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3DHISTECH PANNORAMIC SCAN RX 1.1 User Manual

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PANNORAMIC® SCAN RX
1.1
U
'
G
SER
S
UIDE
November 18, 2021 – Rev.1
FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.

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Summary of Contents for 3DHISTECH PANNORAMIC SCAN RX 1.1

  • Page 1 PANNORAMIC® SCAN RX ’ UIDE November 18, 2021 – Rev.1 FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.

  • Page 2: Table Of Contents

    PANNORAMIC® SCAN RX 1.1 CONTENTS Contents Contents Disclaimer Declaration of Conformity About this User's Guide Character Formats and Symbols Notes Regarding Operational Safety Notes on Warranty Terms and Abbreviations Product Description 1.1 Product overview 1.1.1 Intended use 1.1.2 Features and benefits 1.1.3 Warning and information labels 1.1.4...
  • Page 3 PANNORAMIC® SCAN RX 1.1 CONTENTS 4.1.1 Starting the control software 4.1.2 Exiting Pannoramic® Scanner Software for Research control software Main window functions Hotkeys Scanning Modes and Settings Brightfield scanning mode 5.1.1 Profile settings panel 5.1.2 Microscope control panel 5.1.3 Quick preview functions 5.1.4 Quick microscope functions Fluorescence microscope mode...
  • Page 4 PANNORAMIC® SCAN RX 1.1 CONTENTS 9.3.1 Cleaning the device 9.3.2 Cleaning the magazines 9.3.3 Preventive maintenance Troubleshooting 9.4.1 Fluorescent applications (optional) Maintenance 9.5.1 Removing the protective covers 9.5.2 Removing a slide 9.5.3 Installing and removing the filter module (fluorescent option) 9.5.4 Removing the magazine from the transporting system 9.5.5...

  • Page 5: Disclaimer

    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 damage, indirect damage, consequential damage or incidental damage,...
  • Page 6 RF sources), as these may interfere with the proper operation. Third-party disclaimer 3DHISTECH Ltd. is not liable for damage of whatever nature (including, but not limited to, general or specific damage, indirect damage, consequential damage or incidental damage, including...

  • Page 7: Declaration Of Conformity

    DECLARATION OF CONFORMITY Declaration of Conformity 3DHISTECH Ltd. declares that the product Pannoramic® SCAN RX slide scanner is designed and produced with consideration of specified requirements according to the standards listed below: IEC 61010-1:2010, “Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use –...

  • Page 8: About This User's Guide

    This User's Guide is a part of the Pannoramic® SCAN RX system identified by the relevant article numbers included in the 3DHISTECH Ordering Guide. NOVEMBER 18, 2021 FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.

  • Page 9: Character Formats And Symbols

    PANNORAMIC® SCAN RX 1.1 CHARACTER FORMATS AND SYMBOLS Character Formats and Symbols The following character formats and symbols call your attention in this manual: Example (text in bold) Words or characters that appear on the screen. These include field names, screen and window titles, push-button and menu names, paths or options.

  • Page 10: Notes Regarding Operational Safety

    PANNORAMIC® SCAN RX 1.1 NOTES REGARDING OPERATIONAL SAFETY Notes Regarding Operational Safety The below chapter of this User’s Guide contains information and warnings of a kind that must be followed by owner/operator personnel. Warning and advisory symbols which are used on the base unit of the Pannoramic® SCAN RX and in chapter 1.1.3 Warning and Information Labels have the following meanings:...
  • Page 11 If protective devices are found to be ineffective, the Pannoramic® SCAN RX must be shut down and precautions must be taken to prevent unintended usage. For necessary repair work or work to restore proper operating condition, you should contact the 3DHISTECH Customer Service.
  • Page 12 PANNORAMIC® SCAN RX 1.1 NOTES REGARDING OPERATIONAL SAFETY Warning! If a Lumencor SOLA U-NIR fluorescent illumination unit is used, the corresponding warnings included in the manufacturer’s operating manual have to be observed. Warning! A defective Pannoramic® SCAN RX is not classified as domestic waste. It must be properly disposed in accordance with currently valid legal requirements.
  • Page 13 PANNORAMIC® SCAN RX 1.1 NOTES REGARDING OPERATIONAL SAFETY Caution! Do not position the equipment so that it is difficult to operate 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.

  • Page 14: Notes On Warranty

    NOTES ON WARRANTY Notes on Warranty 3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic® SCAN RX to be free from faults in material and workmanship at the moment of installation. Defects must be notified immediately on identification and maximum efforts must be undertaken to minimize the amount of damage as small as possible.

  • Page 15: Terms And Abbreviations

    PANNORAMIC® SCAN RX 1.1 TERMS AND ABBREVIATIONS Terms and Abbreviations Term Description Comma Separated Value Field of View Numerical Aperture Photobleaching A phenomenon that leads to a dramatic loss of fluorescence emission intensity (a fluorophore permanently loses the ability to fluoresce) due to photon-induced chemical damage and covalent modification, therefore fluorescent signals cannot be properly detected.

  • Page 16: Product Description

    PANNORAMIC® SCAN RX 1.1 PRODUCT DESCRIPTION Product Description 1.1 Product overview 1.1.1 Intended use The Pannoramic® SCAN RX is designed to digitize biological samples and specimens (histological sections, typically) using transmitted light microscopy of fluorescence microscopy techniques. Warning! After each scanning make sure to inspect the digital slide for over-exposed areas. If the slide has been scanned based on improperly set parameters, it can highly affect the result because of information loss.
  • Page 17 PANNORAMIC® SCAN RX 1.1 PRODUCT DESCRIPTION • Software-aimed flat-field correction compensation method to create homogeneous slide image • 150-slide automatic loading and scanning • Improved permanent 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 •...

  • Page 18: Warning And Information Labels

    PANNORAMIC® SCAN RX 1.1 PRODUCT DESCRIPTION 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 NOVEMBER 18, 2021 FOR RESEARCH USE ONLY.

  • Page 19: Base Unit

    PANNORAMIC® SCAN RX 1.1 PRODUCT DESCRIPTION Notice: symbol at the feeder area refers to the possibility of exposure to biological hazards whenever handling slides. This symbol is used as the biohazard label because there is no appropriate symbol for this biohazard level. The biological hazard is minimal because the minimally hazardous sample is enclosed between the glass slide and the coverslip.

  • Page 20: System Overview

    PANNORAMIC® SCAN RX 1.1 PRODUCT DESCRIPTION 9. Lumencor illumination adapter 10. Lumencor illumination cable Fluorescent option B 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.

  • Page 21: Hardware Options

    PANNORAMIC® SCAN RX 1.1 PRODUCT DESCRIPTION Lumencor SOLA U-NIR fiber-coupled illumination unit (optional) 24 V external power supply unit Lumencor SPECTRA 6 Light Engine (optional) Monitor Mouse Control computer Keyboard Pannoramic® SCAN RX base unit 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.
  • Page 22 Notice: If Lumencor SPECTRA 6 unit is ordered, the custom light source and filter modules can be variable. For more information, contact 3DHISTECH customer service. NOVEMBER 18, 2021 FOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES.

  • Page 23: Control Software

    PANNORAMIC® SCAN RX 1.1 PRODUCT DESCRIPTION Objectives • Zeiss Plan-Apochromat 10x/NA 0.30 (only FL mode) • Zeiss Plan-Apochromat 20×/NA 0.8 • Zeiss Plan-Apochromat 40× Corr/NA 0.95 Warning! Do not change correction collar settings on 40×/NA objective, if you need it to be set, contact customer service.
  • Page 24 PANNORAMIC® SCAN RX 1.1 PRODUCT DESCRIPTION • 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™...

  • Page 25: Installation

    PANNORAMIC® SCAN RX 1.1 INSTALLATION 2 Installation Warning! The installation of Pannoramic® SCAN RX must be carried out by a trained professional! In any other case the warranty will be automatically voided. The supplier or distributor is not liable for any damages caused by an installation carried out by an unauthorized person. Only qualified service assistants are allowed to install the hardware and software.
  • Page 26 C:\Program Files\3DHISTECH • C:\ProgramData\3DHISTECH • C:\Program Files (x86)\3DHISTECH • (E:\ScannerSwap\ as the SWAP folder by default) We recommend that you use the "SWAP" partition for storing temporary files generated during scanning, as the lack of space required will result in interruption of scanning.

  • Page 27: Control Computer Ports

    PANNORAMIC® SCAN RX 1.1 INSTALLATION 2.2 Control computer ports The following figure shows the location of the connectors to enable easier transportation of the product for a short distance, by disconnecting cables and detaching hardware components from each other. Figure 4. Ports on control computer Status display DVD drive (RW) Power on/off button...

  • Page 28: Connectors And Cables

    All cable connections must be checked for firm seating. Defective cables must not be connected to any part and must be replaced with cables in proper operating condition. Contact 3DHISTECH Support for help in such cases. Caution! It is not recommended to use USB and FireWire cables longer than 2.5 meters.

  • Page 29: Coupling The Lumencor Sola U-Nir Unit With The Scanner

    PANNORAMIC® SCAN RX 1.1 INSTALLATION Warning! Only connect external devices that are safety extra low voltage rated to the instrument to avoid the risk of electrical shock. 2.4 Coupling the Lumencor SOLA U-NIR unit with the scanner To operate the Lumencor SOLA U-NIR fluorescent illumination unit, it has to be connected to the Pannoramic®...

  • Page 30: External Power Supply Unit

    PANNORAMIC® SCAN RX 1.1 INSTALLATION 2.6 External power supply unit For the proper operation of the scanner, the SINPRO – MPU101-108 24V external power supply unit must be connected between the mains power and the device. Front panel: main power switch power supply connector Back panel: detachable power cord to connect the external power supply unit with the main...

  • Page 31: Operating Slides And Magazines

    PANNORAMIC® SCAN RX 1.1 OPERATING SLIDES AND MAGAZINES 3 Operating Slides and Magazines 3.1 Preparing slides and magazines This chapter demonstrates how to prepare slides and magazines. You can use slides and coverslips that meet the following specifications: Slides Cover slips Length 75.0 to 76.0 mm max.
  • Page 32 PANNORAMIC® SCAN RX 1.1 OPERATING SLIDES AND MAGAZINES Warning! Ensure that no part of the mounted coverslip protrudes from the edges of the slide. Use slides with completely dried embedding medium only. Otherwise, the coverslip can be shifted that makes slide insertion less reliable. Not completely dried embedding might also influence the operation of objectives and other device parts.

  • Page 33: Affixing Barcode Stickers To Slides

    PANNORAMIC® SCAN RX 1.1 OPERATING SLIDES AND MAGAZINES 3.2 Affixing barcode stickers to slides This chapter describes how to affix barcode stickers to large slides. Barcodes enable virtual slide identification. Figure 7: Slide with a barcode sticker The label area (1) is recorded by the preview camera and can be displayed by the Pannoramic®...

  • Page 34: Inserting And Removing Slides

    1 of the magazine. Caution! Only original 3DHISTECH magazines are allowed for use with Pannoramic® SCAN RX! To insert or remove a filled magazine from the device, or when transporting it, slightly tilt it to its closed side to prevent the slides from accidentally falling out. Magazines should always be kept clean from dust, broken glass and other mounting media residues.
  • Page 35 PANNORAMIC® SCAN RX 1.1 OPERATING SLIDES AND MAGAZINES To insert and remove magazines Figure 9. Inserting a magazine Warning! Do not reach into the input/output stack movement area of the magazine, while magazines are loaded/unloaded. The flaps (5) shown in Figure 9 must be closed during operation! 1.
  • Page 36 PANNORAMIC® SCAN RX 1.1 OPERATING SLIDES AND MAGAZINES Caution! Make sure that the magazines are not misplaced, because it can cause serious 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.

  • Page 37: Software Description

    PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION 4 Software Description 4.1 Starting/exiting Pannoramic® Scanner Software for Research 4.1.1 Starting the control software To start the program, double-click on the program icon on the desktop. Before software initialization the user interface is opened, and the mode selection icons are displayed.

  • Page 38: Main Window Functions

    PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION 4.2 Main window functions Figure 12. Pannoramic® Scanner Software for Research 1.1 main window The following functions are available for you to select from at the main menu bar: Switch between Microscope and Planner modes Microscope initialization –...
  • Page 39 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION Unload the slide by clicking Unload next to slide image and unload the magazine by clicking Unload all next to the rack image. Set magazine number in the value box at the left of the control bar, then click Change to load another magazine in the feeder. Figure 13.
  • Page 40 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION The following functions are available for you to select from the toolbar: • – Fast Mode Live images are displayed with a frequency of at least 10 images per second. If an exposure time is set to more than 100 ms, the pixel values are multiplied accordingly (for example, if an exposure time of 200 ms is set, the pixel values are multiplied by 2, and the exposure time is reset to 100 ms).
  • Page 41 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION – Scan Properties Unique settings can be defined even for each separate scanning. This function is included on the profile cards as well, added to the slide in Planner mode. • Scan to Local Figure 15.
  • Page 42 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION Click at the left of 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.
  • Page 43 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION • Define/modify ranges within the barcode string when Range is selected at Parsing modes to extract necessary information (Slide name, Profile, Case, Block, Root folder). • If the option Separator is selected at Parsing modes, the character used as a separator in the selected barcode type can be defined in the Separator input field.
  • Page 44 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION Conversion settings • Apply conversion: Turn on to convert the slide to other formats once the scanning has finished. • Keep original MRXS Slide: The original MRXS format of the slide is stored in the local folder.
  • Page 45 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION 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).
  • Page 46 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION DICOM settings Figure 22. DICOM settings ▪ Click Reset to set everything to default. ▪ Frame number maximum (default: 0) ▪ Optical path / frame (default: 3) ▪ Pixel size accuracy (default: 7) ▪ X-Y offset accuracy (default: 5) ▪...
  • Page 47 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION 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. Warning! Make sure that the proper Quant probe (XML file) is selected for the quantification of the slide, as the resulting measurement data will be incorrect.
  • Page 48 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION 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 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION When creating another server connection, define the following details of the server in the Server Editor window: • Display Name • Host Name • Protocol Figure 25. Window of server editor Server Editor stores each of the created server in a list. List entries can be removed, or a new entry can be added if required.
  • Page 50 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION • Slide naming • Barcode parsing: Similar to the settings 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 •...
  • Page 51 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION • EAN-13 • EAN-8 • UPC-A • UPC-E 2D barcode types • Aztec • Data Matrix • PDF417/Compact • Micro PDF417 • • Micro QR • MaxiCode Notice: If embedded barcode library (provided by Vintasoft barcode reader software) is used, refer to Figure 124.
  • Page 52 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION Slide save path • Synchronize server folders: select Folder / Case / Block to synchronize folders. Caution! The current Windows user must have ownership of the destination folder, or, based on the operating system or network system settings write permission must granted for the current user to access the destination folder.
  • Page 53 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION – Start Scan: Scanning of the actual slide or performing the whole previously planned scanning procedure can be initiated. – Stop Scan – Stop actual progress – Take All Previews Figure 28. Take all previews selector Each preview of slides in the tray is taken automatically.
  • Page 54 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION control software automatically saves the preview image of a slide that is loaded 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.
  • Page 55 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION – Open profile Figure 29. Profile browser window The Profile Browser 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.
  • Page 56 PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION Click Search to run search based on the set criteria. Click to make parameters of the selected profile available for editing. Click Reset to restore default parameters. After modification click Save to overwrite existing profile or Save as to create another one. –...

  • Page 57: Hotkeys

    PANNORAMIC® SCAN RX 1.1 SOFTWARE DESCRIPTION 4.3 Hotkeys • Press F1 to open/close hotkeys window • F11 – Enter/Exit fullscreen mode • ESC (in fullscreen mode): Exit from fullscreen mode • CTRL+mousewheel: Zoom in/out • SHIFT+mousewheel: Change Focus by step +36/-36 •...

  • Page 58: Scanning Modes And Settings

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5 Scanning Modes and Settings After microscope initialization, if FL HW option is provided, you can select from the following two modes: • Brightfield scanning mode (See chapter 5.1 Brightfield Scanning Mode for more information.) •...

  • Page 59: Profile Settings Panel

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.1.1 Profile settings panel Objective settings This field displays the objective used for scanning. Figure 33. Objective settings • Objective type 20× or 40× • Output resolution Fix values are: 37× Native for 20× objective, and 73× Native for 40× objective. Focus settings for the scan profile Figure 34.
  • Page 60 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Sample detection This panel offers options for threshold setting and selection of the area to be scanned. Figure 36. Sample detection window • Source: Brightfield preview – a normal type of illumination in the microscope for scanning the slide.
  • Page 61 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Use marker with 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.
  • Page 62 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • Threshold enhancement 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 38.
  • Page 63 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Scanmap A previously saved scanmap can be loaded and applied. • Use Threshold: Preview settings defined in the Microscope Controller Panel / Preview window are applied as the basis of scanmap. • Load scanmap: This function is useful if the slides contain areas of interest that cannot be detected by the preview camera.
  • Page 64 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Figure 39. Focus level and step size • 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.
  • Page 65 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Use Color matrix: Select an applicable preset color profile to be used for Brightfield scanning from the drop-down menu. Settings according to the profile has effect on the color set, color temperature, and gamma value of the scanned image. Separate color matrix can be defined and used for each profile and scanning.

  • Page 66: Microscope Control Panel

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • Use Save compensation image: This function enables the use of previously recorded reference images for all slides. Use this function when the slide is completely covered by the specimen (for example, blood smear) thereby making compensation image capture impossible.
  • Page 67 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 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.
  • Page 68 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Caution! It requires lots of time (since it cannot find focus neither on the edges, nor on specks) to digitize 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.
  • Page 69 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • Manual threshold – Set threshold value manually or calculate value on the actual preview with Calculate Threshold function which is active only if setting the value 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.
  • Page 70 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 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 NOVEMBER 18, 2021 FOR RESEARCH USE ONLY.
  • Page 71 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Preview Toolbar This section is located at the bottom of the preview image. • Save preview – Click this icon to save the image of the slide recorded with the preview camera. •...
  • Page 72 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • Edit – The size of selected area (positive or negative) can be modified at the borderlines or corners. Figure 46. Edited negative and positive selection masks • Crop – Crop the area of the selected area. •...
  • Page 73 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • TMA tool – TMA tool is used for selecting TMA spots on TMA slides. You can set the selection settings on the following four tabs: Figure 47. TMA grid preview • TMA Grid Setting –...
  • Page 74 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • Use selection box restriction – The preview image shows the area that will be digitized with a red 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.
  • Page 75 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Areas that will be scanned These areas are digitized based on user settings (for example, Fill holes in scan area) and not detected by the selected threshold value. Detected sample areas that will be scanned These areas are digitized.
  • Page 76 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Click the button to display barcode label area. To rotate the label area by 180°, click Figure 51: Barcode label area window – Undo / Redo modification made during specifying the Scanmap. These buttons are inactive when Use threshold function is applied.
  • Page 77 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.1.2.2 Exposure indicator Activate Exposure indicator function by clicking . Click to calculate exposure time for the actual Live image. In Brightfield mode there is no option for manually setting the values. Exposure time can be displayed in microsecond, millisecond, and in second. Figure 53.

  • Page 78: Quick Preview Functions

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.1.3 Quick preview functions Use Ctrl+mouse wheel to zoom in or out to the preview area or the Live image. A quick preview function toolset pops up by right-clicking to the preview area. It allows a quick access to main preview-related functions: •...
  • Page 79 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • Autofocus Figure 58. Autofocus • Live tools Figure 59. Live tools Fast mode Screenshot Magnifier Ruler Image processor plugins Add scanmap • Auto exposure Figure 60. Auto exposure NOVEMBER 18, 2021 FOR RESEARCH USE ONLY.

  • Page 80: Fluorescence Microscope Mode

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.2 Fluorescence microscope mode Fluorescence Microscope View consist of three different chapters: • Profile Settings panel: Profile settings containing parameters used for scanning • Microscope Control Panel: Live microscope movement functions • Main functions: Located at below the window header, these functions are identical in both modes.
  • Page 81 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • D: Deconvolution can be activated per channel in this column. Figure 61. Filter table Objective Settings This field displays the objective used for scanning. Objective type: 20×; 40×. Focus Focus settings for the scanning. Focus modes can be the following: •...
  • Page 82 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Figure 62. Focus settings • Auto focus: Focus value is set automatically to match sample characteristics. • Limit the range: You can define focus limits by selecting Limit the range for focusing. You can set the upper and lower limits by selecting the desired value in the selection boxes.
  • Page 83 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 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. Scanning process is initiated with a simple Pre-scan, the located sample with auto threshold is selected, and finally, a Pre-scan in high resolution is launched.
  • Page 84 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Everything within marker To scan everything within the marked area, check the Everything within marker selection box. Alternatively, click in the preview window to activate this function. Figure 63. Scan everything within the marked area (selected / not selected) •...
  • Page 85 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Caution! It requires lots of time (since it cannot find focus neither on the edges, nor on specks) to digitize 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.
  • Page 86 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS To load a mask, click first, then browse for the scanmap to be loaded. • Custom scanmap: The scanmap drawn on the preview image is used for scanning. If the Use selection box restriction function is activated, only the area inside the box is scanned.
  • Page 87 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Figure 67. Focus level and step size Scan settings Figure 68. Scan settings • Change filters after whole slide scanning To optimize speed, filter change should take place after the digitization of the slide with one channel.
  • Page 88 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Caution! If the specimen area is barely visible, it is possible that the Pannoramic® Scanner Software for Research control software will analyze that area as an empty one. • Maximum exposure time – A limit value can be set to determine that the exposure time cannot be longer than the time of focusing and calculation of exposure.
  • Page 89 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Image settings Choose one of the following predefined image formats (and a subsequent custom option) from the Image Quality drop-down list: • Excellent (JPEG: 90) • Good (JPEG: 80) • Medium (JPEG: 60) •...

  • Page 90: Microscope Control Panel

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.2.2 Microscope control panel 5.2.2.1 Preview window Click to open the Preview panel that offers options for threshold 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.
  • Page 91 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Preview Types In FL Microscope mode the following additional preview modes are available: Brightfield preview – a normal type of illumination for scanning. This option is recommended when scanning in Brightfield mode. Pre-scan –...
  • Page 92 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Caution! It requires lots of time (since it cannot find focus neither on the edges, nor on specks) to digitize 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.
  • Page 93 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • Manual threshold Set value manually or calculate value by using the Calculate Threshold function (can be activated only when manual thresholding is selected). 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.
  • Page 94 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Dilate mask Adjust the slider to enlarge or decrease the scanned area. To switch to manual mode, click the top left corner of the button and the required value can be entered in the box Preview Toolbar This section is located at the bottom of the preview image.
  • Page 95 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • – Edit The size of selected area (positive or negative) can be modified at the borderlines or corners. Figure 75. Edited negative and positive selection masks • Crop – Crop the area of the selected area. •...
  • Page 96 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • – Rectangle tool Draw rectangle shaped area. • – Ellipse tool Draw ellipse selection. • – Polygon tool Area selection by defining a polygon shape. Finish area selection by double-clicking with the mouse at or near the starting point. •...
  • Page 97 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • – Clear scanmap The entire scanmap area will be cleared and reset to default. • – Use selection box restriction The preview image shows the area that will be digitized with a red 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.
  • Page 98 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Areas that will be scanned These areas are digitized based on user settings (for example, Fill holes in scan area) and not detected by the selected threshold value. Detected sample areas that will be scanned These areas are digitized.
  • Page 99 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Figure 80. Pseudo-colorized pre-scan image Click the button to display 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.
  • Page 100 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS If you select the Use fine 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 SetI1, SetI2, or SetI3.
  • Page 101 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Select the types of filters you want to use during scanning. You can select the filter types and the number of channels to be used. The values in the EXC column define the excitation of the Lumencor illumination, in TW define exposure time weight, and in the DG the amount of digital gain is displayed.

  • Page 102: Hidden Functions

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Figure 85. Stage positioning panel 5.2.3 Hidden functions 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.

  • Page 103: Quick Microscope Functions

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.2.4 Quick microscope 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 •...
  • Page 104 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • Microscope mode Brightfield Fluorescence Figure 91. Microscope mode • Live tools Fast mode Screenshot Magnifier Ruler Image processor plugins Use pseudo-color Add scanmap Figure 92. Live tools • Auto-exposure Figure 93. Auto-exposure NOVEMBER 18, 2021 FOR RESEARCH USE ONLY.

  • Page 105: Bottom Menu Bar Of The Main Window

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.2.5 Bottom menu bar of the main window Profile History This function can be activated by clicking in Preferences. During setting scanning profile all the previously used parameters will be saved automatically. Each modification in the profile creates a so-called Milestone unit.

  • Page 106: Planner Mode

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.3 Planner mode The whole scanning procedure can be planned in this mode. Assign profiles to slides, modify scan-maps without performing physical loading of slides. In Planner mode not only the scanning of the actually loaded magazine can be planned, but also profile assignment to slides of prepared virtual magazines is available to be performed.
  • Page 107 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Take all previews – Preview images of all the slides in the magazine are taken automatically. Select the required preview type from the following (from top to bottom): Brightfield, Pre-scan, Pre-scan high-resolution, Pre-scan + high-resolution. Figure 97.
  • Page 108 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS Before loading the CSV file, the required settings in the Planner mode must be performed. • Save CSV – Rack number, slide position, slide name, profile name, illumination type data can be saved to a CSV file. Profile management for all the magazines –...

  • Page 109: General Functions At The Magazine Menu

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.3.2 General functions at the magazine menu Rack view mode selector Switch view by clicking the button. Click to add a virtual magazine to the planner, to remove a virtual magazine from the planner. Figure 99.
  • Page 110 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • You can also set Scan properties 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.

  • Page 111: Slide View With Card

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.3.4 Slide view with 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.
  • Page 112 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS By clicking profiles can be added or removed for/from the slide, respectively. The parameters of the assigned profile are displayed in a card. The colors of a Brightfield and a Fluorescence profile cards are different. Figure 105.
  • Page 113 PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • Notes Notice: Once scanning has finished, the thumbnail of the digital slide is added to the card at the bottom. Double click the thumbnail image of the digital slide to open it in Viewer. If scanning is performed to a local destination, the digital slide can be opened in CaseViewer or SlideViewer only, but when scanned to CaseCenter or SlideCenter, it can be opened in InstantViewer™...

  • Page 114: Card Collection View Mode

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS • Objective • Filters (N/A) • Progress • Scan properties: The location of the virtual slide with the selected profile can be defined Scan result Scan duration Scanned FOVs Total no. of FOVs •...

  • Page 115: Profile And Preview Overview On The Planner

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.4 Profile and preview overview on the planner Each of the assigned profiles are checkable and modifiable. The expanding panel at the right side includes all the profile settings, in coherence with the view type of the Profile Setting panel.

  • Page 116: Progress Features

    PANNORAMIC® SCAN RX 1.1 SCANNING MODES AND SETTINGS 5.5 Progress features The progress is 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.

  • Page 117: Settings And Services

    PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES 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. •...
  • Page 118 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES Appearance settings Planner layout editor ▪ Slides with card ▪ Table ▪ Card Collection Initial Preview window position ▪ – Initial position ▪ – Last position ▪ – Center screen Live mode ▪ Rendered –...
  • Page 119 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES Slide settings Unload slide after FL grabbing (N/A) Slide label anonymity – Slide label area is displayed as a clear white image during scanning, patient data will not be visible in CaseViewer or SlideViewer. Do not save label to slide –...
  • Page 120 Scanning History Hardware log Scanner hardware operations are contained 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 ▪...
  • Page 121 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES Software log All the circumstances and states of the slide scanning procedure are saved. LogID is the sequence number of scanning performed on the scanner in use (Profile Name, Illumination mode, Scan type, Scan Start, Scan Finished, URL, Error). Figure 111.
  • Page 122 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES • – Basic settings Figure 112. Basic settings On this panel, you can define the swap file location in the Swap location field, set the value of Shutter auto close time in FL, and define a value in the Number of compensation images the preview camera should take, if needed.
  • Page 123 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES • – Profile behavior settings Figure 113. Profile behavior settings Use profile history save – With this function each profile modification is saved in Profile History from which the different stages can be reloaded. Save interval –...
  • Page 124 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES • – External application call Figure 115. External application call window Two of the three settings are responsible for opening external applications (.exe or .bat) as defined (for example, CaseViewer or SlideViewer software can be opened after scanning is finished).
  • Page 125 You can test whether the Scanning Error Occurred settings work by clicking Caution! If C:\ProgramData\3DHISTECH\SlideScanner\MessengerUserPreferences.xml is missing or damaged, the External application call feature will not be able to read the address book, therefore it will not operate. To solve this issue, the address book must be repaired or created again.
  • Page 126 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES In the Message Call section of the window complex messaging functions can be defined. Here you can setup parameters of the mail server, add or remove users, and set the message body in the Message subject field by entering a text for example, to inform recipients on the location of the scanner, or the slide set you are working with.
  • Page 127 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES • – Report sender settings Figure 117. Report sender settings Add new recipients to the list by clicking + or remove selected from the list by clicking -. To send an example mail to the selected recipient, click .

  • Page 128: Services

    PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES 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 •...
  • Page 129 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES Set Position, Objective type, and Magnification settings of the objective. Use manual camera changer – Changing the cameras is performed manually. Pre-scan objective protection enabled – If activated, slide area near the edges will not be scanned to record fast preview image.
  • Page 130 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES Notice: If Lumencor SPECTRA 6 is configured as illumination unit, the corresponding Enable Lumencor hardware trigger option is displayed on the Filter settings form. Stitching overlap – Set the amount how much the FOVs should extend over. Measure camera rotation –...
  • Page 131 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES On this panel, you can define which filters occupy which turret positions. The actually set filter position is marked at the Current filter hardware position field. Select filter hardware positions from the Filter hardware position: drop-down list. Notice: The maximum number of virtual filters is 50 if you insert Penta filters (and this type is selected from the Filter type list) in the available 10 filter positions in the turret.
  • Page 132 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES • – XYZ-difference This function is available only for fluorescence settings. It can define focus differences among filters to achieve more precise focusing. The XYZ difference feature finds the appropriate XYZ positions when the signal of the different fluorophores colocalize. The refraction of the lens depends on the wavelength of the transmitted light, and it results in different focus points in XYZ for different fluorophores.
  • Page 133 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES Figure 123. Image compensation window (Brightfield) BF cameras field displays the active camera. Currently, there is only one active camera for Brightfield mode. Objectives field displays the objective used for scanning. The Filter for each objective can be set in Fluorescent mode. There might be specks or minor etches on the surface of the compensation slide that require modifying the threshold settings.
  • Page 134 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES 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. Export image – Save compensation image. Figure 125. Compensation images - example NOVEMBER 18, 2021 FOR RESEARCH USE ONLY.
  • Page 135 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES • – Barcode settings Figure 126. Barcode settings By predefining barcode type, foreground color (black or white – the color of the barcode), and other settings, 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.
  • Page 136 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES Click Test run to check that barcode settings are correctly set. Click Reset barcode exposition time to load default exposition time used for barcode reading. Notice: If the figure is not set correctly, or there is no barcode in the barcode area, the software will display the following error message: “Barcode detection unsuccessful! There might be no barcode present.”.
  • Page 137 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES Notice: When having two barcodes on the slide, barcode layout must be consequential. • Resize image – Label image is downsized to 1:4 before barcode reading. • Apply erode algorithm – The 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.
  • Page 138 PANNORAMIC® SCAN RX 1.1 SETTINGS AND SERVICES ▪ Barcode area light ▪ Backlight illumination intensity Objective guide ▪ Step size ▪ X / Y values or navigation arrows ▪ Goto ▪ Goto Preview Origin RGB LED ▪ Set illumination intensity per channel Sync with microscope Calculate white balance Save RGB intensity...

  • Page 139: Point Spread Function

    PANNORAMIC® SCAN RX 1.1 POINT SPREAD FUNCTION 7 Point Spread Function The Point Spread Function (PSF) is a light scattering pattern of the emission of a point-like object interpreted in three-dimensional space. The scanned image is the result of a convolution of the point object and the PSF.
  • Page 140 PANNORAMIC® SCAN RX 1.1 POINT SPREAD FUNCTION 4. Find the focal plane, then use Go within range and + -Range to set how many images the Scanner should take in the Z-direction. (The distance between the two images in Z- direction is 0.2 μm).

  • Page 141: Using Profiles

    PANNORAMIC® SCAN RX 1.1 USING PROFILES 8 Using Profiles Notice: Saved profile settings cannot be applied if using a different type of Pannoramic® scanner. If you want to scan a group of slides, it is advised to save your settings previously in a profile and continue scanning in Automatic mode.
  • Page 142 PANNORAMIC® SCAN RX 1.1 USING PROFILES Fluorescent settings • Filter position(s) • Selected focus channel • Selected stitching channel • Flat field correction (ON/OFF) Intensity statistics Intensity reducing Intensity equalization • Sharpening (ON/OFF) Other settings • Limitation of focus range (ON/OFF) •...

  • Page 143: Troubleshooting And Maintenance

    PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE 9 Troubleshooting and Maintenance 9.1 Activation of the control software The activation of Pannoramic® Scanner Software for Research is required in order to use the service, otherwise the license validation cannot be performed despite possessing a valid Dongle or license file.
  • Page 144 PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE 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.
  • Page 145 PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE 4) Click Next to finalize 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.
  • Page 146 NOTE: The Next button is active only, if the file has successfully been saved. 3) The saved activation request file must be then copied to the device with internet connection, and uploaded to the 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.
  • Page 147 PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE 9) Load this file in the following window (either by clicking Load..., or by drag&drop to the Drop file here... 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.

  • Page 148: Recovery Functions

    TROUBLESHOOTING AND MAINTENANCE If the license file could not be generated due to some reason, the below window appears, and in this case, you must contact 3DHISTECH Support at support@3dhistech.com. 9.2 Recovery functions PSW automated backups allow you to continue scanning after unexpected events within as little time as possible.
  • Page 149 PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE Only plug the device in a socket with protective grounding (earth) contact. Do not operate the device in explosive environment. Disconnect the device from the power outlet before opening it or replacing a part. The product is not equipped with protection against hazardous materials (infectious, toxic, radioactive, corrosive substances or other effects damaging to health).

  • Page 150: Cleaning The Device

    9.4 Troubleshooting This chapter describes the most common troubleshooting solutions for the Pannoramic® SCAN RX product. If any problem arises that does not have solution in this manual, contact 3DHISTECH service support at support@3dhistech.com The product does not start. •...
  • Page 151 Disable Limiting focus range. Poor image quality • Imaging error (for example, chromatic aberrations) • Contact 3DHISTECH Service for support. Warning! Do not modify the camera driver settings, as the default factory settings give the most accurate images. NOVEMBER 18, 2021...

  • Page 152: Fluorescent Applications (Optional)

    TROUBLESHOOTING AND MAINTENANCE Virtual slides show poor stitching in Viewer. • Scan camera is not properly adjusted (for example, due to loose fixture) • Contact 3DHISTECH Service for support. Slide is often positioned incorrectly. • Guiding fault in transport system •...

  • Page 153: Maintenance

    • Lumencor SOLA U-NIR is switched off. • Switch light source on, otherwise contact 3DHISTECH Service for support. 9.5 Maintenance This chapter describes the most common maintenance solutions that can be performed by the user of the product. For maintenance solutions not described in this manual, contact the service personnel.

  • Page 154: Removing A Slide

    PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE Use an open-end wrench (W/F 10) (5) to turn the screws (3) on the lateral sides of the Pannoramic® SCAN RX by 90° anticlockwise, proceeding pairwise (B). Use both hands to take cover (1) carefully off upwards. Caution! Use caution to prevent contact between the safety rails and the scan camera as you take cover off.
  • Page 155 PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE Figure 131. Removal the slide loader Figure 132. Removing a slide Open the protective cover (see chapter 9.5.1 Removing the protective covers). Push locking lever (1) to the left and keep the lever in this position. 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: Installing And Removing The Filter Module (Fluorescent Option)

    PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE Remove slide loader unit. Press clamping lever (4) down. The slide position lock releases. Retrieve slide (3) from the holder. Caution! If the slide is broken, make sure to remove all pieces completely from the device. The edge of the broken area of the slide is sharp and it can lead to injury and contagion! Broken slide can be removed only by a well-trained person! Release clamping lever (4) and turn down the slide loader (2) back into the original...
  • Page 157 PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE Turn off the fluorescent illumination unit. Warning! Crush hazard! Stop the running digitization process and turn off the scanner (refer to chapter 2.7 Power the Scanner On/Off) before you proceed with filter module installation or removal.

  • Page 158: Removing The Magazine From The Transporting System

    PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE 9.5.4 Removing the magazine from the transporting system Figure 134. Removing a magazine Remove the protective covers (see chapter 9.5.1 Removing the Protective Covers). Warning! Crush hazard! Remember to stop the running digitization process, terminate the software session and turn off the power supply before removing a jammed magazine.

  • Page 159: Transporting Pannoramic® Scan Rx

    PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE If the magazine is tilted because of twisted tappets (1), first restore the tappets to their initial position. They are correctly positioned if vertically aligned exactly one above each other. Turn the knurled wheel (4) by hand, until the tappets are in their initial position again and the magazine flatly rests on both horizontal guide rails.
  • Page 160 PANNORAMIC® SCAN RX 1.1 TROUBLESHOOTING AND MAINTENANCE Notice: The base unit has four carrying handles for transporting. Two or four people can carry the base unit using these carrying handles. To determine the appropriate number of transporter people, observe 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.

  • Page 161: Technical Data

    PANNORAMIC® SCAN RX 1.1 TECHNICAL DATA 10 Technical Data Dimensions (width x depth x height) Base unit approx. 740 mm (W) x 530 mm (D) x 450 mm (H) Base unit without fluorescence option approx. 740 mm (W) x 530 mm (D) x 450 mm (H) 24V 100W power supply approx.
  • Page 162 PANNORAMIC® SCAN RX 1.1 TECHNICAL DATA Operating data Intended site closed room facilities Electrical protection class Internal protection degree IP 20 Electrical safety in compliance with IEC 61010-1:2010, IEC 61010-2-081:2015 Over-voltage category Radio interference suppression in accordance with EN 55011 class B Noise immunity in accordance with IEC 61326-2-6:2012 Base unit input voltage...
  • Page 163 PANNORAMIC® SCAN RX 1.1 TECHNICAL DATA Light sources Brightfield illumination Multichannel LED-based with wide Red, Green, Blue emission Average service life ~ 30000 hrs Fluorescent 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)
  • Page 164 PANNORAMIC® SCAN RX 1.1 TECHNICAL DATA Scan cameras Point Grey Grasshopper3 (GS3-U3-51S5M-C) Global Shutter Type CMOS (Sony IMX250) Pixel size 3.45µm × 3.45µm Camera resolution 2448 (H) × 2048 (W) pixel Frames rates 75 fps Bit-depth 10-bit / 12-bit Pixel resolution with 20x objective and 0.63x C-mount 0.27 µm adapter Pixel resolution with 20x objective and 1x C-mount...
  • Page 165 PANNORAMIC® SCAN RX 1.1 TECHNICAL DATA Exposure / shutter time 10 µs .. 20 s Pixel scan rate 46.0 MHz Pixel data rate 184.0 Mpixel/s Region of interest (ROI) horizontal: steps of 32 pixels vertical: steps of 8 pixels Trigger input signals frame trigger, acquire (SMA connectors) Trigger output signals exposure, busy (SMA connectors)

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