immunohistochemistry Marker A stain for example hormone Estrogen Receptor Proges teron Receptor Her 2 EGFR etc Stain Classic pathological stains for example HE March 4 2009 3DHISTECH Ltd Terms and Abbreviations 6 36 ImmunoScreener Module 1 12 User s Guide 1 About the ImmunoScreener Module 1 12 1 About the ImmunoScreener Module 1 12 ImmunoScreener is an optional module for MIRAX Viewer It allows you to perform semi quantitative histopathological examinations of IHC stained slides digitized with MIRAX scanners e Inthe routine pathology you can use ImmunoScreener to check specimens dyed with common JHC stains Such an ImmunoScreener project typically con tains sequential cuts from the same specimen and each slide is treated with a dif ferent stain e Research projects often use ImmunoScreener to check cuts from different speci mens for example from biopsies from the same patient taken at different points in time In such cases the slides would be dyed with the same marker 1 1 ImmunoScreener Module in the MIRAX Product Family For an overview of the workflow see MIRAX Viewer User s Guide Slides MIRAX Scan Local file system PathoNet Ka Image analizis modules 4 A
29. ser s Guide 3 9 Grid Definition 3 9 Grid Definition i Important In multi user projects only the Consolidator user can fit grids to the slides On each slide mark the areas that you want to inspect with one or more grids for exam ple areas with suspected cancer Specify the grid properties name number of rows and columns the size of the grid in um You can also adjust the position of the grid on the slide or rotate enlarge shrink it by dragging the grid borders You can also put several grids on the slides by clicking New Grid E Grid Fitting Slide Zoom 44 M Grid Show Grid Definition Slide Alignment Reference Slide Grid fas Selected Grid grid Parameters Name grid Row g Column 5 Width um 14065 Height um 14766 Operations Slide Alignment March 4 2009 3DHISTECH Ltd 18 36 ImmunoScreener Module 1 12 User s Guide E Grid Fitting Slide Zoom 44 M Grid Show V Color C O Grid Definition Slide Alignment Reference Slide L Grid Selected Grid E L Parameters Name Row Column Width um Height um 34 Operations Slide Alignment March 4 2009 3DHISTECH Ltd 19 36 ImmunoScreener Module 1 12 User s Guide 3 10 Grid fitting amp Grid Fitting Slide Zoom 44 SA I Grid Show Color Opacity 33 Q
30. stain but it is not changed for the old stains ImmunoScreener Project Wizard a User Management Project Data Slide Selection Stain List Scoring Setup Stain Definition March 4 2009 Welcome to the ImmunoScreener project wizard Scoring Setup Scoring setup Active stain list Name Value Color negative 1 ESEN HeMa Her2 ki 67 p53 progesteron Clone scoring schema lt Previous Next gt 3DHISTECH Ltd Cancel 16 36 ImmunoScreener Module 1 12 User s Guide 3 8 Stain Definition 3 8 Stain Definition Mark for each slide which stain is applied on it You can select several slides with Shift Click and Ctrl Click and apply the same stain marker on them in one step ImmunoScreener Project Wizard g a Welcome to the LmmunoScreener project wizard d User Management Stain Definition Project Data R Use the context menu to assign stain to the selected slides Slide Selection Stain List Slide name Stain name 10301 07_ER_I estrogen SETE 10301 07 _HER2 Her2 Stain Definition 10301 07_HE_I 1 HeMa 10301 07_Ki 67_1 ki 67 Clear estrogen HeMa Her2 ki 67 p53 The wizard asks you whether you want to start fitting the grid onto the slides right away You can do grid fitting later To start grid fitting right away select the checkbox in the pop up window March 4 2009 3DHISTECH Ltd 17 36 ImmunoScreener Module 1 12 U
31. t the Grid Fitting wizard a Select Grid Fitting and select the appropriate option either For All Slides or For Selected Slides b Right click a slide that you want to change the grid of and select Grid Fit ting from the shortcut menu 3 Modify the grid as needed 4 Save the changes by clicking Finish on the Slide Alignment tab March 4 2009 3DHISTECH Ltd 25 36 ImmunoScreener Module 1 12 User s Guide 5 Working with ImmunoScreener Gallery 5 Working with ImmunoScreener Gallery 5 1 Enlarging the Preview Window To make the preview window as large as possible you can hide the panel in the Im munoScreener gallery you are working on by clicking the border between the panel and the preview window 5 2 Display Options of ImmunoScreener Gallery In the gallery you can determine the size of the preview of the fields by setting Zoom The gallery provides multiple visualization options for the ImmunoScreener project which you can change at the left side of the window By default ImmunoScreener shows the annotations the grid fields as thumbnails in the following order of importance group by slides group by grids group by fields To modify the display order set the primary and secondary ordering principle in the Or der by area and click z to refresh the gallery If you are evaluating an ImmunoScreener project from the same specimen where the slides were handled with different stains order the thumbnails by Stai
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