3DHISTECH Pannoramic DESK User Manual
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3DHISTECH Pannoramic DESK User Manual

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Pannoramic DESK
1.15
User's Guide
March 13, 2012
Rev. 1

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Summary of Contents for 3DHISTECH Pannoramic DESK

  • Page 1 Pannoramic DESK 1.15 User’s Guide March 13, 2012 Rev. 1...

  • Page 2: Table Of Contents

    3 Preparing Slides......................20 3.1 Affixing Barcode Stickers to Slides...................21 3.2 Inserting and Removing Slides....................22 4 Software Description....................25 4.1 Starting / Exiting Pannoramic DESK Software Application............25 4.1.1 Starting the software............................25 4.1.2 Exiting the software............................25 4.2 Options.............................25 4.2.1 Barcode Settings.............................26 4.2.2 Image Compensation.............................29...
  • Page 3 Pannoramic DESK 1.15 User’s Guide 4.3.3 Preview tab..............................40 4.3.4 Preview area scanned by preview camera.....................43 4.3.5 Focus tab................................49 4.3.6 Service tab..............................51 4.3.7 Display field and toolbar for live images......................52 4.3.8 Start Scan................................53 4.3.9 Scan To Server..............................54 4.4 Using Profiles...........................59 5 Troubleshooting and Maintenance................61 5.1 Safety Information........................61...

  • Page 4: Disclaimer

    IP are the sole properties of the 3DHISTECH Ltd. 3DHISTECH Ltd. is not liable for damage of whatever nature (including, but not limited to, general or specific damage, indirect damage, consequential damage or incidental damage, including the...
  • Page 5 Pannoramic DESK 1.15 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 1.15 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 1.15 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 Pannoramic DESK 1.15 User’s Guide Remember to unplug the power cord before you open the Pannoramic DESK or replace a fuse! Disconnect plug! Use only electric fuses which are rated for the specified nominal current. You Warning! are prohibited from using makeshift fuses or short-circuiting of a fuse holder.

  • Page 10: Notes On Warranty

    Pannoramic DESK 1.15 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 1.15 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 (typically histological sections). The target users of the product can work for example, in education, research, industry or medical sectors.

  • Page 13: Warning And Information Labels

    Pannoramic DESK 1.15 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 March 13, 2012 –...

  • Page 14: Base Unit

    1.2 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. March 13, 2012 – Rev. 1 3DHISTECH Ltd.

  • Page 15: Hardware Options

    Pannoramic DESK 1.15 User’s Guide 1 Product Description Figure 3 – Pannoramic DESK system overview 1. 24 V external power supply unit 2. Pannoramic DESK base unit 3. Monitor 4. Mouse 5. Control computer 6. Keyboard 1.2.2 Hardware Options The configuration of the control computer and monitor can vary depending on the product order.
  • Page 16 0.63× adapter 1× adapter Warning! The installation of the cameras in Pannoramic DESK must be carried out by trained professionals! 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 17: Control Software

    Pannoramic DESK 1.15 User’s Guide 1 Product Description Base Unit options Pannoramic DESK Basic Scan Option / Fast Option – base unit equipped with Stingray F146C • IRF or CIS VCC-F52U25CL camera for Brightfield scanning Objectives Carl Zeiss Plan-Apochromat 20×/NA 0.8 •...

  • Page 18: 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 19: Connectors And Cables

    Pannoramic DESK 1.15 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 20: Preparing Slides

    Pannoramic DESK 1.15 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 21: Affixing Barcode Stickers To Slides

    Pannoramic DESK 1.15 User’s Guide 3 Preparing Slides Warning! Do not change correction collar settings on 40×/NA objective, if you need it to be set, contact customer service. 3.1 Affixing Barcode Stickers to Slides This section describes how to affix barcode stickers to slides. Barcodes enable virtual slide identification.

  • Page 22: Inserting And Removing Slides

    1.65 mm (including the barcodes and the slide). 3.2 Inserting and Removing Slides Pannoramic DESK features a manual feed for one single slide. To insert a slide Caution! Incorrect slide insertion may break the glass. Always make sure that slides are correctly inserted in the tray.
  • Page 23 Pannoramic DESK 1.15 User’s Guide 3 Preparing Slides 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. Caution! When opening the slide insert door, fingers may be pinched during operation.
  • Page 24 The preview image is displayed in the preview area of the control software. 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.

  • Page 25: Software Description

    Pannoramic DESK 1.15 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 26: Barcode Settings

    Pannoramic DESK 1.15 User’s Guide 4 Software Description 4.2.1 Barcode Settings Figure 9 – Barcode settings Caution! To enable barcode reading, you must install Matrox Imaging Library first. For more information, see the Matrox Imaging Library Installation Guide on the Pannoramic Installation Disk.
  • Page 27 Pannoramic DESK 1.15 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 28 Pannoramic DESK 1.15 User’s Guide 4 Software Description 1D Barcode Types You can select the following 1D barcode types: Code 128 • Code 93 • EAN 8 • EAN 13 • UPC-A • 2D Barcode Types You can select the following 2D barcode types: Data Matrix •...

  • Page 29: Image Compensation

    Pannoramic DESK 1.15 User’s Guide 4 Software Description Barcode Image Compensation Click Use barcode compensation image to use the previously created compensation image for scanning the label area. The compensation image improves the effectiveness of barcode reading. 1. Select a slide with a label area covered fully by a white sticker.

  • Page 30: Microscope Settings

    Pannoramic DESK 1.15 User’s Guide 4 Software Description Preview Settings There might be specks or minor etches on the surface of the compensation slide that require modifying the threshold settings. Therefore, the scanner will not use those areas for the creation of the compensation images.
  • Page 31 Pannoramic DESK 1.15 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 32 Pannoramic DESK 1.15 User’s Guide 4 Software Description Camera Rotation Figure 13 – Camera rotation March 13, 2012 3DHISTECH Ltd. 32(75)
  • Page 33 Pannoramic DESK 1.15 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 34: External Application Call Settings

    Pannoramic DESK 1.15 User’s Guide 4 Software Description 4.2.4 External Application Call Settings Figure 15 – External Application Call Settings These settings open any external application (.exe or .bat) as defined. For example, it might start the Viewer software after finishing scanning, or stop the computer after scanning is finished.

  • Page 35: Using Brightfield Manual Mode

    Pannoramic DESK 1.15 User’s Guide 4 Software Description You can test whether the Error Occurred Call settings work by clicking . By moving the mouse over the buttons, the software displays information about the setting you are interested 4.3 Using Brightfield Manual Mode The Brightfield Manual mode is perfect for digitizing slides that require unique settings, or single slides.

  • Page 36: Routine Work Tab

    Pannoramic DESK 1.15 User’s Guide 4 Software Description 4.3.1 Routine work tab Figure 17 – 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 37 Pannoramic DESK 1.15 User’s Guide 4 Software Description You can also use the barcode as a slide name if a compatible barcode sticker is affixed on • the slide. To do this, click . It will automatically detect the barcode on the slide, and the number or string will appear in the Slide Name field.

  • Page 38: Scan Options Window

    Pannoramic DESK 1.15 User’s Guide 4 Software Description 4.3.2 Scan Options window Figure 18 – Scan options window 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 –...
  • Page 39 Pannoramic DESK 1.15 User’s Guide 4 Software Description Scan Settings Interpolated focus distance – the distance of focal points can be set to create a focus map, • based on which the software calculates interpolated focus values (one step in distance means one FOV).

  • Page 40: Preview Tab

    Pannoramic DESK 1.15 User’s Guide 4 Software Description 4.3.3 Preview tab The Preview tab offers options for threshold setting and selection of the area to be scanned. Figure 19 – Preview tab Use threshold Scan specimen with auto threshold – This automatically detects the specimen in the preview •...
  • Page 41 Pannoramic DESK 1.15 User’s Guide 4 Software Description Scan specimen with user set threshold – This sets the sensitivity of the specimen detection. • To set the desired threshold value manually, change the setting in the Specimen threshold level selection box in the range of 0-255. The default value is 35.
  • Page 42 Pannoramic DESK 1.15 User’s Guide 4 Software Description Figure 21 – Preview image with and without coverslip edge Caution! It requires lots of time and memory (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 43: Preview Area Scanned By Preview Camera

    Pannoramic DESK 1.15 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 44 Pannoramic DESK 1.15 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 45 Pannoramic DESK 1.15 User’s Guide 4 Software Description Preview toolbar You can find the preview toolbar at the bottom of the preview image. Figure 24 – Preview toolbar You can select the area to be scanned with the different tools on the toolbar: Square tool •...
  • Page 46 Pannoramic DESK 1.15 User’s Guide 4 Software Description Figure 25 – Not scanned selection 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 26 –...
  • Page 47 Pannoramic DESK 1.15 User’s Guide 4 Software Description Block tab Figure 27 – TMA tool: Block Set the TMA block type in this tab. 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 48 Pannoramic DESK 1.15 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 49: Focus Tab

    Pannoramic DESK 1.15 User’s Guide 4 Software Description Label area To rotate the label area by 180°, select the Rotate image by 180 degree checkbox. Figure 30 – Label area 4.3.5 Focus tab Figure 31 – Focus tab March 13, 2012 3DHISTECH Ltd.
  • Page 50 Pannoramic DESK 1.15 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 51: Service Tab

    Pannoramic DESK 1.15 User’s Guide 4 Software Description Figure 32 – Focus level and step size 4.3.6 Service tab Figure 33 – 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 Opening the protective cover).

  • Page 52: Display Field And Toolbar For Live Images

    Pannoramic DESK 1.15 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 53: Start Scan

    Pannoramic DESK 1.15 User’s Guide 4 Software Description – One pixel on the monitor corresponds to one pixel on the camera • – The live image completely fills the display area • – Displays or hides the vertical and horizontal scale bars •...

  • Page 54: Scan To Server

    4.3.9 Scan To Server If you want to scan directly to a server, first you have to install the ScanToServer which is an embedded application that can be run under the Pannoramic DESK scanner software. Follow these steps to install the ScanToServer application: 1.
  • Page 55 Pannoramic DESK 1.15 User’s Guide 4 Software Description 3. Click Finish to finalize the installation process of the ScanToServer application. To setup connection with a designated server, follow the steps below: 1. Click Scan Options on the Routine Work tab panel.
  • Page 56 Pannoramic DESK 1.15 User’s Guide 4 Software Description 2. Select the Scan to CaseCenter option in the Scan Option window, then click Connect. Figure 36 – 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 57 Pannoramic DESK 1.15 User’s Guide 4 Software Description Slide settings in the CaseCenter window 1. In the Routine work tab panel, click the button. 2. The CaseCenter window opens. Figure 38 – Scan to Server window Slide data is displayed in a form.
  • Page 58 Pannoramic DESK 1.15 User’s Guide 4 Software Description Figure 39 – Profile selection in the CaseCenter window Profile can be added by selecting a list entry from the Profile drop-down list. • Select a folder where the slide will be scanned to. After clicking the Folder drop- •...

  • Page 59: Using Profiles

    Pannoramic DESK 1.15 User’s Guide 4 Software Description After restarting the scanner software a dialog window appears when scanning to • server is performed previously. Click Yes to use the last used server, or No to define a different one.
  • Page 60 Pannoramic DESK 1.15 User’s Guide 4 Software Description Determination of the area to be scanned Use of automatic threshold specimen • Use of specimen threshold value • Use of marker pen threshold and specimen threshold values • Remove coverslip function (ON/OFF) •...

  • Page 61: Troubleshooting And Maintenance

    Pannoramic DESK 1.15 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 62: 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. March 13, 2012 - Rev. 1 3DHISTECH Ltd.
  • Page 63 Pannoramic DESK 1.15 User’s Guide 5 Troubleshooting and Maintenance 4. Remove slide manually (see section 5.3.5 Removing the slide). 5. Reattach protective covers. 6. Connect power plug and turn power supply on. 7. Launch the scanner software. Illumination error! Probably the lamp has burned out. Please turn off the scanner and check the...
  • Page 64 Pannoramic DESK 1.15 User’s Guide 5 Troubleshooting and Maintenance Virtual slides show poor stitching in Pannoramic Viewer Scan camera not properly adjusted (for example, due to loose fixture) • Contact 3DHISTECH Service for support. • Slide is often positioned incorrectly Guiding fault in transport system •...

  • Page 65: 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 66: Replacing The Halogen Lamp

    Pannoramic DESK 1.15 User’s Guide 5 Troubleshooting and Maintenance 1. Unscrew both Allen screws (2) from the holes (1) located at the sides 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 67 Pannoramic DESK 1.15 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 68: Removing A Slide

    Pannoramic DESK 1.15 User’s Guide 5 Troubleshooting and Maintenance 14. Connect power plug and turn power supply on. 15. Launch control software. 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 69: 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 70 5 Troubleshooting and Maintenance Caution! Be sure that the scan camera is not moved during transportation. 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.

  • Page 71: Technical Data

    Pannoramic DESK 1.15 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 72 Pannoramic DESK 1.15 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 73 Pannoramic DESK 1.15 User’s Guide 6 Technical Data Slide identification Slides are identified by preview camera (TIS DFK21F04): Barcode area is saved as image and label is interpreted as a character string, with capability for interpretation of the following types of 1D and...
  • Page 74 Pannoramic DESK 1.15 User’s Guide 6 Technical Data CIS VCC-F52U25CL camera 1/1.8” PS IT CCD Pixel size 4.40×4.40 µm Camera resolution 1624(H) × 1224(V) pixel Camera max. speed up to 30 frames per second Bit-depth 10 bit Pixel resolution with 20x objective and 1x C-mount adapter 0.22µm...

  • Page 75: Index

    Halogen lamp......................3, 63, 65, 66, 72 Marker..........................41, 44, 60 Pannoramic............................6 Pannoramic DESK...2, 3, 6, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 54, 62, 65, 69, 70 Pannoramic MIDI..........................6 Pannoramic Viewer......................17, 50, 62, 64 Preview............3, 12, 19, 21, 24, 25, 30, 35, 40, 42, 43, 44, 45, 48, 50, 73...

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