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3DHISTECH PANNORAMIC MIDI RX 1.0, User Manual

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3DHISTECH PANNORAMIC MIDI RX 1.0 User Manual Download Page 74

PANNORAMIC®  CONFOCAL  RX 1.0 

SCANNING  MODES AND SETTINGS 

 

 

 

MAY 13, 2021 

73

 

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

•

 

Autofocus 

 

Figure 56: Autofocus 

•

 

Live tools 

 

Figure 57: Live tools 

o

 

Fast mode 

o

 

Screenshot 

o

 

Magnifier 

o

 

Ruler 

o

 

Image processor plugins 

o

 

Add scanmap 

 

•

 

Auto exposure 

 

Figure 58: Auto exposure 

 

Summary of Contents for PANNORAMIC MIDI RX 1.0

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

Page 2: ... 17 1 1 5 Connector panel 18 1 2 System overview 19 1 2 1 Pannoramic ConfocalRX System 19 1 2 2 Hardware options 20 1 2 3 Control software 21 2 Installation 22 2 1 Operation system of the control computer 22 2 2 Control computer ports 24 2 3 Connectors and cables 24 2 4 Power the scanneron off 25 3 Operating Slides and Trays 26 3 1 Preparing slides and trays 26 3 2 Affixing barcode stickers to sli...

Page 3: ...ck microscope functions 97 5 2 5 Bottom menu bar of themain window 100 5 3 Planner mode 101 5 3 1 General functions at the main menu 101 5 3 2 General functions at the tray menu 103 5 3 3 General functions at the slidemenu 104 5 3 4 Slide view with card 105 5 3 5 Table view mode 108 5 3 6 Card collection view mode 109 5 4 Profile and preview overview on the planner 109 5 5 Progress features 110 6 ...

Page 4: ...141 9 4 Troubleshooting 141 9 4 1 Fluorescent applications 143 9 5 Maintenance 144 9 5 1 Opening the service door 144 9 5 2 Replacing fuses of the main powerswitch 145 9 5 3 Removing and refilling thepipette 146 9 5 4 Removing a slide 149 9 5 5 Installing and removing filter cubes 150 9 5 6 Transporting 153 9 5 7 Removing and cleaning the condenser 154 10 Technical Data 157 ...

Page 5: ...6 P101036 PCT IB2005 050351 EP 1789831 US7 663 078 P0301911 PCT HU04 00019 EP 1644767 US 7327515 Theabove mentioned grantedpatents grantedutility model registered trademarks pending internationaland nationalpatentapplications and theothercorresponding IP arethesole properties of the3DHISTECHLtd 3DHISTECHLtd is notliablefordamageofwhatevernature including butnotlimited to general or specificdamage ...

Page 6: ...ble fordamageof whatevernature 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 ...

Page 7: ...below IEC 61010 1 2010 ed 3 Safetyrequirementsforelectricalequipmentformeasurement control and laboratory use Part1 Generalrequirements EN 61326 1 2013 Electricalequipmentformeasurement controlandlaboratoryuse EMC requirements Part1 Generalrequirements EN 61010 1 2010 Safety requirements forelectricalequipmentformeasurement control and laboratory use Part1 Generalrequirements EN 61326 1 2013 EN 55...

Page 8: ...theproduct described Beforeoperating thedevice you mustcarefully read this instructionmanual and adhereto all WARNING and CAUTIONnotices refer to chapterNotes RegardingOperational Safety formoreinformation anda copy should bekeptin theclose proximity ornearthe scannerforreferencewheneverrequired This User s Guideis a part of thePannoramic ConfocalRX systemidentified by therelevant article numbers ...

Page 9: ...creen 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 documentorto otherdocuments Warning It mightcauseirreversibledamageorharmto theuserof theproductortheproductitself if this instruction is notfollowed Caution It mightcausetheproductto notwork properl...

Page 10: ...ross beltarea of thetray guide and thesafety plate during operation Pleasenotethatthedigitizing process has to beinterrupted and thetray moved via softwareto theoutputposition beforeremoval Thetwo hinges of theservicedoor Theinnerside of thedooropenermechanism When reaching by thepipetteunitinto thefarthestarea of the device ThePannoramic ConfocalRX includingany of itsoriginalaccessory components ...

Page 11: ...erendered ineffective by extension cables withoutprotective earth ground conductor Warning Never operatethedevice in explosion risk environment Warning If protectivedevices arefound to beineffective thePannoramic ConfocalRX mustbeshut down and precautions mustbetaken to preventunintended usage Fornecessary repair work orwork to restoreproperoperating condition youshouldcontactthe3DHISTECH Customer...

Page 12: ...roneous results Warning A defective Pannoramic ConfocalRX is notclassified as domesticwaste Itmustbe properly disposed in accordancewith currently valid legalrequirements 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 is performe...

Page 13: ...rvicing willbeidenticalwith levelof theoriginal equipment Notice Electric powerto thePannoramic ConfocalRX is supplied via an externalmains power supply unit Itallows foroperation atlinevoltages in therangeof 100 V to 240 V 10 50 60 Hz withoutany extra facilities required forvoltagetransformation Thereis no furtheroperator user action required in caseof residualrisks Special attention should bepai...

Page 14: ... a faultless productforreplacement No warrantywillbeaccepted in cases of natural wear notably wearand tear orimproperproducthandling TheProductManufacturerwillrefuseany liability in theeventof damageresulting fromfaulty operation negligenceorunauthorized interventioninto theproduct notably from the replacementof productparts ortheusageof accessory parts from othermanufacturers Any such case willvo...

Page 15: ...luoresce 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 interactive image that y...

Page 16: ...Operating personnelmustbefully awareof thepotentialdangers whicha particular field of application involves ThePannoramic ConfocalRX is a precision instrumentwhich may suffera significantreductionin operationalfunctions oreven physicaldestruction following interventionperformed in any nonconformingmanner Warning Aftereach scanning makesureto inspectthedigitalslideforover exposed areas In casethe sl...

Page 17: ...rFL preview imaging Up to 4 filter cubes quad ordual forfluorescence NOTE Thenumberof channels availabledepends on thetypeof theapplied fluorescent illumination device High end fluorescentillumination device LumencorSPECTRA LightEngine Multiband filtersupport FL scanning with a low noise 16 bitscientificCMOSpco edge5 5 camera Software aimed flat field correction compensation method to createhomoge...

Page 18: ...C PROCEDURES 1 1 3 Warning and informationlabels Thefollowing figurecontains thelabels used on theback panel and on theinsideof Pannoramic ConfocalRX main unit Figure 1 Warning and information labels 1 1 4 Base unit Thefollowing figureshows themain outerparts of thedevice Figure 2 Main parts of the base unit ...

Page 19: ...ray feeder door 4 Cable outlet 5 Connector panel USB port power supply connector fusebox 6 Transport handle 4xatthe fourcorners of the device 7 On Off button 1 1 5 Connector panel Thefollowing figuredetails thesub assemblies of theconnectorpanel Figure 3 Sub assemblies of the connector panel 1 USBport forcontrollerPC 2 Fusebox 3 Main power switch 4 Main power inlet ...

Page 20: ...S 1 2 System overview Thestandard scopeof delivery of theproduct includes thefollowing hardwareand software components 1 2 1 Pannoramic Confocal RX System Thefollowing figureshows themain partsof thePannoramic ConfocalRX system Figure 4 Pannoramic Confocal RX system overview 1 Pannoramic ConfocalRX baseunit 2 Slide tray ...

Page 21: ...ld and Fluorescent applications allowing fastscanning andan outstandinglow read outnoise Cooled with Peltier element Warning Theinstallation of thecameras in Pannoramic ConfocalRX mustbecarried outby trained professionals In anyothercasethewarranty willbeautomatically voided Thesupplieror distributoris notliableforany damages caused by an installationcarried outby an unauthorized person Base Unit ...

Page 22: ...cent illumination unit Description LumencorSPECTRA LightEngine illumination unit 1 2 3 Control software Pannoramic ScannerSoftwarefor research controlsoftware Optional o Barcodereader licensed feature o Convertersoftware 2 3 2RTM onlyavailablein Fullscannerinstallmode Accesory softwarecomponents fully functional o CaseCenterand SlideCenter o CaseViewerand SlideViewer o Track Sign o QuantCenter His...

Page 23: ...tion of thedevicemustbe performed when ithas been installed on thedesk In casethedevice has been moved to anotherlocation recalibration mustbeperformedby a qualified and experienced technician Only qualified serviceassistantsareallowed to installthehardwareand software Theproductis ready foruseafterinstallation Caution If the temperatureof thelocation wherethescanneris operated is much lowerthan t...

Page 24: ...nerSwap as theSWAP folderby default We recommend thatyou usethe 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...

Page 25: ...stance by disconnectingcables and detachinghardwarecomponents from each other Figure 5 Ports on control computer 1 DVDdrive RW 2 4xUSB port 3 Audio in out 3 5mmJack ports 4 Poweron off button 5 Powersupply connector 6 6xUSB port 7 Network ports 8 Monitorport 9 MatroxSolios CameraLink ports forpco edge5 5 camera 2 3 Connectors and cables Caution It is not recommended to useUSBcables longerthan 2 5 ...

Page 26: ...rolcomputer USB to RS232 serialcommunication cable between Pannoramic ConfocalRX and controlcomputerforLumencorfluorescentillumination unit CameraLink cables between pco edge5 5 camera and controlcomputer Video cable between monitorand controlcomputer Warning Only connectexternaldevices thatare safety extra low voltagerated to the instrumentto avoid therisk of electrical shock 2 4 Power the scanne...

Page 27: ...tions of slides and coverslips Warning Do NOT use aslide when itis broken oritsedges arenot properly cutorgrounded Using such slides can lead to injury Warning If using immersion liquidforconfocalscanning makesurethatyou applycoverslips on each slide you aregoing to scan in a way thatwatercannotenterunderneath thecoverslip since it may impairthesection and falsify correctevaluation Ensurethatno pa...

Page 28: ...een slideedges and the edges of themounted coverslip should be1 2 mm and they should beparallelwith each other Notice Fluorescentsignals becomemoreeasily detectableforthescanner thereforeresulting in a brighterand betterimage by treating theslidewith a formula thatpreventsrapid photobleachingof fluorescentreagents during theprotocol 3 2 Affixing barcode stickers to slides This section describes ho...

Page 29: ...een thestickerand the label area outerlimits Itis vitalfor barcodeidentification Do notletbarcodesticker protrudefrom slideedges orstick on thecoverslip surface 3 The thickness ofthebarcodesticker on the slidemustnotexceed 0 4 mm Do not stick morethan fourbarcodestickers overeach otherand theoverallthickness must mustbekeptbelow 1 65 mm including thebarcodes and theslide 3 3 Inserting and removing...

Page 30: ...rrectly inserted in the tray Theedgeof thebroken area of the slideis sharp and itsremovalcan lead to injury and contagion Broken slidecan beremoved only by a well trained person Only original3DHISTECHtrays areallowed forusewith Pannoramic ConfocalRX Notice Thecoverslip and the labelarea should beon thetop Notice If you wantto scan frozen samples load only oneslidea time sincethe scanning process i...

Page 31: ...itizing slides thetray is moved to theoutputposition whereitcan beremoved Caution To insertorremovea filled tray from thedevice firstcheck tray forincorrectly inserted slides refer to Figure 8 and always ensurealso when movingthetray slightlytiltitto its closed side to preventtheslides from accidentally falling out Insertsshouldalways bekept clean from dust broken glass and othermountingmedia resi...

Page 32: ...ttons represent Microscopeand Plannerscannermodes andthe Service mode Figure 10 Mode selection window Microscopemode for digitization of individualslides 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...

Page 33: ...n menu bar Switch between Microscopeand Plannermodes Microscopeinitialization Allmotors and thepreview camera during start up Switch between Brightfield modeand Fluorescencemode Thecamera setforthe selected modeis initialized Slide tray control Upon clicking theslideicon or entering slideposition numberattherightside theslidecan be loaded Unload theslideby clicking Unload nextto slideimageand unlo...

Page 34: ...edon the slideicon If you wantto modify slidestatus forexample if theicon representsa wetslide status although a dry slidehas been loaded right click on theslideicon and select Changecurrentslidestatus wet dry to modify slidestatus Select Skip to mark theslideto beskipped When in Servicemode see chapter6Settings and services formoreinformation additional functions areavailableforyou to selectfor s...

Page 35: ...tion of scanning quality Click Reload pipetteto inform Pannoramic ScannerSoftwareforResearchcontrolsoftware that you haverefilled thepipette Pipettestatus is displayed and continuouslyupdatedduringoperation Thequantityof the immersion fluid contained in thepipetteis visualized by thelevel of bluefilling of the icon Pipetteis fully loaded Pipetteis half full can beused withoutthesoftware promptingy...

Page 36: ...sed pixels Saves the currentimageas BMP orJPEG file Thefollowing functions areavailableforyou to selectfrom thetoolbar Fastmode Liveimages aredisplayed with a frequency of atleast10 images persecond If an exposuretimeis set to morethan 100 ms thepixelvalues are multiplied accordingly forexample if an exposure timeof 200 ms is set thepixel values aremultiplied by 2 and theexposuretimeis resetto 100...

Page 37: ...filecards as well added to theslide in Plannermode Scan to Local Figure 14 Scan to Local Slidenaming Slide namecan bedefined manually orautomatically If you wantto nametheslidemanually turn on the Manual naming function and if you wantto generateslidenamebased on the corresponding settings setin Preferences activateGeneratefunction Barcode parsing Selectthetypeof barcodeprofilefrom thedrop downlis...

Page 38: ...TIC PROCEDURES Figure 15 Select type of barcode profile Click atthe leftof alist item to open the Barcode editorwindow in which thesettings of the selected profilecan be edited Figure 16 Barcode editor window If you click Add newitem on thelist blank inputfields willbe displayed Figure 17 Create new barcode ...

Page 39: ... Parsing settings Click to delete rangevalues setforthe correspondingfield o EnableParse subfolders to makeitavailableto create subfolders when parsing datafrom thebarcode Typenameof thesubfolderin the Folder1 Folder2 etc fields depending on thedepth you wantto define o Click Saveto apply settings and click Createnew at thetop of the panelto create a new profileitem Slidesavepath Set destination f...

Page 40: ...originalMRXSslidewillbedeleted afterthe conversion is complete Target format Theslideis converted to the selected finalformat Click oneof the buttons to definethe finalslideformat MRXS Tiled TIFF Roche TIFF SVS DICOM Click to open MRXS Tiled TIFF and DICOMconversion settings panel o MRXS settings Figure 19 MRXS settings Click Reset to set everything to default Select ChangeJPG compression rate to ...

Page 41: ...selected Filesize is smaller butsomeof the viewers cannothandleit TIFF type Automatic theconverterautomaticallyselectsthemost appropriatemethod based on thesizeof thesourceslide Force simpletiff TIFF files use32 bitoffset addressing therefore filesize is limited to a maximum of 4Gb Force big tiff Big TIFF files use64 bitoffsetaddressing allowing thecreation of biggerTIFF files Compression type Jpe...

Page 42: ...t 3 Tilepool size default 1000 UTC timein minutes default 0 Basicoffset table activeby default Shared planeposition activeby default Shared optical reference activeby default Conversion savepath Thefoldersetin this boxis designed to storethefinalslides after conversion Conversionprogressis displayed in theConverterqueuewindowof theconverter Figure 22 Conversion window Quantsettings Run QuantCenter...

Page 43: ...twareforResearchcontrolsoftware is compatiblewith licensed QuantCenter applicationonly otherwise itmay closedueto an error Click to assign theappropriateQuantprobeto thedigitalslide If the scanning of slidehas finished theprogress of Quantevaluationis displayed in the QuantCenter Processing Queuewindow Forfurtherinformationon QuantCenter pleaseread QuantCenter User s Guide Othersettings Scan separ...

Page 44: ...rver settings Select the dedicated serverto which you wantto scan from the Server drop down list Click the arrow to show thelist of saved serverprofiles orclick Add newitem atthe bottom of thelist to createanotherserverconnection When creating anotherserverconnection definethe following details of theserverin the Server Editorwindow Display Name HostName Protocol ...

Page 45: ... removed ora new entry can be added if required With the Filters function you can narrowdowntheresultsby searching fora specificserver data By double clicking a listitem serverdatawillbeloaded in the Scan to Server panel Afterloading serverdata usernameand passwordis required to beadded forauthenticationand accessing theserver If connection is successful a green checkmark is displayed in thewindow...

Page 46: ...s of theScan to local panel barcode settings forparsing can bemodified in theBarcodeEditorwindow Figure 26 Window of Barcode Editor If using MIL forbarcodereading you can selectthefollowing barcodetypes 1Dbarcode types o Code39 o Code128 o Code16K o Interleaved 2 of 5 o Standard 2 of 5 o IATA 2 of 5 o Matrix2 of 5 o Telepen o Code93 o Code11 o MSI o Codabar o Patch Code ...

Page 47: ...rver sidebarcodeparsing option can beselected if CaseCenterand SlideCenter is connected to thesupported HIS LIS This way thebarcoderead by thesoftwareis being identified and thepredefined location of thatspecificcase in CaseCenterand SlideCenter is automatically selected as scanning destination based on theCaseID containing slideand patientdatastored on HIS LIS Therefore Folder Case Block and Slid...

Page 48: ...computermustbeavailableto setin the Conversion savepath field as the destination of theconverted slide o If the userselects a fileformatotherthan MRXS TIFF SVS etc only a folder on the localcomputercan be selected as thepath of the converted slide Quantsettings o Run QuantCenter Turn this functionon forautomaticevaluationof the completed digitalslideby using theintegrated QuantCenter rightafterthe...

Page 49: ...ke All Previews Figure 27 Take all previews selector Each preview of slides in the tray is taken automatically Preview typesarethefollowing from top to bottom Brightfield Darkfield Pre Scan Pre Scan High Resolution Pre Scan High Resolution ActivateRetake Preview forall the slides in the magazineif necessary This operationcan be initiated from theslidepreview window as well Auto attach Theactually ...

Page 50: ... containing a listof previously saved profiles Based on the Illumination type profiles aregroupedinto two clusters Brightfieldand Fluorescence Additional profiles can be created after clicking Create You can also search for aspecific profileby filtering based on thefollowing data Profilename Objectivetype None 20x 40x Confocalmode None TrueConfocalRX Semi confocal Widefield Multilayermode Extended...

Page 51: ...elected profileavailableforediting Aftermodificationclick Save to overwriteexisting profileor Save as to create anotherone Save Profile Theselected profilecan besaved in this window aftertypingtheprofilename into thetextfield and clicking Save as Note thatthis function is notavailablein Plannermode Reset Zoom This function is activeonly in Live view at1 1 magnification Liveimagemagnification Setti...

Page 52: ... USE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES Help In the Aboutwindowtheversion of the Pannoramic ScannerSoftwareforResearch control softwareand licensing details areincluded Figure 29 About window 4 3 Hotkeys Press F1 to open closehotkeys window F11 Enter Exitfullscreen mode ...

Page 53: ...en 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 navigationtree ...

Page 54: ... o Microscopemode availableonly if Services orSettings modeis active o Settings seechapter6Settings and services formoreinformation o Services seechapter6 Settings and services formoreinformation In accordancewith theselected mode the ProfileSettings Panel and theMicroscopeControl Panel views aremodified 5 1 Brightfield Scanning Mode MicroscopeView consistof threedifferentsections Main functions L...

Page 55: ...settheupperand lowerlimitsby selecting thedesired value in the selection boxes This is usefulif focusing was nottargeted on thespecimen buton a spoton thecoverslip Focus distance thedistanceof focalpointscan besetto create a focus map based on which thesoftwarecalculates interpolated focus values onestep in distancemeans oneFOV Auto focus Focus valueis setautomatically to match samplecharacteristi...

Page 56: ...review window is modified this valueis automaticallyapplied by theprofilein theProfileSettings panel o Specimen threshold This valueis definablemanually This setsthesensitivity of thespecimen detection To set thedesired threshold valuemanually changethesetting in theSpecimen threshold level selection boxin therangeof 0 255 Smallervalues resultin a moresensitivescanning meaning thatmoreareas will b...

Page 57: ...ned area If this option is selected only thearea encircled with a markerpen willbe scanned You can definethethreshold levelby changing thethreshold valuein theUse markerwith threshold selection boxin therangeof 0 255 This sets thesensitivity of thespecimen detection insidethemarkerarea To setthe desired threshold valuemanually changethesetting in theSpecimen threshold selection boxin therangeof 0 ...

Page 58: ... to 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 smallsampleobjectsthat otherwisewould notbescanned o Removespecks If selected thescann...

Page 59: ...n menu 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 It is usefulif you only wantto scan thearea thatis equivalentwith thesize of the coverslip so externalspecks will notbe scanned Multilayermode Select Singlelayeroption if you wantto scan a si...

Page 60: ...Thepurposeof deconvolutionis to producea sharperimage buttheuseof a deconvolution algorithmcan significantly increasethetimethattakes to create a digitalslide Thecapacity of deconvolutionis minimum96GBRAM Scan settings Stop and go A scanning method during whichtheslidetray stands stillduring recording theFOV then itmoves on so thatthescannercan record the nextFOV Use Colormatrix Selectan applicabl...

Page 61: ...les Thedefaultsetting is 80 o PNG Lossless compressed imageformat o BMP Lossless uncompressed imageformat butlargerfiles dueto less effectivecompression Itis a raw datafile Stitching UseStitching function enables theseamless stitchingof digitaltiles Use saved compensationimage TheUsesaved compensation image function enables theuseof previously recorded reference images forallslides Usethis functio...

Page 62: ...ow ThePreview panel offers options forthreshold setting andselection of thearea to be scanned Figure 40 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 scanmapis displayed automaticallyin theProfileScanmap Source setting Selectablescanmap types arethefollowing Usethresho...

Page 63: ...ingin Brightfield mode Darkfield preview preview imageis created with transmitted Darkfield illumination Makesureto selectthis option in Fluorescentmode RemoveCoverslip If selected the edges of thecoverslip are notdetected as specimen to bescanned Dependingon thethreshold level itis possiblethattheedges of the coverslip are detected as areas to bedigitized Figure 41 Preview image with and without ...

Page 64: ...erslip function firstswitch to Custom Scanmap Fill holes insidescanmap If selected theholes insidethespecimen willalso be scanned Often theseholes contain smallsampleobjectsthatotherwisewould notbe scanned Removespecks If selected thescannerdoes notdigitizeobjectssmallerthan the predetermined size This helps filtering specks and otheruninterestingobjectsout Set themaximum volumeof specks manually ...

Page 65: ...tbeidentified as required for digitization forexample weak contrast itcan help to encircle completely thespecimen with a black markerpen You haveto draw a fullcircle with thepen to enablethedetection Markerpen detection will makespecimen detection easierby limiting thescanned area Manual setting ofUsemarker with threshold If this option is selected only thearea encircled with a markerpen will besc...

Page 66: ... to savethe imageof thesliderecorded with thepreview camera Save scanmap Click this icon to savethe currently selected areas to scanmap Position To position thespecimen holderthatholds thecurrentslide click Position sampleandthen click on thearea of intereston thepreview image This will definetheLive imagethatyou can access from the Liveview Union Add theselected areas to thepreview Mark area fors...

Page 67: ...cle You can select thearea to be scanned with thedifferent tools on the Previewtoolbar Placefocus point You can add manualfocus pointson thepreview image thecoordinates of the manualfocus pointsyouadd arelisted on theFocus settings panel NOTE Themaximum numberof focus pointsthatyoucan manually add is 100 Rectangletool Draw rectangleshaped area Ellipsetool Draw ellipse selection Polygon tool Area s...

Page 68: ...column numbers and spotshape roundorrectangle Figure 46 TMA tool Grid selector Delete TMA grid by clicking the X atthe top rightcorner and rotategrid by clicking the icon at thebottom rightcorner Enterthenumberof rows and columns in theRows and Columns fields orselecttheappropriatevalues with the arrows Enterthe distancebetween two spotson theX and theY axis in µm in the Core distancefields orsele...

Page 69: ... equivalentwith the size of the coverslip so externalspecks will notbescanned Thepreview image shows thearea thatwill be digitized with a red and oran orangemask If the Use selection boxis enabled and thecrop function is selected a black frame displayed in theimage Figure 47 Use selection box Thefollowing colors areused in the preview imageto demonstratedigitization and selection settings Figure 4...

Page 70: ...hemarkeris 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 funct...

Page 71: ... Settheupperand lowerlimitsby selecting the desired valuein the selection boxes By using set Range theLower limitvalueis setto 32 of the currentfocus valueand the Upperlimitvalueis setto 32 of the currentfocus value This is useful if Auto Focus does notfind thefocus on thespecimen buton thecoverslip Also this makesthe focusing sequencefaster Formanualfocusingdefinethemanualfocus step sizeby adjust...

Page 72: ... y theamplitudeof atany pairof coordinates x y is called the intensity orgray level of the imageatthatpoint Thepixelintensity atthecoordinatepointing atwith thecursoris displayed in theImageIntensity window Figure 52 Window of Image Intensity 5 1 2 5 Stage positioning Click to activateStage Positioning Tool to navigateon theslide so to perform microscope movementson theLiveimagewith this controlfu...

Page 73: ... by right clickingto thepreview area Itallows a quick access to main functions Drag Draw Erase Rotatepreviews Settings o Toggledeletion always on top o Resetzoom o Window auto size o Clean scanmap Figure 54 Quick toolset 5 1 4 Quick microscope functions A quick microscopefunctions toolcan be displayed upon right clicking on thebackgroundof the main window outsidethepreview window Itincludes quick ...

Page 74: ... MAY 13 2021 73 FOR RESEARCH USE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES Autofocus Figure 56 Autofocus Livetools Figure 57 Live tools o Fastmode o Screenshot o Magnifier o Ruler o Imageprocessorplugins o Add scanmap Auto exposure Figure 58 Auto exposure ...

Page 75: ...anning Exp Time If Auto Exp is inactive exposuretimeof each 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 with pco edge 5 5 from 0 to 6...

Page 76: ...n error freecutimagewith less illumination derivingfrom layers thatareoutof focus on theotherhand imageis brighterthan in Confocalmode and darker than theimagecreated in transformed widefield mode o Widefield This option is recommendedto gain less illuminationloss the resulting imagehas no diffractionnoise no plane parallelshift norcalibration error Scanning timecan befourtimes fasterwhen digitizi...

Page 77: ...edesired preview position by clicking Setin thetable of interpolated focus If you wantto go back to any of thepreviously setfocus points click the appropriate Goto button To deletethe stored values click the otherproperfocus pointorturn off the function Thesoftwarecalculates a coarse focus levelfrom thethreevalues determined this way as a basis forthefinefocusing routine Youcan only define thestar...

Page 78: ...rkfield sampledetection is performed with transmitted Darkfield illumination forlow intensitysamples o Pre scan creates a fastFL preview imagethatis displayed in theProfile Wizard window Scanning process takes a coupleof minutes only andit cannotbeinterrupted o Pre scan high resolution creates a High ResolutionfastFL preview imageof every FOV within theselected area in singlelayerDAPI with an illu...

Page 79: ...utitis possible thatsomeof the smallerspecimen areas willnotbe digitized Auto Threshold By clicking thespecimen willautomatically bedetected in thepreview image Caution Makesurethatthe detection resultis acceptable foryou Otherwise setthethreshold value manually orappend missingareas with thehelp of appropriatefunctions in the Preview window o Use marker with threshold If the specimen cannotbeiden...

Page 80: ...lection 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 possiblethat theedges of thecoverslip are detected as areas to be digitized Figure 64 Preview im...

Page 81: ... notdigitizeobjectssmaller than thepredetermined size This helps filtering specks and other uninteresting objectsout Setthemaximum sizeof specks notto bedigitized by adjusting theSpecksizeslider o Dilatemask Adjustthesliderto enlargeordecreasethe scanned area The edgeis extended discretely by 100 µm each time Scanmap option Thepreviously saved scanmap can beloaded foruse Selectoneof thefollowing a...

Page 82: ...also be sharp This method guarantees themaximumdepth of sharpness however itreduces digitization speed Z Stack For Extended focus and Z Stack scanning methods you can determine thedesired numberof focus levels with the Levels selection box Thecurrent focus valueis the initiallevel If you set 5 forexample then theinitiallevel plus four two focus levels aboveand below theFOVs are captured Therefore ...

Page 83: ...s afterwholeslidescan Changefilters ateach field ofview two statebutton To optimizespeed filterchangetakes placeafterthe digitization of theslidewith onechannel Filters arechanged 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 cha...

Page 84: ...wing threeoptions can beselected from thedrop down list o Intensity statistics legacy compensation algorithm o Reduceintensity pixel levelanalyzation of theacquired imageduring which thebackground of theimageis reduced based on thecomparisonof the imagerecorded by thecamera and thecompensation image o Intensity equalization pixel levelanalyzation of theacquired image a one by onetypeimagecompensat...

Page 85: ...gis displayed on which you can select from differentimageformats Accordingly further adjustmentscan bemade exceptif PNG orBMP imageformatis selected Figure 70 Image encoding window Compression o BMP Lossless uncompressed imageformat butlargerfiles dueto less effectivecompression Itis a raw datafile o PNG Lossless compressed imageformat o JPG Thequality can beset in the valuebox Greatervalues resul...

Page 86: ... forthreshold setting andselection 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 scanmapis displayed automaticallyin theProfileScanmap Source setting Selectablescanmap types arethefollowing Usethreshold Load previously saved ...

Page 87: ... 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 theProfileWizard window Scanning process takes a coupleof minutes only and cannotbeinterrupted o Pre scan high resolution creates a High ResolutionfastFL preview imageof every FOV within theselected...

Page 88: ...tecting algorithm Fill holes in scanmap If selected theholes insidethespecimen will also be scanned Often theseholes contain small sampleobjectsthatotherwisewould notbescanned Removespecks If selected thescannerdoes notdigitizeobjectssmallerthan thepredetermined size This helps filtering specks and otheruninterestingobjectsout Set themaximum volumeof specks manually in thesetting window Threshold ...

Page 89: ...men cannotbeidentified as required fordigitization forexample 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 90: ...review camera Save scanmap Click this icon to savethe currently selected areas to scanmap Previewarea settings o Position To position thespecimen holderthatholds thecurrentslide click Position sampleand then click on thearea of intereston the preview image This will definetheLive imagethatyou can access from the Liveview o Union Add theselected areas to thepreview Mark area forscanning based on th...

Page 91: ...sitive selection masks o Crop Crop thearea of theselected area o PlaceCircle You can select the area to bescanned with thedifferenttools on the Preview toolbar o Placefocus point You can add manualfocus pointson thepreview image thecoordinates of themanualfocus pointsyou add arelisted on the Focus settings panel NOTE Themaximum numberof focus pointsthatyoucan manually add is 100 Rectangletool Draw...

Page 92: ...ady been placed on the preview image Setgrid parameters row and columnnumbers andspotshape round or rectangle Figure 77 TMA tool Grid selector Delete TMA grid by clicking the X atthe top rightcorner and rotategrid by clicking the icon at thebottom rightcorner Enterthenumberof rows and columns in theRows and Columns fields orselecttheappropriatevalues with the arrows Enterthedistancebetween two spo...

Page 93: ...the area thatis equivalentwith thesizeof the coverslip so externalspecks will notbe scanned Thepreview imageshows thearea thatwill bedigitized with a red and oran orangemask If the Useselection boxis enabled thereis a black framedisplayed in the image Figure 78 Use selection box Thefollowing colors areused in the preview imageto demonstratedigitization and selection settings Figure 79 Colors in pr...

Page 94: ... the Preview panel the preview camera detects the marker pen The inside areas appear in 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 image is shown but layer information is still valid Note that while this function is active none of the other preview function...

Page 95: ...window 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 thecurrent field of view automatically by clicking Auto focus button If you select theUse finefocus option thecoarsefocus levelis calculated from threedifferent focus pointsof t...

Page 96: ...ntfocus value This is useful if Auto Focus does notfind thefocus on thespecimen buton thecoverslip Also this makesthe focusing sequencefaster Formanualfocusingdefinethemanualfocus step sizeby adjusting the Step sizesliderand use thetwo arrow buttons to focus manually This is usefulwhen youareinterested in an area that remained blurry with Auto Focus forexample thespecimen is thickerin thatarea Thi...

Page 97: ...bemodified by the softwarewhen calculating Auto Exposuretime ImageIntensity Click to open Imageintensity panel An imageis defined as a two dimensionalfunctionf 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 Intensi...

Page 98: ...ops up by rightclicking any of thecontrolmenu items Itallows a quick access to main functions and forFL thesearethefollowing Drag Draw Erase Retakepreview Settings o Toggledelation always on top o ResetZoom o Window auto size o ClearScanmap 5 2 4 Quick microscope functions A quick microscopefunctions toolcan bedisplayed upon right clicking on thebackgroundof the main window outsidethepreview windo...

Page 99: ...AL RX 1 0 SCANNING MODES AND SETTINGS MAY 13 2021 98 FOR RESEARCH USE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES Autofocus Figure 88 Autofocus Objectivetype Figure 89 Objective type o 20x o 40x Filters Figure 90 Filters ...

Page 100: ...USE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES Microscopemode Figure 91 Microscope mode o Brightfield o Fluorescence 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 101: ...tageunitsarelinked 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 th...

Page 102: ...es forplanningscans located underthe Preferences PlannerLayoutSelectormenu Slide view with card Table Card collection 5 3 1 General functions atthe main menu Microscope Plannerselector Horizontal Vertical selector Availablein Slideview with card mode Stage Control Availableafterinitialization uponclicking theslideicon orentering slide position numberattherightside theslidecan beloaded Scan to Avai...

Page 103: ...n beloaded Save plan A scanning plan containingallparameters and profileassignmentwill be saved Load CSV Rack number slideposition slidename barcode optional profile name illuminationtypedatafrom a CSV filecan beloaded Note thatby the Barcodeparameterin theCSV file thebarcodeof theslidecan be specified butthis parameteris optionaland does notneed to bespecified Warning To preventcasemix up ALWAYSp...

Page 104: ...orall racks Detach currentprofilefrom allracks Detach profiles from racks Clearplanner Clearall slide resultfrom every rack Figure 98 Profile management for all the magazines menu Jump to scanned Loads theplannerview of theactualslide during scanning Settings Help 5 3 2 General functions atthe traymenu Rack viewmodeselector Severalothertrays can be added to theplanner Figure 99 Rack view mode sele...

Page 105: ...o set multipleslidepositions as empty Forsingleslides enter setslideposition with thearrows in the Rangeto skip box orright click on a slide and select Skip Click Reset atthe Slides settings barto cancel slide selections as empty orright click the thumbnailof a slideselected as skipped and click Reset Figure 100 General functions at the slide menu You can apply a selected profileto adefined rangeo...

Page 106: ...ties settings to allselected slides and related profiles Figure 102 ScanContext selector 5 3 4 Slide view with card Select from Preferences Appearancesettings Plannerlayoutselectorto activatethis view Depending on theactualview preferenceselected at slide positions can havea horizontalorverticallayout Slidepreview and thelistof theassigned profiles aredisplayed Figure 103 Horizontal slide view wit...

Page 107: ...CEDURES Figure 104 Vertical slide view with card By clicking or profiles can beadded orremoved for from theslide respectively The parameters of theassigned profile aredisplayed in a card Thecolors of a Brightfield and a Fluorescenceprofilecards aredifferent Figure 105 Brightfield profile card and Fluorescence profile card ...

Page 108: ...visible NOTE If slide status is marked as Failed deletestatus beforescanning by clicking If the virtualslideis created thescanning is finished thelocation path of the destination folderis displayed To re scan and thus recreatetheslide click at thefrontof the displayed path to startthescanning process over Priority scan Scan properties ProfileeditorforScheduler Notes NOTE Oncescanning has finished ...

Page 109: ...emore than oneprofileassigned to it and theseprofiles can eitherbe BF or FL if thescanneris capable to operatein thesetwo scanning modes Figure 106 Table view mode In Table view thefollowing information aredisplayedin theprofilestrip based on theloaded profile Profilename Illumination Priority Quantprobe Objectivetype Filters Progress Scan properties thelocation of thevirtualslide with theselected...

Page 110: ...n view mode If you click the button at Appearancesettings each of theslidepreviews aredisplayed in thewindow Add profiles by clicking and detach profiles by clicking Functions arethe sameas with the othermodes Figure 107 Card collection mode 5 4 Profile and preview overview on the planner Figure 108 Profile editor for Scheduler window in Planner mode ...

Page 111: ...ing the scanning process Every aforementionedProfilesetting can bemodified depending on thescan profiletype being Brightfield orFluorescence Click to load the plannerview of theactualslide during scanning 5 5 Progress features Theprogress is visibleboth in Microscopeand Plannermodes wheneverthereis a running hardwareoperation orscanning procedure Progress contentcan bethereforedifferent depending ...

Page 112: ...OCEDURES 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 usersettings thathaveglobaleffecton theGUI and someof itsfunctions Figure 110 Settings ...

Page 113: ...n resultviewer Open digitalslidewith InstantViewer in web browser or CaseViewer and SlideViewerwhen scanningto server Defaultilluminationmodeselector Brightfield orFluorescencemode Simplified Scan Progress forBrightfield scanningonly Screenshotfolder Set the folderforstoring screenshotsby clicking Browse Otherwise the C Users Username Picturesfolderis used by default Slidesettings Unload slideafte...

Page 114: ...tatebarcodeimageby 180 degrees Unload slideafterplannerscan Scanning History Hardware log Scannerhardwareoperationsarecontained in this log To enablethis function firstthe databasefrom the followingfoldermustbeloaded C ProgramData 3DHISTECH SlideScanner HWLogDataBase Thefollowing motormovementsarerecorded in thelog list o Camera Changer o ConfocalRX o DFP Light o Filter Wheel o General o Halogen L...

Page 115: ... Illumination mode Scan type Scan Start Scan Finished URL Error Figure 111 Scanning log Filtering forthefollowing parameters is available o Scanning date o Profilename o Illumination mode o URL o Slide name o Slide index o Tray index General naming settings Naming pattern Theset string defines theslidenaming pattern shownby theexamplebelow thetext box Click Reset to set pattern to default Theabbre...

Page 116: ...ivating 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 Fora morecomfortableand saferuse turn on PlannerAutosave functionto save a scan plan and by defining a location in thePlannera...

Page 117: ...leHistory from which thedifferentstages can bereloaded Save interval Profilecontentis automatically saved atthespecified timeframes Enablesetting offocus time Parameters Short Normal Long related to focus timewill be enabled on theprofilesettings panel Normal is setas default Pre Scan settings Figure 114 Pre scan settings Unlikescan settings in MicroscopeorPlannermode Pre Scan toolbarincludes thes...

Page 118: ...reresponsibleforopening externalapplications exeor bat as defined forexample CaseViewerand SlideViewer softwarecan beopened afterscanningis finished Thesecalls can run only thefollowing scripts cmd bat exe Theapplication cannothandlescriptlanguages thatarenotsupportedby theWindows Operation System You can defineexternalapplication callsettings forthefollowing cases Slidescanning has finished Scann...

Page 119: ... well Run defines thewindow modethattheexternalapplication willstartin The following windowmodes can beset Normalwindow Minimized Maximized You can test whetherthe Scanning ErrorOccurred settings work by clicking Caution If C ProgramData 3DHISTECH SlideScanner MessengerUserPreferences xml is missingor damaged theExternal applicationcall featurewillnotbeableto read theaddress book thereforeit willn...

Page 120: ... activated themessages willbe sentthrough secured connection If you haveproperly setmessengersettings click Save Click Add newuserin theMessageCall section of theExternalapplication call settings window then enter Display nameand Address of therecipient Select messagefunctions underthe Send Messageif field fortheselected recipients from thedrop downlistatthetop of thesection Click Deleteuser if yo...

Page 121: ... see chapter8 5 1Openingthe service door Slideremoved Click this button to notify thesoftwarethatyou haveremovedtheslidemanually PSF settings This panelserves to specify PointSpread Function values PSF values arerequired to usethenew deconvolution function Click Add filterto add anotherfilterto thelist Figure 118 PSF settings 6 2 Services ActivateServices by clicking atthe rightsideof themain menu...

Page 122: ...ersion settings of the objective Use manual camera changer Changing thecameras is performedmanually Pre Scan objectiveprotection enabled If activated slidearea neartheedges will notbe scanned to record fastpreview image If inactive FastPreview processing becomes slower Cameras ActivateBF and or FL modeforthecamera Thesoftwareautomatically loads thecamera settings upon clicking the Testand apply ca...

Page 123: ...ed Schemeis defined by thecolorcalibration slide o Legacy a Colorschemecalibrated fortheprevious softwareversion is applied o Raw the colorinformation of therecorded raw imageis applied WhitePoint o D65 color temperatureaccording to a standard illuminantD65 whitepoint valueis applied 6500K daylight o D50 colortemperatureaccording to a standard illuminantD50 whitepoint valueis applied 5000K horizon...

Page 124: ...ccupy which turretpositions Theactually set filter position is marked atthe Currentfilterhardwareposition field Select filter hardwarepositions fromthe Filterhardwareposition drop down list Notice Themaximum numberof virtualfilters is 20 if you insert Pentafilters and this typeis selected from theFiltertypelist in the available4 filterpositions in theturret Movefilter wheel to insertposition Enabl...

Page 125: ...heck Availableforscanning Set LumencorLEDlightsource setExcitation and Emission wavelength Bandwidth values fortheselected filter Set Pseudo color Select Channels used forgrayscaleconversion Select EnableLumencorhardwaretrigger Click Saveto savesettings Z difference This function is availableonly forfluorescencesettings itenables you to setthebasicfocus differences between the filters This facilit...

Page 126: ...y oneactive camera forBrightfield mode Objectives field displays theobjectiveused forscanning Theremightbespecks or minoretches on thesurfaceof thecompensation slide thatrequiremodifyingthethreshold settings Therefore thescannerwillnotuse thoseareas forthe creation of thecompensation images To modify thethreshold settings setthedesired threshold valuein thebox To create thecompensation image s cli...

Page 127: ...ing Pannoramic ScannerSoftware forResearch controlsoftware To display an imageof thebarcodearea click You can redefinethebarcodereading area by dragging theedges of thebluesquare To check whetherthebarcodereading settings are correct display thebarcodedigitsin the Barcode field by clicking If thelabel area is notcorrectly illuminated adjust BarcodeLEDintensity value Click to check that barcodesett...

Page 128: ...for barcode NOTE New compensation imageforbarcodecan berecorded only if MIL is used forbarcodeidentification Barcode types o Linear o Stacked linear o Postal o Two dimensional Second barcode priority Thesoftwareis capableto read two barcodes atthe sametime If activated thesecond barcodewillbe thebarcodeused forslide identification Notice When having two barcodes on theslide barcodelayoutmustbe con...

Page 129: ...gure 125 Microscope control settings Illumination o Condensorcovered o Brightfield illumination o Barcodearea light o Backlightillumination intensity Objectiveguide o Step size o X Y values ornavigation arrows o Goto o Goto Preview Origin RGB LED Set illumination intensity perchannel Sync with microscope Calculatewhitebalance Save RGB intensity ...

Page 130: ...e loading operation can bechecked foreach of theslides on thetray Click Insert tray if the prepared tray is placed onto the feederplateand pushed in Click Start slideinserttest button to launch theprocess Slides areloaded in butpreview imagewillnotberecorded Slides will be tested in cycles based on the valuesetin the Loading cyclepertray field Click Removetray when finished ...

Page 131: ...ayfrom 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 thecontrol softwareis as follows 1 In Microscopemode settheappropriatefluorescenceparametersaccordingto section 5 2 Itis wor...

Page 132: ...sequence 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 Folde...

Page 133: ...e Scan 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 specimenthresh...

Page 134: ...centsettings Filter position s Selected focus channel Selected stitching channel Flat field correction ON OFF Intensity statistics Intensity reducing Intensity equalization Sharpening ON OFF Othersettings Limitation of focus range ON OFF Enable disableMultilayeroptions Useof extended focus orZ stack step size and focus level ...

Page 135: ... exclusively on thecontrolcomputer of 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...

Page 136: ...ARCH 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 137: ...finalize installation if thesoftwareis activated during installation so the activation is performed and thecontrolsoftwareis ready foruse Offline activation 1 If the serveris notconnected to theinternet then Offlineactivation can beselected only To perform offlineactivation a device with internetconnection is needed to beat hand Click Nextto continue ...

Page 138: ... to 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 ste...

Page 139: ... filehere 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 ScannerSoftwareforRe...

Page 140: ...f you aresurethateverything is completely unchanged aftertheprevious run If anything has changed oryou areunsure click No Formorecomfortableand saferuse the Plannerautosave functionallows thetaking of automaticbackups whilecreating a scan plan Thebackups areplaced in thedefaultdocument folderof the actualwindows userand can beloaded by clicking the Load plan button 9 3 Safety information Check cab...

Page 141: ...ended to dip a pieceof cloth into clean waterand gently rub problematicareas Forthe cleaning of innerparts of thePannoramic ConfocalRX useEthanol 9 3 2 Cleaning the objectives During immersionscanning fluidmay getto thestage slide tray and the objectives Beforeusing the dry objectivealways makesureto clean theseareas at thefollowing cases On Service panels when clicking Clean Microscope When switc...

Page 142: ...lutions forthePannoramic Confocal RX product If any problem arises thatdoes nothavesolutionin this manual contacttheservice personnel The productdoes notstart Powersupply is interrupted 1 Makesurethatthe powerswitch is on state 1 2 Check cable connections Pannoramic ScannerSoftwareforResearch control softwarehas stopped Slidejammed 1 Exit controlsoftware 2 Switch off controlcomputerand thepowersup...

Page 143: ... o Contact 3DHISTECHServiceforsupport Warning Do not modify thecamera driversettings as thedefaultfactory settings givethemost accurateimages Imageis oflowintensity ornoisy o Thescannabledepth of tissueis highly based on thelight absorptioncapacity of thesample If scanning a thickertissuesample theresulting imagemaybecome noisy dueto thecharacteristics of confocal imaging and theloss of intensity ...

Page 144: ...vated o Deactivatethe Extended focusing optionif notrequired Z stackoption is activated o Deactivatethe Z stackoption if notrequired Imageis outof focus in Manual mode Focus rangelimitis activated o Deactivatethe Limiting focus range option Focus rangesetting is incorrect o Changefocus rangesetting All individualimages showa shading effect Algorithm failedto find empty imagefields o Capturea refer...

Page 145: ...r To removethepipette perform othermaintenancework orif therunningdigitizationprocedure is interrupted becauseof slideortray jamming theservicedoorof Pannoramic ConfocalRX need to beopened to eliminatetheproblem Exceptforthe filterchangeand pipetteremoval beforeopening theservicedoor exit Pannoramic ScannerSoftwareforResearchcontrol software switch off powersupplyand disconnectpowercables Figure 1...

Page 146: ...of doorhinges 9 5 2 Replacing fusesof the main powerswitch 1 Switch off the main powersupply anddisconnectthepowersupply cable see section 1 1 4Base Unit 2 Thefusecompartmentis located abovethemain powersupply switch attheback sideof thePannoramic ConfocalRX 3 Releaselock 1 by pushing theleverupwards so theinsert 2 can be pulled out Figure 129 Fuse compartment 4 Removeinsertfrom thecompartment Fig...

Page 147: ...ng quantityin thepipetteis too low thesoftwareinstructsyou to removethepipette unitand refillwith distilled water Makesurethatonly premium quality distilled water conductanceis less than 10 µS cm is used NOTE Two types of pipettethatcan beused Type 1 and Type 2 according to thepurchase order Type2 pipettecan contain a higheramountof distilled water Follow thebelow steps to removeand refillthe pipe...

Page 148: ...emovalmustbeperformed by an experienced and trainedperson only If the pipetteunit is removed with notenoughcare theskin of yourhand can bebruised Figure 132 Type 2 pipette 4 Rotatetheknob anti clockwiseto empty thepipetteentirely Type1 OR Removethetop cap of thepipette Type 2 5 Dip the pipettehead into thecontainerfordistilled water and rotateknob clockwiseuntil endpoint to pump up thenecessary am...

Page 149: ...CE MAY 13 2021 148 FOR RESEARCH USE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES 6 Place thepipetteback to its seating and makesurethatthereis no gap remaining atthe connectorarea 7 Closethe servicedoorby pushing any of thetwo buttons atthesides of thedoorframe ...

Page 150: ...twaresession and turn thepoweroff Any manipulation performedon a mechanicalcomponentmustbefollowed by a completedevice initialization routine softwarerestart Figure 133 Removing a slide 1 Open servicedoor see chapter9 5 1Openingthe service door 2 Moveclamp 1 to theleft so theslide could be easily removed 3 While holding theclamp pushed to theleft removetheslide 2 carefully Caution If the slideis b...

Page 151: ...nceordamagedwhen handled improperly Filtercubes Filter cubes aresupplied in a polyethylenecase each casecan hold up to four filter cubes Each filtercubehas a label showing theexcitation emission and dichroic wavelengths Each filtercubeis comprised of oneexcitation filterand two emission filters Figure 134 Filter cube Theinstrumentis equipped with filtercubes which are user replaceable Itwillbe nec...

Page 152: ...o theCC88 makesurethatitis on standby orturned off beforeopening thefilterturretdoor 1 Open theservice doorof Pannoramic ConfocalRX 2 Open filterturretdoor 3 Manually rotatetheturretto thedesired position Figure 135 Filter turret 4 Insertthefilter cubealong theguiding spokes of thefilterwheeluntilthelocating magnet pulls thefilter cube Figure 136 Inserting the filter cube ...

Page 153: ...lter cube 6 Check that thefilter cubeis flush with thewheel Warning Failureto insert thefilter cubeproperly could resultin damageto theinstrumentand or filter cube as well as compromisingtheopticalperformanceof theinstrument 7 Repeatfrom step 2 to insertthe nextfilter cube 8 When all filter cubes havebeen inserted closethe filterturretdoor Theinstrumentwill undergo itsinitialization proceduredurin...

Page 154: ...itusing thesecarrying handles To determinetheappropriatenumberof transporter people observethelaws of yourcountry regarding load carrying capacity limitations You can find theweightdataof the baseunitin section 10 Technical Data To transportPannoramic ConfocalRX do thefollowing 1 Switch powersupply off see section 1 1 4Base Unit and detach allothercables 2 Pullall fourcarrying handles marked with ...

Page 155: ... PROCEDURES Figure 139 Transporting handles 9 5 7 Removing andcleaning the condenser Thequality intensity cleanness of theresulting imageis highlyaffected by theconditionof the condenser thereforeitis advised to removetheunitand clean thesurfaceof thecondenserlens on a weekly basis Figure 140 Removal of the condenser unit ...

Page 156: ...ing lever 1 downwardsto releasethelock 4 Hold the condenserunit 2 by itshandleand pullitoutwards 5 Place thecondenserunitonto a pieceof cloth lint freeand clean Follow thebelow steps to ensuretheunitis in good condition 1 Check thesurfaceof the condenserlens If itneeds cleaning usea lens cleaning brush to removedustparticles If thereremain someparticles visibleon thelens usea clean lens cleaning c...

Page 157: ...ethatthegroovesof themalepartof the dovetailjointis clean Figure 142 Dovetail grooves Reinstallunitby following thebelow procedure 1 By caring attention to applying theunitcorrectly so thatjointelementsareinterlocking gently slidethecondenserunitback to its position Figure 143 Reinstallation of the condenser unit 2 Lock the unitby moving theleverupwards 3 Closethe servicedoor ...

Page 158: ...ox 1000 mm Table 3 Weight and dimension specifications Environmental 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 25 75 Operation Permissible ambient temperature 10 C to 35 C Permissible relative air humidity 25 75 Altitude at installation site max 2000 m A...

Page 159: ...IEC 61010 1 2001 IEC 61010 2 101 2002 Over voltage category II Radio interference suppression in accordance with EN 55011 class B Noise immunity in accordance with EN 61326 2 6 2012 Base unit input voltage 100 240V AC Power consumption of the complete device max 350W Fuses 2x T3 15A 250V Lightsources Brightfield illumination 3CCD equivalent separated R G B LED Average service life of LED 25 000 hr...

Page 160: ...focus plane 0 4 µm FWHM with 40x 1 2NA objective Cooling Peltier with forced air fan Connection type Dual Camera Link Full 10 taps 85MHz Control computer minimum systemrequirements Operating System Microsoft Windows 10 Professional 64 bit EN CPU Intel Xeon Silver 4110 RAM 96 GB DDR4 Hard disk 256 GB SSD 1 TB HDD 2 TB HDD Optical drive DVD RW Display 96 dpi Graphics Full HD 1920 1080 Input devices ...

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