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3DHISTECH Ltd. Pannoramic SCAN II 2.0 User Manual

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Pannoramic SCAN II
2.0
User's Guide
June 4, 2018
Rev. 2
PSII123-UG-EN-Rev2
For research and education uses only, not for use in diagnostic procedures.

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Summary of Contents for 3DHISTECH Ltd. Pannoramic SCAN II 2.0

  • Page 1 Pannoramic SCAN II User’s Guide June 4, 2018 Rev. 2 PSII123-UG-EN-Rev2 For research and education uses only, not for use in diagnostic procedures.

  • Page 2: Table Of Contents

    Pannoramic SCAN II 2.0 User’s Guide Contents Disclaimer........................5 Character Formats and Symbols..................7 Declaration of Conformity....................8 Notes Regarding Operational Safety................9 Notes on Warranty......................11 Terms and Abbreviations....................12 1 Product Description....................13 1.1 Product Overview........................13 1.1.1 Intended Use..............................13 1.1.2 Features and Benefits............................13...
  • Page 3 Pannoramic SCAN II 2.0 User’s Guide 5.1.1 Profile Settings Panel.............................47 5.1.2 Microscope Control Panel..........................54 5.1.3 Quick microscope functions..........................65 5.2 Fluorescence Microscope Mode.....................68 5.2.1 Profile Settings panel.............................68 5.2.2 Microscope Control Panel..........................77 5.2.3 Hidden functions............................88 5.2.4 Quick Microscope functions..........................89 5.2.5 Bottom menu bar of the main window......................92 5.3 Planner mode..........................94...

  • Page 4: June

    Pannoramic SCAN II 2.0 User’s Guide Packing the SCAN II scanner......................140 Packing the accessories.......................140 Closing the package........................140 Handling of the package......................141 Index........................... 142 June 4, 2018 - Rev. 2 3DHISTECH Ltd. 4(142) For research and education uses only, not for use in diagnostic procedures.

  • Page 5: Disclaimer

    Pannoramic SCAN II 2.0 User’s Guide Disclaimer Copyright © 2001-2018 3DHISTECH Ltd. All rights reserved. Intellectual property related to the 3DHISTECH products are as follows: EP 1,789,831; US 7,663,078; EP 2,024,772; JP 2009-512685; US 12/301,781; EP 1,644,767; JP 2007- 516451; US7,327,515; EP 1,994,398; JP 2008-557835; US 12/281,566; U0700210; US 6,246,785;...
  • Page 6 Pannoramic SCAN II 2.0 User’s Guide Further Information For the latest information on 3DHISTECH products and services, please visit our website at the following URL: http ://www.3dhistech.com Or contact the distributor: Richard Allan Scientific Co. Subsidiary of Thermo Fisher Scientific...

  • Page 7: Character Formats And Symbols

    Pannoramic SCAN II 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 8: Declaration Of Conformity

    Pannoramic SCAN II 2.0 User’s Guide 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 9: Notes Regarding Operational Safety

    Pannoramic SCAN II 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 section 1.1.3 Warning and Information Labels have the following meanings:...
  • Page 10 Pannoramic SCAN II 2.0 User’s Guide Notes Regarding Operational Safety Check that your local line voltage is compatible with Pannoramic SCAN II Warning! specifications before you turn power on. Remember to unplug the power cord before you open the Pannoramic SCAN II Disconnect plug! main unit for maintenance.

  • Page 11: Notes On Warranty

    Pannoramic SCAN II 2.0 User’s Guide Notes on Warranty Notes on Warranty We at Thermo Fisher Scientific are proud of our quality, reliability and of our after-sales service. We continuously strive to improve our service to our customers. Please ask a Thermo Fisher Scientific representative about Service Contracts which can keep your purchase in peak condition for many years to come.

  • Page 12: Terms And Abbreviations

    Pannoramic SCAN II 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 13: Product Description

    Pannoramic SCAN II 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).
  • Page 14 Pannoramic SCAN II 2.0 User’s Guide 1 Product Description FL scanning with a low noise, 16-bit scientific CMOS pco.edge 4.2 camera • Software-aimed flat-field correction compensation method to create homogenous slide • image 150 slide automatic loading and scanning •...

  • Page 15: Warning And Information Labels

    Pannoramic SCAN II 2.0 User’s Guide 1 Product Description 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 16: Base Unit

    Pannoramic SCAN II 2.0 User’s Guide 1 Product Description 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 17: System Overview

    Pannoramic SCAN II 2.0 User’s Guide 1 Product Description 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 18: Hardware Options

    Pannoramic SCAN II 2.0 User’s Guide 1 Product Description 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 19 Pannoramic SCAN II 2.0 User’s Guide 1 Product Description Warning! The installation of the cameras in Pannoramic SCAN II must be carried out by trained professionals, otherwise the warranty will be automatically voided. The supplier or distributor is not liable for any damages caused by an installation carried out by an unprofessional person.

  • Page 20: Control Software

    Pannoramic SCAN II 2.0 User’s Guide 1 Product Description 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 21 Pannoramic SCAN II 2.0 User’s Guide 1 Product Description TMA module • 3D Reconstruction module • QuantCenter, HistoQuant, NuclearQuant, MembraneQuant, CISHQuant, FISHQuant, and • DensitoQuant modules TumorBoard module • E-School Encoder • June 4, 2018 - Rev. 2 3DHISTECH Ltd.

  • Page 22: Installation

    Pannoramic SCAN II 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 23: Connectors And Cables

    Pannoramic SCAN II 2.0 User’s Guide 2 Installation 1. Status display 2. DVD drive (RW) 3. Power on/off button 4. Earphone and microphone 3.5mm Jack ports 5. 2x USB port 6. Power supply connector 7. PS/2 mouse port 8. PS/2 keyboard port 9.

  • Page 24: Coupling The Lumencor Sola Sm Ii Unit With The Scanner

    Pannoramic SCAN II 2.0 User’s Guide 2 Installation Power supply cable (between 230V/110V and Lumencor SPECTRA 6 unit) • Power supply cable (between 230V/110V and control computer) • Power supply cable (between 230V/110V and external power supply unit) • Power supply cable (between 230V/110V and Lumencor SOLA SM II fluorescent illumination •...
  • Page 25 Pannoramic SCAN II 2.0 User’s Guide 2 Installation 4. Connect TTL trigger cable between pco.edge 4.2 camera (out 4) or Point Grey Grasshopper 3 camera and the Lumencor SPECTRA 6 unit (TTL port), and USB-to-RS232 communication cable between the Lumencor SPECTRA 6 unit and the computer.

  • Page 26: Operating Slides And Magazines

    Pannoramic SCAN II 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 27: Affixing Barcode Stickers To Slides

    Pannoramic SCAN II 2.0 User’s Guide 3 Operating Slides and Magazines Note: The distance between slide edges and the edges of the mounted coverslip should be 1-2 mm, and they should be parallel with each other. Note: Fluorescent signals become more easily detectable for the scanner,...

  • Page 28: Inserting And Removing Slides

    Pannoramic SCAN II 2.0 User’s Guide 3 Operating Slides and Magazines To affix barcode stickers to slides, do the following: 1. Peel off the barcode sticker (2) from the roll. 2. Stick it on the colored label area (1) of the slide, on the specimen side.
  • Page 29 Pannoramic SCAN II 2.0 User’s Guide 3 Operating Slides and Magazines Caution! Incorrect slide insertion may break the glass. Always make sure that slides are correctly inserted in the magazine. The edge of the broken area of the slide is sharp and its removal can lead to injury and contagion! Broken slide can be removed only by a well-trained person! The magazines can contain a maximum of 25 slides.
  • Page 30 Pannoramic SCAN II 2.0 User’s Guide 3 Operating Slides and Magazines To insert and remove magazines Figure 8 – Inserting a magazine Warning! Do not reach into the input/output stack movement area of the magazine, while magazines are loaded/unloaded. The doors must be closed during operation! 1.
  • Page 31 Pannoramic SCAN II 2.0 User’s Guide 3 Operating Slides and Magazines Caution! Make sure that the magazines are not misplaced, because it can cause serious damages in the feeding mechanism. Note: The input stack can be filled with a maximum of 6 magazines in addition to the one in the magazine loader.

  • Page 32: Software Description

    Pannoramic SCAN II 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 \...

  • Page 33: Main Window Functions

    Pannoramic SCAN II 2.0 User’s Guide 4 Software Description 4.2 Main window functions Figure 10 – Pannoramic Scanner 2.0 main window The following functions are available for you to select from at the main menu bar: – Switch between Microscope and Planner modes –...
  • Page 34 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description Upon clicking the slide icon or entering slide position number at the right side, the slide can be loaded. Unload the slide by clicking Unload next to slide image, and unload the magazine by clicking Unload next to the rack image.
  • Page 35 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description an exposure time of 200 ms is set, the pixel values are multiplied by 2, and the exposure time is reset to 100 ms). Therefore the resulting images will have a higher noise level.
  • Page 36 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description Scan separately: The FOV areas of the preview image will be scanned and saved ◦ separately as discrete digital slides. Figure 11 – Scan Properties window Scan to Server • Server: the drop-down list includes all the saved servers. Click Add new item ... to create ◦...
  • Page 37 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description Figure 13 – Window of server editor After loading server data, user name and password is required to be added for authentication and accessing the server. If connection is successful, a green checkmark is displayed in the window.
  • Page 38 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description Figure 14 – Window of Barcode Editor You can select the following barcode types: 1D barcode types *Code 39 ◦ Code 128 ◦ Code 16K ◦ *Interleaved 2 of 5 ◦...
  • Page 39 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description 2D barcode types Aztec ◦ Data Matrix ◦ PDF417/Compact ◦ Micro PDF417 ◦ ◦ Micro QR ◦ MaxiCode ◦ – Start Scan Scanning of the actual slide or performing the whole previously planned scanning procedure can be initiated.
  • Page 40 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description – Open profile 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...
  • Page 41 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description – 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 42 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description Appearance settings View Mode Selector ◦ Text mode ▪ Icon mode ▪ Float Text mode ▪ Float Icon mode ▪ Style selector ◦ Black Jelly ▪ Flat style ▪ Black Jelly P1000 ▪...
  • Page 43 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description Slide settings Take preview automatically – This function is designed to take preview images of slides ◦ automatically, once they are loaded. Unload slide after FL grabbing ◦ Slide label anonymity – Slide label area is displayed as a clear white image during ◦...
  • Page 44 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description Shutter ▪ Slide Scanner ▪ Stage ▪ Waterpump ▪ Software log ◦ All of the circumstances and states of the slide scanning procedure is saved. LogID is the sequence number of scanning performed on the scanner in use. (Profile Name,...
  • Page 45 Pannoramic SCAN II 2.0 User’s Guide 4 Software Description Email Settings An e-mail can be sent automatically about every failure and error that is occurred during scanning to the specified address. The log files are compressed into a ZIP file, that is attached to the mail.

  • Page 46: Scanning Modes And Settings

    Pannoramic SCAN II 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 section 5.1 Brightfield Scanning Mode for more information) •...

  • Page 47: Profile Settings Panel

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 5.1.1 Profile Settings Panel Objective settings This field displays the objective used for scanning. Objective type: 20x; 40x Focus settings for the scan profile Figure 18 – Focus settings for scan profile Limit the range: You can define focus limits by selecting Limit the range for focusing.
  • Page 48 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Thresholding: The manually specified value is used for thresholding during scanning. Preview • image of the loaded slide is displayed in the Preview window, and when modifying any of the parameter values, it will have effect on the preview image.
  • Page 49 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Auto Threshold ◦ By clicking the specimen will automatically be detected in the preview image. Caution! Make sure that the detection result is acceptable for you. Otherwise, set the threshold value manually or append missing areas with the help of appropriate functions in the Preview window.
  • Page 50 Pannoramic SCAN II 2.0 User’s Guide 5 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.
  • Page 51 Pannoramic SCAN II 2.0 User’s Guide 5 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.
  • Page 52 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Z-stack scan mode: Both 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 starting point.
  • Page 53 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 54: Microscope Control Panel

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 55 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 56 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 57 Pannoramic SCAN II 2.0 User’s Guide 5 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.
  • Page 58 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 59 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Figure 27 – Edited negative and positive selection masks. Crop : Crop the area of the selected area. • Place Circle : You can select the area to be scanned with the different tools on the •...
  • Page 60 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 61 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Figure 29 – Preview image The following colors are used in the preview image to demonstrate digitization and selection settings: Figure 30 – Colors in preview image and Label area switching button June 4, 2018 - Rev.
  • Page 62 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 63 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Click the button to display barcode label area. To rotate the label area by 180°, click Figure 31 – Barcode label area window 5.1.2.2 Focus Indicator Click to activate the Focus indicator function. Search for the sharpest focus on the current field of view automatically by clicking - Auto focus button.
  • Page 64 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Image Intensity Click to open Image intensity settings window. 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 65: Quick Microscope Functions

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 5.1.2.5 Quick preview functions Use Ctrl+mouse wheel to zoom in or out to the preview area or the Live image. A quick preview function tool pops up by right-clicking to the preview area. It allows a quick access to...
  • Page 66 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Focus • Figure 38 – Focus Autofocus ◦ Set coarse focus point ◦ Set interpolated focus point 1 ◦ Set interpolated focus point 2 ◦ Set interpolated focus point 3 ◦...
  • Page 67 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Add scanmap ◦ Auto exposure • June 4, 2018 - Rev. 2 3DHISTECH Ltd. 67(142) For research and education uses only, not for use in diagnostic procedures.

  • Page 68: Fluorescence Microscope Mode

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 69 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings E : Multilayer option: Select Extended focus or Z-stack scanning for the required channels in • accordance with the scanning mode set in the profile. Figure 39 – Filter table Objective Settings This field displays the objective used for scanning.
  • Page 70 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings speed up the focusing process. If you deselect the Use fine focus checkbox, the software immediately starts scanning on the basis of the interpolated values, without pre-fine- focusing. Auto focus: Focus value is set automatically to match sample characteristics.
  • Page 71 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Fluorescent PreScan (+HR) - 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 72 Pannoramic SCAN II 2.0 User’s Guide 5 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 40 – Scan everything within the marked area (selected / not selected) Threshold enhancement •...
  • Page 73 Pannoramic SCAN II 2.0 User’s Guide 5 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.
  • Page 74 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 75 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Note: Make sure to select the Change filters at each field of view option if using multi band filter for multi-channel digitization. Caution! If the specimen area is barely visible, it is possible that the software will analyze that area as an empty one.
  • Page 76 Pannoramic SCAN II 2.0 User’s Guide 5 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) •...

  • Page 77: Microscope Control Panel

    Pannoramic SCAN II 2.0 User’s Guide 5 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 44 – Pre-scan preview image Threshold options This section is located at right side of the preview window.
  • Page 78 Pannoramic SCAN II 2.0 User’s Guide 5 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.
  • Page 79 Pannoramic SCAN II 2.0 User’s Guide 5 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.
  • Page 80 Pannoramic SCAN II 2.0 User’s Guide 5 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.
  • Page 81 Pannoramic SCAN II 2.0 User’s Guide 5 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 82 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Figure 48 – Edited negative and positive selection masks Crop : Crop the area of the selected area. • Place Circle : You can select the area to be scanned with the different tools on the •...
  • Page 83 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Figure 49 – TMA tool: Grid selector Delete TMA grid by clicking the X at the top right corner, and rotate grid by clicking the icon at the bottom right corner. Enter the number of rows and columns in the Rows and Columns fields or select the appropriate values with the arrows.
  • Page 84 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 85 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 86 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Figure 53 – Pseudo-colorized pre-scan image 5.2.2.2 Focus Indicator Click to activate the Focus indicator function. Search for the sharpest focus on the current field of view automatically by clicking - Auto focus button.
  • Page 87 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 5.2.2.3 Exposure Indicator Exposure time for the live image can be calculated by using the Calculated Exposure function . It is available to switch between microsecond, millisecond, and second units for the reading of exposure time.

  • Page 88: Hidden Functions

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 5.2.2.4 Stage positioning After clicking you can 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 89: Quick Microscope Functions

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Settings • Toggle delation always on top ◦ Reset Zoom ◦ Window auto-size ◦ Clear Scanmap ◦ 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).
  • Page 90 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Objective type • Figure 61 – Objective type ◦ ◦ Filters • Figure 62 – Filters Microscope mode • Brightfield ◦ Fluorescence ◦ Figure 63 – Microscope mode June 4, 2018 - Rev. 2 3DHISTECH Ltd.
  • Page 91 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Live tools • Fast mode ◦ Screenshot ◦ Magnifier ◦ Ruler ◦ Image processor plugins ◦ Use pseudo-color ◦ Add scanmap ◦ Figure 64 – Live tools Auto-exposure •...

  • Page 92: Bottom Menu Bar Of The Main Window

    Pannoramic SCAN II 2.0 User’s Guide 5 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 of the previously used parameter will be saved automatically.
  • Page 93 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Figure 68 – Profile history tree June 4, 2018 - Rev. 2 3DHISTECH Ltd. 93(142) For research and education uses only, not for use in diagnostic procedures.

  • Page 94: Planner Mode

    Pannoramic SCAN II 2.0 User’s Guide 5 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 95: General Functions At The Main Menu

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 96 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Clear planner • Figure 70 – Planner menu Jump to scanned – Loads the planner view of the actual slide during scanning Preferences Help June 4, 2018 - Rev. 2 3DHISTECH Ltd.

  • Page 97: General Functions At The Magazine Menu

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 5.3.2 General functions at the magazine menu Rack view mode selector Switch view by clicking this button. Click to add a virtual magazine to the planner, and remove a magazine from the planner.

  • Page 98: Slide View With Card

    Pannoramic SCAN II 2.0 User’s Guide 5 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 99 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Figure 73 – Vertical 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 100 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 101: Table View Mode

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 102: Card Collection View Mode

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 103: Profile And Preview Overview On The Planner

    Pannoramic SCAN II 2.0 User’s Guide 5 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 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 104: Progress Features

    Pannoramic SCAN II 2.0 User’s Guide 5 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.
  • Page 105 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Magnification ◦ Use manual camera changer – Changing the cameras is performed manually. ◦ Prescan objective protection enabled – If activated, slide area near the edges will not be ◦...
  • Page 106 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Brightfield ICC Profile ◦ 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.
  • Page 107 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 ▪...
  • Page 108 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Check Available for scanning ◦ Set Lumencor LED light source, set Excitation and Emission wavelength / bandwidth ◦ values for the selected filter. Set Pseudo-color ◦ Select channels used for grayscale conversion ◦...
  • Page 109 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 110 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Grab new comp ▪ Click this button to create a new compensation image for barcode. NOTE: New compensation image for barcode can be recorded only if MIL is used for barcode identification.

  • Page 111: Settings

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 5.6.2 Settings Activate Settings by clicking at the right side of the main menu bar. – Basic settings • On this panel, you can define the swap file location, set shutter auto close time in FL, and create new compensation image for preview camera if needed.
  • Page 112 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and 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).
  • Page 113 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings For Scanning error has occurred: "<ERRORTEXT>" – transfers the • error message Run defines the window mode that the external application will start in. The following window modes can be set: Normal window •...
  • Page 114 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings If you have properly set messenger settings, click Save. • Click Add new user in the Message Call section of the External application call • settings window then enter Display name and Address of the recipient. Select message functions under the Send Message if: field for the selected recipients (from the drop-down list at the top of the section).

  • Page 115: Hosting

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings – Emergency slide operations • 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 section 7.3.1 Opening the protective...
  • Page 116 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Hosting a teleconsultation session 1. Select Hosting from the microscope mode menu 2. Type in your nickname used during the session 3. Click Start hosting 4. The software displays the hosting address and the port number Join teleconsultation as a client 1.

  • Page 117: Using Profiles

    Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings 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 118 Pannoramic SCAN II 2.0 User’s Guide 5 Scanning modes and settings Use of removing specks according to the set value (ON/OFF) • Use saved scan area • Use selection box (ON/OFF) • Fluorescent settings Filter position(s) • Selected focus channel •...

  • Page 119: Troubleshooting And Maintenance

    Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance 6 Troubleshooting and Maintenance 6.1 Safety Information Check cables, plugs and connections before operation, and if defective or cannot be replaced, contact Thermo Fisher Scientific Service for support. Check whether the device is compatible with your local line voltage. It can operate at line voltages 100V to 240V and 50/60 Hz.

  • Page 120: Cleaning The Device

    Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance Lumencor SOLA SM II illumination unit Keep inflammable and combustible materials outside the range of Lumencor SOLA SM II • illumination unit. Do not expose yourself to the UV radiation of the Lumencor SOLA SM II illumination unit.

  • Page 121: Troubleshooting

    Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance 6.2 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 Thermo Fisher Scientific service support.
  • Page 122 Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance Virtual slide is improperly focused almost across its entire surface Focus range enabled • Disable Limiting focus range. • Poor image quality Imaging error (for example, chromatic aberrations) • Contact Thermo Fisher ScientificService for support.

  • Page 123: Fluorescent Applications (Optional)

    Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance Focus range setting is incorrect • Change focus range setting. • All individual images show a shading effect Algorithm failed to find empty image fields • Capture a reference image with a blank slide (see section 4.2.2 Image •...

  • Page 124: Maintenance

    Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance 6.3 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 125: Removing A Slide

    Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance 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 126 Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance Figure 80 – Removing the slide loader Figure 81 – Removing a slide 1. Open the protective cover (see section 5.3.1 Removing the protective covers). 2. Push locking lever (1) to the left, and keep the lever in this position.

  • Page 127: Installing And Removing The Filter Module (Fluorescent Option)

    Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance 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 128 Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance Warning! Crush hazard! Stop the running digitization process before you proceed with filter module installation or removal. 2. Pull protective cover halves apart or remove the right part completely (see section 5.3.1 Removing the protective covers).

  • Page 129: Removing The Magazine From The Transporting System

    Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance 6.3.4 Removing the magazine from the transporting system Figure 83 – Removing a magazine 1. Remove the protective covers (see section 5.3.1 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 130: Transporting Pannoramic Scan Ii

    Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance 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 131 Pannoramic SCAN II 2.0 User’s Guide 6 Troubleshooting and Maintenance 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 132: Technical Data

    Pannoramic SCAN II 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 133 Pannoramic SCAN II 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 134 Pannoramic SCAN II 2.0 User’s Guide 7 Technical Data This User’s Guide describes Lumencor Spectra 6 Light Engine and Lumencor SOLA SM II as light sources. Scan cameras Point Grey Grasshopper3 (GS3-U3-51S5M-C) Global Shutter Type CMOS (Sony IMX250) Pixel size 3.45µm ×...
  • Page 135 Pannoramic SCAN II 2.0 User’s Guide 7 Technical Data Control computer, minimum system requirements Operating System Microsoft Windows 7 Professional SP1 64-bit EN Xeon E5-2609v3 1.90GHz 15MB cache 32 GB DDR4 Hard disk 1.5 TB Optical drive DVD-RW Display 96 dpi Graphics SXGA (1280×1024, True color)

  • Page 136: Appendix - Packaging Instructions

    Pannoramic SCAN II 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 137 Pannoramic SCAN II 2.0 User’s Guide Appendix – Packaging instructions 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 138: Packaging

    Pannoramic SCAN II 2.0 User’s Guide Appendix – Packaging instructions 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 139 Pannoramic SCAN II 2.0 User’s Guide Appendix – Packaging instructions Figure 3. June 4, 2018 - Rev. 2 3DHISTECH Ltd. 139(142) For research and education uses only, not for use in diagnostic procedures.

  • Page 140: Packing The Scan Ii Scanner

    Pannoramic SCAN II 2.0 User’s Guide Appendix – Packaging instructions Packing the SCAN II scanner The most sensitive and most heavy unit is the SCAN II scanner. Please handle it with care, the weight of the device is more than 29 kg.

  • Page 141: Handling Of The Package

    Pannoramic SCAN II 2.0 User’s Guide Appendix – Packaging instructions 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 142: Index

    Pannoramic SCAN II 2.0 User’s Guide Index Index Barcode.....................20, 27, 28, 29, 37, 106, 107 Brightfield........................13, 19, 112, 115 CaseCenter..........................20, 37 Compensation image......................112, 115 Control software....................20, 106, 119, 122, 125 Fluorescent..............13, 18, 19, 20, 24, 27, 115, 116, 121, 125, 130 Focus....................14, 20, 106, 115, 116, 120, 121...

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