3D Histech PANNORAMIC SCAN RX User Manual Download Page 102

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PANNORAMIC® SCAN RX 1.0

SCANNING MODES AND SETTINGS

MAY 13, 2021

101

FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES .

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Microscope mode

Brightfield

Fluorescence

Figure 91. Microscope mode

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Live tools

Fast mode

Screenshot

Magnifier

Ruler

Image processor plugins

Use pseudo-color

Add scanmap

Figure 92. Live tools

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Auto-exposure

Figure 93. Auto-exposure

Summary of Contents for PANNORAMIC SCAN RX

Page 1: ...PANNORAMIC SCAN RX 1 0 USER S GUIDE FOR RESEARCH USEONLY NOT FORUSEIN DIAGNOSTIC PROCEDURES May 13 2021 Rev 1 ...

Page 2: ...nit 18 1 2 System Overview 19 1 2 1 Pannoramic SCANRX system 19 1 2 2 Hardware Options 20 1 2 3 Control Software 22 2 Installation 24 2 1 Operation System of the Control Computer 24 2 2 Control ComputerPorts 26 2 3 Connectors and Cables 27 2 4 Coupling theLumencor SOLA SMUnitwith the Scanner 28 2 5 Coupling theLumencor Spectra 6 Unit with the Scanner 28 2 6 External Power Supply Unit 29 2 7 Power ...

Page 3: ...nel 77 5 2 2 MicroscopeControl Panel 87 5 2 3 Hidden Functions 99 5 2 4 Quick MicroscopeFunctions 100 5 2 5 Bottom Menu Barof the Main Window 102 5 3 Planner Mode 103 5 3 1 General Functions at the Main Menu 103 5 3 2 General Functions at the Magazine Menu 106 5 3 3 General Functions at the Slide Menu 106 5 3 4 Slide View with Card 108 5 3 5 Table View Mode 110 5 3 6 Card Collection View Mode 111 ...

Page 4: ...Preventive Maintenance 145 9 4 Troubleshooting 145 9 4 1 Fluorescent Applications Optional 147 9 5 Maintenance 148 9 5 1 Removing the Protective Covers 148 9 5 2 Removing a Slide 149 9 5 3 Installing and Removing theFilter Module Fluorescent Option 151 9 5 4 Removing the Magazinefrom the Transporting System 153 9 5 5 Transporting Pannoramic SCANRX 154 10 Technical Data 156 ...

Page 5: ... P101036 PCT IB2005 050351 EP 1789831 US7 663 078 P0301911 PCT HU04 00019 EP 1644767 US7327515 Theabovementioned granted patents granted utilitymodel registeredtrademarks pending internationaland nationalpatentapplications and theothercorresponding IP arethesole properties of the3DHISTECHLtd 3DHISTECHLtd is notliablefordamageofwhatevernature including butnotlimited to general or specificdamage ind...

Page 6: ...including butnotlimited to general or specificdamage indirectdamage consequentialdamageorincidentaldamage including damageresulting fromlostprofits interruptionof business loss of business information pecuniary loss orsimilardamage thatstems fromoris associated with theincorporated partof this Productthatis madeby a third party company THE SOFTWARE IS PROVIDED AS IS ANDWITHOUT WARRANTY OF ANY KIND...

Page 7: ...below IEC 61010 1 2010 Safety RequirementsforElectricalEquipmentforMeasurement Control and Laboratory Use Part1 GeneralRequirements IEC 61010 2 081 2015 Safety requirementsforelectricalequipmentformeasurement controland laboratory use Part2 081 Particularrequirementsforautomaticand semi automaticlaboratory equipmentforanalysis andotherpurposes Thereis no furtheroperator user action required in cas...

Page 8: ... theproduct described Beforeoperating thedevice you mustcarefully read this instructionmanual and adhereto all WARNING and CAUTIONnotices refer to chapter Notes RegardingOperational Safety formoreinformation anda copy should bekeptin theclose to the scannerforreference wheneverrequired This User s Guideis a part of thePannoramic SCANRX system identified by therelevant article numbers included in t...

Page 9: ...en and window titles push buttonand menu names paths oroptions Keys on thekeyboard Forexample function keys such as F11 ortheCtrl Shotkey Example textin bold and italics Cross references withinthis documentor to otherdocuments Warning It mightcauseirreversibledamageorharmto theuserof theproductortheproductitself if this instruction is notfollowed Caution It mightcausetheproductto notwork properly ...

Page 10: ... operation Makesurenotto reach with yourhands into theinstrumentto avoid therisk of crushing yourfingers Pleasenotethatthedigitizing process has to beinterrupted and the slide magazinemoved via softwareto theoutputpositionbeforeremoving it ThePannoramic SCANRX including anyof itsoriginalaccessory components should notbe operated in any otherway than described in chapter1 1 1IntendedUse Any of thef...

Page 11: ...condition youshouldcontactthe3DHISTECH CustomerService Warning Check thatyourlocalline voltageis compatiblewith Pannoramic SCANRX specifications beforeyou turn poweron Warning Only connectexternaldevices to the instrumentwhich areapproved to avoid therisk of electrical shock Warning ThePannoramic SCANRX does notincludeany specialfacilities to protectfrom samples with an etching potentially infecti...

Page 12: ...c SCANRX is a precision instrumentwhichmay suffera significantreduction in operationalfunctions oreven physicaldestructionfollowing intervention performed in any nonconformingmanner Caution In the eventof any non conformingtypeof use including non conforming useof assemblies or singleparts no liability willbeassumed by theManufacturer This shallalso apply to service orrepairwork of any kind which ...

Page 13: ...tto operateand to disconnectthedevice if necessary Notice Thesafety level of the equipmentafterservicing willbeidenticalwith levelof theoriginal equipment Notice Electric powerto thePannoramic SCANRX is supplied via an externalmains powersupply unit Itallows foroperation atlinevoltages in the rangeof 100 V to 240 V 10 50 60 Hz withoutany extra facilities required forvoltagetransformation ...

Page 14: ... delivering a faultless productforreplacement No warrantywillbeaccepted in cases of naturalwear notably wearand tearparts orimproperproducthandling TheProductManufacturerwillrefuseany liability in theeventof damageresulting fromfaulty operation negligence orunauthorizedintervention into theproduct notably fromthe replacementof productparts ortheusageof accessory parts from othermanufacturers Any s...

Page 15: ...e ability to fluoresce due to photon induced chemical damage and covalent modification therefore fluorescent signals cannot be properly detected SWAP A file that is used as a temporary location on the computer to store information that is not currently used by the RAM Virtual Slide Slide A digital image of a thin glass plate on which specimens are mounted for microscopic study a dynamic interactiv...

Page 16: ...1 1 2 Features and Benefits ThePannoramic SCANRX offers world class brightfieldand fluorescentwholeslide scanning on up to 50 virtualfluorescentchannels using9 physicalfluorescentfilter positions An outstanding 0 12 µm pixel in Brightfield and 0 16µm pixel in Fluorescent resolution is achieved with the40 NA 0 95 equivalentto 80 magnificationin BF and 62 magnification in FL Plan Apochromatobjective...

Page 17: ...ng and preview image Imagesharpening both forFluorescenceand Brightfield featurewhichimprovethe visualappearanceof digitalslides Focus algorithm finds thefocus whichis mostappealingto thehuman eye Deconvolution algorithm Compactand robustdevice Good quality and stablemanufacturing Pannoramic SCANRX is an optimalchoiceforcustomers who need highqualitydaily throughputgrantedby theloading capacityof ...

Page 18: ...SE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES 1 1 3 Warning and InformationLabels Thefollowing figurecontains thelabels used on thePannoramic SCANRX mainunit the externalmains powersupply unit and theLumencor SOLA SM illumination unit Figure 1 Warning and information labels ...

Page 19: ...following figureshows themain partsof thebaseunit Figure 2 Main parts of the base unit 1 Protectivecover 2 Outputstack formagazines 3 Inputstack formagazines 4 Protectivecoverfor magazineloader 5 Magazinefeederdoor cover 6 PointGrey Grasshopper3 or pco edge4 2 bi camera 7 Protectiverails Fluorescent option A 8 Lumencor SOLA SM fiber coupledillumination unit 9 Lumencor illumination adapter 10 Lumen...

Page 20: ...cor illumination adapter 10 Lumencor illumination cable 1 2 System Overview Thestandard scopeof delivery of theproduct includes thefollowing hardwareand softwarecomponents 1 2 1 Pannoramic SCAN RX system Thefollowing figureshows themain componentsof thePannoramic SCANRX system Figure 3 Pannoramic SCAN RX system overview 1 Lumencor SOLASM fiber coupledilluminationunit optional 2 24 V externalpowers...

Page 21: ...ouse 6 Controlcomputer 7 Keyboard 8 Pannoramic SCANRX baseunit 9 Slide magazinewith cover 1 2 2 Hardware Options Notice Theconfiguration of thecontrolcomputerandmonitorcan vary dependingon theproduct order Cameras PointGrey Grasshopper3 1 CCDmonochromecamera forhigh quality sensitivefluorescentapplications pco edge4 2 bi Back illuminated 16 bitsCMOSpco edge4 2 bi camera ...

Page 22: ...ption baseunitequipped with Point Grey Grasshopper3 camera forBrightfield scanning no fluorescentaccessories included Pannoramic SCANRX BasicBrightfield and FluorescenceOption baseunitcompletely equipped with pco edge4 2bicamera and Lumencor SOLA SM non triggered or LumencorSPECTRA 6 fluorescentillumination unit with filters forfluorescencescanning Pannoramic SCANRX Advanced Brightfield and Fluore...

Page 23: ...ngs on 40 NA objective if you need itto beset contactcustomerservice Fluorescent Options for Pannoramic SCAN RX Fluorescent illumination unit Description Lumencor SOLA SM Fluorescentillumination unit usewith PointGrey Grasshopper3 camera only LumencorSPECTRA 6 LightEngineilluminationunit 1 2 3 Control Software Pannoramic Scanner Software for Research control software Optional Fluorescence Extended...

Page 24: ...PROCEDURES Convertersoftware 2 3 2RTM onlyavailablein Fullscannerinstallmode CaseViewer or SlideViewer software fully functional Optional CaseCenterorSlideCenter TMA module 3DReconstruction module QuantCenter HistoQuant NuclearQuant MembraneQuant CISHQuant FISHQuant and DensitoQuant modules E School Encoder ...

Page 25: ...placed so thatthereis enough spaceforventilation and forsafe and efficientoperator maintenance Caution If the temperatureof thelocation wherethescanneris operated is much lowerthan the temperatureof theequipment forexample thedeviceis broughtin from an outerstorage or has been transported to thesite pleaseleave enough timeto normalizethe temperaturedifferences beforeoperating thedevicewithin thesa...

Page 26: ...he SWAP partition forstoring temporaryfiles generated during scanning as thelack of spacerequired will resultin interruption of scanning MicrosoftHardwareDriver Updates We are nottaking responsibilityforerrors caused by automatichardwaredriverupdates issued by Microsoft so werecommend thatyou turntheautomaticupdates optionoff Third Party DriverUpdates Warning Automaticupdates of devices drivers ar...

Page 27: ...on of the productfora shortdistance by disconnectingcables and detachinghardware componentsfrom each other Figure 4 Ports on control computer 1 Status display 2 DVDdrive RW 3 Poweron off button 4 Earphoneand microphone3 5mmJack ports 5 2xUSB port 6 Powersupply connector 7 PS 2 mouseport 8 PS 2 keyboard port 9 4xUSB port 10 2xUSB port 11 Network port 12 4xUSB 3 0 ports forPointGrey Grasshopper3 orp...

Page 28: ...ween PointGrey Grasshopper3 camera and controlcomputer pco edge4 2 bi a pair of CameraLink cables between pco edge4 2bicamera and controlcomputer Video cable between monitorand controlcomputer Powersupply cable between 230V 110V andmonitor Powersupply cable between 230V 110V andLumencorSPECTRA6 unit Powersupply cable between 230V 110V andcontrolcomputer Powersupply cable between 230V 110V and24V e...

Page 29: ... Connect thepowersupply cables of both thescannerand theilluminationunit 2 5 Coupling the Lumencor Spectra 6 Unit with the Scanner To operatetheLumencorSpectra 6 LightEnginefluorescentilluminationunit ithas to be connected to the Pannoramic SCANRX baseunit thecamera and thecontrolcomputer 1 Turn thecontrolcomputerand thepco edge 4 2bicamera off 2 Attach LumencorSPECTRA6 fluorescentilluminationunit...

Page 30: ...nitmustbeconnected between themains powerand thedevice Frontpanel 1 main powerswitch 2 powersupply connector Back panel 3 detachablepowercord to connectthe externalpowersupply unitwith themain unit Figure 6 24V external power supply unit 2 7 Power the Scanner On Off To turn thescanneron press down the Isideof therocker switch atthe frontpanel of the 24V externalpowersupply unit Figure 6 1 and pres...

Page 31: ...max 50 mm Thickness 0 90 to 1 2 mm No 1 and No 1 5 0 13 to 0 16 mm and 0 16 to 0 19 mm Corners 45 beveled corners Edges Ground or cut Warning Always wearpersonalprotectiveequipment safetygoggles gloves and coat when working with biohazardousmaterialorslides Warning Do not usea slide when itis broken oritsedges are notproperly cutorgrounded Using such slides can lead to injury Warning If the scanne...

Page 32: ...glass surfaceof a slide usea softtip pen instead formarking area of interest Notice Thedistancebetween slideedges and theedges of the mounted coverslip should be1 2 mm and they should beparallelwith each other Notice Fluorescent signals becomemoreeasily detectableforthescanner thereforeresulting in a brighterand betterimage by treating theslidewith a formula thatpreventsrapid photobleachingof fluo...

Page 33: ...ontrolsoftwareand viewersoftware To affixbarcodestickers to slides do the following 1 Peel off thebarcodesticker 2 from theroll 2 Stick it on thecolored label area 1 of the slide on thespecimen side Caution Ensurethata marginalspaceof 1 2 mm remains on allsides between thestickerand the label area outerlimits Itis vitalfor barcodeidentification Do notletbarcodesticker protrudefrom slideedges orsti...

Page 34: ...n A magazinecan contain a maximum of 25 slides Push slide 1 into themagazine 3 with itsbarcodeend 2 first Thesymbols on theside of the magazinedemonstratetheproperway of insertingslides Notice You should insertseveralslides into a magazinewithoutemptyslots Begin theinsertionon position 1of the magazine Caution Only original3DHISTECHmagazinesareallowed forusewith Pannoramic SCANRX To insertor remov...

Page 35: ...shown in Figure 9mustbeclosed during operation 1 Removemagazinecover beforeyouinsertmagazines Caution Replacemagazinecover when magazineis notcurrently used oris stored fora longer period Thecoverpreventssoiling and mechanicaldamage 2 Open theflap of theinputstack 5 and puta magazine 1 into theinputstack 4 The magazine s rack theback sideof themagazine 2 mustcontactwith theguiderails with its open...

Page 36: ...ious damages in thefeeding mechanism Notice Theinputstack can befilled with a maximum of 6 magazines in additionto theonein the magazineloader Figure 10 Misplaced magazine Caution Do not placemagazines into theoutputstack 3 orremovemagazines withalready digitized slides from thereduring thedigitization process Only removemagazines fromthe outputstack when you havefinished digitization of allslides...

Page 37: ...indowis displayed Figure 11 Mode selection window Microscopemode fordigitization of individual slideorindividualrack set scanning profileof theslide useLive microscope Plannermode plan theentire scanning procedure assign oneormoreprofiles to each slide defineBrightfield and Fluorescenceormixed scanningmodewithin a run definescanning profileto slides included in racks or magazines automated scannin...

Page 38: ...cted modeis initialized Slide magazinecontrol Notice Atslide loading thePannoramic Scanner SoftwareforResearch controlsoftware registers whethera slideis inserted or not Atthe initialization thestagemoves to theslideinsertposition and checks theslide A logging mechanismis also available in theslideloading test Theslide sensorhas an optoelectronicgate and a lever Attheslide loading position the lev...

Page 39: ...idethatis loaded at themomentis highlighted with a bluebackgroundand outerline Objectivechanger Liveviewis on Liveviewis on with the shutterclosed Toolbarfor liveimages Click to display thetoolbarforLiveview Thesefunctions areonly availableforthedisplayed live image i e Liveview is ON butnotavailableforcamera images during digitization When in Normal livemode images aretaken with theuser specified...

Page 40: ...ng images willhavea highernoiselevel This function is usefulforfluorescentliveview where despitethehighernoiselevel the resulting imagewillberefreshed as in normalmode Imageintensity Figure 14 Image intensity Theintensity of thepixel at which thecursoris placed is displayed by I in the Imageintensity window X and Y stand forthe location of thepixel within theimagecoordinatesystem Screenshot Displa...

Page 41: ...aming Slide namecan bedefined manually orautomatically If you wantto nametheslide manually turn on the Manual naming function and if you wantto generateslidenamebased on the corresponding settings setin Preferences activateGeneratefunction Barcode parsing Selectthetypeof barcodeprofilefrom thedrop downlistforslidenaming through parsingthebarcodestring By using Defaultbarcodeprofile thebarcodeof th...

Page 42: ...leftof alist item to open the Barcode editorwindow in which thesettings of the selected profilecan be edited Figure 17 Barcode editor window If you click Add newitem on thelist blank inputfields willbe displayed Figure 18 Create new barcode Define modifyprofilenamein the Nameinputfield selectbarcodetypefrom the Type drop downlist ...

Page 43: ...tforthe correspondingfield EnableParse subfolders to makeitavailableto create subfolders when parsing datafrom thebarcode Typenameof thesubfolderin the Folder1 Folder2 etc fields dependingon thedepth you wantto define Click Saveto apply settings and click Createnew at thetop of the panelto createa new profileitem Slidesavepath Set destination folderin theinputfield by typing in thepath orclicking ...

Page 44: ...iginalMRXSslidewill bedeleted afterthe conversion is complete Target format Theslideis converted to the selected finalformat Click oneof the buttons to definethefinalslideformat MRXS Tiled TIFF Roche TIFF SVS DICOM Click to open MRXS Tiled TIFF and DICOMconversion settings panel o MRXS settings Figure 20 MRXS settings Click Reset to set everything to default Select ChangeJPG compression rate to en...

Page 45: ...ected File size is smaller butsomeof theviewers cannothandleit TIFF type Automatic theconverterautomaticallyselectsthemost appropriatemethod based on thesizeof thesourceslide Force simpletiff TIFF files use32 bitoffsetaddressing therefore file size is limited to a maximum of 4Gb Force big tiff Big TIFF files use64 bitoffsetaddressing allowing thecreation of biggerTIFF files Compression type Jpeg 8...

Page 46: ...3 Pixel sizeaccuracy default 7 X Y offset accuracy default 5 Depth accuracy default 3 Tilepool size default 1000 UTC timein minutes default 0 Basicoffset table activeby default Shared planeposition activeby default Shared optical reference activeby default o Conversion savepath Thefoldersetin this boxis designed to storethefinal slides after conversion Conversion progress is displayedin theConvert...

Page 47: ... as the resulting measurementdatawillbeincorrect Notice ThePannoramic ScannerSoftwarefor Researchsoftwareis compatiblewith licensed QuantCenter applicationonly otherwisethecontrolsoftwaremay closedueto an error Click to assign theappropriateQuantprobeto thedigitalslide If the scanning of slidehas finished theprogress of Quantevaluationis displayed in the QuantCenter Processing Queuewindow Forfurth...

Page 48: ...AGNOSTIC PROCEDURES Scan to Server Figure 24 Scan to Server settings Server settings Select the dedicated serverto which you wantto scan from the Server drop down list Click thearrow to show thelist of saved serverprofiles orclick Add newitem atthe bottom of thelist to create anotherserverconnection ...

Page 49: ...itorstores each of thecreated server in a list Listentries can be removed ora new entry can be added if required With theFilters function you can narrowdownthe resultsby searching fora specificserverdata By double clicking a listitem serverdata will beloaded in the Scan to Server panel Afterloading serverdata usernameand password arerequired to beadded for authentication and accessingtheserver If ...

Page 50: ...thesettings of the Scan to local panel barcode settings forparsing can bemodified in theBarcodeEditorwindow Figure 27 Barcode Editor If using MIL forbarcodereading you can selectthefollowing barcodetypes 1Dbarcode types Code39 Code128 Code16K Interleaved 2 of 5 Standard 2 of 5 IATA 2 of 5 Matrix2 of 5 Telepen Code93 Code11 MSI Codabar Patch Code Pharmacode ...

Page 51: ...arsing option can beselected if CaseCenterorSlideCenter is connected to the supported HIS LIS This waythebarcoderead by thesoftwareis being identified and thepredefinedlocation of thatspecificcasein CaseCenteror SlideCenter is automatically selected as scanning destinationbased on theCaseID containing slideand patientdatastored on HIS LIS Therefore Folder Case Block and Slidenamefield datacannotbe...

Page 52: ...destination folder Conversion settings Referto Scan to local panel seeabove parameterizationand settingsarethe same Quantsettings Run QuantCenter Turn this functionon forautomaticevaluationof thecompleted digitalslideby using theintegrated QuantCenter rightafterthescanninghas finished Othersettings Scan separately TheFOV areas of thepreview imagewillbe scanned and saved separately as discretedigit...

Page 53: ...esolution FL Pre Scan High Resolution FL ActivateRetake Preview forall the slides in the magazineif necessary This operationcan be initiated from theslidepreview window as well Pannoramic ScannerSoftwarefor Research controlsoftwareautomaticallysaves thepreview imageof a slidethatis loaded into the scanner and of which a preview imageis recorded Wheneveryou add a new magazine in Plannermodeas well ...

Page 54: ...leBrowserwindow containinga listof previously saved profiles is opened Based on the Illumination type profiles aregroupedinto two clusters Brightfieldand Fluorescence Additional profiles can be created by clicking Create You can also search fora specificprofileby filtering based on thefollowing data Objectivetype Multilayermode Illumination Filters Modify date Lastusedate ...

Page 55: ...g profileor Save as to create anotherone Save Profile Theselected profilecan besaved in this window aftertypingtheprofilenameinto thetextfield and clicking Save as Figure 30 Save profile Reset Zoom This function is activeonly in Live view at1 1 magnification Liveimagemagnification Settings and Services function descriptionsaredetailed in chapter 6 Settings and Services Help In the Aboutwindow thev...

Page 56: ...C in fullscreen mode Exitfrom fullscreen mode CTRL mousewheel Zoom in out SHIFT mousewheel ChangeFocus by step 36 36 W S ChangeFocus by step 1 1 fine tuning Arrows Movestage within a limited area F2 ChangePseudocolor CTRL F Start Autofocus Left MouseButton Drag Pan view RightMouseButton Open Circlemenu Other CTRL LeftMouseButton in microscopemode open closeleft profile tree and right navigationtre...

Page 57: ...opemode availableonly if Services orSettings modeis active o Settings Seechapter 6 Settings and Services formoreinformation o Services See chapter 6 Settings and Services formoreinformation In accordancewith theselected mode the ProfileSettings Panel and theMicroscope Control Panel views aremodified 5 1 Brightfield Scanning Mode MicroscopeView consistof threedifferent chapters Main functions Locat...

Page 58: ... selecting Limits oftherange for focusing You can set theupperand lowerlimitsby selecting thedesired valuein the selection boxes This is usefulif focusing was not targeted on thespecimen buton a spot on the coverslip Focus distance thedistanceof focalpointscan besetto create a focus map based on which thesoftwarecalculates interpolated focus values onestep in distance is oneFOV Auto focus Focus va...

Page 59: ...eview window is modified this valueis automatically applied by theprofilein theProfileSettings panel o Specimen threshold This valueis definablemanually This setsthesensitivity of thespecimen detection To set thedesired threshold valuemanually changethesetting in the Specimen threshold level selection boxin therangeof 0 255 Thedefaultvalueis 220 Smallervalues resultin a moresensitivescanning meani...

Page 60: ...s option is selected only thearea encircled with a markerpen willbe scanned You can definethethreshold levelby changing thethreshold valuein the Use marker with threshold selection boxin therangeof 0 255 This setsthe sensitivity of thespecimen detection insidethemarkerarea To setthe desired threshold valuemanually changethesetting in the Specimen threshold selection boxin therangeof 0 255 Thedefau...

Page 61: ... digitizecoverslip edges Select Removecoverslip function to eliminatethoseareas Warning Do NOT use Removecoverslip function on TMA slides Thelayoutof TMA slides may mislead thedetecting algorithm o Fill holes insidethescanmap If selected theholes insidethespecimen will also be scanned Often theseholes contain smallsampleobjectsthatotherwisewould notbe scanned o Removespecks If selected thescannerd...

Page 62: ...Selectwhetherto load preview mask orTMA grid Custom scanmap Thescanmap draws manuallyon thepreview imageis used for scanning Use selection boxrestriction If selected only thearea insidetheboxis scanned Itis usefulif you only wantto scan thearea thatis equivalentwith thesizeof thecoverslip so externalspecks will notbe scanned Multilayermode Select Singlelayeroption if you wantto scan a singlelayero...

Page 63: ...deconvolution is to producea sharperimage buttheuseof a deconvolution algorithm can significantly increasethetimethattakes to createa digitalslide Thecapacity of therequired memory for deconvolutionis minimum96GBRAM Scanning Settings Includes theStop and go scanning modeby which theslidetray stands stillduring recording the FOV then itmoves on so thatthescannercan record thenextFOV Use Colormatrix...

Page 64: ...y butlargerfiles Thedefaultsetting is 80 o PNG Lossless compressed imageformat o BMP Lossless uncompressed imageformat butlargerfiles dueto less effective compression Itis a raw datafile Stitching Usethis functionto enabletheseamless stitching of digitaltiles Use Save compensationimage This function enables theuseof previously recorded referenceimages forall slides Usethis function when theslideis...

Page 65: ...review panel offers options forthreshold setting andselection of thearea to be scanned Figure 42 Preview panel Threshold options This section is located at rightsideof the preview window Scanmap Sourceis designed to set which typeof scanmap is used on thepreview image This scanmap is displayed automatically in theProfileScanmap Source setting Selectablescanmap types arethe following Usethreshold L...

Page 66: ...Brightfield mode RemoveCoverslip If selected the edges of thecoverslip are notdetected as specimen to be scanned Depending on thethresholdlevel itis possiblethatthe edges of the coverslip are detected as areas to be digitized Figure 43 Preview image with and without coverslip edge Caution It requires lotsof time since it cannotfind focus neitheron theedges noron specks to digitizecoverslip edges S...

Page 67: ...ion Makesurethatthe detection resultis acceptable foryou Otherwisesetthethreshold value manually Manual threshold Setthreshold valuemanuallyorcalculatevalueon theactual preview with CalculateThreshold functionwhich is activeonly if setting thevalue manually This setsthesensitivity of thespecimen detection To setthedesired threshold valuemanually changethesetting in the Specimen thresholdlevel sele...

Page 68: ... To setthe desired threshold valuemanually changethesetting in the Threshold selection boxin the rangeof 0 255 Thedefaultvalue is 212 Everything within marker This function is availableonly to selectif the Use marker with threshold functionis activated To scan everythingwithin themarkedarea check theScan everything withinmarkerselection box Figure 44 Scan everything within the marker selected not ...

Page 69: ... areas to scanmap Position To position thespecimen holderthatholds thecurrentslide click Position sample andthen click on thearea of intereston thepreview image This will definetheLive imagethatyou can access from the Liveview Union Add theselected areas to thepreview Mark area forscanning based on theshapeselected in the Preview Toolbar This area willnotbe scanned Erase Delete selected areas from...

Page 70: ...rcle You can select thearea to be scanned with thedifferenttools on the Previewtoolbar Placefocus point You can add manualfocus pointson thepreview image the coordinates of themanualfocus pointsyou add arelisted on the Focus settings panel Notice Themaximum numberof focus pointsthatyou can manuallyadd is 100 Rectangletool Draw rectangleshaped area Ellipsetool Draw ellipse selection Polygon tool Ar...

Page 71: ...lumnnumbers and spot shape round orrectangle Figure 48 TMA tool Grid selector Delete TMA grid by clicking the X atthe top rightcornerand rotategrid by clicking the icon at thebottom rightcorner Enterthenumberof rows and columns in the Rows and Columns fields orselecttheappropriatevalues with thearrows Enterthe distancebetween two spotson theX and theY axis in µm in the Coredistance fields or selec...

Page 72: ...is enabled and the crop function is selected a black framedisplayed in theimage and only thearea inside thebox is scanned Itis usefulif you only wantto scan thearea thatis equivalentwith the size of the coverslip so externalspecks will notbescanned Figure 49 Use selection box on the preview image Thefollowing colors areused in the preview imageto demonstratedigitization and selection settings Figu...

Page 73: ...emarkeris selected in thePreview panel the preview camera detectsthe markerpen Theinsideareas appearin red color and will bedigitized Areas scanned in This color is only displayed during scanning Hide all layers All thelayers will be hidden existing butnotvisible Theoriginal preview imageis shown butlayerinformation is stillvalid Note that whilethis function is active noneof theotherpreview functi...

Page 74: ...definefocus limits select Limittherange Settheupperand lowerlimitsby selecting the desired valuein the selection boxes By using Range theLowerlimitvalueis setto 32 of thecurrentfocus valueand the Upper limitvalueis setto 32 of thecurrentfocus value This is usefulif Auto Focus does notfind thefocus on thespecimen buton thecoverslip Also this makes thefocusing sequencefaster Formanualfocusingdefinet...

Page 75: ...litudeof atany pairof coordinates x y is called theintensity orgray levelof the imageatthatpoint Thepixelintensity atthecoordinate pointing atwith thecursoris displayed in theImage Intensity window Figure 54 Window of Image Intensity 5 1 2 3 Stage Positioning Click to activateStage Positioning Tool to navigateon theslide so to perform microscopemovementson theLiveimagewith this controlfunction The...

Page 76: ...lickingto thepreview area Itallows a quick access to main preview related functions Drag Draw Erase Retakepreview Settings o Toggledeletion always on top o Resetzoom o Window auto size o Clean scanmap Figure 56 Quick toolset 5 1 4 Quick Microscope Functions A quick microscopefunctions toolsetcan bedisplayed uponright clicking on the background of themain window outsidethepreview window Itincludes ...

Page 77: ...AY 13 2021 76 FOR RESEARCH USE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES Autofocus Figure 58 Autofocus Livetools Figure 59 Live tools o Fastmode o Screenshot o Magnifier o Ruler o Imageprocessorplugins o Add scanmap Auto exposure Figure 60 Auto exposure ...

Page 78: ...ach filtercan bedefined manually Valuessuch as CalcExposuretimein MicroscopeControlpaneland thosethatare specified manually areloaded in thesefields Valueunitscan bethe following microsecond millisecond second Exc Thegiven valuespecifies theexcitation intensity in percentageof the illumination unit DG DigitalGain This is camera dependent with PointGrey Grasshopper3 the indexvalueranges from 0 to 4...

Page 79: ...currentZ valueby clicking Assign Current Interpolated focus If you selecttheInterpolated focus option thecoarsefocus levelis calculated from threedifferentfocus pointsof thespecimen Carryouta manualfocusing sequencein thepreview imageon thosethreepoints Setthecorrect focus valueof the desired preview position by clicking Setin the tableof interpolated focus If you wantto go back to any of theprevi...

Page 80: ...enness and size of the specimen Focus Exposure Theexposuretimeduring focusing itcan havethreestates o Short o Normal o Long Sampledetection TheSampledetection paneloffers options forsetting threshold andtheselection of scannable areas Source o Brightfield preview a normaltypeof illumination in themicroscopeforscanning theslide This option is recommended whenscanning in Brightfield mode o Pre scan ...

Page 81: ...n therangeof 0 255 Thedefaultvalueis 212 Smallervalues resultin amoresensitivescanning meaningthatmoreareas willbedigitized however this may also includespecks orotherimperfectionsof theslide Greater values resultin a less sensitivescanning butitis possiblethatsomeof thesmaller specimen areas willnotbe digitized o Auto Threshold By clicking thespecimen will automatically bedetected in thepreview i...

Page 82: ...ction box Alternatively click in thepreview window to activatethis function Figure 63 Scan everything within the marked area selected not selected Threshold enhancement o Removecoverslip If selected theedges of the coverslip arenotdetected as specimen to be scanned Depending on thethresholdlevel itis possiblethatthe edges of the coverslip aredetected as areas to bedigitized Figure 64 Preview image...

Page 83: ...thescannerdoes notdigitizeobjectssmallerthan thepredetermined size This helps filtering specks and otheruninteresting objects out Setthe maximum sizeof specks notto bedigitized by adjusting the Speck sizeslider o Dilatemask Adjustthesliderto enlargeordecreasethe scanned area Theedge is extended discretely by 100 µm each time Scanmap option Figure 65 Scanmap settings Thepreviously saved scanmap can...

Page 84: ...o be sharp This method guaranteesthemaximum depthof sharpness however itreduces digitization speed Z Stack ForExtended focus and Z Stack scanning methods you can determinethe desired numberof focus levels with theLevels selection box Thecurrentfocus valueis theinitial level If you set 5 forexample then theinitiallevel plus four two focus levels aboveand below theFOVs arecaptured Therefore itis adv...

Page 85: ...gitization of theslidewith onechannel Changefilters ateach field of view Filters should bechanged foreach field of view if very precise colocalization is required butconsiderthatthis option is moretimeconsuming Notice Makesureto select theChangefilters ateach field ofview option if using multiband filter formulti channeldigitization Caution If the specimen area is barely visible it is possiblethat...

Page 86: ...during whichthe background of theimageis reduced based on thecomparison of theimage recorded by thecamera and thecompensation image o Intensity equalization pixel levelanalyzation of theacquired image a one by onetypeimagecompensationmethodis applied Extended focus Select the typeof theextended focus algorithm used during scanning o Legacy uses originalextended focus algorithm itis recommended for...

Page 87: ...sion o BMP Lossless uncompressed imageformat butlargerfiles dueto less effective compression Itis a raw datafile o PNG Lossless compressed imageformat o JPG Thequality can beset in the valuebox Greatervalues resultin better quality butlargerfiles Thedefaultsetting is 80 Bit depth 8 bit Stitching UseStitching function enables theseamless stitchingof digitaltiles Sharpening Selectthis option to impr...

Page 88: ...threshold setting and selection of thearea to be scanned Figure 71 Pre scan preview image Threshold options This section is located at rightsideof the preview window Scanmap Sourceis designed to set which typeof scanmap is used on thepreview image This scanmap is displayed automatically in theProfileScanmap Source setting Selectablescanmap types arethe following Usethreshold Load previously saved ...

Page 89: ... area in singlelayerDAPI with an illumination timeof 20ms thatis displayed in theProfileWizard window Scanningprocess takes a coupleof minutes only and cannotbeinterrupted o Pre scan high resolution creates a High ResolutionfastFL preview imageof every FOV within theselected area in singlelayerDAPI with an illumination timeof 20ms thatis displayed in theProfile Wizard window Scanning process is in...

Page 90: ...hedetecting algorithm Fill holes in scanmap If selected theholes insidethespecimen will also be scanned Often theseholes contain smallsampleobjectsthatotherwisewould notbe scanned Removespecks If selected thescannerdoes notdigitizeobjectssmallerthan thepredetermined size This helps filtering specks and otheruninterestingobjectsout Set themaximum volumeof specks manually in thesetting window Thresh...

Page 91: ...n cannotbeidentified as required fordigitization for example weak contrast it can help to encircle completely thespecimen with a black markerpen You haveto draw a full circle with the pen to enablethedetection Markerpen detection willmakespecimen detection easierby limiting thescanned area Manual setting ofUsemarker with threshold If this option is selected only thearea encircled with a markerpen ...

Page 92: ...ed with the preview camera Save scanmap Click this icon to save thecurrently selected areas to scanmap Position To position thespecimen holderthatholds thecurrentslide click Position sample andthen click on thearea of intereston thepreview image This will definetheLive imagethatyou can access from the Liveview Union Add theselected areas to thepreview Mark area forscanning based on theshapeselecte...

Page 93: ...ners Figure 75 Edited negative and positive selection masks Crop Crop thearea of theselected area PlaceCircle You can select the area to bescanned with thedifferent tools on thePreviewtoolbar Placefocus point You can add manualfocus pointson thepreview image the coordinates of themanualfocus pointsyou add arelisted on the Focus settings panel Notice Themaximum numberof focus pointsthatyou can manu...

Page 94: ...l TMA Grid Setting This function is enabled only if a TMA grid has already been placed on the preview image Setgrid parameters row and columnnumbers and spot shape round orrectangle Figure 77 TMA tool Grid selector Delete TMA grid by clicking the X atthe top rightcornerand rotategrid by clicking the icon at thebottom rightcorner Enterthenumberof rows and columns in the Rows and Columns fields orse...

Page 95: ...ed and oran orangemask If the Useselection boxis enabled and the crop function is selected a black framedisplayed in theimage and only thearea inside thebox is scanned Itis usefulif you only wantto scan thearea thatis equivalentwith the size of the coverslip so externalspecks will notbescanned Figure 78 Use selection box Thefollowing colors areused in the preview imageto demonstratedigitization an...

Page 96: ...he Preview panel thepreview camera detects themarker pen The inside areas appearin red color and will be digitized Areas scanned in This color is only displayed during scanning Hide all layers All the layers will be hidden existing but not visible The original preview imageis shown but layer information is stillvalid Note that while this function is active none of theother preview functions can be...

Page 97: ...ndow Undo Redo modificationmadeduring specifyingthe Scanmap Thesebuttons are inactivewhen Usethreshold function is applied 5 2 2 2 Focus Indicator Click to activatethe Focus indicatorfunction Search forthesharpestfocuson the currentfield of view automatically by clicking Auto focus button If you select theUse finefocus option thecoarsefocus levelis calculated from three differentfocus pointsof the...

Page 98: ... value This is usefulif Auto Focus does notfind thefocus on thespecimen buton thecoverslip Also this makes thefocusing sequencefaster Formanualfocusingdefinethemanualfocus step sizeby adjusting theStep sizesliderand usethe two arrow buttons to focus manually This is usefulwhen youareinterested in an area thatremained blurry with Auto Focus forexample thespecimen is thickerin that area This does no...

Page 99: ...odified by the softwarewhen calculating Auto Exposuretime Image Intensity Click to open Imageintensity panel An imageis defined as a two dimensionalfunction f x y the amplitudeof atany pairof coordinates x y is called the intensity orgray levelof theimageatthatpoint Thepixel intensity atthecoordinatepointingatwith thecursoris displayed in theImageIntensity window Figure 84 Window of Image Intensit...

Page 100: ...usewheel to zoom in oroutto thepreview area or theLive image Figure 86 Settings of preview quick toolbar A QuickToolbarpops up by rightclicking any of thecontrolmenu items Itallows a quick access to main functions andforFL thesearethefollowing Drag Draw Erase Retakepreview Settings o Toggledeletion always on top o ResetZoom o Window auto size o ClearScanmap ...

Page 101: ...roscope Functions A quick microscopefunctions toolcan bedisplayed upon right clicking on thebackground of the main window outsidethepreview window Itincludes quick access buttons to main functions Figure 87 Quick toolset for microscope Autofocus Figure 88 Autofocus Objectivetype Figure 89 Objective type o 20x o 40x Filters Figure 90 Filters ...

Page 102: ...SE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES Microscopemode o Brightfield o Fluorescence Figure 91 Microscope mode Livetools o Fastmode o Screenshot o Magnifier o Ruler o Imageprocessorplugins o Usepseudo color o Add scanmap Figure 92 Live tools Auto exposure Figure 93 Auto exposure ...

Page 103: ...geunitsarelinked in a row displayed at thebottom leftcornerof the main window Figure 94 Progress of the profile modification history Onceyou aremoving themousecursorovera unitalltheparameters willbecomevisiblein a pop up window Figure 95 Details of parameter modification Upon clicking the button fortheeasierperspicuity modificationscan beobserved in a pop up windowin which both theoriginaland them...

Page 104: ...lanningscans located underthe Preferences PlannerLayoutSelectormenu Slide view with card Table Card collection 5 3 1 General Functions atthe Main Menu Microscope Plannerselector Horizontal Vertical selector Available in Slide view with card mode Stage Control Available after initialization upon clicking the slide icon or entering slide position number at the right side the slide can be loaded Scan...

Page 105: ...racks will be loaded forpreview taking purposes If you wantto retakethe preview of theactually loaded slide theRetake Preview function is availablefrom theQuickToolbarof thepreview window Activate RetakePreview forallthe slides in themagazineif necessary This operation can beinitiated from theslidepreview window as well Load Save Plan menu Opens a drop downmenuincludingthefollowing Load plan The p...

Page 106: ...lluminationtypedata can be saved to a CSV file Profilemanagementforall themagazines Thefollowing profile relatedtasks applicableforthe plannercan beperformed Add currentprofileto all racks Open profileforall racks Detach currentprofilefrom allracks Detach profiles from racks Clearplanner Clearall slide resultsfrom every rack Figure 98 Profile management for all the magazines menu Jump to scanned L...

Page 107: ...slides Detach currentprofilefrom all slides Detach profiles from slides Clearall slide results 5 3 3 General Functions atthe Slide Menu Mark empty slidepositions Definerangein the Rangeto skip boxes to set multipleslide positions as empty For a singleslide enter set slideposition with thearrows in the Rangeto skip boxorright click on a slideand select Skip Figure 100 General functions at the slide...

Page 108: ...erties range to a slide with a profileattached When more profiles areattached to aslide always thelast scan record will be setwith the selected scan property Figure 101 Scan properties range Click to Open ScanContextselectorand click Apply to validatethescan properties settings to all selected slides and related profiles Figure 102 ScanContext selector ...

Page 109: ... with Card Select from Preferences Appearancesettings Plannerlayout selectorto activate this view Depending on theactualview preferenceselected at slide positions can havea horizontalorverticallayout Slidepreview and thelistof theassigned profiles aredisplayed Figure 103 Horizontal Slide view with card Figure 104 Vertical Slide view with card ...

Page 110: ...sof differentcolor o Stored o Edited Scanning modeicon representingBrightfield orFluorescencemode Objectivetype Filter channelcolorbars forFL modeonly Scan progress No of scanned FOVs Scan duration Priority scan Slide actualstatus of the slideis presented here If the slideis underscanning the Scanning if scanninghas been interrupted by someerror the Failed textis visible If slide status is marked ...

Page 111: ...scanned to CaseCenterorSlideCenter itcan beopened in InstantViewer as well depending on thesettings madein Settings Preferences Server scan resultviewer 5 3 5 Table View Mode By clicking each slidewill be displayed in a separaterow Click to assign profileto a slide and to detach a profilefrom a slide A slide can have morethan oneprofileassigned to it and theseprofiles can eitherbeBF or FL if thesc...

Page 112: ...irtualslide with theselected profilecan be defined o Scan result o Scan duration o Scanned FOVs o Totalno of FOVs ProfileeditorforScheduler Notes 5 3 6 Card Collection View Mode If you click the button each of the slide previews are displayed in the window Add profiles by clicking and detach profiles by clicking Functions arethe sameas with the othermodes Figure 107 Card collection view mode ...

Page 113: ...includes all theprofilesettings in coherencewith theview typeof theProfile Setting panel Slidepreview is displayed in thePreview window in which thescanmap can be modified untilbeginningthescanningprocess Every aforementioned profilesetting can be modified depending on the scan profiletype beingeitherBrightfield orFluorescence Figure 108 Selected profile and expanded preview window in Planner mode...

Page 114: ...ss is visibleboth in Microscopeand Plannermodes wheneverthereis a running hardwareoperation orscanning procedure Progress contentcan bethereforedifferent depending on thetypeof therunningprocedure Figure 109 Progress data Thefollowing information is included in theprogress log listduring scanning Filter Elapsed time Location Slide name Free space FOV number ...

Page 115: ...DURES 6 Settings and Services ActivateSettings by clicking and Services by clicking at therightsideof the main menu bar 6 1 Settings ActivateSettings by clicking atthe rightsideof themain menu bar Preferences This panelcontains user settings thathaveglobaleffecton theGUI and someof itsfunctions Figure 110 Settings ...

Page 116: ...ed in an embedded window External legacy live imageis displayed in an externalwindow Defaultscannermodeselector MicroscopeorPlannermode Server scan resultviewer Opens digitalslidewith InstantViewer in web browser or SlideViewerorCaseViewer when scanning to server Defaultilluminationmodeselector Brightfield orFluorescencemode Simplified Scan Progress forBrightfield scanningonly Screenshotfolder Set...

Page 117: ...nditions forbarcodereading so to makesurethat barcodeidentification is successful o Rotatebarcodeimageby 180 degrees o Unload slideafterplannerscan o Enablereloading of magazines with sameslideset o Automaticempty slidepositiondetection Slidepositions of themagazines to which slides are notloaded into willbe detected by the software and slides withoutincludingany marking etching labelon thelabelar...

Page 118: ...ntained in this log To enablethis function firstthe databasefrom thefollowingfoldermustbeloaded C ProgramData 3DHISTECH SlideScanner HWLogDataBase Thefollowing motormovementsarerecorded in thelog list Camera Changer DFP Light Filter Wheel General Halogen Light MicroscopePart MidiLoader ND ObjectiveChanger Preview Light RGBlight Relay Scan Loader Service Shutter Slide Scanner Stage ...

Page 119: ...e Name Illumination mode Scan type Scan Start Scan Finished URL Error Figure 111 Scanning log Filtering forthefollowing parameters is available Scanning date Profilename Illumination mode URL Slide name Slide index Rack index General naming settings Naming pattern Theset string defines theslidenaming pattern shownby the examplebelow thetext box Click Reset to set pattern to default The abbreviatio...

Page 120: ...ting theInspectarea beyond coverslip edge function a compensation imageof thearea beyond thecoverslip area can betaken Consequently whenthis functionis turned off thearea beyondthecoverslip is nottaken into accountby thescannersoftwarewhen creating thecompensation image o Fora morecomfortableand saferuse turn on PlannerAutosave functionto save a scan plan and by defining a location in thePlannerau...

Page 121: ...story from which thedifferentstages can bereloaded o Save interval Profilecontentis automatically saved atthespecified timeframes o Enablesetting offocus time Parameters Short Normal Long related to focus timewill beenabled on the profilesettings panel Normal is setas default Pre scan settings Figure 114 Pre scan settings Unlikescan settings in MicroscopeorPlannermode Pre scantoolbarincludes the s...

Page 122: ...ponsibleforopening externalapplications exeor bat as defined forexample CaseViewerorSlideViewer softwarecan beopened afterscanning is finished Thesecalls can run only thefollowing scripts o cmd o bat o exe Theapplication cannothandlescriptlanguages thatarenotsupportedby theWindows Operation System You can defineexternalapplication callsettings forthefollowing cases Slidescanning has finished Scann...

Page 123: ...ished SLIDENAME transfers theslide name ForScanning error has occurred ERRORTEXT transfers theerror message Notice Pannoramic Scanner SoftwareforResearch controlsoftwarecan providenotonlythe SLIDENAME butthepath of the digitalslideas well Run defines thewindow modethattheexternalapplication willstartin The following windowmodes can beset Normalwindow Minimized Maximized You can test whetherthe Sca...

Page 124: ...p to display theE mailsettings window in which you can dedicatean e mailserverthrough which thesoftwaresends e mails to the selected recipients Figure 116 Messenger Setup window In the E mailSettings window thefollowingparameters can beset MessageType E mail HostAddress Port E mail Authentication UserID and User password arerequired Secure Connection SSL If activated themessages willbesentthrough ...

Page 125: ...licking Emergency slidefunctions This panelcontains controland maintenancefunctions o Emerg Position Theslideholder will bemoved to a position wheretheslidecan be removed manually afteropeningthecover seechapter 9 5 1Removingthe Protective Covers o Slideremoved Click this button to notify thesoftwarethatyou haveremoved theslide manually PSF settings This panelserves to specify PointSpread Function...

Page 126: ...SE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES 6 2 Services ActivateServices by clicking atthe rightsideof themain menu bar Service password Enterpassword firstto enableservicesettings for modification Figure 119 Enter service password Camera settings Figure 120 Camera settings ...

Page 127: ...libration Gammavalueis notincluded sRGB standard Colorschemeis defined by calibration standard Gamma value 2 2 is applied sRGB standard MicroscopeLike Colorschemeis defined by calibration standard Gamma value WhitePoint D50 Legacy A Colorschemecalibrated fortheprevious softwareversion is applied Custom parametersarefreely customizableas follows ColorScheme Calibrated Schemeis defined by thecolorca...

Page 128: ...h theFOVs should extend over o Measurecamera rotation Camera rotation angleis measured o Alpha blending Thetwo images areblended o Lower imageposition Moves theupperimagesideways in distinctive steps o Reset all camera rotation Click this button to setcamera rotation values to default o ActivatePSF generation If activated thePointSpread Function can be generated Follow thesteps described in sectio...

Page 129: ...rs is 50 if you insertPentafilters and this typeis selected from theFiltertypelist in the available10 filterpositions in theturret o Movefilter wheel to insertposition o Enableposition Notice Whenevera selected physicalfilteris disabled thefilteritself mustberemoved from the turret o Select Filtertype Filterchannel and Filtername o Check Availableforscanning o Set LumencorLEDlightsource setExcitat...

Page 130: ...larities Figure 123 Image compensation window o BF cameras field displays theactivecamera Currently thereis only oneactive camera forBrightfield mode o Objectives field displays theobjectiveused forscanning Theremightbespecks or minoretches on thesurfaceof thecompensation slidethat requiremodifyingthethreshold settings Therefore thescannerwillnotusethoseareas forthe creation of thecompensation ima...

Page 131: ...her settings you enablethe Read Barcodeoption when usingthePannoramic ScannerSoftwarefor Research controlsoftware To display an imageof thebarcodearea click Grab label image You can redefinethe barcodereading area by draggingtheedges of the bluesquare To check whetherthe barcodereading settings arecorrect display thebarcodedigitsin the Barcodefield by clicking Read Barcode If the label area is not...

Page 132: ...t o Barcode reader library Select MIL barcodelibrary orEmbedded barcodelibrary o General Barcodesettings Inversebarcodecolor Activateto invertforeground and backgroundcolors of thebarcode Use barcodecompensation A compensation imageis used during barcodereading Grab new comp Click this button to createa new compensation imageforbarcode Notice New compensation imageforbarcodecan berecorded only if ...

Page 133: ...hm TheErode algorithm is run beforebarcodereading Itis a useful function forreading 2Dbarcodetypes sincethealgorithmcompletes thescuffedand faded areas of thebarcodeby applying themorphologicalerodefilterto an image This filter widens and enhances brightareas of theimage Excludecheck digit Checksum valueis ignored whenreadingInterleaved2of5and Code39 barcodetypes Microscopecontrol Figure 125 Micro...

Page 134: ...ulatewhitebalance o Save RGB intensity Slideload tester Figure 126 Slide load tester Slide loading operation can bechecked foreach of theslides in a magazine Click Insert magazineif theprepared magazineormagazines areplaced atthebottom of theinput guiderails Click Start slideinserttest button to launch theprocess Slides areloaded in butpreview imagewillnotbe recorded If Magazinecounteris set to 1 ...

Page 135: ...from thebeads forthemostaccurateresults II GeneratePSF with a third party program III Enterthe generated PSF values into theprogram then deconvolutethesampleimage IV Start scanning with thedeconvolutionfunction activated Thecompleteprocedureforpreparing to executethePSF in thecontrolsoftwareis as follows 1 In Microscopemode settheappropriatefluorescenceparametersaccordingto section 5 2 Itis worth ...

Page 136: ...equence Onceyou havefinished click GeneratePSF button and theScannerwillstartrecording theimagesequence 5 As the laststep of setting thedeconvolution process load generatedPSF resultsinto the software Selectthe appropriatePSF outputforeach of thefilters in Settings modeunder theBrowse tab of thePSF settings Enterthenumberof images in theseries thatthePSF consistof then select thefolderunder Folder...

Page 137: ...n Mode Brightfield Fluorescent Scan Options Focus frequency in Fluorescentmode Focus frequency in Brightfield mode Compression procedure Useof afixed compensation image in Brightfield mode ON OFF Useof Savefocus quality ON OFF Useof Stitching ON OFF Determination ofthearea to bescanned Useof automaticthresholdspecimen Useof specimen threshold value Useof markerpen threshold and specimenthreshold v...

Page 138: ...ilter position s Selected focus channel Selected stitching channel Flat field correction ON OFF o Intensity statistics o Intensity reducing o Intensity equalization Sharpening ON OFF Othersettings Limitation of focus range ON OFF Enable disableMultilayer options Useof extended focus orZ stack step size and focus level Outputresolution ...

Page 139: ...exclusively on thecontrolcomputerof theScanner in the finalphaseof installation butitcan beperformed afterwardsby launching thecontrol software Itthen detectsthatit is in an inactivated status and theactivation wizard is opened and activation can beperformed eitheronlineoroffline Online activation 1 For Onlineactivation a reliableinternetconnection of theserveris necessary Internet connection is c...

Page 140: ...CH USE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES 2 Activation web pageis opened in theembedded browser FirstaccepttheEULA then click Continue 3 Enterall the required datafortheactivation If you do notpossess a registration code theKey field may beleft blank Click Continueif finished ...

Page 141: ...nalize installation if thesoftwareis activated during installation so the activation is performed and thecontrolsoftwareis ready foruse Offline activation 1 If the serveris notconnected to the internet then Offlineactivation can beselected only To perform offlineactivation a devicewith internetconnection is needed to beat hand Click Nextto continue ...

Page 142: ...o the https activation 3dhistech com web page This stepis mandatory only if Offline activation was selected ClickUpload tobrowseordrag drop the TXT file 4 On theActivation page accepttheEULA then click Continue sameas step 2 in Online activation 5 Enterall the required datafortheactivation If you do notpossess a registration code theKey field may beleft blank Click Continueif finished sameas step ...

Page 143: ...ilehere section of thewindow Click Nextto continue NOTE TheNext button turns activeonly if fileupload and validation was successful 10 Upon successfulactivation thefollowing window is displayed Closeinstallation wizard by clicking Finish If you wantto exit thewizard beforefinishing activation a notification appears If youdecideto leave thewizard by clicking Yes thePannoramic ScannerSoftwareforRese...

Page 144: ...re eventstateby clicking Yes Figure 127 Recovery confirmation window Warning Click Yes only if you aresurethateverything is completely unchanged aftertheprevious run If anything has changed oryou areunsure click No Formorecomfortableand saferuse thePlannerautosave functionallows thetaking of automaticbackups whilecreating a scan plan Thebackups areplaced in thedefault documentfolderof theactualwin...

Page 145: ...ard during operationin thearea of inputoroutput Inserts magazines should bemoved through software Neveropen thedeviceunless promptedaccordingly by thesoftware Defectivedevices do notclassify as domesticwaste Disposeof thedevicein compliance with thecurrently valid legalrequirements LumencorSPECTRA 6 illumination unit NEVER switch on theLumencorSPECTRA 6 LightEngineillumination unitwhen itis not co...

Page 146: ...vethe equipmentin an unconditioned environmentwith a storage temperatureabove60 C 140 F orbelow 0 C 32 F whichmay damagetheequipment Maximum operatingtemperatureis 35 C 95 F witha relativehumidity of less than 75 Installit in a room with properairventilation Do not let dustorfingerprintsremainon opticalsurfaces 9 4 Troubleshooting This chapter describes themostcommon troubleshooting solutionsforth...

Page 147: ...anually If a jammed magazinecannotberemoved contact service personnel 5 Reattach protectivecovers 6 Reconnect24V powersupplyand controlcomputerto linepowersupply 7 Switch on the 24 V powersupply 8 Switch on the controlcomputer 9 Launch controlsoftware Virtual slideis improperly focusedalmostacross its entiresurface Focus rangeenabled DisableLimiting focus range Poorimagequality Imaging error for e...

Page 148: ...stackoption is activated Deactivatethe Z stackoption if notrequired Imageis outof focus in Manual mode Focus rangelimitis activated Deactivatethe Limiting focus range option Focus rangesetting is incorrect Changefocus rangesetting All individualimages showa shading effect Algorithm failedto find empty imagefields Capturea referenceimagewith a blank slide 9 4 1 FluorescentApplications Optional The ...

Page 149: ...ened to performany maintenancework andalso to eliminateerrors forexampleslideormagazinejamming Beforeremoving thecovers exit Pannoramic ScannerSoftwareforResearchcontrol software switch off the24 V powersupply and disconnectthepowercables Warning Avoid leaning overthe devicewhen opening it Figure 128 Removal of covers Fiveeccentric screws 3 arelocated on thebottom faceof the baseplate 4 They attac...

Page 150: ...ons To do this turn theeccentric screws clockwise A Caution Makesurethatno cables of the scan camera aresqueezed as you replacethecovers 9 5 2 Removing a Slide If a slide gotjammed orhas suffered breakageduring theprocess of digitization stop the process and if possible movetheslideholderto a position wheretheslidecan be easily removed by clicking the Emerg position button seeEmergency slideoperat...

Page 151: ...emoval the slide loader Figure 130 Removing a slide 1 Open theprotectivecover see chapter 9 5 1Removingthe protective covers 2 Push locking lever 1 to the left and keep thelever in this position 3 Seize the slideloader 2 by theend wherethelever is and turn itup by the necessary degreeto maketheremoving of slidepossible 4 Removeslideloaderunit ...

Page 152: ...ever 4 and turn down theslideloader 2 back into theoriginal position and pullitinwardly untiltheguiding pin connectswith themotorblock groove again 8 Press theslide loaderdown to mechanicalstop position in which thelocking levermust engage 1 Usemoderateforceto press theloaderpartoppositethemotorin clamp direction 2 untilthis partmechanically engages too 9 Closethe protectivecoveragain seechapter 9...

Page 153: ... pads oneon theright oneon theleft lateral sideof themodule and insertitin forward tilted position from aboveinto theupper spring loadedclamps 1 atthefilterwheel Warning Avoid touching the surfaceof thefilters and storethemodules in theirown boxes when not used 6 Press thefilter moduledown untilitsafely connectsto thebottom spring loaded clamps 2 of thefilter wheel Mountingpositionof thefilters ex...

Page 154: ...memberto stop therunning digitization process terminatethesoftware session and turn off thepowersupply beforeremovinga jammed magazine Caution Check thatthemagazineis nottilted so thatit restson both of thehorizontalguiderails 2 If the magazineis in horizontalposition tiltplate 7 with thedriveassembly for horizontalmagazinedrivemotionto thefrontfarenoughforthedriving gear 5 to disengagefrom thedri...

Page 155: ...rein theirinitialposition again and themagazineflatly restson both horizontalguiderails Notice Any manipulation performedon a mechanicalcomponent forexampletransporting system by theusermustbefollowed by a completePannoramic SCANRX initialization routine softwarerestart 9 5 5 Transporting Pannoramic SCAN RX Thefollowing procedureshows howto transportthePannoramic SCANRX in house Fortransporting th...

Page 156: ...observethelaws of yourcountry regarding load carrying capacity limitations You can find theweightdataof the baseunitin chapter 10 Technical Data To transportthePannoramic SCANRX do thefollowing 1 Turn powersupply off and detach allcables 2 Pullcarrying handles out 2 untilmechanicalstop position A 3 Turn carrying handles by 90 B towards thebaseunitto securethem 4 Now you can transportPannoramic SCA...

Page 157: ...approx 189 mm x 90 mm x 44 mm Weight Base unit approx 26kg Base unit with fluorescent option approx 29 kg 24V 100W power supply approx 550 g Ambient conditions Transportation shipment packed Permissible ambient temperature 40 C to 70 C Storage Permissible ambient temperature 0 C to 60 C Permissible relative air humidity non condensing 75 Operation Permissible ambient temperature 10 C to 35 C Permi...

Page 158: ...1 class B Noise immunity in accordance with IEC 61326 2 6 2012 Base unit input voltage 24V DC 1V Power consumption of the complete device 60 VA SINPRO MPU101 108 24Vexternal mains powersupply unit Intended site closed room facilities Electrical protection class I Internal protection degree IP 20 Electrical safety in compliance with UL 2601 1 TÜV EN 60601 CE EN60601 1 2 2001 Over voltage category I...

Page 159: ...ent light source 1 optional SOLA SM 5 solid state sources producing white light Wavelength range 350 680 nm Average service life 20 000 hours Fluorescent light source 2 optional SPECTRA 6 individually addressable solid state light sources Average service life 20 000 hours Previewcamera Preview camera VRmagic VRmC 8 PRO Sensor CMOS rolling shutter Sensor size Resolution 2056x1544 Pixel size 3 2 um ...

Page 160: ...unt adapter 0 17 µm Pixel resolution with 40x objective and 0 63x C mount adapter 0 14µm Pixel resolution with 40x objective and 1x C mount adapter 0 09 µm Connection type USB3 0 pco edge 4 2 bi 13 3 mm 13 3 mm backside illuminated sCMOS Pixel size 6 5 µm x 6 5 µm Camera resolution 2048 x2048 active pixel Diagonal 18 8 mm Shutter mode rolling shutter RS MTF 76 9 lp mm theoretical Fullwell capacity...

Page 161: ...nectors Trigger output signals exposure busy SMA connectors Data interface USB3 1 Gen 1 Time stamp in image 1 µs resolution Control computer minimum systemrequirements Operating System Microsoft Windows 10 Professional 64 bit EN CPU Intel Xeon W 2245 RAM 64 GB DDR4 Hard disk 256 GB SSD 1 TB HDD 2 TB HDD Optical drive DVD RW Display 96 dpi Graphics SXGA 1280 1024 True color Input devices Keyboard m...

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Summary of Contents for PANNORAMIC SCAN RX

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3D Histech PANNORAMIC SCAN RX, User Manual, Page: 102 / 161

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Summary of Contents for PANNORAMIC SCAN RX

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