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3D Histech Pannoramic DESK User Manual

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Pannoramic DESK
1.18.1
User's Guide
May 29, 2014
Rev. 1
PD1.18.1-UG-Rev1

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Summary of Contents for 3D Histech Pannoramic DESK

  • Page 1 Pannoramic DESK 1.18.1 User’s Guide May 29, 2014 Rev. 1 PD1.18.1-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 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 1.18.1 User’s Guide 4.3.4 Preview area scanned by preview camera.....................46 4.3.5 Focus tab................................52 4.3.6 Service tab..............................54 4.3.7 Display field and toolbar for live images......................55 4.3.8 Start Scan................................57 4.4 Scan To Server..........................57 4.5 Using Profiles...........................62 5 Troubleshooting and Maintenance................63 5.1 Safety Information........................63...

  • Page 4: Disclaimer

    Pannoramic DESK 1.18.1 User’s Guide Disclaimer Copyright © 2001-2014 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 1.18.1 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 1.18.1 User’s Guide Declaration Of Conformity 3DHISTECH Ltd. declares that the product Pannoramic DESK 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 1.18.1 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 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 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 1.18.1 User’s Guide Notes on Warranty 3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic DESK 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 1.18.1 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 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 1.18.1 User’s Guide 1 Product Description 1.1.3 Warning and Information Labels The following figure contains the labels used on the Pannoramic DESK main unit and the external mains power supply unit. Figure 1 – Warning and information labels May 29, 2014 –...

  • Page 14: Base Unit

    Pannoramic DESK 1.18.1 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. Protection rail 3. Scan camera 4.

  • Page 15: System Overview

    The standard scope of delivery of the product includes the following hardware and software items. 1.2.1 Pannoramic DESK system The following figure shows the main components of the Pannoramic DESK system. Figure 3 – Pannoramic DESK system overview 1. 24 V external power supply unit 2.

  • Page 16: Hardware Options

    Pannoramic DESK 1.18.1 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 Stingray F146C IRF Medical camera 1 CCD camera for normal brightfield application. CIS VCC-FC60FR19CL CMOS camera for high-quality brightfield applications allowing fast scanning.

  • Page 17: Control Software

    The supplier or distributor is not liable for any damages caused by an installation carried out by an unauthorized person. Base Unit options Pannoramic DESK Basic Scan Option / Fast Option – base unit equipped with Stingray F146C • IRF or CIS VCC-FC60FR19CL camera for Brightfield scanning Objectives Carl Zeiss Plan-Apochromat 20×/NA 0.8...
  • Page 18 Pannoramic DESK 1.18.1 User’s Guide 1 Product Description Pannoramic Viewer software (fully functional) Optional: CaseCenter • Pannoramic Viewer TMA module • 3D Reconstruction module • QuantCenter, HistoQuant, NuclearQuant, MembraneQuant, and DensitoQuant modules • TumorBoard module • E-School Encoder • May 29, 2014 – Rev. 1 3DHISTECH Ltd.

  • Page 19: Installation

    2 Installation 2 Installation Warning! The installation of Pannoramic DESK 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 1.18.1 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 1.18.1 User’s Guide 3 Preparing Slides 3 Preparing Slides You can use all slides and cover slips that meet the following specifications: Slides Cover slips Length 75.0 to 76.2 mm max. 50 mm Width 25.0 to 26.0 mm max.

  • Page 22: Affixing Barcode Stickers To Slides

    Pannoramic DESK 1.18.1 User’s Guide 3 Preparing Slides 3.1 Affixing Barcode Stickers to Slides This section describes how to affix barcode stickers to 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 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 1.18.1 User’s Guide 3 Preparing Slides Note: The cover slip and the label area should be on the top, with the label area pointing towards the slide insert door. Warning! To avoid jamming or breaking slides, ensure that the slide is not tilted and that it rests perfectly horizontally on the specimen holder.
  • Page 25 3 Preparing Slides To remove a slide: 1. Click in Pannoramic DESK control software. The specimen holder moves to the load/unload position 2. Open the slide insert door (1) by pushing it to the left. 3. Open the fixing lever (2) by pulling it to the left.

  • Page 26: Software Description

    Pannoramic DESK 1.18.1 User’s Guide 4 Software Description 4 Software Description 4.1 Starting / Exiting Pannoramic DESK 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 1.18.1 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 1.18.1 User’s Guide 4 Software Description Functions To move the specimen holder to load/unload position, click . You can replace • the slide when it is in this position. Caution! Ensure that the slide is not tilted, and that it rests perfectly horizontally on the stage.
  • Page 29 Pannoramic DESK 1.18.1 User’s Guide 4 Software Description 2D Barcode Types You can select the following 2D barcode types: Data Matrix • PDF417 • MicroPDF417 • Maxicode • QR code • 1D barcodes with check digit (CDV) You can select the following 1D barcodes with check digit (CDV): Code 39 •...

  • Page 30: Image Compensation

    Pannoramic DESK 1.18.1 User’s Guide 4 Software Description 4.2.2 Image Compensation You can use a saved compensation image whenever compensation-related issues occur (deriving from the slide, illumination, staining or embedding medium irregularities). To set compensation parameters properly, follow the instructions below.

  • Page 31: Microscope Settings

    Pannoramic DESK 1.18.1 User’s Guide 4 Software Description Use Selection Box • Select this if you have a compensation slide that has only certain predefined areas for creating compensation images (due to the type of the compensation slide, or because the compensation slide has faded in some areas).
  • Page 32 Pannoramic DESK 1.18.1 User’s Guide 4 Software Description Base Settings Figure 12 – Base settings Objective type You can select the type and the magnification level of the objectives. Camera type Select the correct camera type in Pos. 1: Camera type, then the software automatically loads the camera settings upon clicking the Test and Apply Camera Settings button.
  • Page 33 Pannoramic DESK 1.18.1 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. May 29, 2014 - Rev. 1 3DHISTECH Ltd. 33(77)
  • Page 34 Pannoramic DESK 1.18.1 User’s Guide 4 Software Description Camera Rotation Figure 14 – Camera rotation May 29, 2014 - Rev. 1 3DHISTECH Ltd. 34(77)
  • Page 35 Pannoramic DESK 1.18.1 User’s Guide 4 Software Description 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. Do not modify these settings yourself.

  • Page 36: Event Call Settings

    Pannoramic DESK 1.18.1 User’s Guide 4 Software Description 4.2.4 Event Call Settings Figure 16 – External Application Call Settings 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 scanning is finished).
  • Page 37 Pannoramic DESK 1.18.1 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 .
  • Page 38 Pannoramic DESK 1.18.1 User’s Guide 4 Software Description Secure connection (SSL) – If activated, the messages will be sent through secured • connection. Send Test e-mail – Click this button to send test e-mail to the specified address. • There are 2 feedback messages that come up after sending the e-mail: “An e-mail has been sent to the recipient.”...

  • Page 39: Using Brightfield Manual Mode

    Pannoramic DESK 1.18.1 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 40: Routine Work Tab

    Pannoramic DESK 1.18.1 User’s Guide 4 Software Description 4.3.1 Routine work tab Figure 20 – 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 41: Scan Options Window

    Pannoramic DESK 1.18.1 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. • To select an existing profile from the selection menu, click Load.
  • Page 42 Pannoramic DESK 1.18.1 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 43: Preview Tab

    Pannoramic DESK 1.18.1 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 44 Pannoramic DESK 1.18.1 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 45 Pannoramic DESK 1.18.1 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 46: Preview Area Scanned By Preview Camera

    Pannoramic DESK 1.18.1 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 47 Pannoramic DESK 1.18.1 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 48 Pannoramic DESK 1.18.1 User’s Guide 4 Software Description You can select the area to be scanned with the different tools on the toolbar: Square tool • Ellipse tool • Polygon tool: you can finish the selection process with the polygon tool by •...
  • Page 49 Pannoramic DESK 1.18.1 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 29 – TMA tool: Select To create a new TMA object, click New.
  • Page 50 Pannoramic DESK 1.18.1 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 51 Pannoramic DESK 1.18.1 User’s Guide 4 Software Description Move tab The Move tab allows the rotation and moving of the TMA selection spots that are displayed on the preview image. To move the spots enter the pixel value in the Move field or use the arrows.

  • Page 52: Focus Tab

    Pannoramic DESK 1.18.1 User’s Guide 4 Software Description Label area To rotate the label area by 180°, select the Rotate image by 180 degrees checkbox. Figure 33 – Label area 4.3.5 Focus tab Figure 34 – Focus tab May 29, 2014 - Rev. 1 3DHISTECH Ltd.
  • Page 53 Pannoramic DESK 1.18.1 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 54: Service Tab

    Pannoramic DESK 1.18.1 User’s Guide 4 Software Description Figure 35 – Focus level and step size 4.3.6 Service tab Figure 36 – Service tab This tab contains control and maintenance functions. Emergency Manual Slide Removal Position The specimen holder will be moved to a position where the slide can be removed manually after opening the cover (see section 5.3.1 Removing the protective cover ).).

  • Page 55: Display Field And Toolbar For Live Images

    Pannoramic DESK 1.18.1 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 56 Pannoramic DESK 1.18.1 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 57: Start Scan

    Pannoramic DESK 1.18.1 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 Current Slide Scan Progress.
  • Page 58 Pannoramic DESK 1.18.1 User’s Guide 4 Software Description 2. Select the Scan to CaseCenter option in the Scan Option window, then click Connect. Figure 39 – 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 59 Pannoramic DESK 1.18.1 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. Figure 41 – Server connection established 5.
  • Page 60 Pannoramic DESK 1.18.1 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 61 Pannoramic DESK 1.18.1 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 62: Using Profiles

    Pannoramic DESK 1.18.1 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 63: Troubleshooting And Maintenance

    Pannoramic DESK 1.18.1 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 64: 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. Follow the steps in section 5.3.1 Removing the protective cover. 4. Remove slide manually (see section 5.3.3 Removing a...
  • Page 65 Pannoramic DESK 1.18.1 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 66 Pannoramic DESK 1.18.1 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 67: Maintenance

    5.3.1 Removing the protective cover 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 need to be removed in order to eliminate the problem.

  • Page 68: Replacing The Halogen Lamp

    Pannoramic DESK 1.18.1 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 69 Pannoramic DESK 1.18.1 User’s Guide 5 Troubleshooting and Maintenance Warning! Hot surface! Wait for the lamp surface to cool down. Keep a cool-down time of approximately 15 minutes. When changing the lamp, avoid touching the replacement bulb with the bare fingers! 1.

  • Page 70: Removing A Slide

    Pannoramic DESK 1.18.1 User’s Guide 5 Troubleshooting and Maintenance 5.3.3 Removing a slide If a slide got jammed or has suffered breakage during the process of digitization, stop the process and, if possible, move the slide holder to a position where the slide can be easily removed.

  • Page 71: Transporting Pannoramic Desk

    9. Launch control software. 5.3.4 Transporting Pannoramic DESK The following procedure shows how to transport Pannoramic DESK. Caution! Do not lift or transport Pannoramic DESK 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 1.18.1 User’s Guide 5 Troubleshooting and Maintenance To transport Pannoramic DESK do the following: 1. Turn power supply off and detach all cables. 2. Transport Pannoramic DESK. 3. After finishing transportation, reestablish cable connections. Caution! Readjust camera angle if necessary after transporting and reinstalling the Pannoramic DESK! May 29, 2014 - Rev.

  • Page 73: Technical Data

    Pannoramic DESK 1.18.1 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 74 Pannoramic DESK 1.18.1 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) Over-voltage category...
  • Page 75 Pannoramic DESK 1.18.1 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, with capability for interpretation of the following...
  • Page 76 Pannoramic DESK 1.18.1 User’s Guide 6 Technical Data CIS VCC-FC60FR19CL camera Global Shutter Type CMOS (Diagonal 15.930mm) Pixel size 5.5µm × 5.5µm Camera resolution 2048(H) × 2048(V) pixel Frame rates 17fps / 34fps / 68fps / 135fps Bit-depth 10 bit Pixel resolution with 20x objective and 1x C-mount adapter 0.24µm...

  • Page 77: Index

    Marker..........................44, 47, 62 Pannoramic............................6 Pannoramic DESK..........6, 8, 9, 10, 12, 13, 15, 17, 19, 23, 25, 26, 64, 67, 71, 72 Pannoramic Viewer......................18, 53, 64, 65 Preview............20, 22, 24, 26, 30, 39, 43, 44, 45, 46, 47, 48, 51, 53, 75 RGB..............................56...

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