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1. Diff morph Pr sence de n crose Index mitotique Invasion locale Emboles vasculaires Engainement p rinerveux Media B11 1428 HES ROI ROI 2 Regions of interest 2 B11 1428 CK56 x P Name ROI 1 Surface 4 26 mm2 2 33 mm Average RGB R 198 G 100 B 167 Type Standard Comments Figure 4 General overview of the IPW interface after opening a media Black section Tool bar Tool bar with icon providing navigation display drawing Action tool bar and export functions Copyright CCITI all rights reserved 5 CCITI Viewer User s Manual 2012 1 3 The Media viewing area The media viewing area allows you to work on the image or sequence with review annotation and export functions When opening a slide the viewer displays the digital slide by default at the lowest magnification other settings can be applied when opening the viewer from a CCITI application Several windows and tools are visible on the viewer window as described below aHa Continuous zoom Scroll bar Figure 5 Overview of the media viewing window Red section Left panel Zoom out in at all magnifications continuously by Continuous zoom scroll bar moving the scroll bar up amp down Fixed map of the entire media To visualize current position of the field of view To move rapidly between distant locations Green section upper left corner Preview window
2. a set of pixels and its corresponding zoom level So It s possible 1 That several users create their own ROI on the same image 3 To view a ROI at various zoom levels when navigating through the media 3 To have specific users rights create modify view ROI Remark The creation of a ROI does not modify the image It s just added information to the image which is superimposed on the image The ROI Manager has 2 main functionalities o Drawing Tool Create modify ROI The drawing mode allows you to draw modify edit a ROI on the image o Manager tool of information associated to each ROI The offered possibilities are detailed in the following chapters Copyright CCITI all rights reserved 23 CCITI Viewer User s Manual 2012 3 1 Draw a ROI The drawing mode allows you to draw modify edit ROI on the image To activate the drawing mode click on the button AJ in the action tool bar T Important Note When you are in drawing mode you can t navigate with the mouse in X Y To navigate in X Y in drawing mode you can use the keyboard arrows keys Alternatively go back to the navigation mode by clicking on the navigation button in the action tool bar aa Navigation icon Choose the drawing parameter amp the ROI type The color thickness and especially the type of the ROI must be defined before drawing and or can be edited afterward To choose a specific color and thickness of the draw
3. button e With the zoom scroll bar Click left on one level of the zoom scroll bar to go at the wished magnification Click left on the blue cursor hold on and move up or down to zoom out in s amp AA Sa Ww iO e oe Click left on the level to go at 0 31x ae Click left amp hold on the blue cursor Move up or down to zoom out in 0 31x Figure 9 Zoom in out with the zoom scroll bar e Zoom in on a predefined area Define an area rectangle where you wish to zoom in O Right click on the media and hold on Then draw a rectangle which defines the area you want to zoom in o Release the right mouse button It will automatically zoom in and center on this defined area Copyright CCITI all rights reserved 10 CCITI Viewer User s Manual 2012 2 1 3 Navigation for DICOM sequences To view DICOM sequences at different magnifications several possibilities are available e With the mouse buttons O Click left anywhere on the media to zoom in O Click right anywhere on the media to zoom out Each click change the magnification from 1 level in the zoom scroll bar e With the zoom scroll bar 1 Click left on one level of the zoom scroll bar to go at the wished magnification Click left on the blue cursor hold on and move up or down to zoom out in To navigate in the different images of the sequence there are two possibilities e With the mouse scroll wheel O Scrolling up once with the mouse Move
4. drawn to answer the question You dont have to click on the drawing icon the drawing type is automatically selected by the software After drawing the ROI its distance or surface is automatically calculated and added at the right side of this question as shown below You may draw as many ROI as needed to answer the question the associated distances or surfaces are added and the number of drawn ROI is indicated at the right side of the question name Tumor Yes No 2 22 435 mime 7 70 mm Figure 46 Answered Distance Surface question For Boolean or list of values question according to the answer you choose new contextual question fields may appear In some contexts you will find this icon Ke before some question This gives you access to a knowledge sheet that presents explanations about the questions Click on the icon K before the question This will open a new window with the K sheet in relation with the question At the top left of the form there s a button showing the name of the form It allows the downloading of your answers to the form in an XML format Click on the button to open a new window to download the XML file Forms Criteria Diagnosis Diagnosis Figure 47 Download of the answers to the form For more information about the form functions please consult your application manual Copyright CCITI all rights reserved 39 CCITI Viewer User s Manual 2012 7 Index of toolbar bu
5. mark Region of Interest on the slide at any time during the screening by clicking with the left button of the mouse on the slide see chapter 3 for annotation handling O Click on Valid to start the screening Copyright CCITI all rights reserved 21 CCITI Viewer User s Manual 2012 ROI size 100 pixels ROItype cpandard v Figure 20 Scan slide setting window Remark The level of zoom used by this function will be your current level of zoom when you activate the function You can pause the automatic scan by clicking on the button li To resume it click again on this button To stop the automatic scan click again on the button a l Copyright CCITI all rights reserved 22 CCITI Viewer User s Manual 2012 3 Annotate Digital Images A Region Of Interest ROI corresponds to a part of the image that the user wants to emphasis during his analysis Several reasons are possible want to justify my diagnosis by indicating one or more ROI 11 have a doubt on a specific part of a media want to ask a question about this specific region of the media emphasize a region of the media because it is very rare or very interesting for a learning purpose i want to make measurements area length RGB levels etc or use sections annotation to make a 3D reconstruction A ROI is characterized by 3 A name and a set of optional information describing it 3 A part of the image that means
6. media as soon as the viewer remains opened To recover the default settings click on reset in the settings control window Once the viewer is closed the default settings will be applied automatically at the next opening of the viewer 2 2 3 Grey level Cf chapter 3 4 Access to local Grey level measurement 2 2 4 Preview window The preview window allows you to have a view of the whole media To localize the area you are viewing on the media this area located in the blue rectangle is the area you are viewing in the navigation window Simi fii eai r gt y aw Localization of the gt current field of view Figure 14 Preview window map of the sample Note The dimensions of the blue rectangle are dynamically calculated according to the zoom level Copyright CCITI all rights reserved 14 CCITI Viewer User s Manual 2012 Using the preview window you have two ways to navigate through the media by moving the blue rectangle O Press and hold down the left button of the mouse on the blue rectangle then move the rectangle Point the mouse cursor at the location you want to reach on the sample and left click outside of the blue rectangle It will automatically move the blue rectangle to this area and center the view if possible on the clicked point a Cad M lie ita at A EAC a E a a Pl lh ee a Left click on the region W you want to reach i BEFORE ACTI
7. to the next image in the sequence O Scrolling down once with the mouse Move to the previous image in the sequence e With the Z navigation scroll bar Click left on one level of the Z navigation scroll bar to go at the wished image section Click left on the blue cursor hold on and move up or down to move to wished section Navigate in the different sections of Figure 10 Navigate in a DICOM sequence Copyright CCITI all rights reserved 11 CCITI Viewer User s Manual 2012 2 2 The visualization tools Several buttons in the Toolbar are available to configure your viewing area If you place the mouse cursor on an icon a brief description of the function appears TE Bua42e Hes y m i pt i L S Tr u d r _ a L 5 T E s e A ea gt 27 us F r Figure 11 Contextual description of the icons function The list of the navigation icons and a brief description of the functions are listed below What it does Toggle on off to full screen mode Display control settings Display grey level Display or hide the preview window Display or hide the magnifying glass Display or hide the scale Display or hide the draws done on the media Copyright CCITI all rights reserved 12 CCITI Viewer User s Manual 2012 2 2 1 Full screen mode Remark Function not available with the thin version of the viewer Use the function F11 of your keyboard To extend the IPW viewing window to a full scr
8. CCITI Viewer User s Manual 2012 User s Manual CCITI Viewer 02 11 2012 Version build 20121102 170523375 Copyright CCITI all rights reserved 1 CCITI Viewer User s Manual 2012 Table of Contents 1 VIEWER IMAGING PATHOLOGIST WORKBENCH INTRODUCTION cececcscscecsccsceceecsces 3 1 1 MINIMUM amp RECOMMENDED WORKSTATION CONFIGURATIONS ccccccccccccccccccccccccccccccccccccccscecscecccecccs 3 1 2 GENERAL VIEW OF IPW vcissscscccctcccacdersaccescawcnccaanaeanceeaectandavwecciaeancascdebsesacsasiutacdersesciaensesecsaeuscasies 4 1 3 THE MEDIA VIEWING AREA ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccscccccccccccccccccccccccccsocccccsoeccccs 6 2 MEDIA RE EW coicc E stra stlouts Sowa elev outa wes Ganerenadunnetiae 8 2 1 NAVIGATE INTO THE MEDIA cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccsccccccceccccsocccs 8 211 FY een 1 aa 1 a ee eT 8 9 ed OP ZOOMIN ZOOM 0 am eee em Or nen ne E 9 2 1 3 NAVIGATION FOR DICOM SEQUENCES wisssicsscsusscecesndiauneedtsecncebeeusteudVexeateedbcacetensiveveaabasanidbeeeedessgecesw bese 11 2 2 THE VISUALIZATION TOOLS ssssesssssssosososseosssossosscssossossosessosssssssosssosseosossssossosossosssssssosssssseossssss 12 Zoek FULLSCREEN MODE see E 13 222 DISPLAY CONTROLSETTINGS saceccaccasnsreccceneracdenesacssteacysesieccacdanavesnca stec iA 13 eo SREY WEY E enc ecteavece cia ven cauaova nea cudinaeedsmriin
9. ON AFTER LEFT CLICK Boems n Figure 15 Navigation with the preview window e Change the position of the preview window o Put the mouse cursor inside the preview window outside of the blue rectangle 1 Press and hold down the right or left button then move the window until the wanted position e Change the dimensions of the preview window Put your mouse cursor on the black border of the preview window The cursor shape will change from a hand shape to a double side arrow head shape o Press and hold down the left button on the black border then move the mouse to change the dimensions of the window The proportions of the preview window are automatically preserved Copyright CCITI all rights reserved 15 CCITI Viewer User s Manual 2012 2 2 5 Magnifying glass window The magnifying glass window allows you to have an instant view at the next zoom level or another according to your setup of the part of the media centered on the mouse cursor a j is f x e a W a F x2 extra magnification for the cursor pointed d region achieving x2 5 x1 25 magnification of the field of view Figure 16 Magnifying glass e Change the position of the magnifying glass window Put the mouse cursor in the magnifying glass window 11 Press and hold down the left button then move the window until the wanted position e Change the dimensions of the magnifying glass window Put your mouse cu
10. Yellow section upper right corner To display extra magnification where the mouse Magnifying glass cursor Is pointed Black section lower right corner l l l l g To display horizontal and vertical scaling Scale Bar Pink section central box To navigate through the media XY and zoom Media section Copyright CCITI all rights reserved 6 CCITI Viewer User s Manual 2012 The main components and actions are O The Media section which shows the part of the image according to the zoom level and the positioning X Y on the media The user can navigate through the media by moving in X Y and by zooming in out The preview window by default located on the top left corner of the viewing area It shows a map of the entire media and shows the location of the field of view thanks to the blue rectangle So the user can easily know where is located the region currently reviewed 3 The magnifying glass by default located on the top right corner of the viewing area It shows an extra zoom of the media X2 by default but you can edit it at the location of the mouse cursor For example if a digital slide is shown at x5 magnification the magnifying glass will show the region pointed at x 10 magnification The scale which gives you the horizontal and vertical scales A detailed description of the use of each tool is given in the following chapters Copyright CCITI all rights reserved 7 CCITI V
11. anization of the windows Display each window side by side Display windows in cascade Close all the displayed media To close one of the displayed medias click on the Reduction button located at the top right of the media window CCIM Viewer Build 20120323 093806515 re d 3 B11 1428 HES Paan a lL e GIN B11 1428 HES Figure 18 Closing of the displayed media Copyright CCITI all rights reserved 19 CCITI Viewer User s Manual 2012 2 3 2 Synchronization of media p XY relative Synchronized navigation through several media In multimedia mode you can decide to synchronize the navigation of each media in order to navigate simultaneously in all the media in the same manner It means each movement and change of magnification will be applied to all the selected media It is particularly useful when reviewing HES amp corresponding Immunohistochemistry of a digital slide or when reviewing different phases of a MRI sequence for example O Open all the media to review O Select a reference point on the media that you can easily recognize on each media and position this point in the center of the window or in a corner of each window Take care to select the same magnification for each media O In the left panel select X Y relative choice then click on the synchronization button p Your media are now synchronized To go back to standard n
12. arker annotation is an exception You can mark several time your slide without having to click again on the marker icon To stop the annotation process click again on the Marker icon Alternatively you can right click on the image take care to click in an area outside any drawn ROI A contextual window appears allowing you to choose the ROI to draw Toes h Draw aline Ea Z Draw a polyine S Draw a curve ei EEN C Draw a rectangle i D _ Draw a circle Ai 18 _ Draw a polygon Rees E Draw a surface us E Draw a marker Figure 22 contextual ROI selection Window Copyright CCITI all rights reserved 26 CCITI Viewer User s Manual 2012 3 2 Delete a ROI To delete a draw several possibilities are available Way A Select the draw you want to delete by clicking on the center of it in drawing mode and use the key Del or Suppr on your keyboard Way B Click on the button Select a drawing Ld in the action tool bar then click in the middle of the draw to delete Then click on the button Delete selected drawing R in the action tool bar Way C Select the draw you want to delete and use the right click on it on the border or inside the draw to open the contextual menu Then select Delete in the contextual menu Example delete a draw using the contextual menu Figure 23 Delete a ROI contextual menu Note When a ROI is selected black squares ap
13. ausiouenccevsansceetn 28 3 3 1 ROI EDITOR EDIT THE ASSOCIATED INFORMATION ccceccececcccccsccccccsccceacsceacsceeeacecenceeeaceeeaeeceeeaceeeacess 28 33 2 EDITTHE ROD IDISPLAY PARAMETERS sccvcsciccuccecscsoncasebecauvuiucctbid houkedenesontedvederdawtilentaswuethiuvereeintsiaucencoes 28 Sc IG Ne ee ce iecee seem E R 30 3 4 ACCESS TO LOCAL GREY LEVEL MEASUREMENT cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccsocccs 31 de TE OO IN C TIONS cruci E E 32 A L EXPORT VIEW tree dawcrtoccetrenwenteusuceciedeseousasceuaccnisusecnaueudeuenedeostaneteacuaisutewsducseestetesenstaueteonseacess 32 4 2 EXPORT OF A REGION OF INTEREST cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccsccccccsceccccs 33 4 3 EXPORT A PREDEFINED AREA ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccsccccccsocccccs 34 4 4 EXPORT A FIELD OF VIEW FOV OR A ROI TO WORD OR POWERPOINT ccsceccsceccsceccscescsceccccscecees 35 5 CUSTOMIZE YOUR INTERFACE sccsascistacnsnssctessavacasnaceiasssastiwemeassaecmsnedendswaselenscuiPacacnamsesnesoeveaswse 36 5 1 ORGANIZE WINDOWS ssccscstecewcastaienciwsdenscsciesoscacndavsweusnacacedwesosewesuanssavetawsacasapewasdweansusesestensaneesnaes 36 5 1 1 MODIFY SIZE OF WINDOW Swasecciccanciniscu ccecsumesetsunnsceuascuscsacuaurnseccuanucadedouestacuat vols atieamwsieeauataskaleheataees 36 SA2 DIPARANI E Pe re ORE ee eer ee 36 Bicz IPERSONAIL SE ITINGS cc cvcccucccc
14. ave it where you want on your computer as a JPEG file This will open a dialog box where you will be able to choose the name of the file and where you want to save it on your computer You can decide if you want to export the view with or without the ROI displayed The image is exported along with the media name the viewing magnification and the size x y in mm of the image 08 _2076_5 1 44x Figure 31 jpg exported image with annotation Copyright CCITI all rights reserved 32 CCITI Viewer User s Manual 2012 4 2 Export of a Region of Interest You can export a region of interest To do so select a region of interest then click right on the ROI and select Export in the contextual menu This action allows you two types of export In the Clipboard so you can paste it in a document O Ina file so you can save it where you want on your computer as a JPEG file This will open a dialog box where you will be able to choose where you want to save it on your computer Change the color Change the thickness Figure 32 Export a ROI ia 2 we Alternatively in Drawing mode select a ROI and click on the icon the closest icon from the ROI icons with legend export the selected draw when putting the mouse cursor on it The ROI when exported as a jpg file is exported along with the name of the media the viewing magnification the name of the ROI the surface if relevant and the size of t
15. avigation mode click on the button _ ee EE re Stk oe h Reference _ point ziu Bo g y KY relative Bli 1426 HES Figure 19 Synchronized mode Note If you choose the X Y absolute mode when starting the synchronized mode IPW will synchronize the media using the absolute coordinates of the media Thus this mode is dedicated to images that have the same coordinates like different phases of MRI sequence for example In the case of digital slides it will be useful only if samples have exactly the same position on the slide which has few chances to happen Copyright CCITI all rights reserved 20 CCITI Viewer User s Manual 2012 2 4 Scan slide mode The scan slide function allows you to automatically screen the slide You can define the region to screen and the speed of the movement It is also possible to create annotation during the screening by clicking on the object of interest for example tumor cells in a smear slide For a detailed description of the annotations read the chapter 3 Annotate digital images On the right side of the Action tool bar you can activate the Scan slide function This function allows you to automatically scan the entire specimen or a part of it that you define Y Before entering the scan mode select the wished magnification of screening in the continuous zoom panel To activate it click on the icon A window will appear wher
16. cacnastenssecaoswedinatewsdiedseceaswateruaduceveuedeaslensdudteteusveedessdevaenvaseianasoneesseuce 37 6 FORM AREA amp DIAGNOSTIC ITEMS cccececscecececcccccccscscncececcccccccscncncececcccccccucscscncececseees 38 7 INDEX OF TOOLBAR BUTTONS itecccwscsncecawcdecsancs cass sueataneebededeusewadsisnecanaes vexadsbieaccetenntedimasocrisent 40 Copyright CCITI all rights reserved 2 CCITI Viewer User s Manual 2012 1 Viewer Imaging Pathologist Workbench introduction The Imaging Pathologist Workbench IPW from CCITI is a viewer platform allowing multimedia navigation and offering extended diagnostic tools and items The various media that you can open with the viewer are Digital slides Leica 3DHistech Hamamatsu Carl Zeiss Olympus Aperio IMPN Jpeg images histology macroscopy blot o DICOM images and sequences MRI PET CT r 4 lt i f f E d e a i a Figure 1 Multimedia IPW interface a u eee IPW can work with media installed locally or distantly through internet and the media can be stored on different servers o Client IPW runs a thin client Windows or Mac or a java thick client Windows only Both clients offer the same functionalities except setting of brightness contrast gamma only available in thick client now Security A secured mode for thick client SSL or thin client Https is implemented The applicati
17. ccess the preferences Once in the Preferences window select in the menu the settings you want to modify Don t forget to click on Apply after each modification lf you want to save all the defined settings click on save to create a preference file To load a file saved previously click on the load button ES Preferences ad Advanced Save Load ox cancel Figure 38 Saving the preferences Copyright CCITI all rights reserved 37 CCITI Viewer User s Manual 2012 6 Form area amp diagnostic items To help your diagnosis the viewer allows you to answer a set of questions directly when viewing a media The answers will be recorded with the media and will be available the next viewing Depending on the media a form will be associated or not to the media This set of questions can be configured according to the type of media organ HE Immuno Remark A form can only be shown when only one media is opened at a time Forms Criteria Diagnosis Diagnosis Favor meso wt Papillary architecture Present w Invasion within the core Present favor meso TPresent not significant For meso Micropapillary Absent s Invasion Absent Multilayering Absent w Marked atypia Absent kd Peg shaped mesothelial cells Absent w Nodular aggregates Absent wt Analysis Finished Oes G No lil Figure 39 Example of associated form for mesothelioma
18. diagnosis Various types of questions are possible Boolean question Yes No Analysis Finished Oves No Figure 40 Boolean question List of values question you choose one answer in the list of proposed answers Histological type v Thymic carcinoma Figure 41 List of values question O Integer question you choose one answer an integer in the list of proposed answers Grade 4 5 3 Figure 42 Integer question The same kind of question exists for real numbers O Free text question you answer the question by typing a free text Specify site s Figure 43 Free text question Copyright CCITI all rights reserved 38 CCITI Viewer User s Manual 2012 O Multiple choice question click on an answer in the list to select it The selected answer appears highlighted in blue To select several answers hold on the Ctrl key and click on additional answer in the list Figure 44 Multiple choice questions Computational question Some questions can use calculation based on other filled question like a sum mean value or more complex calculation Distance surface measurement to answer click on the red question The viewer automatically enters the ROI mode Draw a ROI predefined type and color and the viewer will automatically calculate the distance surface of your ROI Figure 45 Distance Surface question This type of question appears in red That means a ROI has to be
19. e as wanted A Circle Click left or right once the circle is drawn ne The circle is a surface amp largest diameter measurement gt Q Click left on the starting point and release the button R Draw the first segment and click left to start a new side Draw asf many sides as you need Polygon To end the polygon click right at the ending point The polygon is a surface amp largest diameter measurement Click left at the starting point and release the button Move the mouse and the area will follow the cursor of the mouse To end the surface click right at the ending point The system will Surface automatically close the surface The surface is a surface amp largest diameter measurement Point the mouse cursor on the structure of interest and click left tof Sowia create a marker of the position The distance surface of the draw is automatically calculated and indicated in the Region Of Interest Manager For the drawings rectangle circle polygon and surface the largest diameter is also indicated Copyright CCITI all rights reserved 25 CCITI Viewer User s Manual 2012 Remark When drawing you can stop your draw at any moment by pushing the ESC key of your keyboard It will cancel the ROI Remark Each time you want to draw an annotation you have to click first on the corresponding icon in the action toolbar even if the drawing type is the same than the previous ROI drawn The m
20. e in Navigation mode it is possible to display or hide the ROI made on the ea image To display hide the ROI click on the icon in the action toolbar Copyright CCITI all rights reserved 17 CCITI Viewer User s Manual 2012 2 3 Multimedia review 2 3 1 Display modes The viewer allows working on one media at a time or with several media at the same time When several media are displayed as thumbnail in the images presentation panel clicking on anew media leads to close the current media reviewed and to open this new media To display several media in the viewing window hold the Ctrl or Shift keyboard key and click with the left button of the mouse on the wanted media Remark Under MAC system to get the discontinuous selection click right in the left panel and select the slides to visualize in the contextual menu that appears B11 1428 HES gt B11 1428 CD45 z 4 fe Fae e OS gt fea we OS oo olsy Ly se J Figure 17 Multimedia review The viewing area is automatically cut in N viewing screens in order to simultaneously visualize navigate through the N images Note When reviewing several media simultaneously it doesn t allow you to visualize the forms associated to each media Copyright CCITI all rights reserved 18 CCITI Viewer User s Manual 2012 The following icons above the thumbnail images presentation panel allow selecting fixed org
21. e you can define the area you want to scan 3 If you want to screen the entire slide don t touch to the thumbnail you only need to adjust the others settings as explained below 3 To define a scanning region you can select one or several existing ROI if you created those ROI previously To select several ROI hold on the Ctrl keyboard key while clicking on corresponding ROI 1 To create a screening region independently of the existing ROI hold on the left button of the mouse and draw a rectangle on the thumbnail Note If you select a ROI on the right panel you have to hold on the Ctrl key and click on the ROI again to unselect it To delete a screening region made independently of the ROI list click on the region on the thumbnail and press the Suppr key O Enter the speed of the movement defined in the Wait box and corresponding to the time the system will display a field of view before shifting to the next one in ms 11 In the Move box select how the system moves from one field of view FOV to another 100 means the system moves from one complete field of view 50 means half of the displayed FOV remains half is replaced by the next area Select if you want a horizontal or vertical screening in the Mode box 3 If ROI has to be created during the screening select the ROI size from 1 to 100 pixels and the associated type standard for 2 opinion etc You can leave a
22. een mode click on the icon on the left side of the tool bar The viewing window will be displayed in full screen allowing having a bigger field of view In the full screen mode only navigation and annotations are possible To fill in forms and select diagnostic items you have to go back to the standard mode sz 2S AMX w OX De 125K Figure 12 Media displayed in full screen mode z To go back to the standard mode click again on the icon 2 2 2 Display control settings Remark Function not available with the thin version of the viewer The viewer displays the media as it has been acquired and in a standardized way However you can decide to modify the display features as brightness contrast or gamma level The modification are only display modification it does not modify the media file itself You can have access to the display control by clicking on the settings icon in the tool bar Access the settings control brightness contrast and gamma correction The settings window appears Left click and hold on the mouse button on the slider of each control and move left or right to modify the brightness contrast or gamma To change the value step by step click on the left or right arrow to decrease or increase the value Copyright CCITI all rights reserved 13 CCITI Viewer User s Manual 2012 Figure 13 Settings of brightness contrast and gamma correction The viewer will record the new settings of the
23. erin sent eetaneaes iaosutadaucuucuti ects eotaesueecuiaseustetadintelaacwacseeee 14 22A PREVIEW WINDOW scecceteceu ren cacccneosrcace nas eren tess niaecstenienencawncwetaceutataueessiacenresteadietpeneuoiscianseaenouace 14 2 2 5 MAGNIFYING GLASS WINDOW cccccecscsceccccccccccacscscececeaeacsceceatatacecsceeeaeacacecessesceeeatatsceseseaeataeacs 16 LLO SCATA corre rec cee ec ae ees eevee cas cain nea Gusset out oeue vate ewueumnerdeeuiaereucurstw cutee ttacissiacevestaeeus 17 227 DPA AIDE ROM oe E case te cease sia enc atinn so necaas EES 17 ZS MULTIMEDIA REVIEW cvs veis secs cercrnaexesc eves vececeveseucbexeceasawsuceesvecawcnnscawseceaweneossucvereaeneeumececveccoeseues 18 Lo LOUSY MODE seeecese cet teers cacti sree eo ese ei Geis E en nese mencuat 18 2 3 2 SYNCHRONIZATION OF MEDIA cecseicareey ora ee cade een tencase niacceccetawaincextsavesereonceresdsncesateadinsrenecunenttantaeeelacs 20 2A SCAN SLIDE MODE sesaria eE EO voc sacuexcrseuenceseacnacouescesncesacswtouseweaeodcasvareuuauesecacueeuorueues 21 3 ANNOTATE DIGITAL IMAGES sisiscsctcccisncascscvosssssnstecsdssswns avetuensseud ue vetont cb aa 23 31 DRAWARO sicee ices nccacennecs stars vies concseassatesessidedcdessanciseeceseses sete semacwesuces senses conc Ouastots wags seewneesers 24 Bk BLE TE AROF en sv wears tees wes arcs cae uso os nda cane swnann sans ones EEEE AEE E 27 39 UT RO e cacsnces tate ne ausmeusesda pes once caustdess bpusdissecuncnal ais weuecanawcees poieeescaus c
24. g a manual move of the ROI will be necessary to adjust the position Example Duplicate a draw using the contextual menu Choose medias Figure 29 Duplicate a ROI Copyright CCITI all rights reserved 30 CCITI Viewer User s Manual 2012 3 4 Access to local Grey level measurement IPW allows you to measure at a precise pixel location the grey level of the pixel o Select a ROI in the ROI manager editor o When a ROI is selected the Display grey level 4 icon becomes active in the toolbar O Click on the display grey level icon and point your mouse cursor at the location you want to measure The value of the pixel and the mean value on the whole selected ROI appears in the bottom left corner of the viewing window as Grey ROI 163 150 for example 163 being the pixel value where the mouse cursor is pointed 150 being the mean value inside the selected ROI 20 GayiRol 136 145 Figure 30 Grey value measurement Copyright CCITI all rights reserved 31 CCITI Viewer User s Manual 2012 4 Export Functions IPW allows exporting information automatically or manually This section deals with the manual export functions 4 1 Export view You can export the current view of the media displayed on the viewing window by clicking the button 7 in the Action tool bar This action allows you two types of export In the Clipboard so you can paste it in a document O Ina file so you can s
25. he picture in X Y and in mm 08_2076_5 1 25x Infiltrate re Fy Figure 33 ROI exported jpg image Copyright CCITI all rights reserved 33 CCITI Viewer User s Manual 2012 4 3 Export a predefined area lf you want to export a rectangular area larger than the field of view at a given magnification it is possible to do it without having to create a ROI 3 In Navigation Mode select the select a region ms icon in the action Toolbar Click on the left button twice to start to draw the region Drag the mouse and click left button to fix the defined region 3 If you draw the region at x5 magnification for example it is possible to export at higher magnification Go to the wanted resolution and click on the Export icon on the right of N Yv the select a region icon miMa oi 11 This will open a dialog box where you will be able to choose where you want to save it on your computer If nothing happens it means the image size is too big for the jpg format Decrease the magnification and try again Note Once you made your selection you can center the field of view on the selection by clicking On the center view on selection icon Copyright CCITI all rights reserved 34 CCITI Viewer User s Manual 2012 4 4 Export a Field of view FOV or a ROI to Word or PowerPoint IPW allows you to easily insert a field of view image in Microsoft Office word or PowerPoint Open M
26. icrosoft Office word or PowerPoint and minimize the window Open your media and navigate to the field of view you want to export Hold on the Ctr keyboard key and click left with the mouse button on the viewing area Hold on the mouse button and drag the field of view to the Word or PowerPoint window You should see the field of view in transparency when dragging o Release the mouse button The field of view is inserted into your document O O LJ Pall LF mN Drag the field of view to the Mi PowerPoint minimized window ER 3 Figure 34 Insert a Field of view in Microsoft Word or PowerPoint To insert a ROI first select a ROI then follow the same procedure Copyright CCITI all rights reserved 35 CCITI Viewer User s Manual 2012 5 Customize your Interface IPW gives you the possibility to customize the way you want to organize you working area 5 1 Organize Windows 5 1 1 Modify size of windows To modify the size of the different panels put your mouse cursor at the border of a panel The mouse cursor changes from a hand shape or arrow shape to a double arrow head shape Left click and hold on the mouse button and move left right or up down to increase decrease the size of a panel or window size of a window Figure 35 Increase decrease the size of the windows 5 1 2 Display Hide panels To display or Hide the Thumbnail panel showing all the images and or the plug in panel containing the for
27. iewer User s Manual 2012 2 Media Review This section gives you all the necessary information to navigate into your media and use the visualization tools 2 1 Navigate into the media 2 1 1 Navigation in X Y To navigate in X Y several possibilities are available e With the mouse left button O Press and hold down the left button then drag the image in the direction you want Release the left button Example f you want to move the media on the right press and hold down the left button on the mouse then move the mouse to the left e With the scroll bars Use the scroll bars to move the media as you would do it with any other application There are 3 ways to use the scroll bars Left Click on the arrows of the scroll bars to move the image up down or left right O Click on any point of the scroll bars outside of the blue rectangle The image will move automatically O Left click and hold on the mouse button on the blue cursor and move the cursor up down or left right Note The scroll bars are not visible when the whole sample can be seen in the viewing window Figure 6 Navigate with the scroll bar Copyright CCITI all rights reserved 8 CCITI Viewer User s Manual 2012 e With the directional arrows of your keyboard By pushing the up arrow you move up the media O By pushing the down arrow you move down the media O By pushing the right arrow you move the media
28. m and the synchronization windows Click on the CCITI icon on the upper left corner of the IPW window O In the drop down menu click on CCITI viewer Thumbnail band or plug in band to display hide the panels G CCITI Viewer Build 20100905 122476750 Preferences Update Load medis gt Mosaic Cascade Show all medias Hid al medas y 08_2076_5 08_2076_CD20 i 98_2076_CO3 s Figure 36 Display Hide the Thumbnail amp plug in panels Copyright CCITI all rights reserved 36 CCITI Viewer User s Manual 2012 5 2 Personal settings IPW allows you to customize your interface to define preferences when the viewer opens It allows you to define which default parameter should be displayed when opening a media For example if you never use the scale you can select that the scale bar will not be visible by default If you draw a ROI with black border most of the time you can define to show the black border selected by default To access the preferences settings click on the CCITI logo on the upper left corner of the IPW window and select CCIT Viewer preferences in the drop down menu Ee CCITI Viewer Build 20100905 122426 50 FS CCITI Viewer F v Thumbs band v Plugins band D placer Taille Update R duire Load a media O Agrandir Moidi X Fermer mera _ Sa i i Show all medias Options ey Hide all medias 08_2076_CDz f v 08_2076_5 08_2076_CD20 08_2076_CD3 Figure 37 A
29. nel To view and navigate through the selected media Viewing area To draw Regions Of Interest Violet section right panel _ To answer diagnostic items associated to the media Form area Orange section right panel List of Regions Of Interest and associated information Regions Of Interest editor lf several media are loaded into the viewer you will see during the loading process at the bottom side of the image presentation panel a status bar indicating how many media remain to be loaded As soon as all the media are loaded the status bar disappears Figure 3 The loading status bar Copyright CCITI all rights reserved 4 CCITI Viewer User s Manual 2012 On the left panel image presentation the name of each media is displayed just above the media thumbnail If the name of the media is too long then it s truncated Simply move your mouse over the thumbnail to see the full name of the media in a tooltip To open a media click with the left button of the mouse Left Click on the corresponding image thumbnail on the left panel The image appears on the central area If standardized form is associated with the media it will appear on the violet section Two sections appear with the media on top side and right side of the image as described below CCITI Viewer Build 20120323 093806515 BA XY relative v J s ea e SX owe Digestif B11 1428 HES Tumeur Yes No
30. on also takes into account the possible use of a proxy O User s right A read only mode is implemented allowing restricting the rights of some users In that case modification of existing regions of interest and existing answers to diagnostic forms is not possible Creating new regions of interest however can be allowed in this mode 1 1 Minimum amp recommended workstation configurations For optimized use of the IPW viewer the following workstation is recommended Minimum configuration required o 1 6 GHz Duo Processor o 1 Go RAM memory 1 1024 x768 screen resolution Recommended optimum configuration o 1 8 GHz Duo Processor or higher o 2 Go RAM memory or higher 1280 x1024 screen resolution or higher When using the thin version of the viewer through internet web browser it is recommended to use the last version of Mozilla Firefox minimal version 3 6 Copyright CCITI all rights reserved 3 CCITI Viewer User s Manual 2012 1 2 General view of IPW When you first open the viewer from your application platform the following interface appears The window is divided in 4 parts described below CCNI Viewer Build 20120323 093806515 ROI edition B11 1428 CD45 B11 1428 CK56 Figure 2 General overview of the IPW interface The interface is divided in 4 areas Red section Left panel Presents all available media in thumbnails form Images presentation Green section central pa
31. pears on it at each line intersection If you don t see such squares your ROI is not selected and you can t edit the ROI Inactive ROI unselected Active ROI selected Figure 24 ROI selection Copyright CCITI all rights reserved 2 CCITI Viewer User s Manual 2012 3 3 Edit a ROI 3 3 1 ROI editor Edit the associated information The region of interest editor allows you to review all the annotations made on an image and to edit information associated with the annotations The region of interest editor is located in the panel immediately at the right side of the viewing window You can display hide this panel by clicking on the toolbar icon The number of annotations and the name of each annotation are indicated in the top part of the ROI manager The system generates automatic naming of the region You can change the name of a region by selecting the corresponding region in the list and by entering the new name in the name field Click valid to save the change Under the name field you have access to the measurements information distance area largest diameter mean RGB levels Mean Grey levels depending on the kind of ROI 1 To change the ROI class select in the drop down menu of the Type field the class you want to associate to the ROI Inthe comments field you can add free text to your ROI Regions of interest 12 E Number of ROI A Infiltrate vessel measuremen
32. rsor on the black border of the magnifying glass window The cursor shape will change from a hand shape to a double side arrow head shape o Press and hold down the left button on the black border then move the mouse to change the dimensions of the window You can edit width and height independently If you click on the corner of the magnifying glass window you will be able to change its dimensions proportionally e Change the extra zoom level of the magnifying glass Put your mouse cursor inside the magnifying glass window Move the mouse wheel up to increase magnification from x2 to x10 Move the mouse wheel down to decrease the magnification level Note Double left click on the magnifying glass window allows extracting the magnifier as an independent window that you can place anywhere on the screen including outside the viewing window To replace back the magnifying glass inside the viewing window double right or left click on the magnifying glass window Alternatively you can click on the red cross of the magnifier window Copyright CCITI all rights reserved 16 CCITI Viewer User s Manual 2012 2 2 6 Scale bar The scale bar is shown by default on the lower right corner of the viewing window The scale bar shows horizontal and vertical scaling The units are automatically calculated depending on the magnification level and shift from millimeters to micrometers when relevant 2 2 7 Display Hide ROI When you ar
33. s available for line polyline rectangle circle and polygon annotations Select the draw you want to reshape and use the right click on it to open the contextual menu Then select reshape in the contextual menu Move the mouse cursor on an intersection Black Square The cursor shift from an arrow shape to a hand shape Left click and release the mouse button then move the mouse to reshape the draw Click left again to end the operation Figure 28 Reshape a ROI Copyright CCITI all rights reserved 29 CCITI Viewer User s Manual 2012 3 3 3 Duplicate a ROI O Select the draw you want to duplicate and use the right click on it to open the contextual menu Then select duplicate in the contextual menu To duplicate the ROI in the current image select in the current media o Move the mouse to move the duplicated ROI to the wanted position Then click left to fix the duplicate draw To duplicate the ROI in other images select in another media To be active all the concerned images have to be opened in the viewing area before using this function o Select the images to duplicate the ROI in the appearing Choose Media window and click validate Note Duplicate a ROI in another media can be useful to highlight the same region in HE and IHC stained slides for example However the system will use absolute X Y position to duplicate the ROI so if both slides are not exactly matchin
34. select before drawing the wished settings in the drop down menus of the following icons in the action tool bar HE OP PL Standard For advice Justification __ RCP Tumor 7 5 4 4 i s J il il i d t Select ROI type Select thickness Figure 21 ROI display amp type parameters Copyright CCITI all rights reserved 24 CCITI Viewer User s Manual 2012 Choose the type of draw Choose the type of draw in the action tool bar Type of 5 Click left once on the starting point and release the button VA Click left or right at the ending point x The Line ROI is also a length measurement Click left on the starting point and release the button N de A Then move the mouse and click left to finish a first segment Draw as N RUSY i AN i many segments as you need x ARRS Click left on the starting point and release the button Move the mouse the curve will follow the cursor of the mouse To end the curve click left or right at the ending point The curve is also a length measurement Click left at the starting point and release the button Move the mouse in the wished direction to enlarge the rectangle as wanted Rectangle Click left or right once the rectangle is drawn The rectangle is a surface amp largest diameter measurement Click left at the starting point and release the button tok O Move the mouse in the wished direction to enlarge the circl
35. t B n tructure length ROI list with currently selected ROI e a ROI 37 highlighted in blue ROI 40 v Name Lymphocyte Infiltrate Corn ROI Name Surface 1 66 mm2 2 82 mm Average RGB R 194 G 114 B 179 Type For advice C ROI Type Comments Can you check if there is CD20 cells in this region rn Comments free text area Figure 25 ROI manager Editor 3 3 2 Edit the ROI display parameters You can modify the way the ROI is displayed by using a contextual menu associated with the ROI e Change the color and the thickness of draws Before drawing Use the buttons Ci and E in the action tool bar Click on the little arrow to display the various options After drawing Select the draw of which you want to change the appearance Use the right click on the draw to open the contextual menu Then go to change the color or to change the thickness Example Change the color amp Change the border thickness Copyright CCITI all rights reserved 28 CCITI Viewer User s Manual 2012 Figure 26 Modify ROI color and border thickness e Move a draw Select the draw you want to move and use the right click on it to open the contextual menu Then select Move in the contextual menu O Then move the mouse to move your draw Then click left to fix the draw Example move a draw using the contextual menu Figure 27 Move a ROI e Reshape a draw The function i
36. to the right O By pushing the left arrow you move the media to the left Note Each push on an arrow generates a slight move of the field of view Hold the key for a continuous move on the side e With the preview window See chapter 2 2 The visualization tools for a description of the function 2 1 2 Zoom in Zoom out To view the sample at different magnifications several possibilities are available e With the mouse scroll wheel O Scrolling up once with the mouse zoom in O Scrolling down once with the mouse zoom out The mouse scroll wheel feature allows you to navigate between the magnification levels of the scroll bar for example zoom continuously between x5 and x10 magnification levels e With the mouse buttons O Click left anywhere on the media to zoom in Each click change the magnification from 1 level in the zoom scroll bar Example zoom in from zoom level x5 to zoom level x10 by clicking once with the left mouse button 1 left click Figure 7 Zoom in with the left mouse button Remark when you click to zoom in it will automatically zoom by centering the image on the point of the slide on which you have clicked Copyright CCITI all rights reserved 9 CCITI Viewer User s Manual 2012 O Click right anywhere on the media to zoom out Example Zoom out from zoom level x10 to zoom level x5 by clicking once with the right mouse button Figure 8 Zoom out with the right mouse
37. ttons Toggle on off to full screen mode fy Not available with the thin s version of the viewer gt F11 of Delete a selected ROI keyboard Display control settings hp Export a selected ROI Not available with the thin version of the viewer M Select Line ROI Display Grey Level Select Polyline ROI wy Display hide the preview window S Select Curve ROI P Display hide the magnifying glass Display hide the draws done on the Select Circle ROI media Select Rectangle ROI ad Display hide the scale P Q Select Polygon ROI Export a Field Of View 24 Select Surface ROI Q Activate Navigation Mode Select Marker ROI Activate Drawing Mode Standard Select the type of ROI ty 9 Select a region Clear a region Select color of the ROI Export a selected area i Select thickness border of the ROI p Center view on selected region Activate the screening mode w Pause the screening Copyright CCITI all rights reserved 40

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