3D Histech Pannoramic DESK II User Manual
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3D Histech Pannoramic DESK II User Manual

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Pannoramic DESK II
1.22
User's Guide
June 24, 2016
Rev. 1
PDII122-UG-Rev1

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Summary of Contents for 3D Histech Pannoramic DESK II

  • Page 1 Pannoramic DESK II 1.22 User’s Guide June 24, 2016 Rev. 1 PDII122-UG-Rev1...

  • Page 2: Table Of Contents

    3 Preparing Slides......................21 3.1 Affixing Barcode Stickers to Slides...................22 3.2 Inserting and Removing Slides....................23 4 Software Description....................26 4.1 Starting / Exiting Pannoramic DESK II Software Application............26 4.1.1 Starting the software............................26 4.1.2 Exiting the software............................26 4.2 Options.............................26 4.2.1 Barcode Settings.............................27 4.2.2 Image Compensation.............................30...
  • Page 3 Pannoramic DESK II 1.22 User’s Guide 4.3.4 Preview area scanned by preview camera.....................47 4.3.5 Focus tab................................53 4.3.6 Service tab..............................55 4.3.7 Display field and toolbar for live images......................56 4.3.8 Start Scan................................58 4.4 Scan To Server..........................58 4.5 Using Profiles...........................63 5 Troubleshooting and Maintenance................64 5.1 Safety Information........................64...

  • Page 4: Disclaimer

    Pannoramic DESK II 1.22 User’s Guide Disclaimer Copyright © 2001-2016 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 5 Pannoramic DESK II 1.22 User’s Guide Third-Party Disclaimer (LibTIFF – TIFF Library and Utilities) 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 damage...

  • Page 6: Declaration Of Conformity

    Pannoramic DESK II 1.22 User’s Guide Declaration Of Conformity 3DHISTECH Ltd. declares that the product Pannoramic DESK II slide scanner is designed and produced with consideration of specified requirements according to the ISO 13485:2003 and IEC 61326-2- 6:2005 standards, and conforms to the directives and other standards listed below: IEC 61010-1:2001 (ed.

  • Page 7: Character Formats And Symbols

    Pannoramic DESK II 1.22 User’s Guide Character Formats and Symbols Example Words or characters that appear on the screen. These include field names, screen and window titles, push-button 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: 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 DESK II and in the section 1.1.3 Warning and Information Labels have the following meanings:...
  • Page 9 The front door is equipped with an interlock switch. If the door is opened while a Warning! digitization process is running, the process will be stopped instantly. A defective Pannoramic DESK II is not classified as domestic waste. It must be Warning! properly disposed in accordance with currently valid legal requirements.

  • Page 10: Notes On Warranty

    Pannoramic DESK II 1.22 User’s Guide Notes on Warranty 3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic DESK 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 11: Terms And Abbreviations

    Pannoramic DESK II 1.22 User’s Guide 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: a dynamic, interactive image that you can manage, save, magnify, zoom, name, evaluate, annotate, mark and comment, send to a colleague electronically for co- operation or advice, and so on.

  • Page 12: Product Description

    1.1 Product Overview 1.1.1 Intended Use Pannoramic DESK II is designed to use transmitted light 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 13: Warning And Information Labels

    Pannoramic DESK II 1.22 User’s Guide 1 Product Description 1.1.3 Warning and Information Labels The following figure contains the labels used on the Pannoramic DESK II main unit and the external mains power supply unit. Figure 1 – Warning and information labels June 24, 2016 –...

  • Page 14: Base Unit

    Pannoramic DESK II 1.22 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 the base unit 1. Protective cover 2. Sliding door 3. Scan camera June 24, 2016 –...

  • Page 15: System Overview

    The standard scope of delivery of the product includes the following hardware and software items. 1.2.1 Pannoramic DESK II system The following figure shows the main components of the Pannoramic DESK II system. Figure 3 – Pannoramic DESK II system overview 1.

  • Page 16: Hardware Options

    Pannoramic DESK II 1.22 User’s Guide 1 Product Description 1.2.2 Hardware Options The configuration of the control computer and monitor can vary depending on the product order. Cameras Point Grey Grasshopper 3 Color 1 CCD monochrome camera for normal brightfield scanning...
  • Page 17 Pannoramic DESK II Base Brightfield Option – base unit equipped with Point Grey • Grasshopper 3 color camera for Brightfield scanning Pannoramic DESK II Fast Brightfield Option – base unit equipped with Adimec QUARTZ Q- • 12A180 camera for Brightfield scanning Objectives Carl Zeiss Plan-Apochromat 20×/NA 0.8...

  • Page 18: Control Software

    Pannoramic DESK II 1.22 User’s Guide 1 Product Description 1.2.3 Control Software Pannoramic Scanner control software Optional: Extended focus • Z-stack • Barcode reader (licensed feature) • Pannoramic Viewer software (fully functional) Optional: CaseCenter • Pannoramic Viewer TMA module •...

  • Page 19: Installation

    2 Installation 2 Installation Warning! The installation of Pannoramic DESK 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 20: Connectors And Cables

    Pannoramic DESK II 1.22 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 21: Preparing Slides

    Pannoramic DESK II 1.22 User’s Guide 3 Preparing Slides 3 Preparing Slides You can use all large slides and cover slips that meet the following specifications: Slides Cover slips Length 75.0 to 76.0 mm max. 50 mm Width 51.0 to 52.0 mm max.

  • Page 22: Affixing Barcode Stickers To Slides

    Pannoramic DESK II 1.22 User’s Guide 3 Preparing Slides 3.1 Affixing Barcode Stickers to Slides This section describes how to affix barcode stickers to large slides. Barcodes enable virtual slide identification. Figure 5 – Slide with a barcode sticker The label area (1) is recorded by the preview camera, and can be displayed by the control and viewer software.

  • Page 23: Inserting And Removing Slides

    Broken slide can be removed only by a well-trained person! Figure 6 – Inserting and removing a slide 1. Click in Pannoramic DESK II control software. The specimen holder moves to the load/unload position. 2. Open the slide insert door (1) by pushing it to the left.
  • Page 24 Pannoramic DESK II 1.22 User’s Guide 3 Preparing Slides 3. Open the fixing lever (2) by pulling it to the left. 4. Put the slide (4) you want to scan in the specimen holder (3). Note: The cover slip and the label area should be on the top, with the label area pointing towards the slide insert door.
  • Page 25 The preview image is displayed in the preview area of the control software. To remove a slide: 1. Click in Pannoramic DESK II control software. The specimen holder moves to the load/unload position 2. Open the slide insert door (1) by pushing it to the left.

  • Page 26: Software Description

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description 4 Software Description 4.1 Starting / Exiting Pannoramic DESK II Software Application 4.1.1 Starting the software At the startup of the program you can select the manual scanning mode for the scan software.

  • Page 27: Barcode Settings

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description 4.2.1 Barcode Settings Figure 9 – Barcode settings Barcode settings can be modified in the Barcode Settings window. By predefining the 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 28 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Note: You can only scan the barcode type that you have previously set. If you want to read several barcode types, you always have to set the current barcode type before reading it.
  • Page 29 Pannoramic DESK II 1.22 User’s Guide 4 Software Description 1D Barcode Types You can select the following 1D barcode types: *Code 39 • Code 128 • Code 16K • *Interleaved 2 of 5 • Standard 2 of 5 • IATA 2 of 5 •...

  • Page 30: Image Compensation

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description Exclude check digit (default is ON) If activated, the check digit value (last digit of the barcode), an additional checking number of the barcode will also be analyzed as a barcode number.
  • Page 31 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Brightfield Compensation Figure 10 – Brightfield Compensation Camera Selection This field displays the active camera. Currently, there is only one active camera for Brightfield mode. Objective Selection The installed objective is selected for creating a new compensation image.
  • Page 32 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Image Browser panel Figure 11 – Image Browser This function displays the created compensation image. June 24, 2016 - Rev. 1 3DHISTECH Ltd. 32(76)

  • Page 33: Microscope Settings

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description 4.2.3 Microscope Settings By moving the mouse over the buttons, the software displays information about the setting you are interested in. Base Settings Figure 12 – Base settings Objective type You can select the type and the magnification level of the objectives.
  • Page 34 Pannoramic DESK II 1.22 User’s Guide 4 Software Description 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 35 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Filter Settings Figure 13 – Filter settings The settings on this panel apply to Fluorescent mode, therefore irrelevant and inactive. June 24, 2016 - Rev. 1 3DHISTECH Ltd. 35(76)
  • Page 36 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Camera Rotation Figure 14 – Camera rotation Caution! If you have transported the product, or changed the camera, there is a possibility, that the camera does not display the images properly. If you experience such problems, contact service support.

  • Page 37: Event Call Settings

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description 4.2.4 Event Call Settings Figure 15 – Event Call Settings By moving the mouse cursor over the buttons, the software displays information about the setting you are interested in. Two of the three settings are responsible for opening external applications (.exe or .bat) as defined (for example, Pannoramic Viewer software can be opened after...
  • Page 38 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Run defines the window mode that the external application will start in. The following window modes can be set: Normal window • Minimized • Maximized • You can test whether the Scanning Error Occurred settings work by clicking In the Message Call section of the window complex messaging functions can be defined.
  • Page 39 Pannoramic DESK II 1.22 User’s Guide 4 Software Description In the Messenger Setup window the following parameters can be set: Message Type – E-mail (SMTP) • Host Address • Authentication – User ID and User Password are required. • Secure connection (SSL) – If activated, the messages will be sent through secured •...

  • Page 40: Using Brightfield Manual Mode

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description 4.3 Using Brightfield Manual Mode The Brightfield Manual mode is perfect for digitizing slides that require unique settings, or single slides. You can use this mode to set the scanning, preview, and image quality settings. You can also set profile settings here, and start scanning in Brightfield Manual mode.

  • Page 41: Routine Work Tab

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description 4.3.1 Routine work tab Figure 19 – Routine work tab The Routine work tab provides the following basic digitization functions: To insert and remove slides To move the specimen holder to load/unload position, click •...

  • Page 42: Scan Options Window

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description To administer profiles, use the Scan Profiles field. The current profile name is displayed at the bottom left corner of the screen. • To save the current profile, click Save. •...
  • Page 43 Pannoramic DESK II 1.22 User’s Guide 4 Software Description These settings will determine the resulting quality and storage location of the virtual slide. You can choose the following image formats in the Image Encoding field: JPEG – The quality can be adjusted with the JPEG quality factor slider. Greater values result •...

  • Page 44: Preview Tab

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description The Scanned slide destination field determines where to digitize the virtual slides. To be able to choose the Scan To CaseCenter function, you have to install the ScanToServer • application. For information on how to install and use the ScanToServer application, see section 4.4 Scan To...
  • Page 45 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Use threshold Scan specimen with auto threshold – This automatically detects the specimen in the preview • image. Important! Make sure that the detection result is acceptable for you. Otherwise set the threshold value manually or append missing areas with the help of Scanned function located at the preview toolbar.
  • Page 46 Pannoramic DESK II 1.22 User’s Guide 4 Software Description 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 47: Preview Area Scanned By Preview Camera

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description Use saved scan area This function is useful if the slides contain areas of interest that cannot be detected by the preview camera. This function along with saving profiles helps to scan all slides with the most adequate settings.
  • Page 48 Pannoramic DESK II 1.22 User’s Guide 4 Software Description 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. Detected sample areas that will be scanned These areas are digitized.
  • Page 49 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Navigation Tool: This tool offers easy and punctual slide navigation in distinctive steps. Set Step Size (FoV) – 1, ½, or ¼ to determine the size of movement in proportion of one FOV. Click an arrow to move to the required direction with the set step size.
  • Page 50 Pannoramic DESK II 1.22 User’s Guide 4 Software Description TMA tool TMA tool is used for selecting TMA spots on TMA slides. You can set the selection settings on the following four tabs: Select tab Figure 28 – TMA tool: Select To create a new TMA object, click New.
  • Page 51 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Set the type of TMA block on this panel. 1. Select the shape of the TMA spots (Rectangle spots or Circle spots). 2. Enter the number of rows and columns in the Rows and Columns fields or select the appropriate values with the arrows.
  • Page 52 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Figure 31 – TMA tool Move tab with preview June 24, 2016 - Rev. 1 3DHISTECH Ltd. 52(76)

  • Page 53: Focus Tab

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description Label area To rotate the label area by 180°, select the Rotate image by 180 degrees checkbox. Figure 32 – Label area 4.3.5 Focus tab Figure 33 – Focus tab June 24, 2016 - Rev. 1 3DHISTECH Ltd.
  • Page 54 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Live To display a live image of the current specimen in the Live image display field, click . It will work only if you select an area in the preview image with the Position sample.

  • Page 55: Service Tab

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description Figure 34 – Focus level and step size 4.3.6 Service tab Figure 35 – Service tab This tab contains control and maintenance functions. Show images during scanning If you select this option, you will be able to see the currently scanned image field during scanning in the live image display field.

  • Page 56: Display Field And Toolbar For Live Images

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description 4.3.7 Display field and toolbar for live images The display field for live images displays images of the scan camera. The live image is displayed if no current digitization process is running or Show images during scanning option is enabled.
  • Page 57 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Toolbar for live images The toolbar is only available for the displayed live image, but not available for camera images during digitization. – Zoom in • – Zoom out • – One pixel on the monitor corresponds to one pixel on the camera •...

  • Page 58: Start Scan

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description 4.3.8 Start Scan To start digitization process, click after checking all settings. Caution! Before starting digitization process ensure that you have enough free space on the destination drive. You can check the available free disk space in the last line (Available disk space) of the information area of Scan Progress.
  • Page 59 Pannoramic DESK II 1.22 User’s Guide 4 Software Description 2. Select the Scan to CaseCenter option in the Scan Option window, then click Connect. Figure 38 – Scan to CaseCenter option 3. Type in or select the server address from the Connect to: drop-down list, and give the User name and Password.
  • Page 60 Pannoramic DESK II 1.22 User’s Guide 4 Software Description 4. Click the Connect button in the Scan Options window to connect to the server. If the connection is established the server status will be modified from Not connected to Connected.
  • Page 61 Pannoramic DESK II 1.22 User’s Guide 4 Software Description Use masks for automatic fills. Activate the Use mask option and the mask fields • turn fillable. To save masks, click the Save Mask button, then fill the slide data fields. To modify masks click Set Mask.
  • Page 62 Pannoramic DESK II 1.22 User’s Guide 4 Software Description To erase/reset fields to default, click the Reset all button. • If modification is done to the folder tree of the CaseCenter server while the Scan To • Server window is open, click Update Tree to refresh the tree view.

  • Page 63: Using Profiles

    Pannoramic DESK II 1.22 User’s Guide 4 Software Description 4.5 Using Profiles Note: Saved profile settings cannot be applied if using a different type of Pannoramic scanner. The following settings are saved in a profile: Scan Mode Brightfield • Scan Options Focus frequency •...

  • Page 64: Troubleshooting And Maintenance

    Pannoramic DESK II 1.22 User’s Guide 5 Troubleshooting and Maintenance 5 Troubleshooting and Maintenance 5.1 Safety Information Check cables, plugs and connections before operation, and if defective or cannot be replaced, contact 3DHISTECH 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 65: Preventive Maintenance

    • 1. Exit the application software. 2. Switch off the power supply and disconnect the power cable. 3. Remove the protective cover of the Pannoramic DESK II. Follow the steps in section 5.3.1 Removing the protective cover. 4. Remove slide manually (see section 5.3.3 Removing a...

  • Page 66: Replacing The Halogen Lamp

    Pannoramic DESK II 1.22 User’s Guide 5 Troubleshooting and Maintenance 5. Reattach protective covers. 6. Connect power plug and turn power supply on. 7. Launch the scanner software. Black image – Illumination error! Probably the lamp has burned out. Please turn off the scanner...
  • Page 67 Pannoramic DESK II 1.22 User’s Guide 5 Troubleshooting and Maintenance Slide is often positioned incorrectly Guiding fault in transport system • Contact 3DHISTECH Service for support. • Digitization process is extremely slow Extended focusing option is activated • Deactivate the Extended focusing option if not required.

  • Page 68: Maintenance

    To replace the halogen lamp, (or to perform other maintenance work) and to interrupt a running digitization procedure because of slide jamming, the protective cover of the Pannoramic DESK II need to be removed in order to eliminate the problem.

  • Page 69: Removing A Slide

    Pannoramic DESK II 1.22 User’s Guide 5 Troubleshooting and Maintenance 1. Remove both Allen screws (2) located at the left and right sides of the cover (1) by using an Allen screwdriver (3). 2. Carefully push the cover (5) horizontally frontward with light pressure until it can be removed completely from the basic unit (4).
  • Page 70 Pannoramic DESK II 1.22 User’s Guide 5 Troubleshooting and Maintenance Figure 47 – Removing a slide 1. Exit control software. 2. Switch off power supply and disconnect power cable. 3. Remove the cover (see section 5.3.1 Removing the protective cover ).

  • Page 71: Transporting Pannoramic Desk Ii

    5.3.3 Transporting Pannoramic DESK II The following procedure shows how to transport Pannoramic DESK II. Caution! Do not lift or transport Pannoramic DESK II by holding its protective covers! Note: The base unit does not have carrying handles for transporting. One or two persons can carry the base unit by holding it by its base plate.
  • Page 72 Pannoramic DESK II 1.22 User’s Guide 6 Technical Data 6 Technical Data Dimensions (width x depth x height) Base unit approx. 266 mm (W) x 306 mm (D) x 249 mm (H) 24V 100W power supply approx. 189 mm x 90 mm x 44 mm...
  • Page 73 Pannoramic DESK II 1.22 User’s Guide 6 Technical Data Operating data Intended site closed room facilities Electrical protection class Internal protection degree IP 20 Electrical safety in compliance with DIN EN 61010-1:2001, DIN EN 61010-2- 101:2002 (IEC 61010-1:2001, IEC 61010-2-101:2002)

  • Page 74: Technical Data

    Pannoramic DESK II 1.22 User’s Guide 6 Technical Data Slide identification Slides are identified by a VRmagic VRmC-8+ PRO preview camera. Label area is saved as an image and the barcode is interpreted as a character string. Scan cameras Adimec QUARTZ Q-12A180 camera Global Shutter CMOS Pixel size5.5µm ×...
  • Page 75 Pannoramic DESK II 1.22 User’s Guide 6 Technical Data Control computer, minimum system requirements Operating System Microsoft Windows 7 SP1 64-bit EN Intel Core i5-4590 8 GB DDR3-1600 Hard disk 1 TB Optical drive DVD-RW Display 96 dpi Graphics SXGA (1280 × 1024, True color)

  • Page 76: Index

    Marker..........................45, 48, 63 Pannoramic............................6 Pannoramic DESK II........6, 8, 9, 10, 12, 13, 15, 17, 19, 23, 25, 26, 65, 68, 72, 73 Pannoramic Viewer......................18, 54, 65, 66 Preview............20, 22, 24, 26, 31, 40, 44, 45, 46, 47, 48, 49, 51, 52, 54, 76 RGB..............................57...

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