Coolscope webslide_vs_manual
Contents
1. Figure 8 The New Slide dialog The New Slide dialog contains the following fields Name When a slide is scanned the files that comprise the WebSlide virtual slide are placed in a single folder This folder known as a WebSlide virtual slide folder is a Windows folder The name of the WebSlide virtual slide folder is auto assigned and is auto incremented starting from VS000000 by the WebSlide VS program at the completion of each scan Title The name of the WebSlide virtual slide as it is commonly referred to A short description of the specimen for example Normal Lung or Slide1 is often used as Title Title is also known as WebSlide Title or Slide Name Recommended SlideTray Folder The SlideTray Folder under which the WebSlide virtual slide is listed by the SlideTray program A short description of category or type for example Normal Histology or Dr Smith is often used as SlideTray Folder Recommended Note The SlideTray program searches for and builds a SlideTray tree and folder hierar chy listing of found WebSlide virtual slides The SlideTray listing is typically passed to another program such as WebSlide Browser thereby allowing the user to select a WebSlide virtual slide to view or work with The folder component of SlideTray tree and folder hierarchy is provided by the SlideTray Folder field of the New Slide window The value entered into the Slide Tray Folder field corresponds to the SlideTray2. w x Cancel Figure 51 The Scan Options Z Stack tab To enable Z stack check the Enable Z Stack Acquisition checkbox and click the OK button Z stack is configurable for each high magnification objective 5x 10x 20x 40x Step Size defines the distance along the Z axis separating each of the nine stepped images The higher the value for Step Size the greater the depth of virtual focusing Note As the magnification of the high magnification objective is increased less depth and therefore a smaller Step Size value is required to virtual focus through the speci men Post Scan Options Post scan options provides the ability to automatically perform certain operations upon scan completion To access the post scan options click Setup Scan Options or click the Displays the Scan Options window Standard Toolbar button The Scan Options General tab appears as shown in Figure 52 Scan Options General Folders Z Stack Post Scan Options _ Close this application Close this application and launch the WebSlide Server Shut down the COOLSCOPE VS v OK X Cancel Figure 52 The Scan Options General tab The Post Scan Options fieldset contains the following post scan options Close this application Closes the WebSlide VS program upon scan completion Close this application and launch the WebSlide Server Closes the WebSlide VS program and launches
3. gt Initial Z value Cancel Figure 19 The Adjust Z window To adjust the Z value click and drag the slider or click within the slider bar The Image window is updated The initial Z value is indicated by a hash and the current Z value is indicated at the top of the Adjust Z window To accept the current Z value click the OK button To discard any change in Z value thereby reverting the Z value to its initial value click the Cancel button Camera settings Camera settings are configurable and stored separately for each high magnification objective To adjust the camera settings for the currently selected objective click Command Advanced Camera Settings The Camera Settings window appears as shown in Figure 20 Camera Settings i S Shutter Speed 1760 sec w Lamp Intensity 34 gt Preserve camera settings after autofocus or objective change White Balance B Refresh Default settings vr Figure 20 Camera Settings Shutter speed defines the length of time the COOLSCOPE VS instrument s shutter is open during image capture The larger the value for shutter speed the brighter the captured images Use the Shutter Speed drop down to select a shutter soeed The Image window is updated Lamp intensity defines the brightness of the COOLSCOPE VS instrument s LED during image capture The larger the value for lamp intensity the brighter the captured images Use the
4. Scan Browse VS Server Exit Figure 45 The COOLSCOPE VS Suite Menu gt CoolAlign And WebSlide Virtual Slide Folder Locations When a slide is scanned the files that comprise the WebSlide virtual slide are placed in a single folder This folder known as a WebSlide virtual slide folder is a Windows folder The name of the WebSlide virtual slide folder is auto assigned and is auto incremented starting from VSO00000 by the WebSlide VS program at start and completion of each scan respectively When the WebSlide VS program is closed the WebSlide virtual slide folders created during that WebSlide VS session are auto matically processed and rooted on the WebSlide Server LE by the CoolAlign program During this process the CoolAlign program moves WebSlide virtual slide folders from a Scanning Folder to a Destination Folder The Scanning Folder defines the location of the WebSlide virtual slide folders as created during scan time The default location for the Scanning Folder is C Program Files Nikon COOLSCOPE VS Scanning The Destination Folder defines the location of the WebSlide virtual slide folders after processing by the CoolAlign program The default location for the Destination Folder is C Program Files Bacus Labs WebSlide Server WebSlides Known as the WebSlides Folder C Program Files Bacus Labs WebSlide Server WebSlides is the default location provided for rooting WebSlide virtual slide folders on the WebSlide S
5. when the WebSlide VS program is closed each WebSlide virtual slide folder created during that WebSlide VS session is automatically processed and rooted on the WebSlide Server LE by the CoolAlign program As a result when the WebSlide Server LE is started the WebSlide virtual slides are immediately available for viewing over a network The Slide View image provides 0 03x 0 06x 0 11x 0 22x views of the WebSlide virtual slide The Field View image provides 5x 10x 20x and 40x views of the WebSlide virtual slide assuming the 40x objective was selected for the high magnification scan Configuring The WebSlide VS Program To Communicate With The COOLSCOPE VS Instrument The WebSlide VS program and the COOLSCOPE VS instrument communicate with one another via TCP IP This implies that the PC running the WebSlide VS program and the COOLSCOPE VS instrument must be properly networked to one another either directly through the use of a cross over cable or indirectly through the use of an Intranet or the Internet and that the WebSlide VS program must be correctly informed of the COOLSCOPE VS instrument s Network Settings Note For additional information on connecting the PC running the WebSlide VS pro gram and the COOLSCOPE VS instrument to a network please see the Networking Functions section of the Nikon COOLSCOPE User s Manual The COOLSCOPE VS Instrument s Network Settings The COOLSCOPE VS instrument s factory Network Settings
6. 18 Acquiring The Field View Image To complete the capturing of a WebSlide virtual slide a high magnification scan is performed The high magnification scan cap tures a series of images each representing a single field of view under the selected high magnification objective These captured images or tiles are aligned during viewing and constitute an image of the outlined region s of interest known as the Field View image The Slide View image displayed in the WebSlide VS window is the starting point for and provides all the functionality required for acquiring the Field View image After selecting an objective for the high magnification scan simple mouse gestures are performed on the Slide View image to outline the region s of interest to be scanned Although default settings are provided and are recom mended advanced user options include adjusting Camera Settings described above configuring Auto Focus and enabling Z Stack To acquire the Field View image Select a high magnification objective Outline the region s of interest to be scanned Configure Auto Focus if necessary Run the high magnification scan St nt Dt Dt 1 2 3 4 Important Note A right mouse click must be performed on a point of interest on the Slide View image before selecting a high magnification objective or outlining a region s of interest for the high magnification scan Selecting An Objective For The High Magnification Scan The foll
7. Folder under which the WebSlide virtual slide is listed by the SlideTray program Patient ID Patient ID Optional Accession Accession Optional Operator ID Operator ID Optional 10 An example of text entered into the fields of the New Slide window as displayed by WebSlide Browser is shown in Figure 9 WebStide Browser eu File Edit Help eB S01 8 WebSlide Address http 192 168 1 120 a WebSlide SlideTray Favorites Server Link Creator Help Welcome to the WebSlide Server E q Welcome to the WebSlide Server Slide Name W SlideTray Folder field Title field E Tile field vsti Pain ID Patient ID field Accession Accession field Scanne dat 6 27 2004 11 04 29 AM Figure 9 WebSlide Browser displaying the text entered into the fields of the New Slide window Enter text into the fields of the New Scan window as appropriate Then place a clean glass slide into the COOLSCOPE VS instru ment s slide holder and click the New Slide dialog s Scan button as shown in Figure 10 New Slide Slide Information Name vS000000 Title SlideT ray Folder oa Patient ID Accession Operator ID Do not press the Tray Open Close Switch when a running the WebSlide VS X 10265300992 bytes free 8353 image capacity program Cancel Scan Figure 10 The New Slide dialog Scan button Note For information on corre
8. WebSlide Server LE upon scan completion Shut down the COOLSCOPE VS Turns off the COOLSCOPE VS instrument upon scan completion Check the box es corresponding to the post scan actions to be performed upon scan completion and click the OK button Ld Note The CoolAlign program is automatically launched whenever the WebSlide VS pro gram is closed 31
9. are shown in Figure 1 The settings required of the WebSlide VS program IP address User ID and Pass Word are indicated Netliork Settings IP Address User ID Pass Word mi aco DASA Figure 1 The COOLSCOPE VS instrument s Network Settings required by the WebSlide VS program Note For information on obtaining or changing the COOLSCOPE VS instruments Network Settings please see the Networking Functions section of the Nikon COOLSCOPE User s Manual The WebSlide VS Program s COOLSCOPE Properties Network Tab When the WebSlide VS program is started it automatically attempts to communicate with a COOLSCOPE VS instrument By default the first time the WebSlide VS program is run it attempts to communicate with a COOLSCOPE VS instrument having the COOLSCOPE VS instrument s factory Network Settings as shown in Figure 1 above If the PC running the WebSlide VS program and the COOLSCOPE VS instrument are properly networked to one another and if the COOLSCOPE VS instrument s Network Settings are that of the factory when the WebSlide VS program is run the first time it is able to communicate with the COOLSCOPE VS instrument and the WebSlide VS window reports Connected to the COOLSCOPE successfully The system is ready to use as shown in Figure 2 Oy Webble FS hal Bie gii Ye Be JE ay Tree i the COM SOIR in Nr VS Veron 1h Fireman vid Figure 2 The WebSlide VS program communicating with the COOLSCOP
10. ir imn i Fir ic ETP logged in OK LT wi ce X Care Webkid Yiye 1 Paa vig Figure 5 The WebSlide VS program communicating with the COOLSCOPE VS instrument Click the OK button to close the WebSlide VS program s COOLSCOPE Properties dialog The WebSlide VS Window To start the WebSlide VS program open the COOLSCOPE VS Suite Menu and click the Scan button Alternatively click Start Programs Nikon WebSlide VS or if running Windows XP click Start All Programs Nikon WebSlide VS If the WebSlide VS program and the COOLSCOPE VS instrument are properly communicating with one another the WebSlide VS window appears as shown in Figure 6 Standard Toolbar Main Menu Title Bar all Oy Weh lide YE fie pi php Be An ay Tree to the CORSON ein Webi V3 Vernon 1h Fireman i Status Bar Figure 6 The WebSlide VS window Note If the WebSlide VS program and the COOLSCOPE VS instrument are unable to communicate with one another please see the Configuring The WebSlide VS Program To Communicate With The COOLSCOPE VS Instrument section of this manual The WebSlide VS window Status Bar indicates the WebSlide VS program version number and the COOLSCOPE VS instrument firmware version number as shown in Figure 7 1 Webilide VS Jag fe tet Jp en re ao Er Tree i the LO SCOTT sn Webads VS yea G Praa vie ng WebSlide VS COOLSCOPE VS instrument program version firmware version Figure 7 The WebSlid
11. on the New slide button in the main window to start scanning a new slide or Exit this program to either view the slide you just scanned or to serve it on network to be shared with other users Figure 42 The Scanning Complete window To scan a new slide click File New Slide or click the Start a New Slide to scan Standard Toolbar button To close the WebSlide VS program click File Exit or click the Close window button 9 When the WebSlide VS program is closed two things happen First if a high magnification scan was run to completion the WebSlide virtual slide folder s created during that WebSlide VS session are automatically processed by the CoolAlign program which appears minimized on the desktop as shown in Figure 43 Ef CootAtign a x Figure 43 The CoolAlign window minimized on the desktop Click the Restore Up button to display the CoolAlign window shown in Figure 44 _ 2 CoolAlign Kay X Slide List Progress 45000021 Curent Operation Aligning Bottom Neighbor Tie 68 Best 0 Image 69 out of 81 tiles Best 0 Diff 25100155 Time Remaining 00 00 19 Time Elapsed 00 01 38 Avg Time Field 00 00 01 461 See eeseeeeeeens Cancel Figure 44 The CoolAlign window 32 Second the COOLSCOPE VS Suite Menu appears as shown in Figure 45 Click the appropriate button as needed gt COOLSCOPE VS 5acus s sana Vemine Men The Eyes of Science COOLSCOPE VS
12. right mouse click to close the polygon The image tiles corresponding to the fields of view to be scanned are drawn as shown in Figure 28 i gt maa oz El Sx Figure 28 The image tiles to be scanned 23 Use Trace Mode to avoid scanning non tissue containing areas of the slide as shown in Figure 29 Trace Mode Yes Rectangle Mode No JENS J Boo StU Sane eee Figure 29 Using Trace mode to avoid scanning non tissue containing areas of the slide In examples such as that shown in Figure 29 using Trace Mode to avoid including non tissue containing areas of the slide in the high magnification scan provides two benefits First a lesser number of fields of view need to be captured which reduces scan time Second fewer images to capture implies less hard disk space required to store the resultant WebSlide virtual slide Defining multiple scan segments An outlined region of interest for the high magnification scan is known as a scan segment Using Rectangle and or Trace Mode multiple scan segments may be defined as part of the high magnification scan as shown in Figure 30 a few kan Pe ar j Ja wal u E iy Als alte Mode Pa iS hen oe Figure 30 Multiple scan segments defined Note Each scan segment is scanned using the same high magnification objective select ed for the first scan segment defined In other words different scan segments cannot be scanned with different high magnification
13. window appears as shown in Figure 34 Click the tab 5x 10x 20x or 40x corresponding to the high magnification objective of interest The Auto Focus field set of the COOLSCOPE Properties window contains the settings for configuring auto focus Objective tabs Auto Focus fieldset COOLSCOPE IB 5x 10x 7 20x 40x Network Camera Settings Auto Focus Cal Focus every 8 C1 This objective uses the C1 COOLSCOPE custom mode Only focus if the field content value is gt 10 011 Use precision focus if the Z change is gt 450 fal Default settings Figure 34 The COOLSCOPE Properties window 21 Focus every As the number of fields of view to be captured in the high magnification scan increases the time required to auto focus each field of view may become prohibitive To alleviate this issue rather than performing an auto focus on each field of view the Focus Every feature of the WebSlide VS program can be used to perform an auto focus on every second third forth etc field of view The Z value returned by auto focus is then used to capture subsequent fields of view until the next auto focus is performed By reducing the total number of auto focus operations performed during the high magnification scan the Focus Every feature reduces overall scan times Focus every defines the frequency of performing an auto focus Focus every 0 Scan the entire outlined region of interest using the Z va
14. Click the Network tab to display the WebSlide VS program s COOLSCOPE Properties Network tab Enter the COOLSCOPE VS instrument s Network Settings into the appropriate fields as shown in Figure 4 COOLSCOPE Properties 5x 10x 204 40x Network COOLSCOPE Address and Login Settings Host Name 192 168 10 2 IP Address or Domain Name of the COOLSCOPE Enter COOLSCOPE VS instrument s IP Address User Name anonymous Enter COOLSCOPE VS instrument s User ID Password none Enter COOLSCOPE VS instrument s Pass Word Connect Figure 4 Entering the COOLSCOPE VS instrument s Network Settings into the WebSlide VS program s COOLSCOPE Properties Network tab After entering the COOLSCOPE VS instrument s IP Address User ID and Pass Word into the corresponding fields of the WebSlide VS program s COOLSCOPE Properties Network tab click the Connect button If the WebSlide VS program is able to communicate with the COOLSCOPE VS instrument the WebSlide VS program s COOLSCOPE Properties Network tab reports Telnet connected OK and FTP connected OK and the WebSlide VS window is updated to report Connected to the COOLSCOPE successfully The system is ready to use as shown in Figure 5 Weile S el x Be tt pee er re J Communication er amacha io the COM SORT eucceubully successful s EOOLECHBE Properiin a ae es fio itr har TE Fax ra Maras 1 ee Are Corral Telnet logged in OK
15. E VS instrument If the PC running the WebSlide VS program and the COOLSCOPE VS instrument are not properly networked to one another or if the COOLSCOPE VS instrument s Network Settings are not that of the factory when the WebSlide VS program is run the first time it is unable to communicate with the COOLSCOPE VS instrument and the WebSlide VS window reports such including a list of possible causes for the failed communication as shown in Figure 3 5 WebStide YS sl fe en Be An FIT sans cald ant b ak 17 Tas Varna iea G Pae v 77 Figure 3 The WebSlide VS program not communicating with the COOLSCOPE VS instrument ae Note The list of possible causes for the failed communication presented by the WebSlide VS program is provided intelligently and therefore serves as a good starting point for resolving any communication difficulties After ensuring that the PC running the WebSlide VS program and the COOLSCOPE VS instrument are properly networked to one another it is essential to ensure that the WebSlide VS program has the correct COOLSCOPE VS instrument s Network Settings The COOLSCOPE VS instrument s Network Settings are entered into the WebSlide VS program s COOLSCOPE Properties Network tab To access the WebSlide VS program s COOLSCOPE Properties Network tab click Setup COOLSCOPE Properties or click the Displays the COOLSCOPE Properties window Standard Toolbar button 9 The COOLSCOPE Properties dialog appears
16. Ei Le By Figure 12 Point mode and the field of view under the COOLSCOPE VS instrument s high magnification objective outlined Important Note A right mouse click must be performed on a point of interest on the Slide View image before selecting a high magnification objective or outlining a region s of interest for the high magnification scan 13 The Image Window The Image window displays a captured image of the current field of view under the COOLSCOPE VS instrument s high magnifi cation objective Opening the Image window To open the Image window click View Image or click the Displays the Image window Standard Toolbar button window appears as shown in Figure 13 The Image Si a i te Se ie en Kak Met e A AL m The Image window R es i Figure 13 The Image window displays the field of view under the COOLSCOPE VS instruments high magnification objective The Image window itself is shown in Figure 14 Standard Toolbar Main Menu Title Bar Figure 14 The Image window 14 Repositioning the slide the Image window supports two types of mouse point and click operations to reposition the slide under the COOLSCOPE VS instruments high magnification objectives 1 A left mouse click centers the clicked point under the objective 2 Aright mouse click centers the clicked point under the objective and performs an auto focus Left or ri
17. Lamp Intensity up and down arrows to indicate a Lamp intensity value or click within the Lamp Intensity field and type in a value To update the Image window using the new lamp intensity value click the Refresh button 17 Preserve camera settings after auto focus or objective change instructs the COOLSCOPE VS instrument to use the indicated camera settings for capturing each field of view To preserve the indicated camera settings after auto focus or objective change check the Preserve camera settings after auto focus or objective change checkbox To allow the COOLSCOPE VS instrument to automatically adjust its camera setting values on the fly uncheck the Preserve camera settings after auto focus or objective change checkbox Important Note When capturing a WebSlide virtual slide to ensure even lighting a throughout the high magnification scan it is highly recommended that the Preserve cam era settings after auto focus or objective change checkbox is checked White balance normalizes the COOLSCOPE VS instrument s camera Red Green and Blue i e RGB channels To normalize the camera RGB channels click the White Balance button The camera RGB channels are normalized and the Image window is updated Refresh instructs the COOLSCOPE VS instrument to recapture the current field of view using the indicated camera setting val ues To recapture the current field of view using the indicated camera setting values click the Refresh butto
18. WebSlide VS Bacus Laboratories Inc 410 Eisenhower Lane North Lombard IL 60148 Tel 630 424 9750 rev 201005 Table Of Contents in Lin OCC 1 01 1 sci PEN EEE EEE E ACH FPRSEHEDERSUSAESUEER 3 Configuring The WebSlide VS Program To Communicate With The COOLSCOPE VS Instrument 0008 4 The COOLSCOPE VS Instrument s Network Settings ccccccccsessesssseseeeeeeeeeeeseeceeeeasneneeeeeeeseeeeeeenssenseeseneees 4 The WebSlide VS Program s COOLSCOPE Properties Network Tab n2220anan000nnnnonnnnnnnnnnnnnnnnnnnnnnn 5 The WebS10e amp V5 WIRJOW eu a a ee ae se ee se se eases eee 8 Acal ring Ihe SINGS View Image 2 essen Late eat 10 Viewing The Slide Under The High Magnification Objectives_ uu 22an00000nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnen 13 FOME NOQG aaa Ten ee ee E E A E 13 The Image WINGOW issc EEEa EEEE a EE E EEE E EEEE EAEE EA 14 Opening the Image WIHGOW ze anne ae ana 14 FIEDOSITIONING the SINGS 2uu 2innnsiniee een anna heran een nenne sheet 15 Changing the ODJECUVE Zee ee ee es een 16 A Y and Z CO0OrdIMaleS zuuczenens nee sn Banane een nenn EEe Hrn r a NSAN AAEN ANEN AEAEE NREN 16 FOCUSING the Teld 01 VIEW sine ea na ae Jats Aa ren rn near 17 Camera SOUS au een te ee ee ae a ee euren 17 Reacguire the Image vn see een sedate een 18 Saving image to hard disk or copying to clipboard uuuuuuuueeeennnnnnnnnnnnnnnnnnnnnnnnnnnnnn
19. ace the tip of the mouse cursor over a clearly recognizable and defined point on the Slide View image and click the right mouse button The clicked point is to be centered under the COOLSCOPE VS instrument s objective and an auto focus is per formed 4 Open the Image window and identify the point that was clicked on the Slide View image If necessary use the Image window to navigate the slide 5 In the Image Windows place the mouse cursor cross hair over the point that was clicked in the Image window and click the right mouse button as shown in Figure 48 The clicked point is centered under the COOLSCOPE VS instrument s objective and the Image window is updated 1 The Slide 2 The 5x high magnification objec View image tive and Point Mode selected a EJ ECO TS PS OH gt NE EM HA Pn m 4 Open the Image window and identify the point that was clicked in the Slide View image 5 Place mouse courser cross hair over the point and click the right 3 Right click a clearly mouse button recognizable and defined point on the Slide View image EA Yi IOS ET Se Figure 48 The steps in setting X Y offset 33 6 In the Image window click Command Advanced Setup X Y Offset as shown in Figure 49 6 In the Image window click Command Advanced Setup X Y Offset ERES dad i FRR he hn AMG OS L S Sebo habe Y offset feo the macro image Figure 49 Setting the X Y offset 7 The Confirm Set
20. blank fields of view for the performance of auto focus Only focus if the field content value is gt ensures that the Z values returned by auto focus are representative of fields of view containing tissue The third issue concerning auto focus is the fidelity of auto focus The Z values returned by auto focus performed on representa tive fields of view containing tissue often differ but not by much If the Z value returned by an auto focus performed on a repre sentative field of view containing tissue differs greatly from that of the preceding auto focus an inaccurate auto focus may have occurred If the Z value of such an auto focus is used to capture subsequent fields of view the subsequent fields of view are like ly to be captured out of focus To alleviate this issue the Use precision focus if the Z change is gt feature of the WebSlide VS program sets a Z change threshold value above which the Z value returned by auto focus is rejected and a precision auto focus is performed The Z value returned by the precision auto focus is then used to capture subsequent fields of view until the next auto focus is performed Auto focus settings for the high magnification scan are configurable and are stored separately for each high magnification objec tive To configure auto focus for a high magnification objective click Setup COOLSCOPE Properties or click the Displays the COOLSCOPE Properties window Standard Toolbar button The COOLSCOPE Properties
21. canning pattern performed by the WebSlide VS program Each scan segment is scanned starting with the top leftmost field of view The scan then moves left to right across the first row down to the right most field of view in the second row right to left across the second row down to the leftmost field of view in the third row left to right across the third row etc in a snake like fashion as shown in Figure 32 Figure 32 Raster scanning 25 Recommended Trace Mode scan segment shapes Trace Mode scan segment whose outline presents gaps along the X axis are not recommended Rather use Trace Mode to define multiple scan segments each of which not presenting a gap along the X axis as shown in Figure 33 Y axis gaps X axis gaps Two allowed scan segments gt gt Figure 33 Recommended Trace mode scan segment shapes 26 Configuring Auto Focus For The High Magnification Scan During the high magnification scan the COOLSCOPE VS instrument s built in auto focus routine may be used to adjust Z as the scan is run There are three main issues concerning auto focus The first issue is the frequency of performing an auto focus As the number of fields of view to be captured in the high magnification scan increases the time required to auto focus each field of view may become prohibitive To alleviate this issue rather than performing an auto focus on each field of view the Focus Every feature of the WebSlide VS program can be us
22. cision focus if the Z change Click the tab 5x 10x 20x or 40x corresponding to the high magnification objective of interest To change the Use precision focus if the Z change is gt value click within the Use precision focus if the Z change is gt field and type in a new value or use the up and down arrows to select a new value To register the new value and close the COOLSCOPE Properties window click the OK button To restore the Auto Focus default values for the selected high magnification objective including Use precision focus if the Z change is gt click the Default settings button and then click the OK button 30 Running The High Magnification Scan After selecting an objective outlining a region of interest and if necessary configuring auto focus one is ready to run the high magnification scan To start the high magnification scan click Scan Start or click the Start the scan Standard Toolbar button The COOLSCOPE VS instrument s camera is initialized the Scan Progress window appears and the captured fields of view are shaded green as shown in Figure 39 Betis wa ii AROS BE uh amm U o o Eee ne e s a rete et ae Tie Fang OOOO m po ee en Mit Scan Progress window Captured fields of view shaded green S u van 56 Pld Interval 06 285 Figure 39 The high magnification scan in progress The Scan Progress window indicates the total number images to be captured the c
23. ctly placing a glass slide in the COOLSCOPE VS instru ment s slide holder please see the Nikon COOLSCOPE User s Manual Important Note Do not press the COOLSCOPE VS instrument s Tray Open Close Switch when running the WebSlide VS program The COOLSCOPE VS instrument s Tray Open Close Switch is intended for use in conjunction with the COOLSCOPE VS instru ment s Multi Screen display The WebSlide VS program automatically ejects and retracts the COOLSCOPE VS instrument s slide holder as needed 11 When the Scan button is clicked the slide holder is retracted into the COOLSCOPE VS instrument and the 0 22x macro scan of the entire slide is automatically performed When the macro scan is finished the Slide View image is displayed in the WebSlide VS window as shown in Figure 11 TEE Bin ir jeo Obmann a HLO TS 0S H gt 8 Fim a Mid Pam x Scroll bar Scroll bar Figure 11 The Slide View image The Slide View image displayed in the WebSlide VS window is a static image Use the scroll bars as necessary to reposition the Slide View image within the WebSlide VS window 12 Viewing The Slide Under The High Magnification Objectives Mouse point and click operations performed on the Slide View image move the slide under the COOLSCOPE VS instrument s high magnification objectives 5x 10x 20x and 40x high magnification objectives are available The field of view under the selected objective is displayed
24. d Toolbar button 9 The COOLSCOPE Properties window appears as shown in Figure 37 COOLSCOPE Properties 5x 10 20 40 Network Camera Settings Auto Focus a Focus every 8 This objective uses the C1 COOLSCOPE custom mode Only focus if the field content value is gt 10 5 Field content value Use precision focus if the Z change is gt 450 el Default settings Figure 37 COOLSCOPE Properties Field content value 29 Click the tab 5x 10x 20x or 40x corresponding to the high magnification objective of interest To change the Only focus if the field content value is gt value click within the Only focus if the field content value is gt field and type in a new value or use the up and down arrows to select a new value To register the new value and close the COOLSCOPE Properties window click the OK button To restore the Auto Focus default values for the selected high magnification objective including Only focus if the field content value is gt click the Default settings button and then click the OK button Use precision focus if the Z change is gt The Z values returned by auto focus performed on representative fields of view containing tissue often differ but not by much If the Z value returned by an auto focus performed on a representative field of view containing tissue differs greatly from that of the preceding auto focus an inaccurate auto focus may have occurred If
25. e VS program and the COOLSCOPE VS instrument firmware version numbers Acquiring The Slide View Image When a glass slide is retracted into the COOLSCOPE VS instrument two macro images at 0 22x magnification are automatically captured These images are aligned during viewing and constitute an image of the entire slide known as the Slide View image Mouse point and click operations performed on the Slide View image move the slide under the COOLSCOPE VS instrument s high magnification objectives 5x 10x 20x and 40x high magnification objectives are available The field of view under the selected objective is displayed in the Image window Using simple mouse point and click operations and the Image window the user is able to navigate and view the slide under the COOLSCOPE VS instrument s high magnification objectives If capturing a WebsSlide virtual slide this functionality also allows the user to determine the objective to be used for and the region s of interest to be scanned in the second high magnification scan To acquire the Slide View image click File New Slide or click the Start a New Slide to scan Standard Toolbar button The COOLSCOPE VS instrument s slide holder is ejected and the New Slide dialog appears as shown in Figure 8 New Slide Slide Information Name vS000000 Title SlideTray Folder a am Patient ID Accession Operator ID sas N iM 10265300992 bytes free 3353 image capacity
26. ective buttons Selected objective green File Edit Command Objective View amp G B X 41053 Y 13917 Z 30474 20x Selected objective listed Figure 17 The currently selected objective indicated Note The WebSlide VS window Standard Toolbar also indicates and can be used to change the high magnification objective X Y and Z coordinates The Image window Status Bar indicates the slide X and Y coordinate values corresponding to the top left hand corner of the Image window and the Z coordinate value corresponding to focal plane as shown in Figure 18 File Edit Command Objective view E DAG RL rn 5x 10x 20x 40x u er K 4 X 41053 Y 13917 Z 30474 20x X Y and Z Figure 18 The X Y and Z coordinate values indicated 16 Focusing the field of view To auto focus the field of view displayed in the Image window click Command Auto Focus or click the Perform automatic focus Standard Toolbar button An auto focus is performed and the Image window is updated To manually focus the field of view displayed in the Image window roll the mouse wheel The Image window is updated for each notch the wheel mouse is rolled Alternatively click Command Adjust Z or click the Displays the Adjust Z window Standard Toolbar button amp The Adjust Z window appears as shown in Figure 19 Adjust Z zZ 31133 Current Z value 30533 Slider bar Slider
27. ed to perform an auto focus on every second third forth etc field of view The Z value returned by auto focus is then used to capture subsequent fields of view until the next auto focus is performed By reducing the total number of auto focus operations performed during the high magnification scan the Focus Every feature reduces overall scan times The second issue concerning auto focus is field content The Z value returned by an auto focus performed on a blank or a nearly blank field of view often differs greatly from the Z value returned by an auto focus performed on a representative field of view containing tissue If the Focus Every value is set to 2 or greater the Z value returned by auto focus is used to capture subse quent fields of view until the next auto focus is performed If the Z value returned by an auto focus on a blank or a nearly blank field of view is used to capture subsequent fields of view the subsequent fields of view are often captured out of focus To allevi ate this issue the Only focus if the field content value is gt feature of the WebSlide VS program sets a field content threshold value above which a field of view is accepted for the performance of an auto focus If a field of view queued for auto focus has field content value below the threshold the Z value returned by the preceding auto focus is used to capture that field of view and the next field of view is queued for auto focus By rejecting blank or nearly
28. en it The Directory Name field indicates the currently selected directory To change the location of appropriate folder Scanning or Destination click the OK button Click the OK button to close the Scan Options Folder dialog Important Note In order for the CoolAlign program to root WebSlide virtual slides on the WebSlide Server LE the Destination Folder must be C Program Files Bacus Labs WebSlide Server WebSlides or a Virtual WebSlide Folder For additional informa tion on Virtual WebSlide Folders please see the WebSlide Server LE manual 34 Additional Settings And Options X Y Offset Mouse point and click operations performed on the Slide View image move the slide within the COOLSCOPE VS instrument Specifically the point clicked on the Slide View image is to be centered under the COOLSCOPE VS high magnification objective The Image window displays the current field of view under the COOLSCOPE VS instrument s objective X Y offset translates the Slide View image and the Image window X Y axis coordinate systems in a process known as centration such that a point clicked in the Slide View image appears centered in the Image window Note It is recommended that the X Y offset is set soon after initially running the WebSlide VS program Once the X Y offset is set reset only as needed To set the X Y offset 1 Acquire the Slide View image 2 If necessary select the 5x high magnification objective and Point Mode 3 Pl
29. erver LE Hence a default behavior of the CoolAlign program is to root WebSlide virtual slide fold ers on the WebSlide Server LE Although the default location for Scanning Folder and Destination Folder is satisfactory in most cases there may arise a need to change the location of one or both To change the location of the Scanning Folder and or the Destination Folder click Setup Scan Options or click the Displays the Scan Options window Standard Toolbar button Then click the Folders tab to display the Scan Options Folders tab as shown in Figure 46 Scan Options General Folders 2 Stack Scanning Folder C Program Files Nikon COOLSCOPE YS4Scanning Select Destination Folder C Program Files Bacus Labs WebSlide Server ebSlides v OK X Cancel Figure 46 The Scan Options Folders tab To select a new directory for the Scanning Folder and or the Destination Folder click the appropriate Select button The Select Directory dialog appears as shown in Figure 47 Select Directory Directory Name C Program Files Bacus Labs WebSlide Server WebSlides Directories Files E EA gt Program Files gt Bacus Labs gt WebSlide Server PB Weides Sf EN Drives BI c v Figure 47 The Select Directory dialog Use the Drives dropdown to select a drive Use the Directories tree to locate the desired directory and double click on the directo ry to op
30. et to 2 or greater the Z value returned by auto focus is used to capture subsequent fields of view until the next auto focus is performed If the Z value returned by an auto focus on a blank or a nearly blank field of view is used to capture subsequent fields of view the subsequent fields of view are often captured out of focus To alleviate this issue the Only focus if the field content value is gt feature of the WebSlide VS program sets a field content threshold value above which a field of view is accepted for the performance of an auto focus If a field of view queued for auto focus has field content value below the threshold the Z value returned by the preceding auto focus is used to capture that field of view and the next field of view is queued for auto focus By rejecting blank or nearly blank fields of view for the performance of auto focus Only focus if the field content value is gt ensures that the Z values returned by auto focus are representative of fields of view containing tissue The Only focus if the field content value is gt value is configurable and is stored separately for each high magnification objective A default Only focus if the field content value is gt value is provided and is recommended as a starting point for each high mag nification objective To change the Only focus if the field content value is gt value click Setup COOLSCOPE Properties or click the Displays the COOLSCOPE Properties window Standar
31. ght click a point within the Image window The point clicked is repositioned to the center of the Image window as shown in Figure 15 Eo Image Repositioning the stage x File Edit Command Objective View sn 40x 20x 4ilx DE 4 x 39849 Y 12931 Z 30546 5x Repositioning the stage Figure 15 Mouse point and click to reposition the slide in the Image window The Image window also supports mouse click and drag operations to reposition the slide under the COOLSCOPE VS instru ment s high magnification objectives To click and drag place the mouse cursor over the over the Image window and press the left mouse button With the left mouse button still pressed move the mouse cursor to a new location within the Image window The slide is repositioned as shown in Figure 16 When the left mouse button is released the partially painted portion of the Image window is filled File Edit Command Objective view o oo 2 5x 10x 20x 40x X 40589 Y 13584 Z 29861 5x Figure 16 Mouse click and drag to reposition the slide in the Image window 15 Changing the objective To change the objective click one of the high magnification objective buttons i e 5x 10x 20x or 40x in the Image window Standard Toolbar The objective is changed and the Image window is updated The currently selected objective is indicated by green in the Image window Standard Toolbar and in the Status Bar as shown in Figure 17 Obj
32. high magnification objective A default Focus every value is provided and is recommended as a starting point for each high magnification objective To change the Focus every value click Setup COOLSCOPE Properties or click the Displays the COOLSCOPE Properties window Standard Toolbar button The COOLSCOPE Properties window appears as shown in Figure 35 COOLSCOPE Properties 5x 10x 20 40x Network Camera Settings Auto Focus Focus every 3 Cal cq This objective uses the C1 Bonner fal COOLSCOPE custom mode Only focus if the field content value is gt 10 11 Use precision focus if the Z change s gt 450 Default settings Figure 35 COOLSCOPE Properties Focus every Click the tab 5x 10x 20x or 40x corresponding to the high magnification objective of interest To change the Focus every value click within the Focus every field and type in a new value or use the up and down arrows to select a new value To regis ter the new value and close the COOLSCOPE Properties window click the OK button To restore the Auto Focus default values for the selected high magnification objective including Focus every click the Default settings button and then click the OK button 28 Only focus if the field content value is gt Field content is expressed as percent i e 0 100 and is a function of the optical density of the central portion of the field of view If the cen
33. in the Image window Using simple mouse point and click operations and the Image window the user is able to navigate and view the slide under the COOLSCOPE VS instrument s high magnification objectives If capturing a WebSlide virtual slide this functionality also allows the user to determine the objective to be used for and the region s of interest to be scanned in the high magnification scan Point Mode Mouse point and click operations performed on the Slide View image move the slide within the COOLSCOPE VS instrument Specifically the point clicked on the Slide View image is centered under the COOLSCOPE VS high magnification objective This mode of operation where mouse point and click operations performed on the Slide View image centers the clicked point under the COOLSCOPE VS instrument s high magnification objective is known as Point Mode Point Mode is the default mode of the WebSlide VS window upon acquisition of the Slide View image Two types of mouse point and click operations are available in Point Mode 1 A left mouse click centers the clicked point under the objective 2 A right mouse click centers the clicked point under the objective and performs an auto focus Left or right click a point of interest on the Slide View image The field of view under the COOLSCOPE VS instrument s high mag nification objective is outlined in red on the Slide View image as shown in Figure 12 Point Mode Field of View T a To PA
34. lected objective is displayed in the Image window Using mouse point and click operations and the Image window the user is able to navigate and view the slide under the COOLSCOPE VS instrument s high magnification objectives If capturing a WebsSlide virtual slide this functionality also allows the user to determine the objective to be used for and the region s of interest to be scanned in the high magnification scan The Slide View image displayed in the WebSlide VS window is the starting point for and provides all the functionality required for the high magnification scan After selecting an objective for the high magnification scan simple mouse gestures are performed on the Slide View image to outline the region s of interest to be scanned Advanced user options include adjusting Camera Settings configuring Auto Focus and enabling Z Stack The high magnification scan captures a series of images each representing a sin gle field of view under the selected high magnification objective These captured images or tiles are aligned during viewing and constitute an image of the outlined region s of interest known as the Field View image A WebSlide virtual slide consists of the data structures and the image tiles corresponding to both the Slide View image and the Field View image During scanning the files that comprise a WebSlide virtual slide are placed in a single folder known as a Webslide virtual slide folder Upon the completion of scanning
35. lue returned by the last focus performed Best suited for 5x and 10x high magnification scans Important Note Focus every 0 implies that an auto focus or a manual focus must be performed preferably within the outlined region of interest before commencing the high magnification scan Focus every 1 Perform an auto focus on every field of view within the outlined region of interest Best suited for small scans or scans involving specimens of varying thickness Focus every 2 Perform an auto focus on every second field of view within the outlined region of interest The Z value returned by an auto focus is used to capture subsequent fields of view until the next auto focus is performed Focus every 3 Perform an auto focus on every third field of view within the outlined region of interest The Z value returned by an auto focus is used to capture subsequent fields of view until the next auto focus is performed Focus every x Perform an auto focus on every x field of view within the outlined region of interest The Z value returned by an auto focus is used to capture subsequent fields of view until the next auto focus is performed Note With high magnification scans using the 20x or 40x objective and or with a speci men having greatly varying thickness it is recommended that the Focus every value is not increased too far from the default value The Focus every value is configurable and is stored separately for each
36. n The Image window is updated Default settings restores the camera setting values for the selected high magnification objective to their default factory values Each high magnification objective has its own default camera setting values To restore the camera setting values for the selected high magnification objective to their default values click the Default settings button The camera settings are restored to their default values and the Image window is updated To accept the current camera setting values for the selected high magnification objective click the OK button To discard any change to the camera setting values for the selected high magnification objective thereby reverting the settings to their initial val ues click the Cancel button Reacquire the image To reacquire the field of view displayed in the Image window click Command Refresh or click the Reacquire the image Standard Toolbar button l Saving image to hard disk or copying to clipboard To save the field of view image displayed in the Image window to hard disk click File Save Image As To copy the field of view displayed in the Image window to the Clipboard click Edit Copy the image to the clipboard Changing size To change the size of the Image window click View Two options are available 1 640x480 and 2 1280x960 Closing To close the Image window click File Close or click the close button at the top right hand corner of the Image window 3
37. nnnnnnnnnnnnnnn nen 18 CHANGING SIE 2 ann ee ea ee seem ea 18 GIOSING aan men ee ee ee 18 Acalir ng The Field VIEW Mage z 0 0 28 0000 Ss Em Hirn DH a a Ren EHER ER 19 Selecting An Objective For The High Magnification Scan uuuuuuuuueeenennnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nn 19 Objectives and the number of images to be captured during the high magnification scan 20 Outlining The Region s Of Interest For The High Magnification Scan uruuuseseeennnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnenn 21 PRECIAEIGIS Mod sirrane e ONERE DEA Aa OaE aa DA ENEUEEELTAERE ER NIE EEENENEENEERSSERHEEUREEDE 22 Trace Mode sisisi os aa aE EAE AEA SNAAR NEEN 23 Defining multiple scan segments u nn 24 Deleting 3 scan Segment suusssuissinnsunangssnnceem enden an aA a ana A aE AAEE aE ENEA EENE 25 Hasler scanning ULE EN ssis iosin eaaa Sec res aaa aiaa a Henna Enns RENN 25 Recommended Trace Mode scan segment shapes uuurerennnnnnnnnenonnnnnnnnnennnnnnnnnnennnnnnnnnnennnnnnnnnneennnn 26 Configuring Auto Focus For The High Magnification Scan uuuuuuu000nnnnnnnnnnonnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 27 FOCUS GVEIY serisine EEEREN EEEE EEEE E AEE EE EE E SAA EERON 28 Only focus if the field content value is gt 22222000200000nnnn2nnnnnnnnnnunonnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnen 29 Use precision focus if the Z change iS gt _ uuuuuusnnannnnnnnnnnnnnnnnnnnnnnnnnn
38. nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn 30 Running The High Magnification Scan sicssicisiscssissssicnsesaccccinnssusessnnceucutasuasueessecassieneonsssannsinendabsnccevsussuuusysbeeeciaei 31 CoolAlign And WebSlide Virtual Slide Folder Locations cccceeeeescescesssseeneeeeeeeeeneceeseesseeeneeeeseeaonaecoeasnesseeesensaaeaoas 34 Additional Settings And Options 9 49 15 E E E E E ace esac aes aes ee ae cere E E pe geen sec ee eee eects 35 PS 6 GR ee Pe ee ee ee re nee ene ae ae ee 36 PO SU SCAN OPIONS een ae ne a ee 37 Introduction The WebSlide VS program software is a program for WebSlide virtual slide capture from the COOLSCOPE VS instrument WebSlide virtual slide capture from the COOLSCOPE VS instrument involves two scans 1 A0 22 x magnification scan of the entire slide producing the Slide View image 2 A high magnification i e 5x 10x 20x or 40x scan of a user defined region of interest producing the Field View image When a glass slide is retracted into the COOLSCOPE VS instrument two macro images at 0 22x magnification are automatically captured These images are aligned during viewing and constitute an image of the entire slide known as the Slide View image Mouse point and click operations performed on the Slide View image move the slide under the COOLSCOPE VS instrument s high magnification objectives 5x 10x 20x and 40x high magnification objectives are available The field of view under the se
39. objectives 24 The first scan segment is identified by the appearance of a ff in first field of view to be scanned in that scan segment The sec ond scan segment is identified by the appearance of a in first field of view to be scanned in that scan segment defined etc Scan segments may overlap Important Note The WebSlide VS program is intended as a region of interest WebSlide virtual slide scanner As such it is recommended that a single scan segment not include more than 400 tiles Hence and in particular when using the 20x or 40x objective for the high magnification scan rather than outlining a single large area of interest for the high magnification scan it is recommended that multiple smaller areas of interest are outlined each including less than 400 tiles Deleting a scan segment To delete a scan segment from the high magnification scan click Edit Delete a Scan Segment or click the Displays the Delete Scan Segment window Standard Toolbar button amp The Delete a Scan Segment window appears as shown in Figure 31 Delete a Scan Segment Anl Seg 1 R Anl Seg 2 Trace Figure 31 The Delete a Scan Segment window The scan segments are listed and are identified by Segment number and the Mode i e Rectangle or Trace type To delete a scan segment from the high magnification scan click on the scan segment to select it and then click the OK button Raster scanning pattern Raster scan is the s
40. owing objectives are available for the high magnification scan 5x 10x 20x and 40x To select an objective click Objective and select an high magnification objective from the dropdown or click one of the high magnification objective buttons i e 5x 10x 20x or 40x in the WebSlide VS window Standard Toolbar as shown in Figure 21 Objective dropdown Objective buttons 5 WebUlide WE Ba pi pp Cie few ev mai Yo FOR Fi ae By Figure 21 Selecting an objective for the high magnification scan 19 The currently selected objective is indicated by green in the WebSlide VS window Standard Toolbar and in the Status Bar as shown in Figure 22 Selected objective green Selected objective listed Figure 22 The currently selected objective indicated Objectives and the number of images to be captured during the high magnification scan Each increase in high magnification objective reduces the size the field of view by half along both the X and Y axis Hence each increase in high magnification objective requires approximately a four fold increase in the number of fields of view to be captured in order to scan a fixed area as shown in Figure 23 5x 6 tiles 10x 24 tiles 20x 96 tiles 40x 384 tiles Figure 23 Each increase in objective requires an approximate four fold increase in the number of fields of view to be captured 20 Outlining The Region s Of Interest For The High Magnification Scan To o
41. the Z value of such an auto focus is used to capture subse quent fields of view the subsequent fields of view are likely to be captured out of focus To alleviate this issue the Use precision focus if the Z change is gt feature of the WebSlide VS program sets a Z change thresh old value above which the Z value returned by auto focus is rejected and a precision auto focus is performed The Z value returned by the precision auto focus is then used to capture subsequent fields of view until the next auto focus is performed The Use precision focus if the Z change is gt value is configurable and is stored separately for each high magnification objective A default Use precision focus if the Z change is gt value is provided and is recommended as a starting point for each high mag nification objective To change the Use precision focus if the Z change is gt value click Setup COOLSCOPE Properties or click the Displays the COOLSCOPE Properties window Standard Toolbar button The COOLSCOPE Properties window appears as shown in Figure 38 COOLSCOPE Properties 5x 10x 20 40x Network Camera Settings Auto Focus a Ca cg This objective uses thect Forusevew 8 ii COOLSCOPE custom mode Only focus if the field content value is gt 10 11 Use precision focus if the Z change is gt 450 A Use precision focus if the Z change Default settings Figure 38 COOLSCOPE Properties Use pre
42. tral portion of the field of view is blank or is partially filled with lightly stained tissue the field content value is low If the central portion of the field of view is filled with darkly stained tissue the field content value is high as shown in Figure 36 Field content 0 Field content 1 Field content 39 Field content 84 p dey on eee Ld Siege ray os ieee kd e rey on bmg Ld rey os ieee Ld fe i Ce Gee See Pe Bm Cae Gee See fe i Ce Gee See m y DO a m 4 D m m a D D B m a E AE O EEE des E a I b h ie k E sO a b i m ie ay ik Ai 7 el He 3 i os i Ar j ae an rolls i F A z e ee ara ae z ipa 7 7 er a a HT m J a uh m oy 7 s Fe f f ad a F re oe ee m Ag ee iss Kl on s gue a 4 es ii u k tien ae i uy ma P i Ti em eae Tri EA Tim iE Zn Pa Th EEEN Fe bare Da P E ERA mn m Dra Fae 2 Figure 36 Field content Two instances where the central portion of a field of view may contain little to no tissue are 1 The outlined region of interest for the high magnification scan includes non tissue containing areas of the slide 2 The the tissue within the field of view is loose or highly vacuolated The Z value returned by an auto focus performed on a blank or a nearly blank field of view often differs greatly from the Z value returned by an auto focus performed on a representative field of view containing tissue If the Focus Every value is s
43. up XY Offset dialog appears as shown in Figure 50 To set the X Y offset click the Yes button Points click on the Slide View image now appear centered in the Image window 9 This command is used to set the centration between the macro image and the micro images Please read the help and be Familiar with this command wy before using it Do you wish to continue Figure 50 The Confirm Setup XY Offset dialog Z Stack Z stack provides the ability to virtual focus a WebSlide virtual slide This is accomplished by capturing a series of nine images for each field of view rather than one Four of the images are captured using Z values stepped incrementally greater than that returned by auto focus and four of the images are captured using Z values stepped incrementally less than that returned by auto focus The ninth image is captured using the Z values returned by auto focus During viewing simple mouse or keyboard ges tures are used to cycle through the series of nine focal plane images in what is known as virtual focus 36 To enable Z stack click Setup Scan Options or click the Displays the Scan Options window Standard Toolbar button Then click the Z Stack tab to display the Scan Options Z Stack tab as shown in Figure 51 Scan Options General Folders Z Stack Z Stack Mulitple Image Plane Acquisition Enable Z Stack Acquisition 5x Step Size 120 10x Step Size 60 f 20x Step Size 30 40x Step Size 15
44. urrent image being captured the time remain ing and reports when an auto focus or a precision focus is being performed as shown in Figure 40 Image Time Remaining Scan Prog ii Z Trash U Time Remaining 00 02 00 ES FE ES EE EE ZT EEE Sk oe Oy ce Tr eg ga a s es Fi un ALA z a e ed u r P gt on rs ie 3 SS EBAY gt SKA Auto Focus in progress x ig A TIPTA L we ee eg Figure 40 The Scan Progress window 31 To pause the high magnification scan click Scan Pause or click the Pause the active Scan Standard Toolbar button Il To resume the high magnification scan click the Continue the Scan Standard Toolbar button To end i e abort the high magnification scan click Scan End or click the End the active Scan Standard Toolbar button The Confirm window appears as shown in Figure 41 Confirm X 9 Please confirm ending the scan No final scan data will be saved Is this OK J Figure 41 The Confirm window To end the high magnification scan click the Yes button If the high magnification scan is ended a WebSlide virtual slide is not created To resume the high magnification scan click the No button At the completion of the high magnification scan the Scanning Complete window appears as shown in Figure 42 Click the OK button to close the Scanning Complete window Alarm Scanning Complete At this point you may click on the OK button and either click
45. utline a region of interest for the high magnification scan click the Mode dropdown button as shown in Figure 24 Mode dropdown i gt 2 ae Y EI es 5x Figure 24 Outlining a region of interest for the high magnification scan There are two Modes by which a region of interest is outlined 1 Rectangle Mode 2 Trace Mode 21 Rectangle Mode To draw a rectangle around a region of interest select Rectangle in the Mode dropdown Place the mouse cursor at the top left hand corner of the region of interest and press the left mouse button With the left mouse button still pressed move the mouse cursor to the bottom right hand corner of the region of interest as shown in Figure 25 a TAGER JBE 1 AB aS Ze Sx Figure 25 Rectangle Mode for outlining a region of interest Release the left mouse button and the image tiles corresponding to the fields of view to be scanned are drawn as shown in Figure 26 e J Be pE je tew kan ECO TEJE TDPI m Tan ann Wa Pi x nee he Oe ix Figure 26 The image tiles to be scanned 22 Trace Mode To draw a polygon around a region of interest Select Trace in the Mode dropdown Left mouse click on the Slide View image to define the corners of the polygon as shown in Figure 27 RGR JB EB l a Sma gt maa Yo eT i A Sx Figure 27 Trace Mode for outlining a region of interest After defining the last corner of the polygon
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