IH-Lab Module 1.11 User's Guide June 30, 2008
Contents
1. iz os 3DHISTECH IH Lab Module 1 11 User s Guide June 30 2008 IH Lab Module 1 11 User s Guide Contents Diels la Ce er hee ee ee ee ee ee ee 4 FORME TY Des GiGi VO S aastasaavcaseantceredsudda vas saanaveulecaccak E 5 MEPIS ANG FO ONG VISE IOINS a a E an vecenes cee conga E EE E A NE T E AE 6 FADO the TEE EAD MOGUIC EL SEE anita E R RAR 7 1 1 IH Lab Module in the MIRAX Product Family ccccccccccccseeesee sence eee eeeeeeeeeeeesaaeeesaanenegs 7 1 2 Overview of the IH Lab Module 1 11 ccccccccccccee cece eee eeeeeeeeeeeeeseasaateeseeuseteetsauaaneenes 7 OE els WM ON EROS EET A 8 Te JR COGS A E E nase ctedanmenana aneauteaanuaui aa ante A E E 9 Daar SCONING SCHEMING a oiagmngnanieonauaratengnabeemienhaatonanesee neuatenenenaninr ease 10 1 2 4 Reusing Stain Definitions and Scoring SCNEMES ccceceeee cece cece eeeeeeeeeeeeeeeenags 10 1 2 5 Multi User Mode and Score COnsolidation ccccccceeeee cece eee eee eee eeeeeeesaeeeesaneeees 10 Be aber COUT wears esc E acess esutewonsede E EE 10 1 4 IH Lab and HistoQuant Measurement ViSUAlIZATION cccceeeeeesseeeeeeeeueueeeeauenenauenes 11 2 Installing the IH Lab module for MIRAX ViCWETL cccccccceeeeee eee eee eee e een E eee E eens 12 244 Licensing Of MIRAX PrOGU CUS AE EAR ER 12 Bg PEET SUS RE ea ces se cate cee sere tee ce ces ee atte eee ce es cee es ee ce ne eee Eee eee 12 2 3 Installing the Application Bundle ssssssessessssenessnnssnsnssnssne2. July 1 2008 3DHISTECH Ltd 22 30 IH Lab Module 1 11 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 IH Lab 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 IH Lab project because this is the only way to show the scores in the output July 1 2008 ST ERIS ESTO atragem fone Crear 6 cet eia Fi 9606 07 ER 1131304 stregen mors ihan GES of reacted 111 i ae ER 1 4 f Di earagen more Then S of mai T 8808407 FR I O estrogen I more Shan Sei of raai 1 ST HERS 2 os Hard sf ET week moribrene 1 ST HERS a fa OS Hard T 1107 maden Taira arnas 24 1 weg recente EREA ETRE PS of mi e aT E TELTIS ETEME PE of raie a BEDE KET a i Ga MESS of reacted SET HET IS PS O PE Se u a passa ee a od ected 1 i ST pa ia 14 pS Sod mudei 5 Sey poise sS Ol pss 13 od huske Fd 3DHISTECH Ltd progesteran i 76 85 of puck so Brogesioron 16 25 of muld fF poepen 1 55 of reached 11 progetieron i Miti gf Pusch 15 23 30 IH Lab Module 1 11 User s Guide 6 Scoring Slides in an IH Lab Project 6 Scoring Slides in an IH Lab Project 6 1 Scoring Options e From the gallery e s
3. To make the preview window as large as possible you can hide the panel in the IH Lab gallery you are working on click the border between the panel and the preview window 5 2 Display Options of an IH Lab Gallery In the gallery we can determine the size of the preview of the fields by setting the Zoom The gallery provides multiple visualization options for the IH Lab project which we can change by many ways at the left side of the window By default IH Lab shows the annotations the grid fields as thumbnails in the following order of importance 1 group by slides 2 group by grids 3 group by fields To modify the display order set the primary and secondary ordering principle in the Or der by area and click on to refresh the gallery If you are evaluating an IH Lab project from the same specimen in which the slides were handled with different stains order the thumbnails by Stain If you want to check your consistency in scoring order the thumbnails by Score FE BER Gea be ry os i ae ee a E gt Se OO OF ER JATO agaa I OOH AO HET Is 7 Oian 3 HAT PRIIT Os mi FR acor 1000 07 HERD ST OS Herds T stent POSH OF pS 7 Os pea yi PRAT Ot propane cal 1000 0907 ER I fr 1000 07 HERZ 1001 07 KT 1030107 _ pF I der FA I kee MIB 1 fe p53 E ptcgettenon Sone OE i Hot HR SQuan BOE IONER ERE sey or ERAO IHAT i 1301 07 O 67 Jrg 0716 67 M6 sth Nt pid TTA TAT 1030107 PR JFR O propesteree 1
4. using marker counter TER MIRAX Viewer Local 10301 07 Ki 67 I Pe File Settings Window Help x ER B tf lo 5 OBS es i Er SQ ORE mal O kd rYA m RAL ino Displayed area width 450 um height 256 pm Step 50 at A Ea ER ER fo ES EO EE Magrification jo Progress E p 2 3 J ay F 5 Annotation Name 30 Overall Area 0 04 Number of Markers 183 Frequency of Markers 4 576E 03 Preview Number Rel Number Frequency Viewing history i 34 186 8 502E 02 C Preview and 149 81 4 3 726E 03 viewing history Delete Viewing History 5 ey Module IHLab UserM 1 4 IH Lab and HistoQuant Measurement Visualization You can also use IH Lab with other MIRAX Viewer modules 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 entire slide set in an IH Lab project e With Measurement Visualization you can display the HistoQuant measurements as a scatterplot a histogram or as a gallery of pictures You can also export your results into a CSV file or as an HTML picture gallery July 1 2008 3DHISTECH Ltd 11 30 IH Lab Module 1 11 User s Guide 2 Installing the IH Lab module for MIRAX Viewer 2 Installing the IH Lab module for MIRAX Viewer 2 1 Licensing of MIRAX Products Mirax software is purchased with a valid lic
5. Project As name cannot be modified later be cautious to incorporate all needed information into the name of the new project The IH Lab Project will be located within the folder of its slides which can be visualized after pushing update Tree button in the left side of the Mirax Viewer screen July 1 2008 3DHISTECH Ltd 13 30 IH Lab Module 1 11 User s Guide 3 3 Define at Least One User on User Management 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 for the project for example patient name s and the corresponding IDs or registry numbers if it is needed You may skip this option 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 IH Lab 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 TH Lat Project Wired y g gt Welkome to the IH Lab project wizard Lie Han Sie Selector uii Elde Selechom Sian Lat Path Tia
6. 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 LIDTIFF 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 services please visit http www 3DHISTECH com July 1 2008 3DHISTECH Ltd 4 30 IH Lab Module 1 11 User s Guide Font Types and Symbols Example Abbreviation or term t
7. a 27 Far EK DO BIA AAA G arr a E E E E A EE E E E E E AE 27 7 4 Exporting One Annotation as a Picture from an IH Lab Gallery cccccccccceeeeeeeeeeeeeeeees 28 8 Working with IH Lab in Multi User MOde ccccccccc cece eee REE ERE NERE ERE REEL ERE E ENE RENEE REE 29 9 Using HistoQuant and IH Lap TOGCINEl sisceeesstecsvasvdeciwansarcerersteniwurshereveessesecsawesxisen ners oress 30 July 1 2008 3DHISTECH Ltd 3 30 IH Lab Module 1 11 User s Guide Disclaimer Disclaimer Copyright 2001 2008 3DHISTECH Ltd All rights reserved The following patents are pending for 3DHISTECH products WO 2006 030326 P0700409 and 11 826 752 3DHISTECH Ltd is not liable for damage of whatever nature including but not limited to general or specific damage indirect damage consequential damage or incidental damage including the results of the analysis of the digitized slides for example change of health status related to erroneous diagnosis from the digitalized slide s 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 Commander scripts CAUTION For research and education uses only not for use in diagnostic procedures This product has not been approved or cleared as a medical device by the U
8. 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 IH Lab projects allow you to correlate the different antigens and per form measurements for example with a separately available MIRAX Viewer module HistoQuant Grid A set of annotations used in IH Lab They are independent of other annotations for example HistoQuant annotations 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 IH Lab project in which you created or modified them but you can also save them onto the slides IH Lab Gallery An IH Lab 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 IH Lab project An IH Lab project is a set of slides that you want to evaluate with each other In multi user IH Lab projects only the Consolidator can modi fy the project add or remove slides add or remove stains IHC Immunohistochemistr
9. e a Erde 21 4 4 Adding OF REMOVING Stains vcsesssdscunnntontiariodeaed exdoviamiendaad endontemsdanadentondeanWedeneewis 21 A Ml I FAG El VON Gli artageae stares R 21 5 Working with an H Lab Gallery cece cee ceeece ee eeeeeeeeeenseennneeeeeeeeesseeenaseeeanteesenanenenanegs 22 July 1 2008 3DHISTECH Ltd 2 30 IH Lab Module 1 11 User s Guide 5 1 Enlarging the Preview WiINdOW ccccccccccsseneneneeeeeeeeseeeeesseennanneeeeeeeeeeeanteesanneesenanees 22 5 2 Display Options of an IH Lab Gallery ccc eee cece cece eee e eens eeeeeeeeeeeeageeeeenaaenees 22 5 3 Setting Which Labels Are Visible in the HTML Export cc cccccccccseeee sence eee ker ERR ke 23 6 Scoring Slides in an TH LAD Project ccccsscceees see eneeeeeeeeeesseecceseneeeecuneessantessenaeetsuneeseas 24 OU SCO OPON atic oes cree EE E EEEE E EE E E EE EE 24 6 1 1 Scoring in the IH Lab Gallery ssssssssssssssssnssessnnssssnssnsnssnsnnsnssnenassnnsnenenssenn 24 012 SEGUE lal SOFA wasencanaseenrtsaeranraaascnossciqanraneteannsmarssaaaarrgeuecianasesaraeceneeneen es 25 OL FF SEAT a SING SNAG rea a E 25 A MWN IO EL tase cyan EEE E R AAE A EA EEA EA 26 7 Exporting Information from an IH Lab Project cccccccece cece eee ee esses eee ELLLER RENEE ERR REE 27 7 1 Exporting Data from an IH Lab Project to a CSV File cccccccccccee cece ects eee eeeeeeeeeeeeeeeeees 27 Fe EXPONO aN HEME FilGresurananenecsantaivrannnanswaaneasesssucattnanciatmasmianeea aa
10. ense file Mirax 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 IH Lab 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 11 version Running on Microsoft Windows XP Hardware minimum Pentium P4 3GHz 1GB RAM recommended Pentium C2D DualCore 2 GHz 2GB RAM Disk space MIRAX Viewer bundled with the IH Lab module minimum 88 MB 2 3 Installing the Application Bundle l Start the setup exe file that you received on a DVD or downloaded in a compressed file 2 Follow the instructions in the installation wizard July 1 2008 3DHISTECH Ltd 12 30 IH Lab Module 1 11 User s Guide 3 Creating an IH Lab Project 3 Creating an IH Lab Project Before You Start Make sure that the slides that you want to add to the IH Lab project are all in one folder at a location that you can access from MIRAX Viewer 3 1 Create New IH Lab Project IH Lab projects are handled and created within Mirax Viewer In the Project Tree right click the folder in which you want to create the IH Lab project select Create new IH Lab Project from the menu and enter a name for the new project Now IH Lab Project Wizard is launched and helps You to go through all steps 3 2 Give Name for the New IH Lab
11. equential scoring e per slide 6 1 1 Scoring in the IH Lab Gallery 1 Open the IH Lab project 2 Click Gallery in the project menu and display the thumbnails 3 Score the grid fields s Cenlbery SET ES POO OS estrogen i i DESOT ES 1 1 Dieng i W ES NIe T SESE ESS J30 eairogen i i 2356 07 ES id fa O ieo Dee MEAS PD Herz Ps fs Pol a JA OS ert T f e s ae 1 e We z eebogen L Hia Ht fe REET MIB 1 i e53 Ome PEO EON Opa I SESE PEIO IPSN I 720508 nana geo eee eee ye Path peeti a 7 pita vak membrane 2 ob 0 eerie incomplehe members 3 LOD merase ondere menor 4 21 3 erate Ponies membrane 5 JIS dere empie rene amp j HEE moia mennee membrane 7 SLOG moderate ncongiete membrane 5 G17 dere mennee mami are F TUG dere reonip manbai LO BSS Meiers krone membrane li j OL Modes incomplete membrane i lz re burar cats O e 1S Aron complete mamira IS e SEK cong complete mandeme 14 Paget Store To change the order of the display before you start scoring change the grouping settings in the Order by frame To score the annotations in the order they are displayed in the gallery start sequential scoring To score the annotations one by one right click each thumbnail and select the score from the shortcut menu 6 1 2 Sequential Sco
12. hat is explained in section page Example i Words or characters that appear on the screen These in clude 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 AN Warning Indicates that you need an additional module to use the feature or that there are prerequisites for the task Important Contains an important piece of information or a recommen dation The application will work if you choose not to follow the recommendation but its performance might be less than optimal v Tip Contains a suggestion about using the application in some other way or to some interesting purpose July 1 2008 3DHISTECH Ltd Font Types and Symbols 5 30 IH Lab Module 1 11 User s Guide Terms and Abbreviations Annotation Area of interest on the digitized slide Consolidator An additional user in a multi user IH Lab project who can see the scores given by all the other users and who can consoli date them Cumulative CSV ex port Summary line appended to an existing CSV file in which you compile longitudinal or otherwise cumulative data Evaluator A user who checks each field in each grid on each slide and assigns it a score In a multi user IH Lab project evaluators do not see each other s scores Field A
13. he export menu you can export your added values and scores to a CSV comma sep areted vaule 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 Open the IH Lab project From the menu select Export and then select what data you want to export from the IH Lab project Full export data from the IH Lab project including a summary line exported into its own CSV file Cumulative export summary line appended to an existing CSV file in which you compile longitudinal or otherwise cumulative data 7 2 Exporting an HTML File Tip IH Lab does not export the scores to the HTML file Add the scores to the annotation label before you export the IH Lab Gallery and you will see the score above each annotation 1 Open the IH Lab gallery 2 Click iA on the top panel and then 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 or save all list ed pictures as image files BMP JPEG or PNG 1 Open the IH Lab gallery 2 Click E on the panel and then select Save to Picture s from the shortcut menu July 1 2008 3DHISTECH Ltd 27 30 IH Lab Module 1 11 User s Guide 7 3 Exporting an image 3 Set the magnification level and the format and then save the pictu
14. ing 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 exactly cover the same area on each of them Repeat these steps for each slide that you want to use in this IH Lab project Save the grid to the slide if You want to further analyze annotations with Marker Counter or Histoquant Click Finish to create the IH Lab project 3 11 Creating Annotations Inside an IH Lab Grid IH Lab grids are annotations that you create when you create the IH Lab project You can nevertheless use further annotations on the slides There might be already annota tions on a slide or you might want to create HistoQuant annotations that are smaller than the grid field if you have the optional HistoQuant module you can perform measure ments on the HistoQuant annotations July 1 2008 3DHISTECH Ltd 18 30 IH Lab Module 1 11 User s Guide 3 11 Creating Annotations Inside an IH Lab Grid 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 module only cap
15. nensensnsnsnnnassenensnnnennene 12 3 Creating an IH Lab PrO 6 Clin srcussansacunsiveseeu caansstwnaesandweaensasuateasagusiansapanteesseunaaannianabeainrtees 13 3 1 Create New IH Lab FiO 16 Claires ey cata cdses ne tamatanaeetaecess wolawiacienaneasetesetaaueswiansennatueds 13 3 2 Give Name for the New IH Lab Project cccccccccccccccccccccccccecececececeeeeeeeeeeeeeseeteuneats 13 3 3 Define at Least One User on User Management SCreen cccceeeeee eee eeeeeeeeeeeneneeees 14 APOE T Wo AM ape abc eres bese ba cis etnee eaters a eee abe a a beeeeoe cease eh eees EE 14 Da BILTEST HU Ol ansancuaiacencumsacenguaiasenauuiaceeanpiatentns eacanenaiuceatessaeasqnpaneenenaecescane une cang tees 14 BOs SUI A EET ESS EET TEE EET sedan cseweveeseon E E 15 F COMING SUID ARNESEN staseseeates senu ncndoeneebesseenciaceun seems sew enasoree oben ssnnededsennetesceraeesses 15 JO SAM DeM ON oncsaccees teangensneaseaustonssensteatveusteanbersteaseasstennsensseasbestonnsecnnerindtasseness 16 CP RE RD nE e EEE E EE E E E E P EE A EEN 17 ALO G EN tet E AT EA A E A AAA ner 18 3 11 Creating Annotations Inside an IH Lab Grid s sessssssssssnssrsnsnrsrenrsnnrnrnrnsnnnernrnens 18 A ree Gabriel OlCCU EEN ovat unaaesu caanem ENE E E arter 20 4 1 Options in the IH Lap Proj SC ccascsiedensactadensnesscaneusascanraansdencessscaransnidenausaseseeniaenias 20 Ae Modifying an LeMLab PlOlGGl ao ED renen 20 4 3 Adding OF REMOVING SIDS SigcncaucvaceSoodugay basenatebnedees
16. nitions and Scoring Schemes You can reuse stains and scoring schemes defined in other IH Lab projects The defini tions are saved in a file IHLabConfig xml and you can copy it to the machine of other MIRAX Viewer users 1 2 5 Multi User Mode and Score Consolidation IH Lab can handle scores from several evaluators and average their results It also cre ates a Consolidator user for each multi user report to facilitate score consolidation 1 3 Marker Counter MIRAX Viewer includes Marker Counter to count cells and objects manually You can move and reset Marker Counter on the screen and you can define the counter categories Marker Counter uses Marker Counter automatically generates the values and shows them in a pop up window You can use this tool for example to keep track of the following data in an annotation or per a standard area for example 1 um Marker Counter determines the number of marked objects percentage of positive cells and as derived information the individual or average intensity of marked objects within their category All measured parameters can be stored in the digital slide or they can be exported to database Create marker categories H i gh light ta rget area create an annotation Select m arker categ ory from menu Place markers in annotation Export image Aen eae of annotation July 1 2008 3DHISTECH Ltd 10 30 IH Lab Module 1 11 User s Guide 1 3 Marker Counter And an example of
17. ores or to support the Consolidator s decisions in hard to decide cases For example 1 Evaluate the cuts from the specimen with possibly cancerous cells and score them manually as positive negative in IH Lab 2 Create an algorithm on an annotation with easy to decide positive negative stains in HistoQuant for the same positive negative parameter and run the algo rithm on all fields in the IH Lab project 3 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 easer for the Evaluators to score the IH Lab Gallery Create IH Lab project Fit grids Section 4 1 Section 4 2 Create HistoQuant annotations Inside fields Section Aa score fields in IH Lab Gallery Section 5 2 Consolidate scores Secoton 5 5 Export picture gallery Export data to CSW aie NE Section 4 4 July 1 2008 3DHISTECH Ltd 30 30
18. port 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 positive 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 would be too large Several grids You can put several grids on the slides scoring is done per annotation that is per grid field IH Lab calculates 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 IH Lab an notations on the same slide without any problems If you want to use HistoQuant you can run HistoQuant algorithms on either type of annotations Grids on several slides in the You can analyze several slides in a project and get a better project overview of a specimen Furthermore you can export the data into one report July 1 2008 3DHISTECH Ltd 9 30 IH Lab Module 1 11 User s Guide 1 2 Overview of the IH Lab Module 1 11 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 IH Lab computes the final score for each annotation each field in each grid on each slide 1 2 4 Reusing Stain Defi
19. ra Seba Chan Dair red Seira July 1 2008 3DHISTECH Ltd 14 30 IH Lab Module 1 11 User s Guide 3 6 Stain List 3 6 Stain List Specify which markers are used in the actual project Use checkboxes to add marker for the marker list You can also add new stains here IM Lab Project Wizard u ay Welcome to the IH Lab project mund 4 E ped Ban Slam Lit Pesati Ma Thi Selector Sien Lii Torry Hup ien Deira Grd Saig 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 stain but the scoring scheme is not changed for the other old stain July 1 2008 3DHISTECH Ltd 15 30 IH Lab Module 1 11 User s Guide 3 7 Scoring Setup TH La Projet Wizard i i cy Welcome te the IH Lab project ward E Ua Hansy Dourig Setup Pratt Data ER Tiie jaor Hang San List les han 1 of nucke sorta ETP Mn Daini 6 1 ol rcii ae TESB of rede 25 30 ofl rd SG ll aiei HEER ll maii SEBY oll matii BEJBY of masii TEGE ol riei Chores doting oceans 3 8 Stain Definition Mark for each slide which stain is applied to it You can select several slides with Shift Click and Ctrl Click and apply the same stain marker to
20. res 7 4 Exporting One Annotation as a Picture from an IH Lab Gallery Listed images can be exported at arbitrary magnification into a HTML file or save all list ed pictures as image files BMP JPEG or PNG 1 Open the IH Lab gallery 2 Right click the annotation that you want to export 3 Set the magnification level and the format and then save the picture July 1 2008 3DHISTECH Ltd 28 30 IH Lab Module 1 11 User s Guide 8 Working with IH Lab in Multi User Mode 8 Working with IH Lab in Multi User Mode If several users are assigned to an IH Lab project the application automatically 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 July 1 2008 3DHISTECH Ltd 29 30 IH Lab Module 1 11 User s Guide 9 Using HistoQuant and IH Lab Together 9 Using HistoQuant and IH Lab Together You can use IH Lab and HistoQuant together to perform measurements regarding the markers used on the slides If you first score a slide set with IH Lab you can create and run a HistoQuant algorithm on the grid annotations to cross check the manual sc
21. ring July 1 2008 3DHISTECH Ltd 24 30 IH Lab Module 1 11 User s Guide 6 1 Scoring Options Sequential scoring is a comfortable way to go through and score each fields of the grids You can launch this option by clicking in the Gallery In the window appears only one field for evaluation and by clicking the score at the bottom toolbar the next field is com ing up automatically pg Gallery POIT ps FAO a Pe Po 6 1 3 Scoring a Single Slide p Open the IH Lab project 2 Right click the slide that you want to score select Final Score from the shortcut menu and then select the score ET 0 postin miia i 1 4 0 polia mdai EE 15 privene 5 1000 07 ki 16 25 postive niea J 26 ates nude 5 hj d a rachel 6 kE 46 55 paire iei 7 S665 poii racked g bee Fo perches ruched 9 TEGS postive nucke 10 95 pote rude 1 July 1 2008 3DHISTECH Ltd 25 30 IH Lab Module 1 11 User s Guide 6 2 Marking Slides 6 2 Marking Slides You can flag slides in IH Lab projects for example to mark the ones that you have al ready scored 1 Start the IH Lab project 2 Right click the slide that you want to flag and select Marked from the shortcut menu July 1 2008 3DHISTECH Ltd 26 30 IH Lab Module 1 11 User s Guide 7 Exporting Information from an IH Lab Project 7 Exporting Information from an IH Lab Project 7 1 Exporting Data from an IH Lab Project to a CSV File In t
22. s decision making in targeted therapy or in marker validation It also makes your evaluations more reliable with IH Lab you make subjective slide scoring more accurate and you make it measurable because you compare areas and scores on digitized MIRAX slides which is a more reliable method than analyzing the actual slides empirically under traditional microscopes July 1 2008 3DHISTECH Ltd 7 30 IH Lab Module 1 11 User s Guide 1 2 Overview of the IH Lab Module 1 11 1 2 1 Workflow The following figure summarizes your workflow You can also use IH Lab together with your colleagues In this case each team member scores the slides and then one team member consolidates the scores For instructions on how to consolidate scores see 8 Working with IH Lab in Multi User Mode p 29 July 1 2008 3DHISTECH Ltd 8 30 IH Lab Module 1 11 User s Guide 1 2 Overview of the IH Lab Module 1 11 1 2 2 Grids In routine pathology an IH Lab project contains slides from the same specimen In such cases grids are typically put on the same area on each slide for example on a group of cancer cells ast Sk i s7 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 IH Lab helps you rotate and align the grid throughout several cuts from the same speci men This allows you to obtain a re
23. t fields or put fields back into the grid July 1 2008 3DHISTECH Ltd 20 30 IH Lab Module 1 11 User s Guide 4 3 Adding or Removing Slides 4 3 Adding or Removing Slides The way of adding or removing slides from the IH Lab project 1 Start the IH Lab project 2 Select Manage gt Add Remove Slide s 3 Add or remove slides as needed gt Browse for slides to add gt Clear the checkbox of the slide s that you want to remove 4 Click OK to update the IL Lab project The way of removing a slide quickly 1 Start the IH Lab project 2 Right click the slide to be removed and then select Remove Slide 4 4 Adding or Removing Stains 1 Start the IH Lab project 2 Select Manage gt Stain Manager 3 Add or remove stains as needed and then click OK 4 5 Changing the Grid 4 Important In multi user projects only the Consolidator user can fit or modify grids 1 Start the IH Lab project 2 Start the Grid Fitting wizard gt Select Grid Fitting and then select the appropriate option For All Slides or For Selected Slides gt Right click a slide for which you want to change the grid and then select Grid Fitting from the shortcut menu 3 Modify the grid as needed 4 Save the changes click Finish on the Slide Alignment tab July 1 2008 3DHISTECH Ltd 21 30 IH Lab Module 1 11 User s Guide 5 Working with an IH Lab Gallery 5 Working with an IH Lab Gallery 5 1 Enlarging the Preview Window
24. them in one step TH La Project Wizard gt i cy Welcome to the IH Lab project warid r E Ura Hanar Slam Demon Piet ta Side Selection Sige Liat Chie harme ee ES Soning Seip 25607 HE Stan Dardi 7555 07 HER ee 55 07 KHT re 38607 p83 C Wine De coi por be Aor Sign Ba em cheba eel ikiga 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 up coming window July 1 2008 3DHISTECH Ltd 16 30 IH Lab Module 1 11 User s Guide 3 9 Grid Definition 3 9 Grid Definition 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 for example areas with suspect ed cancer with one or more grids Specify the grid properties name number of rows and columns the size of the grid in um You can also adjust the position the grid on the slide or rotate enlarge shrink it by drag ging the grid borders You can also put several grids on the slides click the New Grid button E Grid Fitting E Grid Fitting Selected Grid estrogen Parameters Name estrogen Row 5 Column 5 Width um 10000 Height um 10000 July 1 2008 Width um 1199 Height um 200 3DHISTECH Ltd 17 30 IH Lab Module 1 11 User s Guide 3 10 Grid fitting 3 10 Grid fitt
25. tions are exported to the CSV output file Annotation descriptions are for internal use in MIRAX Viewer and HistoQuant 3 Repeat step 2 for each area on which you want to run the algorithm You will be able to run other algorithms on these annotations July 1 2008 3DHISTECH Ltd 19 30 IH Lab Module 1 11 User s Guide 4 Handling an IH Lab Project 4 Handling an IH Lab Project 4 1 Options in the IH Lab Project You can manage slides stains perform grid fitting open gallery and export options from IH Lab Toolbar or by directly choosing from the option by right clicking the mouse on the slide You can also mark slides give a final score or open the slide or HistoQuant module E Pilah new moi ih 0T EF bi a 4 2 Modifying an IH Lab Project Important If you modify an IH Lab the scores related to the slide stain or grid are lost for all users who have already submitted scores to the project Most of the settings of an IH Lab 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 IH Lab projects which slides are included in the project they can add or delete slides which stains are used in the project they can add or delete stains how many grids are used in the project they can add or delete grids grid layout they can modify the size of a grid they can change the number of rows or columns they can knock ou
26. y Marker A stain for example hormone Estrogen Receptor Proges teron Receptor Her 2 EGFR etc Stain Classic pathological stains for example HE 3DHISTECH Ltd July 1 2008 Terms and Abbreviations 6 30 IH Lab Module 1 11 User s Guide 1 About the IH Lab Module 1 11 1 About the IH Lab Module 1 11 IH Lab is an optional module for MIRAX Viewer It allows you to perform semi quantita tive histopathological examinations of IHC stained slides digitized with MIRAX scanners e In the routine pathology you can use IH LAB to check specimens dyed with common IHC stains Such an IH Lab project typically contains sequential cuts from the same specimen and each slide is treated with a different stain e Research projects often use IH Lab to check cuts from different specimens 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 IH Lab Module in the MIRAX Product Family For an overview of the workflow see MIRAX Viewer User s Guide 2 MIT FAS Local BEES E el Server file system Bright eld TIA slides slides Flurorescent slides MIR AS Viewer a 4 Digitized PathoMet E School slides With the IH Lab 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 MIRAX Slide Serv er 1 2 Overview of the IH Lab Module 1 11 IH Lab support
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