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Pannoramic Viewer 1.15 User's Guide

1. Marker category settings You can manage marker categories on the Settings tab There is a possibility of deleting and also adding them from the Used categories to the Saved categories column and vice versa pe Marker categories Add Modify Settings Used categories Saved categories y negative negative ome gt e ioe Apply Cancel 7 Click Apply to save changes and leave the window open or OK to save and close the window 8 Click Cancel to abandon changes and exit window June 7 2011 Rev 1 3DHISTECH Ltd 61 68 Pannoramic Viewer 1 15 User s Guide 5 Working with Marker Counter licensed feature 5 1 1 Using existing marker categories 1 Create an annotation on the target area 2 Select the marker category and place markers on the objects to be measured in the target area r Manage Marker Category Select Marker Category t Y positive negative 3 If you want to delete markers right click on them and select Delete 4 Clickthe 1 button and select the Marker Counter Statistics menu item 5 The Marker Counter Statistics window appears on the screen showing values for each category regarding the overall area number relative number and frequency of markers within the given annotation 1 Y Show Annotations Annotation Hame Show Measurement Annotations Dalias cee mm2 Show Measurement Data Mumber of Markers F Ep Y Show Markers Frequency of Markers 319E 00 El sl Y Mar
2. oooccccnnoccononncnnnncnnonccnnnnnnonanononnnonononrnnnnnnnrnnnrnnnnnnnnrnnnnrnnnnnnnnnnons 40 3 7 Working with ARNOLatiON Sonsonate 41 3 7 1 Creating Annotations in Pannoramic Viewer ssssssssssessesssesserssersreeseresererresrresrrerrosrreseresresseseesesesreeeseseee 42 DIZ Mana 28 ANNO ONS aeaa EE E EEE RA E TT AER 44 3 8 Measuring in a Digital Slide o occoooccnncnnnnnonocononarononanonnonarononanonnonaronnrnonrnonrnnnononcnononnnos 47 3 8 1 Length E UA 47 3 8 2 Determination of perimeter and surface area ooooncncnccccnonononnnnonnnonnnnnnnonononnnnnnnonnnnnnnnnononnnnnnnnnnnnnnrnnnnnrnnnnnnnos 47 3 9 Displaying Information Relating to a Digital Slide coooocccoooconnnnonnnonacononarononaronnnnnonos 48 3 9 1 Explanations to digital slide related infOrMatiOn ccccccsssssecccceceeseeecccceceeseeecccseaeaseececeseauaseeseessuauaeeeeeesaes 48 SAO Babb OCS S SING arccec AQ e E E A 51 3 11 Exporting Slides from Pannoramic ViCWEL c ccccecccsecccseceeseccceececnseeeneeeneeseeenceeeeeuseeeeeeess 52 AM A A AS 52 SALA WINE Tola asr A purse cc se csiaie Sau sare AE de seater aeesemeat enact 53 3 11 3 Export to TIFF Image Pannoramic Slide or to MetaXML ccccccssssseeccccceeeeecceeceeeeseeeceeeseascesaueeseneeeeaeees 54 Sal Z VA OnE SRO S11 Oasis 56 313 Recording Tracking Istoric 56 3 13 1 Retrieving the tracking MIStOrY mnsaranisn diodes 57 4 Working with TM
3. 3DHISTECH Pannoramic Viewer 1 15 User s Guide June 7 2011 PV1 15 UG EN Rev1 Rev 1 Pannoramic Viewer 1 15 User s Guide Contents DISC ANIC sis a roo ob 4 Character Formats and OVI ONS mireia astas incurable 6 Terms and aDDreviatIONS unan ii 7 Keyboard quick Tere rente irrita 8 1 About Pannoramic VI Wes ais diia 10 LLODHISTECH Produccion ni tia 10 12 Marker COUNT Fannie 11 2 Installing Pannoramic Viewer Lil ion 12 2 1 Requirements for Installing and Using Pannoramic VieWerT cccoooccnccncnnnonocnnoncnnncncncncncnononnnos 12 ER A A N A A E ade A dion aaaasbed aon 12 2 3 Uninstalling Pannoramic ViEWeL ccccssecccsssccceesececenececescecsesececeaecessuecesseeeesegecesseeseeeueeeeees 20 2 4 Starting Pannoramic Viewer for the First TiM c oocccncnncnnnnncnnccnanononacononnnonnonarononaronnnnanonenanos 20 2 5 Pannoramic Viewer Start Up OPtiOns cccsccssccssccssccsscesccesecesccescsesessscssecesececescscsecseeeees 21 AA A E O ag anise eases 22 25 A Slide window CT AUIS iaa din cio 22 A A o O ceaustaccesscduuee 24 A VY O O E So o o n 24 2 5 5 External Application Call for Image Capture ooocccccncnccnononnnnnnnonanononnnnnnnaronnnnnnnnnnronnnnnnrnnnrnnnnnrnnrnnnnrononnnnnanoss 24 2 5 6 External Application Call for Annotation Export ccccccccccsssssececcccssesseccccsseeeececesseeaeeeeeessuanseseacesseseeaaes 25 2 07 Enable the Use of EL COGIIVG picada in 26 2 6 Configuring the On Screen
4. TMA Master Marker Diameter 600 porn f 1000 um 1500 pra 2000 pro Line color 3 Click OK or Cancel 4 When placing markers with the left mouse button mind that the crosshair cursor in the slide window is presented as the center point of the marker a y ETOT EA age Or z 1 e Na ro o Ml aS ieee eo L amp Aa Delete A i 1 a Co zi e rae ode es a i 3 A A T 1 7 ra a la a A zn _ sing TE e A ie June 7 2011 Rev 1 3DHISTECH Ltd 58 68 Pannoramic Viewer 1 15 User s Guide 4 Working with TMA Master Marker 5 You can drag a marker on the slide by the ring area of the marker a hand cursor appears 6 Toremove a marker right click on the marker and select Delete If you press the nf button then select Manage option you will be available only to move and delete markers The slide containing TMA Master markers can be used later with the TMA Master software application to determine which areas of the donor block should be transferred to the recipient block For more information see TMA Grand Master 1 0 User s Guide or TMA Master 1 14 SP1 User s Guide June 7 2011 Rev 1 3DHISTECH Ltd 59 68 Pannoramic Viewer 1 15 User s Guide 5 Working with Marker Counter licensed feature 5 Working with Marker Counter licensed feature With Marker Counter you can create marker categories and place markers to point to specific areas of an annotation 5 1 Managing Marker
5. This value however can be specifically matched to each digital slide later on Slide Tracking History Color This property defines the color of the tracing mask Slide tracking history Change color with the Ctrl C hotkey June 7 2011 Rev 1 3DHISTECH Ltd 23 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 2 5 3 Resolution Screen resolution is for setting the currently connected monitor s display screen resolution in units of DPI refer to section 2 1 2 5 4 Viewer Show thumbnails This option defines if the thumbnail view screen of digital slides is to be in ON or OFF state when a Pannoramic Viewer session starts If the preview image takes much time to build up for example when accessing a remote server this option can be turned off It can be turned on again at any time during the program session Show slide tree This option defines if the register card view tree view of the digital slides is to be displayed or not when starting the Pannoramic Viewer session 2 5 5 External Application Call for Image Capture The snapshot function allows you to export the displayed image to raster image viewers or editors refer to section 3 9 1 The related settings can be made in this area are as follows Application This option defines the program to which the image information is exported Browse for the folder of the application and select the executable file Start in
6. PP SU E NE E TE 6 7 23 25 29 35 39 43 45 49 50 FUO SCAN Larrea ee cocos licor natal 3 10 23 29 37 40 50 55 G eo tiesto 22 38 65 66 H PUTS UO ti PP EE eo A 39 41 66 L A o Une E 7 41 44 52 57 M AELE AP I ER OO cen shkence nee baat 2 3 11 55 58 59 60 61 62 66 Measures 3 7 34 38 44 45 46 47 51 65 66 A y qq OT 7 MUS riada 7 21 53 p We LATS 21 8 VIEW e ia 11 R e A O E PEU A 39 S SCA ter PO latir 66 E A EI oy pemenanpeaacasubssauapabodses sass caetecosaarveebaseranereneas E 7 SO OP seen E o IA 10 11 o A E PU Po A 11 T TEICCONSUITATION cccecceccesccssceccesceeseeccesseusceseesseuccessesseeseesseeceeseesseeseneeeenss 10 11 28 30 31 49 65 U lol o 0 APC Eu e o A oo sanesencautees 11 June 7 2011 Rev 1 3DHISTECH Ltd 68 68
7. Scale encata 26 3 Working with the Pannoramic Viewer sesesesessssssececesssssoecesecesososcoecesesoeoecseccesoesoeesecsesoeseeeee 28 3 1 Managing Folders in the Navigation Tree ccccccsssecccssececesececescecseseceseeceseeeeeseeeeeeeeeeeeees 28 3 2 Opening Digital Slides atico dotes 29 3 2 1 Ope ing slides loca Mastin 29 3 2 2 Opening slides from a 3DHISTECH CaseCenter SCrvelr cccsssssececcccssessececceseuesscceeeseeussecceeeseeanseceeeseeseaeesenes 29 3 3 Upload Slides to Case Conte annie 30 A e on A A 33 sA L e nn o EOR 33 3 4 2 Displaying information ON the slide oooccccccoconoconnnnnonanncononnnnnnnncnnnnnnnononnnnnnnonanornnnnnnonannnnnnnnnnnnnonnnnannoss 33 ES he es SI e eo 34 3 4 4 Dragging and moving the slide up down and left right ccccccnnnnnnninonanaoaoaonnnnnnnnnnnononononononananananannn non onnonos 34 3 4 5 Setting the magnification eve nasa a 35 3 4 6 Previewing a smaller area with a higher magnificatiON ccccoooonnconnnnnononnconnnnonanonnnnnnnonanononnnnnonnnnnnnnnnonnnnos 35 sA LO ON W Ao nn o E e nn 36 June 7 2011 Rev 1 3DHISTECH Ltd 2 68 Pannoramic Viewer 1 15 User s Guide 34 8 Rotating o o E E A 36 3 5 Working with Fluorescent Slides ooooccccooononononononacononnnonnonarononarononnnnnnonrononarononanonnonanonos 37 36 Changing Image Properties 38 3 0 1 SECM p colors on a SUB 38 3 6 2 Setting up colors on a fluorescent slide
8. T Pannoramic Viewer 1 15 RTM Setup Check computer for installed versions 3DHISTECH Preuninstall Installed Pannoramic Viewer version 1 15 00 44 Installed 3DHISTECH s Applications version 1 15 0 10 Uninstall You must remove these apllications first To do that press Uninstall button SDHISTECH Ltd lt Back Next gt 10 If the uninstall wizard window opens click Next TA Fannoramic Viewer 1 15 BETA Uninstall Welcome to the Pannoramic Viewer 1 15 BETA Uninstall Wizard This wizard will guide you through the uninstallation of Pannoramic Viewer 1 15 BETA Before starting the uninstallation make sure Pannoramic Viewer 1 15 BETA is not running Click Next to continue June 7 2011 Rev 1 3DHISTECH Ltd 17 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 11 The wizard automatically detects the folder of the previously installed application Click Uninstall to proceed T Pannoramic Viewer 1 15 BETA Uninstall E Uninstall Pannoramic Viewer 1 15 BETA Remove Pannoramic Viewer 1 15 BETA from your computer S4DHISTECH Pannoramic Viewer 1 15 BETA will be uninstalled from the following folder Click Uninstall to start the uninstallation Uninstalling from C Program Files 3DHISTECHWiewer SCHISTECH Ltd A progress bar and an information box is displayed showing the status of the uninstallation process When the uninstallation is completed successfully click Ne
9. User Name test Password 4 Secure connection E Cancel 3 Set upload parameters and click OK Slide Upload for Teleconsultation Access Fights W Public iw Allow saving W Read only Automatic Delete fram Server 5 Days ED 23 1 2 Today 2010 02 22 Remote Path E k mr test lastni mr test lastni Test Dania Cancel Access Rights You can share the slide by selecting Public make the slide Read only and or downloadable by selecting Allow saving Automatic Delete from Server Set the date of deletion from the drop down list 1 2 3 5 Days 1 2 3 Weeks User Defined or Never The date can be selected in the calendar as well Remote Path Select the location of the slide on the server June 7 2011 Rev 1 3DHISTECH Ltd 31 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 4 You can add more slides to the list change Slide Parameters and remove slides by clicking the Delete from List button in the Slide Upload window Slide Upload AI IS A Prepared for upload 10301 07_HE_1 1 CASLIDES N010307 07_HE_1 1 Prepared for upload Slide Parameters Delete from List Start Upload Close When all the slides you want to upload to the CaseCenter server are listed in the window press the Start Upload button 5 To update the tree click the Refresh button Local J eleconsultation Server Joined server Sdes
10. click the Preview and tracking history radio button in the panel or to select it as default choose the Preview and Slide tracking history option in the Options window refer to section 2 5 2 The position mask appears as a color mask Click the color bar to switch between the colors red green blue of the tracing mask To remove the tracing mask click the Delete Tracking History button The intensity of a color indicates the magnification at which a particular sub area was examined Brighter color shadings suggest greater magnification factors A position is not saved unless a certain magnification level was exceeded Otherwise no diagnosis is possible June 7 2011 Rev 1 3DHISTECH Ltd 57 68 Pannoramic Viewer 1 15 User s Guide 4 Working with TMA Master Marker 4 Working with TMA Master Marker TMA Master Marker feature allows you to place markers on TMA Master slides that the TMA Master control software analyzes and uses the markers as selected areas of the tissue to be removed from the donor block and transported to the recipient block 4 1 Create TMA Master Marker 1 Click the ihr button on the slide window toolbar and select the Create menu 2 Set the diameter of the marker that corresponds to the size of the puncher in the TMA Master unit You can also choose a distinctive color for the marker s either of different or same sizes Each time you want to change the marker diameter and or color click the nf button
11. press F11 on the keyboard 3 4 4 Dragging and moving the slide up down and left right H r Use clicks in the preview window rather than holding down the mouse button when you move around on a slide Pannoramic Viewer renders the image faster if you move the mouse in discrete steps rather than with a continuous movement When using Ergodrive as the operating device for moving the image press the button defined for X Y resolution change to enable faster movement June 7 2011 Rev 1 3DHISTECH Ltd 34 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer To enable moving and dragging click the R s button in the slide toolbar Then use any of the following two options a With the mouse Click an anchor point in the slide hold the left mouse button and drag the slide to the desired direction b From the keyboard Click the area of the slide that you want to inspect then use the arrow keys on the keyboard to move the image up down or left right c With the Ergodrive Turning the upper knob Y moves the slide horizontally and turning the lower knob X moves the slide vertically 3 4 5 Setting the magnification level You can set the magnification level in the toolbar at the top of the slide window ES E EZ ox EE ERA Magniication 15 Use one of the preset magnification levels e Fit the entire specimen is visible fits into window e 1 1 one camera pixel corresponds to one pixel on the
12. step size Filtere FITC 46HE Exposure time me Digital gal Number of focus level Focus step size Filters Rhodamine Exposure time me Digital gain Number of focus level Focus step size Image parameters Image compression Image file format Quality Factor Rotate Barcode Label Area by 180 Plan 4 pochromat Dx IE Asiolam Mim Aev 3 0 322500 0 322500 04 03 2009 11 56 58 01 20 33 240 76 MByte 30656 50688 1815 We outerOs Ok 3 9 1 Explanations to digital slide related information Optical parameters e Objective name Shows the name of the objective used for imaging e Objective magnification The given specimen was digitized with an objective with a physical magnification of 20x June 7 2011 Rev 1 3DHISTECH Ltd 48 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer e Camera adapter magnification Shows the magnification of the TV adapter this information appears only if digitization was carried out with version 1 9 or higher e Optovar magnification Shows the magnification of the Optovar used this information appears only if digitization was carried out with version 1 9 or higher This information is displayed only for digital slides digitized in the brightfield mode e Camera type AxioCam Mm Rev 3 was used to digitize the digital slide e Micrometer pixel X Pixel resolution is 0 322500 um in X direction for thi
13. A Master Marker csccscscsscsssscsccccscsccsceccsceccecsccscesecsceccecccecscscccececececeees 58 4 1 Create TMA Master Market ainia iaa 58 5 Working with Marker Counter licensed feature ccsccsccsscscssccsccsccsccsccsscsscsccececcscesescscess 60 5 LH Managing Marker Cate cone eric cnaciss 60 5 1 1 Using existing Marker CAtCQOLICS cccccccccsssssecccceccessseccccecausssececeecauuseeceesesueueeeceseeaeaseeceesseauaseeceesauaaaseeeeesaes 62 5 12 Exporting Marker Counter results asis 62 BE ONS ani 64 Appendix Toolbar BUTTONS vice scccaccescstccosccscrsdnacscikessccensecnseceanecuinsuanseasesansavatresunewiesiaimiexstenswaneneed 65 ReTerencOS oa uate cute lotto AN E EE A A E E ca euedeueiesseessusaeeese 67 June 7 2011 Rev 1 3DHISTECH Ltd 3 68 Pannoramic Viewer 1 15 User s Guide Disclaimer Copyright O 2001 2011 3DHISTECH Ltd All rights reserved Intellectual property related to the 3DHISTECH products are as follows EP 1 789 831 US 7 663 078 EP 2 024 772 JP 2009 512685 US 12 301 781 EP 1 644 767 JP 2007 516451 US7 327 515 EP 1 994 398 JP 2008 557835 US 12 281 566 U0700210 US 6 246 785 HU0900142 HUO700404 PCT HU2007 000065 EP 08762668 5 US 12 663 537 PCT AT2006 000492 JP 2008 542552 EP 06817469 US 12 095 545 PCT AT2006 000493 EP 06817470 5 US 12 095 596 HU0900741 US 61 264 732 US 11 826 752 PO401870 PCT IB2005 050344 US 11 662 976 HUO700409 US 12 042 050 US 77 636 144
14. Categories AN Important The size of the markers is magnification dependent it is proportional to the magnification used as they are defined in Marker Manager If the magnification is lower the size of the markers is smaller 1 To setup a Marker Annotation press the 2 button on the slide window toolbar 2 Select the Manage Marker Category menu item pe Marker categories Modify Settings Hame positive Fill color Line color fe Filled circles f Transparent circles Diameter 10 um Line width 1 ae W Add to saved categories soy com 3 On the Add tab in the Marker categories window give the name of the marker category select unique Fill and Line colors if necessary 4 Choose Filled circles or Transparent circles to determine the visualization type of markers 5 Type in the Diameter and Line width values of markers 6 Check Add to saved categories to add the marker category to Saved categories June 7 2011 Rev 1 3DHISTECH Ltd 60 68 Pannoramic Viewer 1 15 User s Guide 5 Working with Marker Counter licensed feature Modify Marker categories On the Modify tab of the Marker categories window select a category and modify its attributes if necessary pe Marker categories Add Modif Settings Select positive Hame positive Fill color Line color a 1 f Filled circles f Transparent circles Diameter 50 um Line width 1 ae soy com
15. SDHISTECH Ltd June 7 2011 Rev 1 3DHISTECH Ltd 15 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 A progress bar and an information box is displayed showing the status of the installation process 1 Pannoramic Viewer 1 15 RTM Setup Installing Please wait while Pannoramic Viewer 1 15 RTM is being installed SUOHISTECH Registering C Program Files Common Files SDHISTECH ClCHand all Output folder C Program Files SDHISTECH Wiewer Data Templates Extract mail_temp txt 100 Extract SlideRep1 htm 100 Output folder C Windows system32 Extract IplWrapper dil 100 Extract C Windows lsystem32Wgzlib dll 100 Created uninstaller C Program Files 3DHISTECH Wiewer Uninstall Viewer exe Output folder C Program Files Common Files 3DHISTECH Extract C Program Files Common Files S30HISTECH CICHand dll 100 Registering C Program Files Common Files 3DHISTECH CICHand dll SCHISTECH Ltd Next gt Cancel 8 Click Finish when the installation is complete 1 Pannoramic Viewer 1 15 RTM Setup n Completing the Pannoramic Viewer 1 15 RIM Setup Wizard Pannoramic Viewer 1 15 RTM has been installed on your computer Click Finish to dose this wizard June 7 2011 Rev 1 3DHISTECH Ltd 16 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 9 If you have a different version of the application it must be uninstalled first
16. UAS TECA Preuninstall Uninstalled Pannoramic Viewer version 1 15 00 44 Uninstalled 3DHISTECH s Applications version 1 15 0 10 Uninstall To continue the installation dick the Next button SCHISTECH Ltd June 7 2011 Rev 1 3DHISTECH Ltd 19 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 AN Important Keep the installation DVD or back up the compressed installation file it is needed for removing the application and also for upgrading the product 2 3 Uninstalling Pannoramic Viewer AN Important The digital slides that you open in Pannoramic Viewer or the files created by the application are not removed when you uninstall Pannoramic Viewer You can remove them manually if you do not need them any more 1 Start the removal process a From the DVD ROM I Insert the DVD into the DVD ROM ll If the start up screen does not appear automatically double click the Pannoramic_Viewer_RTM_15_00_53 exe file in the root directory of the installation disk b From the Programs folder under the Windows Start menu Press the Start menu button in Windows ll Open Program Files 3DHISTECH Viewer folder 2 Select Next Uninstall 2 4 Starting Pannoramic Viewer for the First Time 1 Start the application yy From the FES shortcut on the Desktop e From the Windows menu Start Programs 3DHISTECH Viewer June 7 2011 Rev 1 3DHISTECH Ltd 20 68 P
17. You can define the working path of the exporting process It is recommended to define the path in which the program to be called is located Parameters e lt IMAGE gt When the image data are exported the file name of the digital slide can also be transferred Run Select the size of the window in which the export procedure is presented e Normal window The program is launched in a normal window Minimized The program is displayed in a minimized window June 7 2011 Rev 1 3DHISTECH Ltd 24 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 e Maximized The program is displayed in a maximized window Image format The image format to be exported is defined here The following formats can be selected JPEG TIFF BMP and PNG Quality factor Only if the JPEG image format is selected you can set the quality factor ranges from 1 to 100 This setting is not possible for other image formats External 4pplication Call for Image Capture changes will take effect immediately Application C Program Filestirtariiswti_view32 exe re start in C Program FilesSIrhanview P Parameters s MAGES Rur Normal window Image format PNG vr 2 5 6 External Application Call for Annotation Export When administering annotations the currently displayed digital slide and a selected annotation can be opened in another program refer to section 3 6 2 You can make the corres
18. ameters only for fluorescent slides e Filter 1 B The name of the filter is indicated in brackets It is indicated as defined by the user o Exposure time ms This entry item informs on the exposure time for the individual image fields for this channel e Filter lt n gt The name of the filter is indicated in brackets It is indicated as defined by the user o Exposure time ms This entry item informs on the exposure time for the individual image fields for this channel Image parameters e Image compression This entry item shows whether a compression of the image data was carried out Yes or not No e Image file format This parameter indicates the image file format e Quality factor In the case of a JPEG compression the quality factor is indicated here Preview image Depending on the equipment of the digitizer an additional image of the barcode area is displayed or not Rotate Barcode Label Area by 180 Press this button to rotate the barcode image by 180 June 7 2011 Rev 1 3DHISTECH Ltd 50 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 10 Batch Processing By clicking the EX icon on the bottom of the tree view panel of the main window the selected slides and their annotations will be listed in the Batch Processing window in which an specific Image Analysis application can be selected for each annotation 1 Select the slide then the ann
19. and 007502032 The above mentioned granted patents granted utility model registered trademarks pending international and national patent applications and the other corresponding IP are the sole properties of the 3DHISTECH Ltd 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 S Food and Drug Administration nor any other regulatory authority The data and images obtained or viewed using this product are not intended for clinical or diagnostic use For performance evaluation only the performance characteristics of this product have not been established June 7 2011 Rev 1 3DHISTECH Ltd 4 68 Pannoramic Viewer 1 15 User s Guide Third Party Disclaimer LibTIFF TIFF Lib
20. annoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 e From an annotation link e By opening a slide mrxs file 2 Select the start up options of Pannoramic Viewer in Settings Options 3 Calibrate the slide display scale bar refer to section 2 5 7 2 5 Pannoramic Viewer Start up Options Various parameters are available for a desired user defined graphical appearance of the Pannoramic Viewer once the program has started These properties can be modified by selecting Options in the Settings menu An Options window for Pannoramic Viewer opens Thumbnail changes will take effect immediately Resolution changes will take effect at next Pannorarnic Viewer start Size Type Screen resolution f Small C Barcode area 6 DFI f Normal f Preview camera image Large Low resolution scanned image Viewer changes will take effect immediately Caching W Show thumbnails i Show slide tree Cache Folder CAProgramDatas3DHISTECHWiewertLocalCact vs External Application Call for Image Capture changes will take effect immediately Maximum cache size 50 O MB Application OO Clear Cache Start in FP l A Parameters MIMAGES Run Normal window v fe Preview Image format JPEG f Slide tracking history Slide Window Defaults changes will take effect at next slide open W Show slide preview Bottom Preview Mode We Show preview in full screen mode i Top preview Fit scanned area Quality fac
21. ant applications such as HistoQuant MembraneQuant NuclearQuant FISHQuant and DensitoQuant modules you can define algorithms to measure various parameters on a slide Combined with ImmunoScreener you can run the Quant algorithm on one slide or on a set of slides grouped into an ImmunoScreener project 5 You can upload slides to Pathonet or share slides for E School For more information on E School see E School 1 11 User s Guide One example of a server based teleconsultation solution is www pathonet org 1 2 Marker Counter Pannoramic Viewer includes Marker Counter as a licensed feature to count cells and objects manually You can define counter categories that Marker Counter uses and you can move and reset Marker Counter on screen After creating a Marker Counter annotation and placing markers within the region the application 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 e number of marked objects or labeled areas e percentage of positive cells or examined area e average intensity of marked objects within their category All measured parameters can be stored in the digital slide or can be exported to a database June 7 2011 Rev 1 3DHISTECH Ltd 11 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 2 Installing Pannoramic Viewer 1 15 2 1 Requirements for Installing and Using Pannoramic View
22. ar Image Capture molor Balance cave Brightness Red If Show scale bar E O Co 0 a AAA 0 Copy To Clipboard Export Gamma 1 00 Blue 0 I I I I Cloze 3 Modify the image properties with the editing options for example change its brightness contrast and or gamma correction values as needed If a slide was digitized in fluorescence mode by checking the Align Channel function color channel layers can be individually moved to the desired position with the arrow buttons June 7 2011 Rev 1 3DHISTECH Ltd 52 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer Pe Image Capture mi andtalione Colorozation ssl AAN Show scale bar Brightness J J i Red J J i y DAPI Blue v Contrast 0 Gree 0 DAPI aa Ll Fit Gamma f 1 00 Blue E Rhoden ae 4 Export the image e Click Copy To Clipboard to put the image to the Windows clipboard so that you can use it in another application e By selecting Export the displayed image will be opened with the raster image viewer application set previously in the Options window section 2 5 5 e Click Save to save the image to file into a specific folder 3 11 2 Saving a slide a Manually outside of Pannoramic Viewer e save the Pannoramic Slide and the folder with the same name as the MRXS file b From Pannoramic Viewer e press Ct
23. can be selected for this channel e The channels are displayed in their pseudo colors when the gt button is on To display the digital slide in gray levels this button must be in OFF position For gray level images only one channel can be displayed The button serves to optimize the digital slide for all channels through the Best fit function for optimizing single channels see section 3 5 1 June 7 2011 Rev 1 3DHISTECH Ltd 40 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer e The A button is used to optimize the digital slide for all channels by extending the histogram Min Max for optimizing single channels see section 3 5 1 e By clicking the E button the default settings are restored e The non digitized region of a digital slide is displayed with a grayscale value that has been defined by means of the slider Background color A relatively dark background is recommended slider shifted to the left The El button opens a Properties window which allows contrast brightness gamma and other values to be set for the individual channels For details on the settings see section 3 5 1 DAPI Blue FITE green Rhodamine orange Current 4rea a Eei Best fit Ji 3 PRR 3 7 Working with Annotations You can add layers annotations to digital slides to mark specific areas of the specimen Annotations can be superimposed on a digital slide to show previous
24. dow then click the Auto detect hardware settings button For further information on how to use the Ergodrive see section 6 Ergodrive 2 6 Configuring the on screen scale In Pannoramic Viewer a calibrated scale can be displayed on the digital slide window Because the scale integrates the current values for display screen resolution and pixel geometry the display screen must be properly calibrated before using the application This input is required only once unless your monitor is replaced with a new one or you change your monitor settings 1 Open the Slide Display Scale Setup window by selecting Settings Options Slide Display Scale Setup Slide Display Scale Setup Measure the length of the red line in millimeters and enter it below i Displayed line length kd Measured line length mm Extra slide display zoom factor 1 men June 7 2011 Rev 1 3DHISTECH Ltd 26 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 2 Select the length of the bar measure the displayed line with a ruler then type in the value in millimeters 3 Setthe multiplication factor enables extra zoom on slides 4 To apply settings and close the window click Apply To exit the window without applying changes click Cancel June 7 2011 Rev 1 3DHISTECH Ltd 27 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 Working with the Pannoramic Viewer AN Important Si
25. eft mouse button allow you to mark outline any desired image area For more accurate detection results leave some gap between the outer cells of the area and the outline while creating an annotation The end point of a given freehand drawing line must be located near the starting point for the marked area to be actually enclosed To call the window for specifying annotation parameters click the right mouse button Parameters can be specified in much the same way as for rectangular shaped annotations e Point annotation O To mark just a specific point rather than a whole area the Y button must be turned on To define an annotation click a desired spot with the left mouse button A special input window for definition of properties appears Create or Edit Annotation Annotation parameters Tate Point Annotation Comment Direction Title background color Outline color Cancel An annotation name must be typed into the Title entry field This name will also appear in the digital slide view A Comment to this annotation is an optional entry item A desired frame line color for that annotation can be selected in the Outline color input box A background color for the annotation area can be defined via Title background color Direction allows you to determine how the caption box is displayed to the given point June 7 2011 Rev 1 3DHISTECH Ltd 43 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Vie
26. el 7 Change the background color of the slide in grayscale June 7 2011 Rev 1 3DHISTECH Ltd 37 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 6 Changing Image Properties If the El button is activated the software displays a window where you can make modifications in property settings regarding brightness contrast gamma value and color matching for each single digital slide AN Important If you use a high quality screen the default settings for color reproduction gamma brightness and contrast are adequate These functions are mainly intended for highlighting specific image contents for training and documentation purposes or to match monitor screen features User modified settings are saved specifically for the active digital slide NOTE The applied color settings of the slide is used when creating Gallery or Classification Gallery in the Measurement Visualization module 3 6 1 Setting up colors on a slide When a slide is open click the EJ button on the toolbar to open the Properties window Adjust for histogram Color Adjust Color Ba ance Color Adjust Color Balance Current 4rea EL Best fit i Threshold oo Minh ax Default Save Hdi Brightness Contrast Gamma RGB channels June 7 2011 Rev 1 3DHISTECH Ltd 38 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer Ifthe Current Area button is activa
27. er Operating system Microsoft Windows XP SP3 Windows 7 32 64 bit EN HU Hardware Minimum Pentium P4 1 8 GHz 1GB RAM Recommended Pentium C2D DualCore 2 4 GHz 2GB RAM Monitor Recommended 96 DPI Screen resolution Minimum CRT 1280x960 TFT 1280x1024 Recommended CRT 1600x1200 or better TFT 1680x1050 1920x1080 or better LAN WAN LAN 10 Mbit s or better networking interface Minimum bandwidth to remote servers 1 000 kbit s DSL Disk space Minimum 110 MB 2 2 Installation You receive the Pannoramic Viewer installation files on an installation disk or downloaded in an executable file 1 Start the installation e From the CD DVD ROM I Insert the Pannoramic Viewer installation disk into the CD or DVD ROM ll Ifthe start up screen does not appear automatically launch the Pannoramic_Viewer_RTM_15_00_53 exe file in the root directory of the disk e From the compressed file run the Pannoramic_Viewer_RTM_15_00_53 exe file June 7 2011 Rev 1 3DHISTECH Ltd 12 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 2 Follow the instructions in the installation wizard and click Next to start installation TA Pannoramic Viewer 1 15 RTM Setup Welcome to the Pannoramic Viewer 1 15 RTM Setup Wizard This wizard will guide you through the installation of Pannoramic Viewer 1 15 RTM Itis recommended that you dose all other applicat
28. erver Logged in as mr test lastri E k Sdeserver se agr oz Er mr test lastni ogr 07 El el Test Dania m 4 mr Refresh AN Important When refreshing the tree view of the server the content of the selected folder will be updated only June 7 2011 Rev 1 3DHISTECH Ltd 32 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 4 Viewing Slides 3 4 1 Image creation method Slide images in Pannoramic Viewer are represented by a tiled image pyramid The image pyramid is a hierarchical structure composed of n levels of the same image of different resolutions This allows the rendering engine to grab only that bit of data that is necessary for a particular view of a digital slide image However if the user is zoomed in to a specific area of a large image then only those tiles needed to show the specific areas are downloaded This can lead to very large bandwidth savings because often only some aspects of a large image are interesting to the user The illustration below shows what the image pyramid looks like conceptually At each level of the pyramid the image is scaled down by 4 a factor of 2 in each dimension At the bottom of the pyramid is the given full size image Each set of 2x2 4 neighboring pixels is replaced by their average as the pixel value of the image at the next level This process which reduces the image size by half is repeated n log2N times until fi
29. feature related buttons are displayed in the main toolbar of Pannoramic Viewer after opening a slide Rotate slide 90 left Rotate slide 90 right Rotate slide 180 Flip slide horizontally me g E h Flip slide vertically Slider to rotate slide by from O to 360 degrees Reset rotation June 7 2011 Rev 1 3DHISTECH Ltd 36 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 5 Working with Fluorescent Slides Pannoramic Scanner allows you to create slides with maximum ten channels in fluorescent mode For more information see Pannoramic SCAN 150 1 15 User s Guide When you open a fluorescent slide Pannoramic Viewer offers you options that are available only for these kind of slides SENO tonnage o bh AE eo Magnification 11 69 Progress HAS W Fit scanned area le Preview f Viewing history f Preview and viewing History Delete Viewing History de ff Background color 6 Fi a e 1 Turn on off colors 2 Left click on a label switch on off current channel Right click on a label change the color of the channel pseudo colorization 3 Set optimal brightness value depends on zoom factor all channels 4 Set optimal contrast value depends on zoom factor all channels 5 Set optimal gamma value depends on zoom factor all channels 6 Properties window adjust brightness contrast and gamma channel by chann
30. ic slide DPI Dot Per Inch June 7 2011 Rev 1 3DHISTECH Ltd 7 68 Pannoramic Viewer 1 15 User s Guide Keyboard quick reference Keyboard Description shortcut Up Move slide upwards Down Move slide downwards Left Move slide left Right Move slide right Increase magnification Decrease magnification ESC Exit full screen mode F1 Show help window F2 Fit scanned area to window F3 1x magnification F4 2x magnification F5 5x magnification F6 10x magnification F7 20x magnification F8 40x magnification F9 Display one pixel at the highest resolution of the image on one pixel of the monitor F10 Menu F11 Toggle full screen mode F12 Switch to pan mode Ctrl During pressing Pannoramic Viewer switches to pan mode Ctrl C Change Slide tracking history color Red Green Blue Ctrl F4 Close active slide window Ctrl M Show hide magnifier Ctrl 0O Open slide or 3D project Ctrl P Show hide slide preview panel June 7 2011 Rev 1 3DHISTECH Ltd 8 68 Pannoramic Viewer 1 15 User s Guide Ctrl S Saves slide as a JPEG image file Ctrl T Show hide slide tree Ctrl V Switches between the Fit and Full View modes in the upper preview window on the slide panel In Fit mode the preview window shows only the digitized specimen cut In Full View mode the preview window shows the entire s
31. ically Arranges several windows currently open horizontally one beside the other Tile horizontally Arranges several windows currently open one below the other Hm a Cascade Arranges several windows currently open in a cascade FAA a Synchronize all slide windows Slide windows synchronized Links open windows for simultaneous navigation Full screen Maximizes currently selected window to cover the entire screen area Rotate 90 left Rotates Slide by 90 degrees left Rotate 90 right Rotates Slide by 90 degrees right Rotate 180 Rotates Slide by 180 degrees Flip horizontal Flips Slide horizontally me Ss a Flip vertical Flips Slide vertically Rotate slider Rotates Slide by dragging the slider EN Measurement Visualization Launches a window for the Measurement Visualization Modules HistoQuant MembraneQuant NuclearQuant FISHQuant Digital Slide window toolbar buttons la Show hide preview panel Turns preview image on or off Show hide magnifier Turns magnifier on or off June 7 2011 Rev 1 3DHISTECH Ltd 65 68 Pannoramic Viewer 1 15 User s Guide Appendix Toolbar Buttons m Properties window Shows or hides an operator panel for color matching Pan mode Allows you to shift the window contents using the mouse or keyboard commands if active n Create rectangu
32. ight The friction knob with which you can set the resisting force of the X knob can be accessed when the X knob is pulled down Y knob smoothness Zoom Pan Y X knob smoothness Pan X X Y resolution change Main features of the device e alternative velocities for XYZ e high resolution proportional positioning e fast and sensitive slide positioning across the entire travel range in sub u area at the same time e ergonomic adjustment for friction and height telescopable mechanism June 7 2011 Rev 1 3DHISTECH Ltd 64 68 Appendix Toolbar Buttons Pannoramic Viewer 1 15 User s Guide Appendix Toolbar Buttons Main window toolbar buttons Show slide tree Turns slide tree for digital slides on or off Show thumbnails Turns thumbnail view screen gallery on or off Open slide Opens a dialog window for adding a folder or opening a single digital slide ER New 3D project Launches a 3D project under the 3D Reconstruction Module ES Connect to teleconsultation server Logging in to a teleconsultation server to view digital slides Host teleconsultation If this icon is selected the host will create a group online teleconsultation Join teleconsultation If this icon is selected a client may join a group online teleconsultation if da Disconnect from teleconsultation server Separates the user from teleconsultation server Tile vert
33. ions before starting Setup This will make it possible to update relevant system files without having to reboot your computer Click Next to continue 1 Pannoramic Viewer 1 15 RTM Setup Please review the license terms before installing Pannoramic 3DHISTECH Viewer 1 15RTM Press Page Down to see the rest of the agreement General Terms and Conditions of End User License Agreement of the License for Pannoramic Viewer E PLEASE READ THIS AGREEMENT CAREFULLY THIS END USER LICENSE AGREEMENT EULA IS A VALID AND BINDING AGREEMENT BETWEEN YOU A5 A LICENSEE If you accept the terms of the agreement select the first option below You must accept the agreement to install Pannoramic Viewer 1 15 RTM Click Next to continue 5 I do not accept the terms in the License Agreement 3DHISTECH Ltd June 7 2011 Rev 1 3DHISTECH Ltd 13 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 4 If some of the prerequisites is missing click the Download button A Pannoramic Viewer 1 15 RTM Setup Review the prerequisites of the installation S3DHISTECH status Microsoft Visual C 2008 SP 1 Redistributable x86 Installed Intel Performance Primitives 6 1 1 035 x86 Installation files missing Some of the prerequisites are not found Press Download button to download them SCHISTECH Ltd 5 After the missing item has been installed click Next T Pannoramic Viewer 1 15 RTM Setup Review the prereq
34. isualization Modules O Marker Counter Activates Marker Counter feature licensed optional Digital Slide window toolbar buttons for fluorescence slides only Turn color channels on off Changes between gray level and color view Shows all available channels they can be turned on or off 3 Optimum displaying Optimizes the view according to the Best Fit method for all channels A Optimum channels Optimizes the view according to the Min Max method for all channels x Default colors Resets the settings to the default values Background color This slider is used for setting background color of the slide window June 7 2011 Rev 1 3DHISTECH Ltd 66 68 Pannoramic Viewer 1 15 User s Guide References References Pannoramic SCAN 150 1 15 User s Guide TMA Grand Master 1 0 User s Guide TMA Master 1 14 SP1 User s Guide June 7 2011 Rev 1 3DHISTECH Ltd 67 68 Pannoramic Viewer 1 15 User s Guide References Index A Annotati0N 2 3 7 11 21 25 26 34 41 42 43 44 45 46 47 51 52 55 56 60 62 66 B PCN FO OSS aE EE PP antes eae ctioe se ae psoas smc csainn E E seems aaeanmadeececee 3 51 BN A A A 23 29 39 49 C CE ENE aE E E E E E ee 2 10 11 29 30 32 a A A E A E 38 ES IU a nase esta ects So ns seein E ET 7 45 46 47 62 E OI Sarat o eii oO secues A E 2 3 26 34 35 36 64 F o o E N e e
35. ith pathologists June 7 2011 Rev 1 3DHISTECH Ltd 10 68 Pannoramic Viewer 1 15 User s Guide 1 About Pannoramic Viewer 3 Slides can be opened from the local computer or the CaseCenter via Pannoramic Viewer you can inspect the local slides and you can create annotations on them to mark interesting areas Pannoramic Viewer is a platform for the following applications called modules 4 With the 3D module you can reconstruct a specimen virtually from its cuts as a three dimensional object You can then view this object and recut it along other planes With the TMA module you can view and analyze slide sets in which each slide is a cut from a tissue microarray Combined with the ImmunoScreener module the TMA module provides you with a powerful tool to perform research scale analyses on digital slides With the ImmunoScreener module you can perform an immunohistochemical analysis on a slide set If you purchase the TMA module as well you can run your ImmunoScreener analysis on a tissue microarray and score the TMA project in ImmunoScreener With the Teleconsultation module you can upload slides to a dedicated CaseCenter server and share them with other Pannoramic Viewer users to request their analysis CaseCenter allows you to view remote slides slides stored on a 3DHISTECH CaseCenter server With this application you can also host a Teleconsultation session or participate in a session initiated by another user With the Qu
36. ive Rendering the digital slide is first loaded with a low resolution and afterwards updated with a higher resolution If Progressive Rendering is disabled the complete viewing area of the digital slide is shown with the selected resolution without any intermediate views e Always Progressive Rendering is always carried out e Local Area Network and Internet Progressive Rendering is carried out only if the digital slide is displayed via LAN or the Internet e Internet Progressive Rendering is carried out only if the digital slide is displayed via the Internet recommended setting e Never Progressive Rendering is never carried out Prefetch recommended If this option is active neighboring areas outside the visible zone are loaded This way a faster view build up process is reached Show Scale Bar By enabling this option a scale bar with a scale value appears in the slides window You can also set the colors of the scale bar the text and their background both for brightfield and fluorescent slides Bottom Preview Mode This is to define if the variable preview of a related specimen Preview the tracing mask Slide tracking history or both features Preview and Slide tracking history are displayed by default when a new digital slide is opened Toggle between these modes with the Ctrl Z hotkey Bottom Preview Zoom Allows you to define a default zoom value for displaying the variable preview image
37. ker Counter Statistics Category Number Rel Number Frequency Slide Information negative gt 40 2 927E 00 positive 4 BO E 4 S91E 00 6 If you need an additional marker category which does not exist yet create it 7 Save or export Copy to clipboard the measured parameters and images by clicking the El or the button If the markers are inside of an annotation also free hand annotation they are summed for that region In this way it is very easy to produce cell number area ratios for an actual studying 5 1 2 Exporting Marker Counter results You can display the most important values for each marker category in the Marker Counter window and you can export them as a CSV file June 7 2011 Rev 1 3DHISTECH Ltd 62 68 Pannoramic Viewer 1 15 User s Guide 5 Working with Marker Counter licensed feature e Number of marked objects labeled area or objects standard area e Percentage of positive cells in the cell population for example in a tumor In representative areas the number of positive cells must be divided by the sum of positive and negative cells and multiplied by 100 June 7 2011 Rev 1 3DHISTECH Ltd 63 68 Pannoramic Viewer 1 15 User s Guide 6 Ergodrive 6 Ergodrive Ergodrive is a 3 axes operating device that is able to carry out rapid and accurate slide positioning across the complete travel range within microns The adjustable drive knobs enable an ergonomic adaptation to friction and he
38. lar annotation This function is used to create a rectangular shaped annotation A Create polygonal or freehand annotation This function is used to create a freehand drawn annotation f Create point annotation This function creates an annotation that points to a specific spot D A j Create TMA Master Marker By clicking this button you can place markers on TMA Master slides T J Measurement options Allows you to measure a distance in a virtual slide and or create a measurement annotation Manage locate annotations Opens a window for organizing of the various annotations Create slide report Selects annotations for consolidation in a report Capture image Creates a bitmap snapshot of the virtual slide Show slide on tree By clicking onto this button you can mark the entry that relates to a currently opened virtual slide if the slide tree is shown E 1 Information options Displays a menu for turning view screen for annotations measurement annotations measurement data markers on and off and opening virtual slide information window fot Je Zoom to selected area mode You can select sample areas to be enlarged via mouse selection EO EY EA ES rox Ed Eo 6513 You can select from predefined magnification levels al Visualization Data Visualization data can be displayed as histogram scatter plot or an image gallery available only for Measurement V
39. lide Ctrl Z Change bottom preview mode Preview Slide tracking history Preview Slide tracking history Ctrl Alt V Display the current version of the Pannoramic Viewer June 7 2011 Rev 1 3DHISTECH Ltd 9 68 Pannoramic Viewer 1 15 User s Guide 1 About Pannoramic Viewer 1 About Pannoramic Viewer With Pannoramic Viewer you can inspect serialize and annotate slides digitized with the Pannoramic microscope scanners 1 1 3DHISTECH Product Family Pannoramic Viewer is the core 3DHISTECH product You can purchase additional modules for it to cover various virtual microscopy tasks The Pannoramic products support various tasks in the routine and research pathologist s workflow Brightfield ScanToServer te Fluorescent CaseCenter TMA as PathoNet E School 1 You digitize slides which can also be tissue microarrays or slides stained with fluorescent probes with a 3DHISTECH scanner microscope for example with Pannoramic SCAN 150 For information on the microscopes see Pannoramic SCAN 150 1 15 User s Guide 2 The Pannoramic scanner microscope creates digitized slides that can be saved on a local computer connected to the scanner or if the ScanToServer application is installed the slides can be uploaded through the scanner software directly to the CaseCenter server where slides can be evaluated shared and you can also create Teleconsultation session to discuss specific cases w
40. lide as a thumbnail image in the gallery as taken by the preview camera if the barcode area was recorded by the digitizer Otherwise only the digital slides thumbnail view is displayed e Low resolution scanned image Displays the digital slide as a thumbnail image taken by the scan camera in the gallery Caching You can locate a caching folder and determine the disk cache size 2 5 2 Slide window defaults Show slide preview panel This option displays the preview panel in the window of the digital slide if active Preview panel can be turned off again with the Ctrl P hotkey Show preview panel in full screen mode When selecting full screen mode the slide preview panel is displayed Top preview Fit scanned area If this option is active the preview image shows only that slide area which is actually covered by a specimen for display Show magnifier Allows a magnifier to be superimposed in the top right corner of a digital slide s window The magnifier can always be switched on and off with the Ctrl M hotkey June 7 2011 Rev 1 3DHISTECH Ltd 22 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 Step size Set how much the keyboard arrows shift the image For example if you set the step value to 50 Pannoramic Viewer moves the focus area with half of the image Progressive Rendering This option defines the mode of how the screen is built up and updated With Progress
41. ll slides 3 Select an easy to distinguish detail that is visible on all slides and move it to the center of the window for each slide 4 Click the Ep button in the toolbar to synchronize the slides 3 13 Recording Tracking History O rip You can use the trace that you record as a proof of the inspection procedure June 7 2011 Rev 1 3DHISTECH Ltd 56 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer Pannoramic Viewer can record how you move the mouse on the slide and what magnification levels you select at various spots This tracing mask is saved as a superimposed layer rather than and integral part of the image A position mask is even preserved on closing and reopening of the present digital slide NM Important You do not need to start or stop the recording process Pannoramic Viewer automatically records whatever you do to the slide 3 13 1 Retrieving the tracking history If Preview is ON only a preview of the digital slide is displayed without a position mask If the Tracking history option is selected only the position mask is displayed while the variable preview screen is OFF 400 400 f Preview f Preview f Tracking history f Tracking history f Preview and le Preview and tracking history tracking history Delete Tracking History Delete Tracking History To display both the variable preview screen and the position mask
42. ly created annotations on the slide the Display Annotations feature must be activated after clicking the L button When a new annotation is created Pannoramic Viewer automatically activates this feature June 7 2011 Rev 1 3DHISTECH Ltd 41 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 7 1 Creating Annotations in Pannoramic Viewer ERS a LE _ Rectangular Annotation a MAL N a poparen e Rectangular annotation If the m button is on a rectangle area can be marked by clicking into the digital slide with the left mouse button and keeping it depressed As soon as the button is released you are prompted to enter the name of the annotation Title and a comment in the Create or Edit Annotation window Ce tomes Annotation parameters Title Rectangular Annotation Comment Title background color Cutline color E ee Cancel While the title is a compulsory entry item which is indicated in that digital slide the comment is an optional entry In addition a frame line color Outline color and a background color Title background color can be defined for the caption area June 7 2011 Rev 1 3DHISTECH Ltd 42 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer Freehand annotation If the x button is on a click into the digital slide with the left mouse button sets the starting point for freehand drawing Further clicks with the l
43. monitor You can also enter the magnification level manually in the text field and then click the area that you want to inspect with that magnification Note that the highest magnification ratio that can be achieved on a slide is 2 1 meaning that one pixel of the digital slide is presented on two pixels in the slide window 3 4 6 Previewing a smaller area with a higher magnification 1 To enable the magnifier a small preview window in the top right corner of the slide window click the Sl button on the slide toolbar or use the Ctrl M hotkey 2 Move the mouse cursor to the area that you want to see in the magnifier June 7 2011 Rev 1 3DHISTECH Ltd 35 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 4 7 Zooming Zooming around a point 1 Click the me button on the slide toolbar if not activated 2 Select the point that you want to inspect then zoom with the mouse scroll wheel with the Ergodrive or with keyboard keys e Use the mouse wheel You can modify zoom level by rolling the mouse wheel back and front e Roll the Z wheel of the Ergodrive to zoom in or out e Use the plus and minus keys on the keyboard Zooming to an area 1 Click A on the slide toolbar 2 Select the area that you want to inspect with the left mouse button then release it 3 4 8 Rotating slides With this feature you can rotate slides by degrees and flip them vertically or horizontally The
44. nally an image of only 1 pixel average of entire image is generated as the top of the pyramid 3 4 2 Displaying information on the slide Each digital slide window displays the following two pieces of information e The size of the window currently on display in relation to the specimen and the selected magnification June 7 2011 Rev 1 3DHISTECH Ltd 33 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer e The loading progress of a current view with digital slides available on local sources the loading process is very fast so the progress bar is of secondary signification in this case However where digital slides on remote servers are accessed this bar shows the latest progress state of downloading When clicking the 1 button in the digital slide window a selection menu with information items relating to the digitized digital slide Slide info appears on the display 1 Y Show Annotations Show Measurement Annotations Show Measurement Data Show Markers Marker Counter Statistics Slide Information AN Important Select Show Measurement Data from the Viewer s INFO menu to display detailed measurement information according to annotations only when the analysis process is finished otherwise the slide must be reopened 3 4 3 Using the full screen mode To switch to full screen mode click the m button in the main toolbar or press F11 on the keyboard To return from the full screen mode
45. nce user privileges or access rights depend on Microsoft Windows settings some features of the Pannoramic Viewer may be not accessible for users with limited user permissions 3 1 Managing Folders in the Navigation Tree You can open slides one by one by browsing them from Pannoramic Viewer You can open them faster however if you add their folders to the navigation tree in the application You can add both local and remote folders to the navigation tree AN Important If a folder has been created under a different operation system language and its name contains a letter with double acute accent it cannot be identified by Pannoramic Viewer therefore slides in such folders cannot be opened Adding a folder to the navigation tree 1 Ifthe navigation frame is not visible click to display it 2 Depending on the location of the folder select the Local tab or the Teleconsultation Server tab 3 Inthe toolbar click 3 ES Open Slide or 3D Project Local Network List Preview O Ep Program Files Edo SLIDES 10301 07_HER2 769 MByte WE E SWShare e SWTOOLS oo siywork Update Tree Set Home Folder Add Folder June 7 2011 Rev 1 3DHISTECH Ltd 28 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 4 Browse for the directory that you need and then click Add Folder 5 If you want Pannoramic Viewer to start with this folder every time you open the application click Set H
46. o annotation e exam encrypted link generate link to annotation but only with limited functionality creating and editing are not possible e direct link full path or relative path is created to the slide 8 Open a text editor and copy the link into a text file Exporting annotations 1 Click the E button on the slide toolbar 2 Select the annotation or annotations you want to convert to another format 3 Click Export e Measurement annotations can be exported to a CSV file e Non measurement annotations can be exported to a HTML file that includes a referenced JPG file for each annotation June 7 2011 Rev 1 3DHISTECH Ltd 46 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 8 Measuring in a Digital Slide 3 8 1 Length measurement You can perform length measurement jobs via related annotations Although such annotations are saved and maintained as part of a digital slide they can be deleted again Refer to section 3 6 fora detailed description of the procedure to generate measurement annotations Apart from this working approach it is also possible to perform temporary length measurements gm 1 Pressthe button 2 Select the Measure Distance entry item 3 Define a starting point with the left mouse button and move the mouse to the desired end point keeping it depressed The distance reading from the starting point to the current position is indicated in um If the mo
47. ome Folder Removing a folder from the navigation tree Right click the folder and then select Remove Project from Tree from the shortcut menu 3 2 Opening Digital Slides You can open digital slides from a local storage disk drive or connected drive or remotely from a CaseCenter Pannoramic Viewer behaves differently with brightfield and with fluorescent slides 3 2 1 Opening slides locally To open a slide you can choose from the following options Select File Open e Press Ctri O e Click the gt button in the toolbar e Inthe navigation tree select the Local tab browse for the folder and then double click the slide e Ifthe slide is already displayed as a thumbnail in the preview frame double click the thumbnail 3 2 2 Opening slides from a 3DHISTECH CaseCenter server CaseCenter servers are set up by default so that only authorized users can access them A server administrator must give you a user name and password before you can open slides from the server in Pannoramic Viewer Depending on the type and speed of the connection some Pannoramic Viewer screens may take longer to load from the server than from a local drive 1 Click the Tm icon in the toolbar 2 Enter the URL or the IP address of the CaseCenter and log in to the server with your username and password June 7 2011 Rev 1 3DHISTECH Ltd 29 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer Connect to Telecon
48. otation s from the list 2 Choose the application or applications you want to run 3 Click the Add button to move the process to the Batch Processing List 4 Activate Export Settings options if necessary either removal of a process is available by selecting it and clicking the Remove button 5 Finally click the Batch Processing button when finished 6 After measurements are performed and saved to a file close the window Annotations MISPs Whole slide Every annotation 10301 07_ER_ DensitoQuant_Default 1030107 HE_ F1 Rectangle Annotation FISH_Default 10301 07 HER Freehand Annotation FISH Modified Rectangle Annotation 02 test01 MuclearGuant_ Default Add Remove Batch Processing List Slide Annotation MISP 1030107 ER Modeled Deiat 10301 07 HE_ 1 Annotation _O NuclearQuant_ Default 10301 07_HER2_ Her MembraneGuant 1030107 HER Freehand Annotation MembraneQuant Export Settings W Save Region measurements W Save Cumulative measurements W Save to single CSV Cos June 7 2011 Rev 1 3DHISTECH Ltd 51 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 11 Exporting Slides from Pannoramic Viewer Pannoramic Viewer allows you various possibilities to export slides or annotations to different file formats 3 11 1 Image capture 1 Setthe magnification factor and shift the image in the slide window as needed 2 Click the button in the slide toolb
49. ou can select the annotated areas for export using the button or remove them from the selection using the button Also you can select all the annotations with the button or deselect them with the button June 7 2011 Rev 1 3DHISTECH Ltd 55 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 Destination path The path where your slides will be stored Slides are named after the annotation names if any otherwise you can give an alternative file name AN Warning Depending on your settings the size of the exported area and the number of exported areas the size of the exported file can be quite large in some cases and the process can take unexpectedly long time 3 12 Synchronizing Slides in a Set One of the advantages of virtual microscopy over the traditional microscopes is that once you digitized the slide you can inspect a specimen with different stains In Pannoramic Viewer you can synchronize slides that belong together so when you move one of the slide image s horizontally or vertically Pannoramic Viewer shows the same area in the other s as well Besides magnification levels of the slides are synchronized and when modifying zoom on one slide the same step is applied on the other slide s 1 Open the slides that you want to synchronize It does not matter whether you arrange them in cascading or in any other way 2 Select the same magnification level for a
50. ponding settings in this field Application This option defines the program to which the image information is exported Browse for the folder of the application and select the executable file Start in You can define the working path of the exporting process It is recommended to define the path in which the program to be called is located Parameters When the image data are exported other parameters can also be transferred e lt SLIDE gt The file name and the path of the digital slide currently displayed are transferred e lt X1 gt The x value for the top left corner of the annotation is transferred June 7 2011 Rev 1 3DHISTECH Ltd 25 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 e lt Y1 gt The y value for the top left corner of the annotation is transferred e lt X2 gt The x value for the bottom right corner of the annotation is transferred e lt Y2 gt The y value for the bottom right corner of the annotation is transferred Run Select the size of the window in which the export procedure is presented e Normal window The program is launched in a normal window e Minimized The program is displayed in a minimized window e Maximized The program is displayed in a maximized window 2 5 7 Enable the use of Ergodrive After the Ergodrive has been connected to one of communication ports COM port activate the function in this win
51. rary 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 our website at http www 3dhistech com June 7 2011 Rev 1 3DHISTECH Ltd 5 68 Pannoramic Viewer 1 15 User s Guide Character Formats and Symbols The following character formats and symbols are used in this User s Guide Example Abbreviation or term that is explained in section Terms and abbreviations page 7 E
52. rl S on the keyboard June 7 2011 Rev 1 3DHISTECH Ltd 53 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 11 3 Export to TIFF Image Pannoramic Slide or to MetaXML With the Slide Export function you can export a whole slide or just the annotated areas to TIFF Image Pannoramic Slide or to MetaXML file format Choose Slide Export from the File menu RS Slide Export Original Settings Slide type Fluorescent Image file format JPEG Output Settings File format TIFF Image Magnification 1 1 Tile size JEG y 956 Image codec Uncompressed ROI Selection Available regions Caption Rectangle Annotation Whole Slide Important Output Channels Multichannel Channel Selection Blue DAPI Blue gt Green FITC green Red Rhodamine orange v Regions to be exported Caption Freehand Annotation Quality factor 20 Output Image Information Selected image information Image type TIFF Image Image size 3974 x 4046 Pitels Tile size 256 x 256 Pieles Number of tiles 256 Estimated image file size 48 Megabytes Aggregated Export Information Number of exported images 1 Esitmated total disk size 48 Megabytes Selected Region of Interest men When you save the slide as a TIFF Image the exporting result is a tiled TIFF Therefore applications such as Windows Picture and Fax Viewer cannot open this type of file To save a standard TIFF file u
53. s Title Freehand annotation Comment Title background color Outline color Delete Deletes the selected annotation Save to CSV Saves the information contained in annotations and measurement annotations as a file Values are separated by comma Send Link to Clipboard Copies a link to the selected annotations to the clipboard Export The currently displayed digital slide is opened in a predefined program and the marked annotation is transferred with its position data For information on defining an application see section 2 5 6 Close Terminates this dialog Creating a link to an annotation Tip You can use links to annotations and therefore to slides in E School training or exam materials When you copy the link in the address field of a web browser Pannoramic Viewer opens and the slide to which the annotation belongs is opened not the annotation directly June 7 2011 Rev 1 3DHISTECH Ltd 45 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 1 Click the button on the slide toolbar 2 Select the annotation that you want to save as a link 3 Click Send Link to Clipboard Send Link of Bookmarks to Clipboard o Magnification f meter school link Current 1 of exam encrypted link We Direct link Close e Magnification select the desired magnification level e mview school link choose this option to generate a normal link t
54. s contrast and gamma value on the Color Adjust tab and on RGB channels on the Color Balance tab By clicking the Default button the sliders for brightness and contrast are reset to the default value 0 the gamma value is set to 1 20 brightfield or 1 00 fluorescence Save settings by clicking the Save button Restore is used to recall the settings again This function refers only to the current digital slide If another digital slide is called the saved values will not be available June 7 2011 Rev 1 3DHISTECH Ltd 39 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 6 2 Setting up colors on a fluorescent slide If specimens were digitized in the fluorescence mode all channels are displayed in the bottom part of the image The software supports up to nine channels In the example below three channels were digitized DAPI Alexa 488 and Cy3 age la Cie SG Ee Ee o E 03 0 fo MAA e SAL Magnification 10 09 Progress PO 100 pm o MINS FlrC Ice E 2 te E Background color The pseudo colors are taken over as specified in the Pannoramic Scanner control software before digitization but can still be changed in Pannoramic Viewer There are various options for changing the representation of digital slides e Individual channels can be shown or hidden by clicking on the respective channel e By clicking with the right mouse key on the respective channel another pseudo color
55. s digital slide This value depends on Pannoramic Scanner control software settings and your hardware configuration e Micrometer pixel Y Pixel resolution is 0 322500 um in Y direction for this digital slide This value depends on Pannoramic Scanner control software settings and your hardware configuration Scan information e Scan start This digital slide was digitized on March 4 2009 at 11 56 58 e Scanning duration Digitization time was 1 hour 20 minutes and 33 seconds e File size This digital slide occupies about 240 76 MB of hard drive space AN Important If a digital slide is opened via a teleconsultation server no respective value is indicated e Slide dimensions in pixels width x height The size of this slide is 38 656 x 50 688 pixels each single image has a size of 1 400 x 1 000 pixels in standard configuration AN Important The slide size is referred to the total theoretically digitized area of a specimen not to the actually digitized specimen e Scanned field of view count To create the digital slide a total of 1815 single images were taken June 7 2011 Rev 1 3DHISTECH Ltd 49 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer e Profile name The name of the profile under which the slide was digitized If a slide was digitized in fluorescent mode the individual channels are displayed with the respective parameters Fluorescence par
56. se the image capture function refer to section 3 9 1 June 7 2011 Rev 1 3DHISTECH Ltd 54 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 1 Output settings You can set up the output file parameters in this window region a Output file formats TIFF Image Pannoramic Slide and MetaXML b Magnification the level of magnification c Tile size size of tiles from 256 x 256 up to 2048 x 2048 d Overlap only for Pannoramic Slides and MetaXML the percentage of overlap between two tiles e Image codec for TIFF Image uncompressed or JPEG for Pannoramic Slide JPEG PNG BMP for MetaXML JPEG PNG BMP TIFF f Quality JPEG compression level g Burn in slide annotation if checked in the annotation is burned in the slide as the part of the image h Burnin slide markers can be checked only if you choose TIFF Image or MetaXML as an output format i Output channels modify settings mainly if a fluorescent slide is to be exported It has three options Multi channel a selected channel can be replaced by another one written into the new slide for example you can set a GGR channel instead of BGR Il Single channel one selected channel is written in the new slide III Current View the current color settings is written in the slide 2 ROI Region of Interest Selection You can select the whole slide or just some annotated areas for export Y
57. sultation Server Address 10 130 131 213 User Name test Password 4 Secure connection Cancel After you logged in to the server you can see the remote folders and slides in the navigation tree on the Teleconsultation Server tab 3 3 Upload Slides to CaseCenter 1 You can select any of the following options to upload slides to the server Select a slide or folder containing a set of slides from the tree in the Local tab Right click the slide or folder then choose Upload Slide s to Teleconsultation Server e Batch upload is available when creating a list of slides from various locations folders or disk drives After selecting a folder or slide in the Local tree press the el icon below the Navigation Tree panel Press the el icon to remove slide s from the list il The items added to the list can be uploaded to the server by clicking the icon Local Local fe NO ep 10301 07_HER2 2 cel fad mips E k NO a 10301 07_ER_I g 0 98 Bs all l m E Slide Hame Slide Path TOS01 0F_ HE I 17 O NSLIDES SNO41030 1030 07 HER2 CASLIDES MO 030 June 7 2011 Rev 1 3DHISTECH Ltd 30 68 Pannoramic Viewer 1 15 User s Guide 2 Type in the Address of the server the User Name and Password in the Connect to 3 Working with the Pannoramic Viewer Teleconsultation Server window Click OK to continue Connect to Teleconsultation Server Address 10 130 131 213
58. ted the histogram of the currently displayed image segment is shown If 1 1 is active the histogram for the complete digital slide is shown The option 1 1 is available only if the specimens were digitized by means of a Pannoramic Scanner control software version 1 14 or higher Inthe upper part of the window there is a graphic image of the color values of the currently displayed digital slide or image segment The black line with squares represents the characteristic curve and it can be shifted to left right or upward downward by dragging the squares If brightness contrast gamma or RGB values are changed the sliders below are set automatically to the corresponding positions Representation between the grayscale value ranges from O to 255 and the number of grayscale values is linear For logarithmic representation the log button must be activated Use Best fit button for optimal setting on the basis of the threshold value defined in per thousand In brightfield mode all three color channels RGB are optimized Color Balance tab For fluorescence this function can be executed for each single channel The Min Max button is used for optimal setting by extending the histogram between the minimum and maximum values In brightfield mode all three color channels RGB are optimized Color Balance tab For fluorescence this function can be executed for each single channel The three sliders have a direct influence on brightnes
59. tor eo gt f Preview and slide tracking history Iw Show magnifier Bottom Preview oom e l E E External 4pplication Call for Annotation Export changes will take effect immediately Step size 50 a Fit C 100 a Progressive Rendering gt 200 Application E C Always fe 400 Start in O f Local rea Network and Internet as Slide Tracking History Color Parameters lt SUIDE gt ee la A OY o gt e Internet recommended f Red Never C Green Rur Normal window f Blue We Prefetch recommended a lu Ergodriwe enabled changes will take effect at nest slide oper Brightfield colors Fluorescent colors Auto detect hardware settings COM port Coma cres June 7 2011 Rev 1 3DHISTECH Ltd 21 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 2 5 1 Thumbnail Size This option allows you to determine the size of the various preview images Small Normal or Large displayed when the preview function is on The larger the thumbnail images are the more space is available for the name of the digital slide Type This option defines the representation mode in the thumbnail view e Barcode area Displays only the barcode area as a thumbnail image in the gallery if the barcode area was recorded as an image by the digitizer Otherwise only the digital slides thumbnail view is displayed e Preview camera image Displays the barcode area and the digital s
60. uisites of the installation SDH E ECH Status Microsoft Visual C 2008 SP 1 Redistributable x86 Intel Performance Primitives 6 1 1 035 x86 All of required components are installed To continue dick Install button SDHISTECH Ltd June 7 2011 Rev 1 3DHISTECH Ltd 14 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 6 Choose the installation folder for Pannoramic Viewer Click Browse for locating a different folder than the default one then click Next to continue T Pannoramic Viewer 1 15 RTM Setup Choose Install Location Choose the folder in which to install Pannoramic Viewer 1 15 RTM SDHISTECH Setup will install Pannoramic Viewer 1 15 RTM in the following folder To install in a different folder click Browse and select another folder Click Mext to continue IC Program Files 3DHISTECHWiewer Space required 17 0MB Space available 73 3GB SDHISTECH Ltd 7 Choose the Start menu folder A Pannoramic Viewer 1 15 RTM Setup Choose Start Menu Folder Choose a Start Menu folder for the Pannoramic Viewer 1 15 RTM 3DHISTECH Shortcuts Select the Start Menu folder in which you would like to create the program s shortcuts You can also enter a name to create a new folder 3DHISTECH Pannoramic Viewer AAA Logo 2010 ABBYY FineReader 7 0 Administrative Tools Adobe Artweaver Camtasia Studio 4 DivX Plus Extras and Upgrades GanttProject E Do not create shortcuts
61. use button is released a new starting point can be defined 3 8 2 Determination of perimeter and surface area AN Important Neither a perimeter nor a surface area value can be determined directly To define any of these two parameters an area must be defined at first using rectangular or freehand annotations refer to section 3 6 Having completed this click the button to turn the Manage Annotations window on This window lists the perimeter and surface area values related to the given annotation To save these data click Save to CSV refer to section 3 6 2 June 7 2011 Rev 1 3DHISTECH Ltd 47 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer 3 9 Displaying Information Relating to a Digital Slide After clicking the 1 button and selecting Slide Information a window with information items relating to the digitized digital slide is displayed These information items depend on the hardware used the hardware control software version and the mode of digitization Slide Information Optical parameters Objective name Objective magnification Camera adapter magnification Micrometer piel Scan information Scan start DO MMA yr HH MM SS Scan duration HH MM 55 File size Slide dimensions in pixels width height Scanned field of view count Profile name Fluorescence parameters Filter DAPI Exposure time me Digital gair Number of focus level Focus
62. wer e Measurement annotations A measurement annotation is provided for displaying a required distance or spacing Click the button then select the Create Distance Measurement Annotation entry item By clicking with the left mouse button the marked spot may be chosen as starting point now By keeping that key depressed dragging it accordingly and releasing it the end point of measurement is defined AN Important When you save the slide each annotation is saved as a separate layer if several users mark up the slide with annotations their annotations can be managed and eventually be deleted independently of each other 3 7 2 Managing Annotations e Click the a button on the slide toolbar A window appears showing all the annotations and measurement annotations on the slide Manage Annotations Annotations Rectangular annotation Permeter 1460 3 um Area 132721 9 ume Freehand annotation Perimeter 864 5 um Area 495145 ume Distance Measurement annotations Locate Edit Delete Save ta CSW Send Link to Clipboard Esport Scanmap Locate Changes the main screen view resulting in that the selected annotation is shown Edit Opens another window with options for editing the properties of a previously marked annotation June 7 2011 Rev 1 3DHISTECH Ltd 44 68 Pannoramic Viewer 1 15 User s Guide 3 Working with the Pannoramic Viewer Create or Edit Annotation Annotation parameter
63. xample Words or characters that appear on the screen These include field names screen and window titles pushbuttons and menu names paths or options Keys on the keyboard For example function keys such as F11 or the Ctrl M 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 Important gt gt Contains an important piece of information or a recommendation The application will work if you choose not to follow the recommendation but its performance might be less than optimal Tip Contains a suggestion about using the application in some other way or to some interesting purpose June 7 2011 Rev 1 3DHISTECH Ltd 6 68 Pannoramic Viewer 1 15 User s Guide Terms and abbreviations Annotation A particular detail of a digitized slide Measurement visualization modules perform measurements on annotations CSV format Comma Separated Value Digital slide Slide digitized with a scanner microscope for example Pannoramic Scanner Consists of an MRXS file and a folder with the same name as the MRXS file Field Annotation in an image analysis module Layer A group of objects matching the same stain and size criteria MISP A segmentation and measuring algorithm is stored in a MISP file MRXS File extension of a digitized Pannoram
64. xt T Pannoramic Viewer 1 15 BETA Uninstall Uninstalling Please wait while Pannoramic Viewer 1 15 BETA is being IDHISTECH uninstalled Delete file C Program Files 3DHISTECH Wiewer MView exe Delete file C Program Files Common Files S3DHISTECH SlidelOINet dll Unregistering C Program Files 3DHISTECH Wiewer Data DLLs WIMMeet dll Delete file C Program Files 30HISTECH Wiewer Data DLLs WIMMeet dll Unregistering C Program Files 3DHISTECH Wiewer Data DLLs HTMLReport dll Delete file C Program Files 30HISTECH Wiewer Data DLLs HTMLReport dll Unregistering C Program Files 3DHISTECHWiewer Data DLLs MrxsThumbnailer dll Delete file C Program Files 3DHISTECHWiewerWDataWDLLsWMrxsThumbnailer dll Removing Files Delete file C Program Files 30HISTECH Wiewer ModuleSettings ini Delete file C Program Files 3DHISTECH Wiewer MView exe SCHISTECH Ltd June 7 2011 Rev 1 3DHISTECH Ltd 18 68 Pannoramic Viewer 1 15 User s Guide 2 Installing Pannoramic Viewer 1 15 12 Click Finish to close the wizard i Pannoramic Viewer 1 15 BETA Uninstall a a Completing the Pannoramic Viewer 1 15 BETA Uninstall Wizard Pannoramic Viewer 1 15 BETA has been uninstalled from your computer Click Finish to cose this wizard Cancel 13 After the previously installed applications are removed click Next to launch the installation wizard then follow steps 2 8 Check computer for installed versions S

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