3DHISTECH PANNORAMIC SCAN RX 1.1 User Manual Download Page 45

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PANNORAMIC® SCAN RX 1.1

SOFTWARE DESCRIPTION

NOVEMBER 18, 2021

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

Tiled-TIFF settings

Figure 21. Tiled-TIFF settings

▪

Click

Reset

to set everything to default.

▪

Zero based index in names

: Z-Stack layers of the generated TIFF files will

be indexed starting with 0, and the focus distance of the actual layer will
not be included (inactive by default).

▪

Display FL channels RGB-colorized

: a 24-/48-bit color TIFF image is

generated based on the FL channels. File size is bigger, but most of the
image viewers are capable to open it. An 8-/16-bit grayscale TIFF image will
be generated if not selected. File size is smaller, but some of the viewers
cannot handle it.

▪

TIFF type

▪

Automatic

: the converter automatically selects the most

appropriate method based on the size of the source slide.

▪

Force simple tiff

: TIFF files use 32-bit offset addressing; therefore,

file size is limited to a maximum of 4Gb.

▪

Force big tiff

: Big TIFF files use 64-bit offset addressing allowing

the creation of bigger TIFF files.

▪

Compression type

▪

Jpeg (8-bit)

: compression rate can be set (1-100, default: 80).

▪

Lossless compression 8-bit

▪

Lossless compression native:

color depth of the source slide is

inherited (16-bit is supported).

▪

Uncompressed 8-bit

▪

Uncompressed native:

color depth of the source slide is inherited

(16-bit is supported).

▪

Compression rate

: default is 80, on a scale of 1-100.

▪

Zoom scale

: set the level of zoom at which the TIFF image is created to get

the smallest file size possible.

Summary of Contents for PANNORAMIC SCAN RX 1.1

Page 1: ...PANNORAMIC SCAN RX 1 1 USER S GUIDE FOR RESEARCH USE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES November 18 2021 Rev 1 ...

Page 2: ... 18 1 2 System overview 19 1 2 1 Pannoramic SCAN RX 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 computer ports 26 2 3 Connectors and cables 27 2 4 Coupling the Lumencor SOLA U NIR unit with the scanner 28 2 5 Coupling the Lumencor Spectra 6 unit with the scanner 28 2 6 External power supply unit 29 2 7 ...

Page 3: ...panel 79 5 2 2 Microscope control panel 89 5 2 3 Hidden functions 101 5 2 4 Quick microscope functions 102 5 2 5 Bottom menu bar of the main window 104 5 3 Planner mode 105 5 3 1 General functions at the main menu 105 5 3 2 General functions at the magazine menu 108 5 3 3 General functions at the slide menu 108 5 3 4 Slide view with card 110 5 3 5 Table view mode 112 5 3 6 Card collection view mod...

Page 4: ... Preventive maintenance 149 9 4 Troubleshooting 149 9 4 1 Fluorescent applications optional 151 9 5 Maintenance 152 9 5 1 Removing the protective covers 152 9 5 2 Removing a slide 153 9 5 3 Installing and removing the filter module fluorescent option 155 9 5 4 Removing the magazine from the transporting system 157 9 5 5 Transporting Pannoramic SCAN RX 158 10 Technical Data 160 ...

Page 5: ... 050351 EP 1789831 US 7 663 078 P0301911 PCT HU04 00019 EP 1644767 US 7327515 The above mentioned granted patents granted utility model registered trademarks pending international and national patent applications and the other corresponding IP are the sole properties of the 3DHISTECH Ltd 3DHISTECH Ltd is not liable for damage of whatever nature including but not limited to general or specific dama...

Page 6: ...uding but not limited to general or specific damage indirect damage consequential damage or incidental damage including damage resulting from lost profits interruption of business loss of business information pecuniary loss or similar damage that stems from or is associated with the incorporated part of this Product that is made by a third party company THE SOFTWARE IS PROVIDED AS IS AND WITHOUT W...

Page 7: ... 61010 1 2010 Safety Requirements for Electrical Equipment for Measurement Control and Laboratory Use Part 1 General Requirements IEC 61010 2 081 2015 Safety requirements for electrical equipment for measurement control and laboratory use Part 2 081 Particular requirements for automatic and semi automatic laboratory equipment for analysis and other purposes There is no further operator user action...

Page 8: ...roduct described Before operating the device you must carefully read this instruction manual and adhere to all WARNING and CAUTION notices refer to chapter Notes Regarding Operational Safety for more information and a copy should be kept in the close to the scanner for reference whenever required This User s Guide is a part of the Pannoramic SCAN RX system identified by the relevant article number...

Page 9: ...dow titles push button and menu names paths or options Keys on the keyboard For example function keys such as F11 or the Ctrl S hotkey Example text in bold and italics Cross references within this document or to other documents Warning It might cause irreversible damage or harm to the user of the product or the product itself if this instruction is not followed Caution It might cause the product t...

Page 10: ...ion Make sure not to reach with your hands into the instrument to avoid the risk of crushing your fingers Please note that the digitizing process has to be interrupted and the slide magazine moved via software to the output position before removing it The Pannoramic SCAN RX including any of its original accessory components should not be operated in any other way than described in chapter 1 1 1 In...

Page 11: ...ition you should contact the 3DHISTECH Customer Service Warning Check that your local line voltage is compatible with Pannoramic SCAN RX specifications before you turn power on Warning Only connect external devices to the instrument which are approved to avoid the risk of electrical shock Warning The Pannoramic SCAN RX does not include any special facilities to protect from samples with an etching...

Page 12: ... RX is a precision instrument which may suffer a significant reduction in operational functions or even physical destruction following intervention performed in any nonconforming manner Caution In the event of any non conforming type of use including non conforming use of assemblies or single parts no liability will be assumed by the Manufacturer This shall also apply to service or repair work of ...

Page 13: ...rate and to disconnect the device if necessary Notice The safety level of the equipment after servicing will be identical with level of the original equipment Notice Electric power to the Pannoramic SCAN RX is supplied via an external mains power supply unit It allows for operation at line voltages in the range of 100 V to 240 V 10 50 60 Hz without any extra facilities required for voltage transfo...

Page 14: ...ring a faultless product for replacement No warranty will be accepted in cases of natural wear notably wear and tear parts or improper product handling The Product Manufacturer will refuse any liability in the event of damage resulting from faulty operation negligence or unauthorized intervention into the product notably from the replacement of product parts or the usage of accessory parts from ot...

Page 15: ... the 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 interac...

Page 16: ...fect the functionality of the scanner program 1 1 2 Features and benefits The Pannoramic SCAN RX offers world class brightfield and fluorescent whole slide scanning on up to 50 virtual fluorescent channels using 9 physical fluorescent filter positions An outstanding 0 12 µm pixel in Brightfield and 0 16 µm pixel in Fluorescent resolution is achieved with the 40 NA 0 95 equivalent to 80 magnificati...

Page 17: ...autofocus 3MP camera for barcode reading and preview image Image sharpening both for Fluorescence and Brightfield feature which improve the visual appearance of digital slides Focus algorithm finds the focus which is most appealing to the human eye Deconvolution algorithm Compact and robust device Good quality and stable manufacturing Pannoramic SCAN RX is an optimal choice for customers who need ...

Page 18: ...NLY NOT FOR USE IN DIAGNOSTIC PROCEDURES 1 1 3 Warning and information labels The following figure contains the labels used on the Pannoramic SCAN RX main unit the external mains power supply unit and the Lumencor SOLA U NIR illumination unit Figure 1 Warning and information labels ...

Page 19: ...hazard level The biological hazard is minimal because the minimally hazardous sample is enclosed between the glass slide and the coverslip 1 1 4 Base unit The following figure shows the main parts of the base unit Figure 2 Main parts of the base unit 1 Protective cover 2 Output stack for magazines 3 Input stack for magazines 4 Protective cover for magazine loader 5 Magazine feeder door cover 6 Poi...

Page 20: ...8 Lumencor SPECTRA 6 Light Engine fiber coupled illumination unit 9 Lumencor illumination adapter 10 Lumencor illumination cable 1 2 System overview The standard scope of delivery of the product includes the following hardware and software components 1 2 1 Pannoramic SCAN RX system The following figure shows the main components of the Pannoramic SCAN RX system Figure 3 Pannoramic SCAN RX system ov...

Page 21: ...TRA 6 Light Engine optional 4 Monitor 5 Mouse 6 Control computer 7 Keyboard 8 Pannoramic SCAN RX base unit 9 Slide magazine with cover 1 2 2 Hardware options Notice The configuration of the control computer and monitor can vary depending on the product order Cameras Point Grey Grasshopper 3 1 CCD monochrome camera for high quality sensitive fluorescent applications pco edge 4 2 bi Back illuminated...

Page 22: ...base unit equipped with Point Grey Grasshopper 3 camera for Brightfield scanning no fluorescent accessories included Pannoramic SCAN RX Basic Brightfield and Fluorescence Option base unit completely equipped with pco edge 4 2 bi camera and Lumencor SOLA U NIR non triggered or Lumencor SPECTRA 6 fluorescent illumination unit with filters for fluorescence scanning Pannoramic SCAN RX Advanced Brightf...

Page 23: ...not change correction collar settings on 40 NA objective if you need it to be set contact customer service Fluorescent Options for Pannoramic SCAN RX Fluorescent illumination unit Description Lumencor SOLA U NIR Fluorescent illumination unit use with Point Grey Grasshopper 3 camera only Lumencor SPECTRA 6 Light Engine illumination unit 1 2 3 Control software Pannoramic Scanner Software for Researc...

Page 24: ... Barcode reader Converter software 2 3 2 RTM only available in Full scanner install mode CaseViewer or SlideViewer software fully functional Optional CaseCenter or SlideCenter TMA module 3D Reconstruction module QuantCenter HistoQuant NuclearQuant MembraneQuant CISHQuant FISHQuant and DensitoQuant modules E School Encoder ...

Page 25: ...so that there is enough space for ventilation and for safe and efficient operator maintenance Caution If the temperature of the location where the scanner is operated is much lower than the temperature of the equipment for example the device is brought in from an outer storage or has been transported to the site please leave enough time to normalize the temperature differences before operating the...

Page 26: ...AP partition for storing temporary files generated during scanning as the lack of space required will result in interruption of scanning Microsoft Hardware Driver Updates We are not taking responsibility for errors caused by automatic hardware driver updates issued by Microsoft so we recommend that you turn the automatic updates option off Third Party Driver Updates Warning Automatic updates of de...

Page 27: ...the product for a short distance by disconnecting cables and detaching hardware components from each other Figure 4 Ports on control computer 1 Status display 2 DVD drive RW 3 Power on off button 4 Earphone and microphone 3 5mm Jack ports 5 2x USB port 6 Power supply connector 7 PS 2 mouse port 8 PS 2 keyboard port 9 4x USB port 10 2x USB port 11 Network port 12 4x USB 3 0 ports for Point Grey Gra...

Page 28: ...nt Grey Grasshopper 3 camera and control computer pco edge 4 2 bi a pair of CameraLink cables between pco edge 4 2 bi camera and control computer Video cable between monitor and control computer Power supply cable between 230V 110V and monitor Power supply cable between 230V 110V and Lumencor SPECTRA 6 unit Power supply cable between 230V 110V and control computer Power supply cable between 230V 1...

Page 29: ...ect the power supply cables of both the scanner and the illumination unit 2 5 Coupling the Lumencor Spectra 6 unit with the scanner To operate the Lumencor Spectra 6 Light Engine fluorescent illumination unit it has to be connected to the Pannoramic SCAN RX base unit the camera and the control computer 1 Turn the control computer and the pco edge 4 2 bi camera off 2 Attach Lumencor SPECTRA 6 fluor...

Page 30: ... be connected between the mains power and the device Front panel 1 main power switch 2 power supply connector Back panel 3 detachable power cord to connect the external power supply unit with the main unit Figure 6 24V external power supply unit 2 7 Power the scanner on off To turn the scanner on press down the I side of the rocker switch at the front panel of the 24V external power supply unit Fi...

Page 31: ...ckness 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 wear personal protective equipment safety goggles gloves and coat when working with biohazardous material or slides Warning Do not use a slide when it is broken or its edges are not properly cut or grounded Using such slides can lead to injury Warning If the scann...

Page 32: ...s surface of a slide use a soft tip pen instead for marking area of interest Notice The distance between slide edges and the edges of the mounted coverslip should be 1 2 mm and they should be parallel with each other Notice Fluorescent signals become more easily detectable for the scanner therefore resulting in a brighter and better image by treating the slide with a formula that prevents rapid ph...

Page 33: ...and viewer software To affix barcode stickers to slides do the following 1 Peel off the barcode sticker 2 from the roll 2 Stick it on the colored label area 1 of the slide on the specimen side Caution Ensure that a marginal space of 1 2 mm remains on all sides between the sticker and the label area outer limits It is vital for barcode identification Do not let barcode sticker protrude from slide e...

Page 34: ...can contain a maximum of 25 slides Push slide 1 into the magazine 3 with its barcode end 2 first The symbols on the side of the magazine demonstrate the proper way of inserting slides Notice You should insert several slides into a magazine without empty slots Begin the insertion on position 1 of the magazine Caution Only original 3DHISTECH magazines are allowed for use with Pannoramic SCAN RX To i...

Page 35: ... 9 must be closed during operation 1 Remove magazine cover before you insert magazines Caution Replace magazine cover when magazine is not currently used or is stored for a longer period The cover prevents soiling and mechanical damage 2 Open the flap of the input stack 5 and put a magazine 1 into the input stack 4 The magazine s rack the back side of the magazine 2 must contact with the guide rai...

Page 36: ... damages in the feeding mechanism Notice The input stack can be filled with a maximum of 6 magazines in addition to the one in the magazine loader Figure 10 Misplaced magazine Caution Do not place magazines into the output stack 3 or remove magazines with already digitized slides from there during the digitization process Only remove magazines from the output stack when you have finished digitizat...

Page 37: ... is displayed Figure 11 Mode selection window Microscope mode for digitization of individual slide or individual rack set scanning profile of the slide use Live microscope Planner mode plan the entire scanning procedure assign one or more profiles to each slide define Brightfield and Fluorescence or mixed scanning mode within a run define scanning profile to slides included in racks or magazines a...

Page 38: ...initialized Slide magazine control Notice At slide loading the Pannoramic Scanner Software for Research control software registers whether a slide is inserted or not At the initialization the stage moves to the slide insert position and checks the slide A logging mechanism is also available in the slide loading test The slide sensor has an optoelectronic gate and a lever At the slide loading posit...

Page 39: ...s loaded at the moment is highlighted with a blue background and outer line Objective changer Live view is on Live view is on with the shutter closed Toolbar for live images Click to display the toolbar for Live view These functions are only available for the displayed live image i e Live view is ON but not available for camera images during digitization When in Normal live mode images are taken w...

Page 40: ...ill have a higher noise level This function is useful for fluorescent live view where despite the higher noise level the resulting image will be refreshed as in normal mode Image intensity Figure 14 Image intensity The intensity of the pixel at which the cursor is placed is displayed by I in the Image intensity window X and Y stand for the location of the pixel within the image coordinate system S...

Page 41: ...name can be defined manually or automatically If you want to name the slide manually turn on the Manual naming function and if you want to generate slide name based on the corresponding settings set in Preferences activate Generate function Barcode parsing Select the type of barcode profile from the drop down list for slide naming through parsing the barcode string By using Default barcode profile...

Page 42: ...f a list item to open the Barcode editor window in which the settings of the selected profile can be edited Figure 17 Barcode editor window If you click Add new item on the list blank input fields will be displayed Figure 18 Create new barcode Define modify profile name in the Name input field select barcode type from the Type drop down list ...

Page 43: ...responding field Enable Parse subfolders to make it available to create subfolders when parsing data from the barcode Type name of the subfolder in the Folder1 Folder2 etc fields depending on the depth you want to define Click Save to apply settings and click Create new at the top of the panel to create a new profile item Slide save path Set destination folder in the input field by typing in the p...

Page 44: ...inal MRXS slide will be deleted after the conversion is complete Target format The slide is converted to the selected final format Click one of the buttons to define the final slide format MRXS Tiled TIFF Roche TIFF SVS DICOM Click to open MRXS Tiled TIFF and DICOM conversion settings panel o MRXS settings Figure 20 MRXS settings Click Reset to set everything to default Select Change JPG compressi...

Page 45: ...e size is smaller but some of the viewers cannot handle it TIFF type Automatic the converter automatically selects the most appropriate method based on the size of the source slide Force simple tiff TIFF files use 32 bit offset addressing therefore file size is limited to a maximum of 4Gb Force big tiff Big TIFF files use 64 bit offset addressing allowing the creation of bigger TIFF files Compress...

Page 46: ...l size accuracy default 7 X Y offset accuracy default 5 Depth accuracy default 3 Tile pool size default 1000 UTC time in minutes default 0 Basic offset table active by default Shared plane position active by default Shared optical reference active by default o Conversion save path The folder set in this box is designed to store the final slides after conversion Conversion progress is displayed in ...

Page 47: ...resulting measurement data will be incorrect Notice The Pannoramic Scanner Software for Research software is compatible with licensed QuantCenter application only otherwise the control software may close due to an error Click to assign the appropriate Quant probe to the digital slide If the scanning of slide has finished the progress of Quant evaluation is displayed in the QuantCenter Processing Q...

Page 48: ...OSTIC PROCEDURES Scan to Server Figure 24 Scan to Server settings Server settings Select the dedicated server to which you want to scan from the Server drop down list Click the arrow to show the list of saved server profiles or click Add new item at the bottom of the list to create another server connection ...

Page 49: ...stores each of the created server in a list List entries can be removed or a new entry can be added if required With the Filters function you can narrow down the results by searching for a specific server data By double clicking a list item server data will be loaded in the Scan to Server panel After loading server data username and password are required to be added for authentication and accessin...

Page 50: ...ttings of the Scan to local panel barcode settings for parsing can be modified in the Barcode Editor window Figure 27 Barcode Editor If using MIL for barcode reading you can select the following barcode types 1D barcode types Code 39 Code 128 Code 16K Interleaved 2 of 5 Standard 2 of 5 IATA 2 of 5 Matrix 2 of 5 Telepen Code 93 Code 11 MSI Codabar Patch Code Pharmacode ...

Page 51: ...ption can be selected if CaseCenter or SlideCenter is connected to the supported HIS LIS This way the barcode read by the software is being identified and the predefined location of that specific case in CaseCenter or SlideCenter is automatically selected as scanning destination based on the CaseID containing slide and patient data stored on HIS LIS Therefore Folder Case Block and Slide name field...

Page 52: ...tination folder Conversion settings Refer to Scan to local panel see above parameterization and settings are the same Quant settings Run QuantCenter Turn this function on for automatic evaluation of the completed digital slide by using the integrated QuantCenter right after the scanning has finished Other settings Scan separately The FOV areas of the preview image will be scanned and saved separat...

Page 53: ...an Stop actual progress Take All Previews Figure 28 Take all previews selector Each preview of slides in the tray is taken automatically Preview types are the following from top to bottom Brightfield Pre Scan FL Pre Scan High Resolution FL Pre Scan High Resolution FL Activate Retake Preview for all the slides in the magazine if necessary This operation can be initiated from the slide preview windo...

Page 54: ...ded into the scanner and of which a preview image is recorded Whenever you add a new magazine in Planner mode as well the software asks you whether the magazine has previously been loaded or not Click Yes if the magazine has already been processed then enter the number of the magazine used during the process otherwise click No Auto attach Actual profile is assigned to the loaded slide automaticall...

Page 55: ...owser window containing a list of previously saved profiles is opened Based on the Illumination type profiles are grouped into two clusters Brightfield and Fluorescence Additional profiles can be created by clicking Create You can also search for a specific profile by filtering based on the following data Objective type Multilayer mode Illumination Filters Modify date Last use date ...

Page 56: ...ofile or Save as to create another one Save Profile The selected profile can be saved in this window after typing the profile name into the text field and clicking Save as Figure 30 Save profile Reset Zoom This function is active only in Live view at 1 1 magnification Live image magnification Settings and Services function descriptions are detailed in chapter 6 Settings and Services Help In the Ab...

Page 57: ... fullscreen mode Exit from fullscreen mode CTRL mousewheel Zoom in out SHIFT mousewheel Change Focus by step 36 36 W S Change Focus by step 1 1 fine tuning Arrows Move stage within a limited area F2 Change Pseudocolor CTRL F Start Autofocus Left Mouse Button Drag Pan view Right Mouse Button Open Circle menu Other CTRL Left Mouse Button in microscope mode open close left profile tree and right navi...

Page 58: ...e available only if Services or Settings mode is active o Settings See chapter 6 Settings and Services for more information o Services See chapter 6 Settings and Services for more information In accordance with the selected mode the Profile Settings Panel and the Microscope Control Panel views are modified 5 1 Brightfield scanning mode Microscope View consist of three different chapters Main funct...

Page 59: ...ng Limits of the range for focusing You can set the upper and lower limits by selecting the desired value in the selection boxes This is useful if focusing was not targeted on the specimen but on a spot on the coverslip Focus distance the distance of focal points can be set to create a focus map based on which the software calculates interpolated focus values one step in distance is one FOV Auto f...

Page 60: ...ow is modified this value is automatically applied by the profile in the Profile Settings panel o Specimen threshold This value is definable manually This sets the sensitivity of the specimen detection To set the desired threshold value manually change the setting in the Specimen threshold level selection box in the range of 0 255 The default value is 220 Smaller values result in a more sensitive ...

Page 61: ...on is selected only the area encircled with a marker pen will be scanned You can define the threshold level by changing the threshold value in the Use marker with threshold selection box in the range of 0 255 This sets the sensitivity of the specimen detection inside the marker area To set the desired threshold value manually change the setting in the Specimen threshold selection box in the range ...

Page 62: ...coverslip edges Select Remove coverslip function to eliminate those areas Warning Do NOT use Remove coverslip function on TMA slides The layout of TMA slides may mislead the detecting algorithm o Fill holes inside the scanmap If selected the holes inside the specimen will also be scanned Often these holes contain small sample objects that otherwise would not be scanned o Remove specks If selected ...

Page 63: ...menu Select whether to load preview mask or TMA grid Custom scanmap The scanmap draws manually on the preview image is used for scanning Use selection box restriction If selected only the area inside the box is scanned It is useful if you only want to scan the area that is equivalent with the size of the coverslip so external specks will not be scanned Multilayer mode Select Single layer option if...

Page 64: ...ed with Viewer applications The Z Stack slide contains the extended focus layers Step size determines the spacing between focus levels One step is around 0 2 µm Default settings are Levels 7 Step size 5 The number of iterations the Deconvolution algorithm is run can be determined in the Iteration number for deconvolution value box Figure 40 Focus level settings Notice The purpose of deconvolution ...

Page 65: ...rated for the previous software version is applied Custom Color profile set in Service is applicable if needed Image settings You can choose the following predefined image formats and a subsequent custom option from the Image Quality drop down list in the Image Encoding section of the window Excellent JPEG 90 Good JPEG 80 Medium JPEG 60 Low JPEG 30 Custom If choosing this option the image compress...

Page 66: ...ide with coverslip to grab a compensation image If you select this the software will not create new compensation images for each slide Compensation images are reference images used for white balancing and shading Save focus quality The measurement of focus quality correctness of average focus on layers is saved This option is inactive when Extended focus option is activated 5 1 2 Microscope contro...

Page 67: ...g Use threshold Load previously saved Scanmap from file Custom Scanmap Preview Type setting determines the type of illumination In Brightfield mode the following preview types are available Brightfield preview a normal type of illumination in the microscope for scanning the slide This option is recommended when scanning in Brightfield mode Remove Coverslip If selected the edges of the coverslip ar...

Page 68: ...sing on the coverslip area is not available If you want to use the Remove Coverslip function first switch to Custom Scanmap Fill holes inside scanmap If selected the holes inside the specimen will also be scanned Often these holes contain small sample objects that otherwise would not be scanned Remove specks If selected the scanner does not digitize objects smaller than the predetermined size This...

Page 69: ... threshold If the specimen cannot be identified as required for digitization for example weak contrast it can help to encircle completely the specimen with a black marker pen You have to draw a full circle with the pen to enable the detection Marker pen detection will make specimen detection easier by limiting the scanned area Manual setting of Use marker with threshold If this option is selected ...

Page 70: ...CEDURES Figure 44 Scan everything within the marker selected not selected Dilate mask Adjust the slider to enlarge or decrease the scanned area The edge is extended discretely by entering a new value each time To switch to manual mode click the top left corner of the button and the required value can be entered in the box ...

Page 71: ...o scanmap Position To position the specimen holder that holds the current slide click Position sample and then click on the area of interest on the preview image This will define the Live image that you can access from the Live view Union Add the selected areas to the preview Mark area for scanning based on the shape selected in the Preview Toolbar This area will not be scanned Erase Delete select...

Page 72: ...u can select the area to be scanned with the different tools on the Preview toolbar Place focus point You can add manual focus points on the preview image the coordinates of the manual focus points you add are listed on the Focus settings panel Notice The maximum number of focus points that you can manually add is 100 Rectangle tool Draw rectangle shaped area Ellipse tool Draw ellipse selection Po...

Page 73: ...nd spot shape round or rectangle Figure 48 TMA tool Grid selector Delete TMA grid by clicking the X at the top right corner and rotate grid by clicking the icon at the bottom right corner Enter the number of rows and columns in the Rows and Columns fields or select the appropriate values with the arrows Enter the distance between two spots on the X and the Y axis in µm in the Core distance fields ...

Page 74: ...s enabled and the crop function is selected a black frame displayed in the image and only the area inside the box is scanned It is useful if you only want to scan the area that is equivalent with the size of the coverslip so external specks will not be scanned Figure 49 Use selection box on the preview image The following colors are used in the preview image to demonstrate digitization and selecti...

Page 75: ...r is selected in 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 ...

Page 76: ...imits select Limit the range Set the upper and lower limits by selecting the desired value in the selection boxes By using Range the Lower limit value is set to 32 of the current focus value and the Upper limit value is set to 32 of the current focus value This is useful if Auto Focus does not find the focus on the specimen but on the coverslip Also this makes the focusing sequence faster For manu...

Page 77: ... any pair of coordinates x y is called the intensity or gray level of the image at that point The pixel intensity at the coordinate pointing at with the cursor is displayed in the Image Intensity window Figure 54 Window of Image Intensity 5 1 2 3 Stage positioning Click to activate Stage Positioning Tool to navigate on the slide so to perform microscope movements on the Live image with this contro...

Page 78: ...icking to the preview area It allows a quick access to main preview related functions Drag Draw Erase Retake preview Settings o Toggle deletion always on top o Reset zoom o Window auto size o Clean scanmap Figure 56 Quick toolset 5 1 4 Quick microscope functions A quick microscope functions toolset can be displayed upon right clicking on the background of the main window outside the preview window...

Page 79: ...BER 18 2021 78 FOR RESEARCH USE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES Autofocus Figure 58 Autofocus Live tools Figure 59 Live tools o Fast mode o Screenshot o Magnifier o Ruler o Image processor plugins o Add scanmap Auto exposure Figure 60 Auto exposure ...

Page 80: ...n be defined manually Values such as Calc Exposure time in Microscope Control panel and those that are specified manually are loaded in these fields Value units can be the following microsecond millisecond second Exc The given value specifies the excitation intensity in percentage of the illumination unit DG Digital Gain This is camera dependent with Point Grey Grasshopper 3 the index value ranges...

Page 81: ... Z value by clicking Assign Current Interpolated focus If you select the Interpolated focus option the coarse focus level is calculated from three different focus points of the specimen Carry out a manual focusing sequence in the preview image on those three points Set the correct focus value of the desired preview position by clicking Set in the table of interpolated focus If you want to go back ...

Page 82: ...ess and size of the specimen Focus Exposure The exposure time during focusing it can have three states o Short o Normal o Long Sample detection The Sample detection panel offers options for setting threshold and the selection of scannable areas Source o Brightfield preview a normal type of illumination in the microscope for scanning the slide This option is recommended when scanning in Brightfield...

Page 83: ...0 255 The default value is 212 Smaller values result in a more sensitive scanning meaning that more areas will be digitized however this may also include specks or other imperfections of the slide Greater values result in a less sensitive scanning but it is possible that some of the smaller specimen areas will not be digitized o Auto Threshold By clicking the specimen will automatically be detecte...

Page 84: ...on box Alternatively click in the preview window to activate this function Figure 63 Scan everything within the marked area selected not selected Threshold enhancement o Remove coverslip If selected the edges of the coverslip are not detected as specimen to be scanned Depending on the threshold level it is possible that the edges of the coverslip are detected as areas to be digitized Figure 64 Pre...

Page 85: ...ed o Remove specks If selected the scanner does not digitize objects smaller than the predetermined size This helps filtering specks and other uninteresting objects out Set the maximum size of specks not to be digitized by adjusting the Speck size slider o Dilate mask Adjust the slider to enlarge or decrease the scanned area The edge is extended discretely by 100 µm each time Scanmap option Figure...

Page 86: ...ry in auto manual focus will also be sharp This method guarantees the maximum depth of sharpness however it reduces digitization speed Z Stack For Extended focus and Z Stack scanning methods you can determine the desired number of focus levels with the Levels selection box The current focus value is the initial level If you set 5 for example then the initial level plus four two focus levels above ...

Page 87: ...slide scanning To optimize speed filter change should take place after the digitization of the slide with one channel Change filters at each field of view Filters should be changed for each field of view if very precise colocalization is required but consider that this option is more time consuming Notice Make sure to select the Change filters at each field of view option if using multi band filte...

Page 88: ...tions can be selected from the drop down list o Intensity statistics legacy compensation algorithm o Reduce intensity pixel level analyzation of the acquired image during which the background of the image is reduced based on the comparison of the image recorded by the camera and the compensation image o Intensity equalization pixel level analyzation of the acquired image a one by one type image co...

Page 89: ...f PNG or BMP image format is selected Figure 70 Image encoding window Compression o BMP Lossless uncompressed image format but larger files due to less effective compression It is a raw data file o PNG Lossless compressed image format o JPG The quality can be set in the value box Greater values result in better quality but larger files The default setting is 80 Bit depth 8 bit Stitching Use Stitch...

Page 90: ...hreshold setting and selection of the area to be scanned Figure 71 Pre scan preview image Threshold options This section is located at right side of the preview window Scanmap Source is designed to set which type of scanmap is used on the preview image This scanmap is displayed automatically in the Profile Scanmap Source setting Selectable scanmap types are the following Use threshold Load previou...

Page 91: ...ea in single layer DAPI with an illumination time of 20ms that is displayed in the Profile Wizard window Scanning process takes a couple of minutes only and cannot be interrupted o Pre scan high resolution creates a High Resolution fast FL preview image of every FOV within the selected area in single layer DAPI with an illumination time of 20ms that is displayed in the Profile Wizard window Scanni...

Page 92: ...ng algorithm Fill holes in scanmap If selected the holes inside the specimen will also be scanned Often these holes contain small sample objects that otherwise would not be scanned Remove specks If selected the scanner does not digitize objects smaller than the predetermined size This helps filtering specks and other uninteresting objects out Set the maximum volume of specks manually in the settin...

Page 93: ...n cannot be identified as required for digitization for example weak contrast it can help to encircle completely the specimen with a black marker pen You have to draw a full circle with the pen to enable the detection Marker pen detection will make specimen detection easier by limiting the scanned area Manual setting of Use marker with threshold If this option is selected only the area encircled w...

Page 94: ... with the preview camera Save scanmap Click this icon to save the currently selected areas to scanmap Position To position the specimen holder that holds the current slide click Position sample and then click on the area of interest on the preview image This will define the Live image that you can access from the Live view Union Add the selected areas to the preview Mark area for scanning based on...

Page 95: ...Figure 75 Edited negative and positive selection masks Crop Crop the area of the selected area Place Circle You can select the area to be scanned with the different tools on the Preview toolbar Place focus point You can add manual focus points on the preview image the coordinates of the manual focus points you add are listed on the Focus settings panel Notice The maximum number of focus points tha...

Page 96: ...id Setting This function is enabled only if a TMA grid has already been placed on the preview image Set grid parameters row and column numbers and spot shape round or rectangle Figure 77 TMA tool Grid selector Delete TMA grid by clicking the X at the top right corner and rotate grid by clicking the icon at the bottom right corner Enter the number of rows and columns in the Rows and Columns fields ...

Page 97: ...and or an orange mask If the Use selection box is enabled and the crop function is selected a black frame displayed in the image and only the area inside the box is scanned It is useful if you only want to scan the area that is equivalent with the size of the coverslip so external specks will not be scanned Figure 78 Use selection box The following colors are used in the preview image to demonstra...

Page 98: ... 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 99: ...splay barcode label area To rotate the label area by 180 click Figure 81 Barcode label area window Undo Redo modification made during specifying the Scanmap These buttons are inactive when Use threshold function is applied 5 2 2 2 Focus indicator Click to activate the Focus indicator function Search for the sharpest focus on the current field of view automatically by clicking Auto focus button ...

Page 100: ...without pre fine focusing To define focus limits select Limits of the range Set the upper and lower limits by selecting the desired value in the selection boxes By using Range the Lower limit value is set to 32 of the current focus value and the Upper limit value is set to 32 of the current focus value This is useful if Auto Focus does not find the focus on the specimen but on the coverslip Also t...

Page 101: ...sity field The defined value will be used as maximum when applying Auto Exposition time if you activate the Max excit intensity option Caution To prevent over exposure the Excitation intensity value can be modified by the software when calculating Auto Exposure time Image Intensity Click to open Image intensity panel An image is defined as a two dimensional function f x y the amplitude of at any p...

Page 102: ...Use Ctrl mouse wheel to zoom in or out to the preview area or the Live image Figure 86 Settings of preview quick toolbar A Quick Toolbar pops up by right clicking any of the control menu items It allows a quick access to main functions and for FL these are the following Drag Draw Erase Retake preview Settings o Toggle deletion always on top o Reset Zoom o Window auto size o Clear Scanmap ...

Page 103: ...oscope functions A quick microscope functions tool can be displayed upon right clicking on the background of the main window outside the preview window It includes quick access buttons to main functions Figure 87 Quick toolset for microscope Autofocus Figure 88 Autofocus Objective type Figure 89 Objective type o 20x o 40x Filters Figure 90 Filters ...

Page 104: ...E ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES Microscope mode o Brightfield o Fluorescence Figure 91 Microscope mode Live tools o Fast mode o Screenshot o Magnifier o Ruler o Image processor plugins o Use pseudo color o Add scanmap Figure 92 Live tools Auto exposure Figure 93 Auto exposure ...

Page 105: ... are linked in a row displayed at the bottom left corner of the main window Figure 94 Progress of the profile modification history Once you are moving the mouse cursor over a unit all the parameters will become visible in a pop up window Figure 95 Details of parameter modification Upon clicking the button for the easier perspicuity modifications can be observed in a pop up window in which both the...

Page 106: ...types for planning scans located under the Preferences Planner Layout Selector menu Slide view with card Table Card collection 5 3 1 General functions at the main menu Microscope Planner selector 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 ...

Page 107: ... loaded for preview taking purposes If you want to retake the preview of the actually loaded slide the Retake Preview function is available from the Quick Toolbar of the preview window Activate Retake Preview for all the slides in the magazine if necessary This operation can be initiated from the slide preview window as well Load Save Plan menu Opens a drop down menu including the following Load p...

Page 108: ...ation type data can be saved to a CSV file Profile management for all the magazines The following profile related tasks applicable for the planner can be performed Add current profile to all racks Open profile for all racks Detach current profile from all racks Detach profiles from racks Clear planner Clear all slide results from every rack Figure 98 Profile management for all the magazines menu J...

Page 109: ...des Detach current profile from all slides Detach profiles from slides Clear all slide results 5 3 3 General functions at the slide menu Mark empty slide positions Define range in the Range to skip boxes to set multiple slide positions as empty For a single slide enter set slide position with the arrows in the Range to skip box or right click on a slide and select Skip Figure 100 General functions...

Page 110: ...ties range to a slide with a profile attached When more profiles are attached to a slide always the last scan record will be set with the selected scan property Figure 101 Scan properties range Click to Open ScanContext selector and click Apply to validate the scan properties settings to all selected slides and related profiles Figure 102 ScanContext selector ...

Page 111: ... card Select from Preferences Appearance settings Planner layout selector to activate this view Depending on the actual view preference selected at slide positions can have a horizontal or vertical layout Slide preview and the list of the assigned profiles are displayed Figure 103 Horizontal Slide view with card Figure 104 Vertical Slide view with card ...

Page 112: ...fferent color o Stored o Edited Scanning mode icon representing Brightfield or Fluorescence mode Objective type Filter channel color bars for FL mode only Scan progress No of scanned FOVs Scan duration Priority scan Slide actual status of the slide is presented here If the slide is under scanning the Scanning if scanning has been interrupted by some error the Failed text is visible If slide status...

Page 113: ...anned to CaseCenter or SlideCenter it can be opened in InstantViewer as well depending on the settings made in Settings Preferences Server scan result viewer 5 3 5 Table view mode By clicking each slide will be displayed in a separate row Click to assign profile to a slide and to detach a profile from a slide A slide can have more than one profile assigned to it and these profiles can either be BF...

Page 114: ...tual slide with the selected profile can be defined o Scan result o Scan duration o Scanned FOVs o Total no of FOVs Profile editor for Scheduler 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 are the same as with the other modes Figure 107 Card collection view mo...

Page 115: ...udes all the profile settings in coherence with the view type of the Profile Setting panel Slide preview is displayed in the Preview window in which the scanmap can be modified until beginning the scanning process Every aforementioned profile setting can be modified depending on the scan profile type being either Brightfield or Fluorescence Figure 108 Selected profile and expanded preview window i...

Page 116: ...visible both in Microscope and Planner modes whenever there is a running hardware operation or scanning procedure Progress content can be therefore different depending on the type of the running procedure Figure 109 Progress data The following information is included in the progress log list during scanning Filter Elapsed time Location Slide name Free space FOV number ...

Page 117: ...6 Settings and Services Activate Settings by clicking and Services by clicking at the right side of the main menu bar 6 1 Settings Activate Settings by clicking at the right side of the main menu bar Preferences This panel contains user settings that have global effect on the GUI and some of its functions Figure 110 Settings ...

Page 118: ... an embedded window External legacy live image is displayed in an external window Default scanner mode selector Microscope or Planner mode Server scan result viewer Opens digital slide with InstantViewer in web browser or SlideViewer or CaseViewer when scanning to server Default illumination mode selector Brightfield or Fluorescence mode Simplified Scan Progress for Brightfield scanning only Scree...

Page 119: ...nditions for barcode reading so to make sure that barcode identification is successful o Rotate barcode image by 180 degrees o Unload slide after planner scan o Enable reloading of magazines with same slide set o Automatic empty slide position detection Slide positions of the magazines to which slides are not loaded into will be detected by the software and slides without including any marking etc...

Page 120: ...ned in this log To enable this function first the database from the following folder must be loaded C ProgramData 3DHISTECH SlideScanner HWLogDataBase The following motor movements are recorded in the log list Camera Changer DFP Light Filter Wheel General Halogen Light Microscope Part Midi Loader ND Objective Changer Preview Light RGB light Relay Scan Loader Service Shutter Slide Scanner Stage ...

Page 121: ...e Name Illumination mode Scan type Scan Start Scan Finished URL Error Figure 111 Scanning log Filtering for the following parameters is available Scanning date Profile name Illumination mode URL Slide name Slide index Rack index General naming settings Naming pattern The set string defines the slide naming pattern shown by the example below the text box Click Reset to set pattern to default The ab...

Page 122: ...Inspect area beyond coverslip edge function a compensation image of the area beyond the coverslip area can be taken Consequently when this function is turned off the area beyond the coverslip is not taken into account by the scanner software when creating the compensation image o For a more comfortable and safer use turn on Planner Autosave function to save a scan plan and by defining a location i...

Page 123: ...rom which the different stages can be reloaded o Save interval Profile content is automatically saved at the specified timeframes o Enable setting of focus time Parameters Short Normal Long related to focus time will be enabled on the profile settings panel Normal is set as default Pre scan settings Figure 114 Pre scan settings Unlike scan settings in Microscope or Planner mode Pre scan toolbar in...

Page 124: ...or opening external applications exe or bat as defined for example CaseViewer or SlideViewer software can be opened after scanning is finished These calls can run only the following scripts o cmd o bat o exe The application cannot handle script languages that are not supported by the Windows Operation System You can define external application call settings for the following cases Slide scanning h...

Page 125: ... SLIDENAME transfers the slide name For Scanning error has occurred ERRORTEXT transfers the error message Notice Pannoramic Scanner Software for Research control software can provide not only the SLIDENAME but the path of the digital slide as well Run defines the window mode that the external application will start in The following window modes can be set Normal window Minimized Maximized You can ...

Page 126: ...play the E mail settings window in which you can dedicate an e mail server through which the software sends e mails to the selected recipients Figure 116 Messenger Setup window In the E mail Settings window the following parameters can be set Message Type E mail Host Address Port E mail Authentication User ID and User password are required Secure Connection SSL If activated the messages will be se...

Page 127: ... Emergency slide functions This panel contains control and maintenance functions o Emerg Position The slide holder will be moved to a position where the slide can be removed manually after opening the cover see chapter 9 5 1 Removing the Protective Covers o Slide removed Click this button to notify the software that you have removed the slide manually PSF settings This panel serves to specify Poin...

Page 128: ... ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES 6 2 Services Activate Services by clicking at the right side of the main menu bar Service password Enter password first to enable service settings for modification Figure 119 Enter service password Camera settings Figure 120 Camera settings ...

Page 129: ...ion Gamma value is not included sRGB standard Color scheme is defined by calibration standard Gamma value 2 2 is applied sRGB standard Microscope Like Color scheme is defined by calibration standard Gamma value White Point D50 Legacy A Color scheme calibrated for the previous software version is applied Custom parameters are freely customizable as follows Color Scheme Calibrated Scheme is defined ...

Page 130: ...the FOVs should extend over o Measure camera rotation Camera rotation angle is measured o Alpha blending The two images are blended o Lower image position Moves the upper image sideways in distinctive steps o Reset all camera rotation Click this button to set camera rotation values to default o Activate PSF generation If activated the Point Spread Function can be generated Follow the steps describ...

Page 131: ... if you insert Penta filters and this type is selected from the Filter type list in the available 10 filter positions in the turret o Move filter wheel to insert position o Enable position Notice Whenever a selected physical filter is disabled the filter itself must be removed from the turret o Select Filter type Filter channel and Filter name o Check Available for scanning o Set Lumencor LED ligh...

Page 132: ...YZ position of the beads can easily be defined in each fluorescent channel To this purpose find the focus pane for the beads in each channel and then click Store X Y position in addition to the Z position Mark the round checkbox in the Reference column to select a filter It is only possible to select a reference filter after finding the related XYZ position Click Grab reference image to grab save ...

Page 133: ...shold settings Therefore the scanner will not use those areas for the creation of the compensation images To modify the threshold settings set the desired threshold value in the box To create the compensation image s click Take Comp image Figure 124 Image compensation window Fluorescent To use the Fluorescent image compensation function take a compensation image and use a compensation slide for ea...

Page 134: ...RCH USE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES Click the Stop button to interrupt the process The progress bar at the bottom of the window displays the progress of the compensation image creation o Export image Save compensation image Figure 125 Compensation images example ...

Page 135: ...ings you enable the Read Barcode option when using the Pannoramic Scanner Software for Research control software To display an image of the barcode area click Grab label image You can redefine the barcode reading area by dragging the edges of the blue square To check whether the barcode reading settings are correct display the barcode digits in the Barcode field by clicking Read Barcode If the lab...

Page 136: ...Barcode reader library Select MIL barcode library or Embedded barcode library o General Barcode settings Inverse barcode color Activate to invert foreground and background colors of the barcode Use barcode compensation A compensation image is used during barcode reading Grab new comp Click this button to create a new compensation image for barcode Notice New compensation image for barcode can be r...

Page 137: ... Erode algorithm is run before barcode reading It is a useful function for reading 2D barcode types since the algorithm completes the scuffed and faded areas of the barcode by applying the morphological erode filter to an image This filter widens and enhances bright areas of the image Exclude check digit Checksum value is ignored when reading Interleaved2of5 and Code39 barcode types Microscope con...

Page 138: ...balance o Save RGB intensity Slide load tester Figure 128 Slide load tester Slide loading operation can be checked for each of the slides in a magazine Click Insert magazine if the prepared magazine or magazines are placed at the bottom of the input guide rails Click Start slide insert test button to launch the process Slides are loaded in but preview image will not be recorded If Magazine counter...

Page 139: ...the beads for the most accurate results II Generate PSF with a third party program III Enter the generated PSF values into the program then deconvolute the sample image IV Start scanning with the deconvolution function activated The complete procedure for preparing to execute the PSF in the control software is as follows 1 In Microscope mode set the appropriate fluorescence parameters according to...

Page 140: ...nce you have finished click Generate PSF button and the Scanner will start recording the image sequence 5 As the last step of setting the deconvolution process load generated PSF results into the software Select the appropriate PSF output for each of the filters in Settings mode under the Browse tab of the PSF settings Enter the number of images in the series that the PSF consist of then select th...

Page 141: ...ode Brightfield Fluorescent Scan Options Focus frequency in Fluorescent mode Focus frequency in Brightfield mode Compression procedure Use of a fixed compensation image in Brightfield mode ON OFF Use of Save focus quality ON OFF Use of Stitching ON OFF Determination of the area to be scanned Use of automatic threshold specimen Use of specimen threshold value Use of marker pen threshold and specime...

Page 142: ...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 Other settings Limitation of focus range ON OFF Enable disable Multilayer options Use of extended focus or Z stack step size and focus level Output resolution ...

Page 143: ...ively on the control computer of the Scanner in the final phase of installation but it can be performed afterwards by launching the control software It then detects that it is in an inactivated status and the activation wizard is opened and activation can be performed either online or offline Online activation 1 For Online activation a reliable internet connection of the server is necessary Intern...

Page 144: ...SE ONLY NOT FOR USE IN DIAGNOSTIC PROCEDURES 2 Activation web page is opened in the embedded browser First accept the EULA then click Continue 3 Enter all the required data for the activation If you do not possess a registration code the Key field may be left blank Click Continue if finished ...

Page 145: ...e installation if the software is activated during installation so the activation is performed and the control software is ready for use Offline activation 1 If the server is not connected to the internet then Offline activation can be selected only To perform offline activation a device with internet connection is needed to be at hand Click Next to continue ...

Page 146: ...he https activation 3dhistech com web page This step is mandatory only if Offline activation was selected Click Upload to browse or drag drop the TXT file 4 On the Activation page accept the EULA then click Continue same as step 2 in Online activation 5 Enter all the required data for the activation If you do not possess a registration code the Key field may be left blank Click Continue if finishe...

Page 147: ...re section of the window Click Next to continue NOTE The Next button turns active only if file upload and validation was successful 10 Upon successful activation the following window is displayed Close installation wizard by clicking Finish If you want to exit the wizard before finishing activation a notification appears If you decide to leave the wizard by clicking Yes the Pannoramic Scanner Soft...

Page 148: ...ate by clicking Yes Figure 129 Recovery confirmation window Warning Click Yes only if you are sure that everything is completely unchanged after the previous run If anything has changed or you are unsure click No For more comfortable and safer use the Planner autosave function allows the taking of automatic backups while creating a scan plan The backups are placed in the default document folder of...

Page 149: ...covering it There is crush hazard during operation in the area of input or output Inserts magazines should be moved through software Never open the device unless prompted accordingly by the software Defective devices do not classify as domestic waste Dispose of the device in compliance with the currently valid legal requirements Lumencor SPECTRA 6 illumination unit NEVER switch on the Lumencor SPE...

Page 150: ...s inserting a deteriorated magazine could lead into unsafe loading of slides 9 3 3 Preventive maintenance To prevent fungus growth Do not leave the equipment in an unconditioned environment with a storage temperature above 60 C 140 F or below 0 C 32 F which may damage the equipment Maximum operating temperature is 35 C 95 F with a relative humidity of less than 75 Install it in a room with proper ...

Page 151: ...rol software 2 Switch off control computer and 24V power supply disconnect power cable 3 Remove protective covers see chapter 9 5 1 Removing the Protective Covers 4 Remove magazine manually If a jammed magazine cannot be removed contact service personnel 5 Reattach protective covers 6 Reconnect 24V power supply and control computer to line power supply 7 Switch on the 24 V power supply 8 Switch on...

Page 152: ...ess is extremely slow Extended focusing option is activated Deactivate the Extended focusing option if not required Z stack option is activated Deactivate the Z stack option if not required Image is out of focus in Manual mode Focus range limit is activated Deactivate the Limiting focus range option Focus range setting is incorrect Change focus range setting All individual images show a shading ef...

Page 153: ...ribed in this manual contact the service personnel 9 5 1 Removing the protective covers The protective covers of the Pannoramic SCAN RX must be opened to perform any maintenance work and also to eliminate errors for example slide or magazine jamming Before removing the covers exit Pannoramic Scanner Software for Research control software switch off the 24 V power supply and disconnect the power ca...

Page 154: ...rk put the covers cover 2 at first then cover 1 back into place and lock them in their positions To do this turn the eccentric screws clockwise A Caution Make sure that no cables of the scan camera are squeezed as you replace the covers 9 5 2 Removing a slide If a slide got jammed or has suffered breakage during the process of digitization stop the process and if possible move the slide holder to ...

Page 155: ...e 131 Removal the slide loader Figure 132 Removing a slide 1 Open the protective cover see chapter 9 5 1 Removing the protective covers 2 Push locking lever 1 to the left and keep the lever in this position 3 Seize the slide loader 2 by the end where the lever is and turn it up by the necessary degree to make the removing of slide possible ...

Page 156: ...ined person 7 Release clamping lever 4 and turn down the slide loader 2 back into the original position and pull it inwardly until the guiding pin connects with the motor block groove again 8 Press the slide loader down to mechanical stop position in which the locking lever must engage 1 Use moderate force to press the loader part opposite the motor in clamp direction 2 until this part mechanicall...

Page 157: ...its handling pads one on the right one on the left lateral side of the module and insert it in forward tilted position from above into the upper spring loaded clamps 1 at the filter wheel Warning Avoid touching the surface of the filters and store the modules in their own boxes when not used 6 Press the filter module down until it safely connects to the bottom spring loaded clamps 2 of the filter ...

Page 158: ... running digitization process terminate the software session and turn off the power supply before removing a jammed magazine Caution Check that the magazine is not tilted so that it rests on both of the horizontal guide rails 2 If the magazine is in horizontal position tilt plate 7 with the drive assembly for horizontal magazine drive motion to the front far enough for the driving gear 5 to diseng...

Page 159: ...r initial position again and the magazine flatly rests on both horizontal guide rails Notice Any manipulation performed on a mechanical component for example transporting system by the user must be followed by a complete Pannoramic SCAN RX initialization routine software restart 9 5 5 Transporting Pannoramic SCAN RX The following procedure shows how to transport the Pannoramic SCAN RX in house For...

Page 160: ...ve the laws of your country regarding load carrying capacity limitations You can find the weight data of the base unit in chapter 10 Technical Data To transport the Pannoramic SCAN RX do the following 1 Turn power supply off and detach all cables 2 Pull carrying handles out 2 until mechanical stop position A 3 Turn carrying handles by 90 B towards the base unit to secure them 4 Now you can transpo...

Page 161: ...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 15 C to 35 C Permissible ...

Page 162: ...nity 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 24V external mains power supply 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 II Radio interferen...

Page 163: ...cent light source 1 optional SOLA U NIR 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 Preview camera Preview camera VRmagic VRmC 8 PRO Sensor CMOS rolling shutter Sensor size Resolution 2056x1544 Pixel size 3 ...

Page 164: ...mount 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 USB 3 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 capac...

Page 165: ...nnectors Trigger output signals exposure busy SMA connectors Data interface USB 3 1 Gen 1 Time stamp in image 1 µs resolution Control computer minimum system requirements 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 Keyboar...

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Summary of Contents for PANNORAMIC SCAN RX 1.1

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3DHISTECH PANNORAMIC SCAN RX 1.1, User Manual, Page: 45 / 165

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Summary of Contents for PANNORAMIC SCAN RX 1.1

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