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3DHISTECH Pannoramic SCAN II User Manual

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Pannoramic SCAN II
2.2.0
User's Guide
January 24, 2020
Rev. 2
PSII220-UG-EN-Rev2

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Summary of Contents for 3DHISTECH Pannoramic SCAN II

  • Page 1 Pannoramic SCAN II 2.2.0 User’s Guide January 24, 2020 Rev. 2 PSII220-UG-EN-Rev2...

  • Page 2: Table Of Contents

    Pannoramic SCAN II 2.2.0 User’s Guide Contents Disclaimer........................5 About this User's Guide....................7 Character Formats and Symbols..................8 Declaration of Conformity....................9 Notes Regarding Operational Safety................10 Notes on Warranty......................12 Terms and Abbreviations....................13 1 Product Description....................14 1.1 Product Overview........................14...
  • Page 3 Pannoramic SCAN II 2.2.0 User’s Guide 4.1.1 Starting the software............................35 4.1.2 Exiting the software............................36 4.2 Main window functions......................36 5 Scanning modes and settings..................52 5.1 Brightfield Scanning Mode.......................52 5.1.1 Profile Settings Panel............................54 5.1.2 Microscope Control Panel..........................62 5.1.3 Quick preview functions..........................72 5.1.4 Quick microscope functions...........................73...
  • Page 4 Pannoramic SCAN II 2.2.0 User’s Guide 6.4.5 Transporting Pannoramic® SCAN II.......................144 7 Technical Data......................146 Appendix – Packaging instructions................150 Preparations..........................150 Main parts and their accessories....................150 Packaging.............................152 Packing the SCAN II scanner......................154 Packing the accessories.......................154 Closing the package........................154 Handling of the package......................155 Index...........................

  • 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, including the...
  • Page 6 THE SOFTWARE IS PROVIDED “AS IS” AND WITHOUT WARRANTY OF ANY KIND, EXPRESSED, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. Further Information For the latest information on 3DHISTECH products and services, please visit our website at the following URL: http ://www.3dhistech.com.

  • Page 7: About This User's Guide

    Pannoramic SCAN II 2.2.0 User’s Guide About this User's Guide About this User's Guide The purpose of this manual is to assist the user in the safe and reliable operation of the product described. Before operating the device, you must carefully read this instruction manual, and adhere...

  • Page 8: Character Formats And Symbols

    Pannoramic SCAN II 2.2.0 User’s Guide Character Formats and Symbols Character Formats and Symbols Example Words or characters that appear on the screen. These include field names, screen and window titles, pushbutton and menu names, paths or options. Keys on the keyboard. For example, function keys (such as F11) or the Ctrl+M key combination.

  • Page 9: Declaration Of Conformity

    Character Formats and Symbols Declaration of Conformity 3DHISTECH Ltd. declares that the product Pannoramic® SCAN II 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 - Part 1: General Requirements”...

  • Page 10: Notes Regarding Operational Safety

    Pannoramic SCAN II 2.2.0 User’s Guide Notes Regarding Operational Safety Notes Regarding Operational Safety The below section 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 II and in chapter 1.1.3 Warning and Information Labels have the following meanings:...
  • Page 11 Pannoramic SCAN II 2.2.0 User’s Guide Notes Regarding Operational Safety Electric power to the Pannoramic® SCAN II is supplied via an external mains Note: 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...

  • Page 12: Notes On Warranty

    Notes on Warranty Notes on Warranty 3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic® SCAN II 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 in order to the amount of damage as small as possible.

  • Page 13: Terms And Abbreviations

    Pannoramic SCAN II 2.2.0 User’s Guide Terms and Abbreviations Terms and Abbreviations Comma Separated Value Field of View Numerical Aperture Virtual Slide / Slide A digital image of a thin glass plate on which specimens are mounted for microscopic study:...

  • Page 14: Product Description

    Pannoramic SCAN II 2.2.0 User’s Guide 1 Product Description 1 Product Description 1.1 Product Overview 1.1.1 Intended Use The Pannoramic® SCAN II is designed to use transmitted light and reflected light fluorescence to digitize biological samples and specimens (histological sections, typically). The target users of the product can work for example, in education, research, industrial, or medical sectors.
  • Page 15 Pannoramic SCAN II 2.2.0 User’s Guide 1.1.2 Features and Benefits FL scanning with a low-noise, 16-bit scientific CMOS pco.edge 4.2 camera • Software-aimed flat-field correction compensation method to create homogeneous slide • image 150-slide automatic loading and scanning • Improved permanent autofocus •...

  • Page 16: Warning And Information Labels

    Pannoramic SCAN II 2.2.0 User’s Guide 1.1.3 Warning and Information Labels 1.1.3 Warning and Information Labels The following figure contains the labels used on the Pannoramic® SCAN II main unit, the external mains power supply unit, and the Lumencor SOLA SM II illumination unit.

  • Page 17: Base Unit

    Pannoramic SCAN II 2.2.0 User’s Guide 1.1.4 Base Unit 1.1.4 Base Unit The following figure shows the main parts of the base unit. Figure 2 – Main parts of base unit 1. Protective cover 2. Output stack for magazines 3. Input stack for magazines 4.

  • Page 18: System Overview

    Pannoramic SCAN II 2.2.0 User’s Guide 1.2 System Overview 1.2 System Overview The standard scope of delivery of the product includes the following hardware and software components. 1.2.1 Pannoramic® SCAN II system The following figure shows the main parts of the Pannoramic® SCAN II system.

  • Page 19: Hardware Options

    Pannoramic SCAN II 2.2.0 User’s Guide 1.2.1 Pannoramic® SCAN II system 6. Control computer 7. Keyboard 8. Pannoramic® SCAN II base unit 9. Slide magazine with cover 1.2.2 Hardware Options The configuration of the control computer and monitor can vary depending on the product order.
  • Page 20 NOTE: If Lumencor SPECTRA 6 is ordered, the custom light source and filter modules can be variable. For more information, contact 3DHISTECH customer service. Objectives Plan-Apochromat 10×/NA 0.45 (optional, can be used only for FL scanning) •...

  • Page 21: Control Software

    Pannoramic SCAN II 2.2.0 User’s Guide 1.2.2 Hardware Options Fluorescent Options for Pannoramic® SCAN II Fluorescent illumination unit Description Lumencor SOLA SM II Fluorescent illumination unit (can be used with Point Grey Grasshopper 3 camera only) Lumencor SPECTRA 6 Light Engine illumination unit 1.2.3 Control Software...
  • Page 22 Pannoramic SCAN II 2.2.0 User’s Guide 1.2.3 Control Software TMA module • 3D Reconstruction module • QuantCenter, HistoQuant, NuclearQuant, MembraneQuant, CISHQuant, FISHQuant, and • DensitoQuant modules TumorBoard module • E-School Encoder • January 24, 2020 - Rev. 2 3DHISTECH Ltd.

  • Page 23: Installation

    Pannoramic SCAN II 2.2.0 User’s Guide 2 Installation 2 Installation Warning! The installation of the Pannoramic® SCAN II 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.

  • Page 24: Control Computer Ports

    Pannoramic SCAN II 2.2.0 User’s Guide 2 Installation C:\Program Files (x86)\3DHISTECH • (E:\ScannerSwap\ as the SWAP folder by default) • It is also 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 25: Connectors And Cables

    Warning! All cable connections must be checked for firm seating. A defective cable cannot be applied for connection and must be replaced with a cable that is in proper operating condition. Contact 3DHISTECH Service for support in such cases. Caution! It is not recommended to use USB and FireWire cables longer than 2.5...

  • Page 26: Coupling The Lumencor Sola Sm Ii Unit With The Scanner

    Pannoramic SCAN II 2.2.0 User’s Guide 2 Installation USB-to-RS232 serial communication cable (between Lumencor SPECTRA 6 fluorescent • illumination unit and control computer) Warning! Only connect external devices that are safety extra low voltage rated to the instrument to avoid the risk of electrical shock.

  • Page 27: External Power Supply Unit

    Pannoramic SCAN II 2.2.0 User’s Guide 2 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:...

  • Page 28: Operating Slides And Magazines

    Pannoramic SCAN II 2.2.0 User’s Guide 3 Operating Slides and Magazines 3 Operating Slides and Magazines 3.1 Preparing Slides and Magazines This section demonstrates how to prepare slides and magazines. You can use slides and coverslips that meet the following specifications:...
  • Page 29 Pannoramic SCAN II 2.2.0 User’s Guide 3.1 Preparing Slides and Magazines Warning! Ensure that no part of the mounted coverslip protrudes from the edges of the slide. Use slides only with completely dried embedding medium. If not so, the coverslip can be shifted that makes slide loading less reliable.

  • Page 30: Affixing Barcode Stickers To Slides

    Pannoramic SCAN II 2.2.0 User’s Guide 3.2 Affixing Barcode Stickers to Slides 3.2 Affixing Barcode Stickers to Slides This section describes how to affix barcode stickers to slides. Barcodes enable virtual slide identification. Figure 7 – Slide with a barcode sticker The label area is recorded by the preview camera, and can be displayed by the control and viewer software.

  • Page 31: Inserting And Removing Slides

    Pannoramic SCAN II 2.2.0 User’s Guide 3.3 Inserting and Removing Slides 3.3 Inserting and Removing Slides To insert slides into a magazine Figure 8 – Inserting slides into a magazine Caution! Incorrect slide insertion may break the glass. Always make sure that slides are correctly inserted in the magazine.
  • Page 32 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 II! To insert or remove a filled magazine from the device, or when transporting it without its cover (4), slightly tilt it to its closed side to prevent the slides from accidentally falling out.
  • Page 33 Pannoramic SCAN II 2.2.0 User’s Guide 3.3 Inserting and Removing Slides 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 34 Pannoramic SCAN II 2.2.0 User’s Guide 3.3 Inserting and Removing Slides 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 digitization of all slides.

  • Page 35: Software Description

    Pannoramic SCAN II 2.2.0 User’s Guide 4 Software Description 4 Software Description 4.1 Starting / Exiting Pannoramic® Scanner Software 4.1.1 Starting the software To start the program, double-click on the program icon on the desktop or start it from Start \ Program Files \ 3DHISTECH \ Pannoramic Scanner After software initialization the user interface is opened and the mode selection icons are displayed.

  • Page 36: Exiting The Software

    Pannoramic SCAN II 2.2.0 User’s Guide 4.1.2 Exiting the software 4.1.2 Exiting the software To exit the software, Click X at the main window header to close the program. Note, that when exiting the software, the loaded slide will be automatically unloaded.
  • Page 37 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions Slide/magazine control Upon clicking the slide icon or entering slide position number at the right side and clicking Load, the slide can be loaded. Unload the slide by clicking Unload next to slide image, and unload the magazine by clicking Unload all next to the rack image.
  • Page 38 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions 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 39 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions – 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.
  • Page 40 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions 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. If you click Add new item ... on the list, blank input fields will be displayed.
  • Page 41 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions 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. Click to delete range values set for the corresponding field.
  • Page 42 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions Note: MRXS to MRXS conversion will result in an overlap-free final image (tile fitting is performed without overlapping). 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 ◦...
  • Page 43 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions 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 in order ◦ to get the smallest file size possible.
  • Page 44 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions 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. NOTE: The scanner control software is compatible with licensed QuantCenter application only, otherwise the control software may close due to an error.
  • Page 45 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions Scan to Server • Figure 13 – Scan to Server 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 ...
  • Page 46 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions Figure 14 – 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. With the Filters function you can narrow down the results by searching for a specific server data.
  • Page 47 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions 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 •...
  • Page 48 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions Server-side barcode parsing option can be selected if CaseCenter is connected with ▪ 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 is automatically selected as scanning destination based on the CaseID (containing slide and patient data stored on HIS/LIS).
  • Page 49 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions – Take All Previews Each preview of slides in the magazine is taken automatically. Preview types are the following: - Brightfield • - Pre-Scan (FL) • - Pre-Scan High-Resolution (FL) •...
  • Page 50 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions – Open profile Figure 17 – 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 after clicking Create.
  • Page 51 Pannoramic SCAN II 2.2.0 User’s Guide 4.2 Main window functions – Save Profile The selected profile can be saved in this window after typing the profile name into the text field and clicking Save as. – Reset Zoom This function is active only in Live view at 1:1 magnification.

  • Page 52: Scanning Modes And Settings

    Pannoramic SCAN II 2.2.0 User’s Guide 5 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 •...
  • Page 53 Pannoramic SCAN II 2.2.0 User’s Guide 5.1 Brightfield Scanning Mode January 24, 2020 - Rev. 2 3DHISTECH Ltd. 53(156)

  • Page 54: Profile Settings Panel

    Pannoramic SCAN II 2.2.0 User’s Guide 5.1.1 Profile Settings Panel 5.1.1 Profile Settings Panel Objective settings This field displays the objective used for scanning. Objective type • 20x or 40x ◦ Output resolution • Fix values are: 37x Native for 20x objective, and 73x Native for 40x objective.
  • Page 55 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.1 Profile Settings Panel Sample detection This panel offers options for threshold setting and selection of the area to be scanned. January 24, 2020 - Rev. 2 3DHISTECH Ltd. 55(156)
  • Page 56 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.1 Profile Settings Panel Source: Brightfield preview – a normal type of illumination in the microscope for scanning • the slide. This option is recommended when scanning in Brightfield mode. Thresholding: The manually specified value is used for thresholding during scanning. Preview •...
  • Page 57 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.1 Profile Settings Panel Figure 20 – Scan everything within the marked area (selected / not selected) January 24, 2020 - Rev. 2 3DHISTECH Ltd. 57(156)
  • Page 58 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.1 Profile Settings Panel 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.
  • Page 59 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.1 Profile Settings Panel 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.
  • Page 60 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.1 Profile Settings Panel 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 61 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.1 Profile Settings Panel 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) •...

  • Page 62: Microscope Control Panel

    Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel 5.1.2 Microscope Control Panel The Microscope Control panel includes the main control features of the microscope. 5.1.2.1 Preview Window The Preview panel offers options for threshold setting and selection of the area to be scanned.
  • Page 63 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel 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 •...
  • Page 64 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel Warning! Do NOT use Remove coverslip function on TMA slides! The layout of TMA slides may mislead the detecting algorithm. Fill holes inside scanmap : If selected, the holes inside the specimen will also be scanned.
  • Page 65 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel 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.
  • Page 66 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel Preview Toolbar This section is located at the bottom of the preview image. 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 •...
  • Page 67 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel 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.
  • Page 68 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel 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 69 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel Areas that will be scanned These areas are digitized on the basis of user settings (for example, Fill holes in scan area) and not detected by the selected threshold value.
  • Page 70 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel Click the button to display barcode label area. To rotate the label area by 180°, click Figure 32 – Barcode label area window – Undo / Redo modification made during specifying the Scanmap. These buttons are inactive when Use threshold function is applied.
  • Page 71 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel 5.1.2.3 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 also in second.

  • Page 72: Quick Preview Functions

    Pannoramic SCAN II 2.2.0 User’s Guide 5.1.2 Microscope Control Panel Figure 35 – Window of Image Intensity 5.1.2.5 Stage positioning Click to activate Stage Positioning Tool to navigate on the slide, so to perform microscope movements on the Live image with this control function. The number at the center of the controller defines the step size by which the stage is moved.

  • Page 73: Quick Microscope Functions

    Pannoramic SCAN II 2.2.0 User’s Guide 5.1.3 Quick preview functions Figure 37 – Quick toolset 5.1.4 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: January 24, 2020 - Rev.
  • Page 74 Pannoramic SCAN II 2.2.0 User’s Guide 5.1.4 Quick microscope functions Figure 38 – Quick toolset for microscope Autofocus • Live tools • Fast mode ◦ Screenshot ◦ Magnifier ◦ Ruler ◦ Image processor plugins ◦ Add scanmap ◦ Auto exposure •...

  • Page 75: Fluorescence Microscope Mode

    Pannoramic SCAN II 2.2.0 User’s Guide 5.2 Fluorescence Microscope Mode 5.2 Fluorescence Microscope Mode Fluorescence Microscope View consist of three different sections: Profile Settings panel: Profile settings containing parameters used for scanning. • Microscope Control Panel: Live microscope movement functions •...
  • Page 76 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.1 Profile Settings panel E / Z (Multilayer option): Select Extended focus or Z-stack scanning for the required channels • in accordance with the scanning mode set in the profile. D: Deconvolution can activated per channel in this column.
  • Page 77 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.1 Profile Settings panel To delete the stored values, click the other proper focus point or turn off the function. The software calculates a coarse focus level from the three values determined this way as a basis for the fine focusing routine.
  • Page 78 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.1 Profile Settings panel 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.
  • Page 79 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.1 Profile Settings panel 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 40 – Scan everything within the marked area (selected / not selected) Threshold enhancement •...
  • Page 80 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.1 Profile Settings panel 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.
  • Page 81 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.1 Profile Settings panel Multilayer mode Single layer mode: If none of the filters are selected in the Filters table for multilayer • scanning, this mode is active and can be selected, and Multilayer mode turns inactive.
  • Page 82 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.1 Profile Settings panel 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. Change filters at each field-of-view •...
  • Page 83 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.1 Profile Settings panel Image Correction settings Use Flatfield correction – If this function is active the scanned slide compensates itself with a • special method (light intensity statistical data, not to modify the average intensity of the slide.
  • Page 84 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.1 Profile Settings panel Custom... – If choosing this option, the Image compression setting is displayed on which you • can select from different image formats. Accordingly, further adjustments can be made, except if PNG or BMP image format is selected.

  • Page 85: Microscope Control Panel

    Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel 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 44 – Pre-scan preview image Threshold options This section is located at right side of the preview window.
  • Page 86 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel 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.
  • Page 87 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel 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.
  • Page 88 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel 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.
  • Page 89 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel 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 90 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel Edit : The size of selected area (positive or negative) can be modified at the borderlines • or corners. Figure 48 – Edited negative and positive selection masks Crop : Crop the area of the selected area.
  • Page 91 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel TMA Grid 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).
  • Page 92 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel The following colors are used in the preview image to demonstrate digitization and selection settings: Figure 51 – Colors in preview image and Label area switching button Areas that will be scanned These areas are digitized on the basis of user settings (for example, Fill holes in scan area) and not detected by the selected threshold value.
  • Page 93 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel Marker If Scan area inside the marker is selected in the Preview panel, the preview camera detects the marker pen. The inside areas appear in red color and will be digitized.
  • Page 94 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel Click the button to display barcode label area. To rotate the label area by 180°, click Figure 53 – Barcode label area window – Undo / Redo modification made during specifying the Scanmap. These buttons are inactive when Use threshold function is applied.
  • Page 95 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel For manual focusing define the manual focus step size by adjusting the Step size slider and use the two arrow buttons to focus manually. This is useful when you are interested in an area that remained blurry with Auto Focus (for example, the specimen is thicker in that area).

  • Page 96: Hidden Functions

    Pannoramic SCAN II 2.2.0 User’s Guide 5.2.2 Microscope Control Panel 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 pair of coordinates (x, y) is called the intensity or gray level of the image at that point.

  • Page 97: Quick Microscope Functions

    Pannoramic SCAN II 2.2.0 User’s Guide 5.2.3 Hidden functions 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 •...
  • Page 98 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.4 Quick Microscope functions Objective type • Figure 61 – Objective type ◦ ◦ Filters • Figure 62 – Filters Microscope mode • Brightfield ◦ Fluorescence ◦ Figure 63 – Microscope mode January 24, 2020 - Rev. 2 3DHISTECH Ltd.

  • Page 99: Bottom Menu Bar Of The Main Window

    Pannoramic SCAN II 2.2.0 User’s Guide 5.2.4 Quick Microscope functions Live tools • Fast mode ◦ Screenshot ◦ Magnifier ◦ Ruler ◦ Image processor plugins ◦ Use pseudo-color ◦ Add scanmap ◦ Figure 64 – Live tools Auto-exposure • Figure 65 – Auto-exposure 5.2.5 Bottom menu bar of the main window...
  • Page 100 Pannoramic SCAN II 2.2.0 User’s Guide 5.2.5 Bottom menu bar of the main window Once you are moving the mouse cursor over a unit all of the parameters will become visible in a pop- up window. Figure 67 – Details of parameter modification For the easier perspicuity, modifications can be observed in a pop-up window by clicking the button in which both the original and the modified values are presented.

  • Page 101: Planner Mode

    Pannoramic SCAN II 2.2.0 User’s Guide 5.3 Planner mode 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 102: General Functions At The Main Menu

    Pannoramic SCAN II 2.2.0 User’s Guide 5.3.1 General functions at the main menu 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 can be loaded.
  • Page 103 Pannoramic SCAN II 2.2.0 User’s Guide 5.3.1 General functions at the main menu Load / Save Plan menu – Opens a drop-down menu including the following: Load plan – The previously saved scanning plan can be loaded. • Save plan – A scanning plan containing all parameters and profile assignment will be saved.

  • Page 104: General Functions At The Magazine Menu

    Pannoramic SCAN II 2.2.0 User’s Guide 5.3.2 General functions at the magazine menu 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, and remove a magazine from the planner.

  • Page 105: Slide View With Card

    Pannoramic SCAN II 2.2.0 User’s Guide 5.3.3 General functions at the slide menu By default the Current profile is applied, but you can select another profile by clicking Load profile. Click Add selected profile to apply the selected profile to the slides in the range.
  • Page 106 Pannoramic SCAN II 2.2.0 User’s Guide 5.3.4 Slide view with card Figure 73 – Horizontal slide view with card By clicking profiles can be added or removed for/from the slide, respectively. The parameters of the assigned profile is displayed in a card. The colors of a Brightfield and a Fluorescence profile cards are different.
  • Page 107 Pannoramic SCAN II 2.2.0 User’s Guide 5.3.4 Slide view with card The following information are included in a profile card: Profile name in the top left corner • Profile status is marked with spots of different color: • – Stored ◦...
  • Page 108 Pannoramic SCAN II 2.2.0 User’s Guide 5.3.5 Table view mode 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 or FL if the scanner is capable to operate in these two scanning modes.

  • Page 109: Card Collection View Mode

    Pannoramic SCAN II 2.2.0 User’s Guide 5.3.6 Card collection view mode 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 .

  • Page 110: Profile And Preview Overview On The Planner

    Pannoramic SCAN II 2.2.0 User’s Guide 5.4 Profile and Preview overview on the Planner 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 of 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.

  • Page 111: Progress Features

    Pannoramic SCAN II 2.2.0 User’s Guide 5.5 Progress features 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.

  • Page 112: Settings And Service

    Pannoramic SCAN II 2.2.0 User’s Guide 5.6 Settings and Service 5.6 Settings and Service Activate Settings by clicking and Services by clicking at the right side of the main menu bar. 5.6.1 Settings Activate Settings by clicking at the right side of the main menu bar.
  • Page 113 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.1 Settings Appearance settings View Mode Selector ◦ Text mode ▪ Icon mode ▪ Float Text mode ▪ Float Icon mode ▪ Style selector ◦ Black Jelly ▪ Flat style ▪ Black Jelly light ▪...
  • Page 114 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.1 Settings Default illumination mode selector – Brightfield or Fluorescence mode ▪ Simplified Scan Progress (for Brightfield scanning only) Screenshot folder – Set the folder for storing screenshots by clicking Browse. Otherwise the C:\Users\<Username>\Pictures folder is used by default.
  • Page 115 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.1 Settings Camera Changer ▪ DFP Light ▪ Filter Wheel ▪ General ▪ Halogen Light ▪ Microscope Part ▪ Midi Loader ▪ ▪ Objective Changer ▪ Preview Light ▪ RGB Light ▪ Relay ▪...
  • Page 116 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.1 Settings Filtering for the following parameters is available: Scanning date ▪ Profile name ▪ Illumination mode ▪ ▪ 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).
  • Page 117 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.1 Settings – 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 – Profile content is automatically saved at the specified time-frames.
  • Page 118 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.1 Settings – External application call • Two of the three settings are responsible for opening external applications (.exe or .bat) as defined (for example, CaseViewer software can be opened after scanning is finished). These calls can run only the following scripts: ◦...
  • Page 119 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.1 Settings For Slide scanning has finished and Scanning error has occurred you can define the external software by entering the file path in the Application box, or by browsing for it by clicking If you define parameters in the Parameters field, it will pass them to the software that it starts.
  • Page 120 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.1 Settings Figure 79 – Messenger Setup window In the Messenger Setup window the following parameters can be set: Message Type – E-mail • Host Address • Port • E-mail • Authentication – User ID and User password are required.
  • Page 121 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.1 Settings – Emergency slide functions • This panel contains control and maintenance functions. Emerg. position ◦ The slide holder will be moved to a position where the slide can be removed manually after opening the cover (see chapter 6.4.1 Opening the protective covers).

  • Page 122: Service

    Pannoramic SCAN II 2.2.0 User’s Guide 5.6.2 Service 5.6.2 Service Activate Service by clicking at the right side of the main menu bar. – Service password • Enter password first to enable service settings for modification. – Camera settings •...
  • Page 123 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.2 Service PreScan objective protection enabled – If activated, slide area near the edges will not be ◦ scanned to record fast preview image. If inactive, Fast Preview processing becomes slower. Cameras – Activate BF and/or FL mode for the camera. The software automatically loads ◦...
  • Page 124 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.2 Service Current threshold – Set the desired threshold level in the box. ◦ Use selection box – 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.
  • Page 125 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.2 Service 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 ◦...
  • Page 126 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.2 Service – Z-difference This function is available only for fluorescence settings; it enables you to set the basic focus differences between the filters. This facilitates more precise focusing during scanning. – Image compensation •...
  • Page 127 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.2 Service – 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 control software.
  • Page 128 Pannoramic SCAN II 2.2.0 User’s Guide 5.6.2 Service Note: If you did not set the barcode type 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 129: Hosting

    Pannoramic SCAN II 2.2.0 User’s Guide 5.6.2 Service 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. This filter widens and enhances bright areas of the image Exclude check digit –...
  • Page 130 Pannoramic SCAN II 2.2.0 User’s Guide 5.7 Hosting Warning! The user who starts hosting should not touch the hardware after the control has been passed on to avoid personal injury from possible hardware movements (for example, inserting new cassettes or slides, installing fluorescent filters, etc.).

  • Page 131: Using Profiles

    Pannoramic SCAN II 2.2.0 User’s Guide 5.8 Using Profiles 5.8 Using Profiles Note: 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 132 Pannoramic SCAN II 2.2.0 User’s Guide 5.8 Using Profiles Use saved scan area • Use selection box (ON/OFF) • Fluorescent settings Filter position(s) • Selected focus channel • Selected stitching channel • Flat field correction (ON/OFF) • Intensity statistics •...

  • Page 133: Troubleshooting And Maintenance

    Pannoramic SCAN II 2.2.0 User’s Guide 6 Troubleshooting and Maintenance 6 Troubleshooting and Maintenance 6.1 Recovery functions PSW automated backups allow you to continue scanning after unexpected events within as little time as possible. After the program is restarted and the microscope is initialized, you can confirm the automatic restore of pre-event state by clicking Yes.

  • Page 134: Cleaning The Device

    Pannoramic SCAN II 2.2.0 User’s Guide 6.2 Safety Information Slides that are not used any longer do not classify as domestic waste and must be treated as hazardous materials and disposed in compliance with the currently valid legal requirements. Dust, specks and humidity may decrease or harm the operating capability of the device. Protect it with dust cover when not in use.

  • Page 135: Cleaning The Magazine

    • 6.3 Troubleshooting This section describes the most common troubleshooting solutions for the Pannoramic® SCAN II 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 Power supply is interrupted •...
  • Page 136 Pannoramic SCAN II 2.2.0 User’s Guide 6.3 Troubleshooting 7. Switch on the 24 V power supply. 8. Switch on the control computer. 9. Launch control software. Magazine jammed • 1. Exit control software. 2. Switch off control computer and 24V power supply, disconnect power cable.

  • Page 137: Fluorescent Applications (Optional)

    • No suitable exposure time can be found. Signal is too weak. Lumencor SOLA SM II is switched off • Switch light source on, otherwise contact 3DHISTECH Service for support. • January 24, 2020 - Rev. 2 3DHISTECH Ltd. 137(156)

  • Page 138: Maintenance

    Pannoramic SCAN II 2.2.0 User’s Guide 6.4 Maintenance 6.4 Maintenance This section 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 139: Removing A Slide

    Pannoramic SCAN II 2.2.0 User’s Guide 6.4.1 Removing the protective covers Caution! Use caution to prevent contact between the safety rails and the scan camera as you take cover off. 3. Turn eccentric screw at the front of the base plate by 90° anticlockwise and use both hands to carefully raise and take cover (2) off.
  • Page 140 Pannoramic SCAN II 2.2.0 User’s Guide 6.4.2 Removing a slide Figure 82 – Removing the slide loader Figure 83 – Removing a slide 1. Open the protective cover (see chapter 6.4.1 Removing the protective covers). 2. Push locking lever (1) to the left, and keep the lever in this position.

  • Page 141: Installing And Removing The Filter Module (Fluorescent Option)

    Pannoramic SCAN II 2.2.0 User’s Guide 6.4.2 Removing a slide 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...
  • Page 142 Pannoramic SCAN II 2.2.0 User’s Guide 6.4.3 Installing and Removing the Filter Module (Fluorescent Option) 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 143: Removing The Magazine From The Transporting System

    Pannoramic SCAN II 2.2.0 User’s Guide 6.4.4 Removing the magazine from the transporting system 6.4.4 Removing the magazine from the transporting system Figure 85 – Removing a magazine 1. Remove the protective covers (see chapter 6.4.1 Removing the protective covers).

  • Page 144: Transporting Pannoramic® Scan Ii

    Pannoramic SCAN II 2.2.0 User’s Guide 6.4.4 Removing the magazine from the transporting system 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 disengage from the driving worm gear (6).
  • Page 145 Pannoramic SCAN II 2.2.0 User’s Guide 6.4.5 Transporting Pannoramic® SCAN II Caution! Do not use the blue guide rail bar (1) to raise, shift or transport the Pannoramic® SCAN II! Note: The base unit has four carrying handles for transporting. Two or four people can carry the base unit using these carrying handles.

  • Page 146: Technical Data

    Pannoramic SCAN II 2.2.0 User’s Guide 7 Technical Data 7 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 147 Pannoramic SCAN II 2.2.0 User’s Guide 7 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 61010-2-101:2015, IEC 61010-2-081:2015 Over-voltage category Radio interference suppression...
  • Page 148 Pannoramic SCAN II 2.2.0 User’s Guide 7 Technical Data Light sources Brightfield illumination PAX-601-3 Precision-Aligned Pulsed Xenon Light Source Average service life 1 x 10 flashes Fluorescent light source 1 (optional) SOLA SM II 365 (5 solid-state sources producing white light) Wavelength range 350–680 nm...
  • Page 149 Pannoramic SCAN II 2.2.0 User’s Guide 7 Technical Data pco.edge 4.2 13.3 mm × 13.3 mm sCMOS (CIS2020A) Pixel size 6.5 µm x 6.5 µm Camera resolution 2048 x2048 active pixel Camera max. speed 100 fps at full resolution (2048 × 2048 pixel)

  • Page 150: Appendix - Packaging Instructions

    Pannoramic SCAN II 2.2.0 User’s Guide Appendix – Packaging instructions Appendix – Packaging instructions Figure 1. Preparations 1. Unload the slide from the device by using the scanner software. Remove your slide. 2. Close the scanner software normally. 3. Turn off the scanner with the main switch located on the backside of the device. Disconnect all the cables of the scanner.
  • Page 151 Pannoramic SCAN II 2.2.0 User’s Guide Main parts and their accessories 3. BOX 3 – carton box dedicated for the PC a) PC (placed inside the dedicated foam) b) power cable for PC c) power cable for scanner d) USB cable of the scanner...

  • Page 152: Packaging

    Pannoramic SCAN II 2.2.0 User’s Guide Packaging Packaging The whole system is packed in a big carton box. This is divided into two areas with a vertical carton slab: “Space 1” for accessories (PC, cables, etc.) “Space 2” for BOX 2 (scanner) Figure 2.
  • Page 153 Pannoramic SCAN II 2.2.0 User’s Guide Packaging Figure 3. January 24, 2020 - Rev. 2 3DHISTECH Ltd. 153(156)

  • Page 154: Packing The Scan Ii Scanner

    Pannoramic SCAN II 2.2.0 User’s Guide Packing the SCAN II scanner Packing the SCAN II scanner The most sensitive and heaviest unit is the SCAN II scanner. Please handle with care, the device weighs more than 29kg (65 lbs). Place the scanner into the nylon bag.

  • Page 155: Handling Of The Package

    Pannoramic SCAN II 2.2.0 User’s Guide Handling of the package Handling of the package Please be aware to observe the following instructions on Figure 5: Designation Symbol Explanation The package must always be transported, handled and stored in such a way that the arrows always point upwards.

  • Page 156: Index

    Pannoramic SCAN II 2.2.0 User’s Guide Index Index Barcode......................21, 30, 32, 48, 127, 128 Brightfield........................14, 20, 126, 131 CaseCenter..........................21, 48 Compensation image......................126, 131 Control software..................21, 127, 135, 136, 138, 141 Fluorescent............14, 19, 20, 21, 25, 26, 29, 131, 132, 137, 141, 146 Focus.....................15, 21, 94, 126, 131, 132, 136, 137...

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