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3DHISTECH Pannoramic SCAN 150 User Manual

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Pannoramic SCAN 150
1.14
User's Guide
May 10, 2010
Rev. 1

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Summary of Contents for 3DHISTECH Pannoramic SCAN 150

  • Page 1 Pannoramic SCAN 150 1.14 User’s Guide May 10, 2010 Rev. 1...

  • Page 2: Table Of Contents

    Pannoramic SCAN 150 1.14 User’s Guide Contents Disclaimer........................5 Character Formats and Symbols..................7 Notes Regarding Operational Safety................8 Notes on Warranty......................10 Terms and Abbreviations....................11 1 Product Description....................12 1.1 Product Overview........................12 1.1.1 Intended Use..............................12 1.1.2 Features and Benefits.............................12 1.1.3 Warning and Information Labels........................13 1.1.4 Base Unit................................14...
  • Page 3 Pannoramic SCAN 150 1.14 User’s Guide 4.3.3 Preview tab..............................50 4.3.4 Preview area scanned by preview camera.....................52 4.3.5 Focus tab................................59 4.3.6 Service tab..............................62 4.3.7 Display field and toolbar for live images......................63 4.3.8 Start Scan................................65 4.4 Using Brightfield Automatic Mode..................65 4.4.1 Routine work tab............................65 4.4.2 Barcodes tab..............................67...
  • Page 4 Pannoramic SCAN 150 1.14 User’s Guide Index...........................127 May 10, 2010 3DHISTECH Ltd. 4(127)

  • Page 5: Disclaimer

    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 resulting from lost profits, interruption of business, loss of business information, pecuniary loss or similar damage) that stems from or is associated with the incorporated part of this Product that is made by Silicon Graphics Inc.
  • Page 6 OF DAMAGE, AND ON ANY THEORY OF LIABILITY, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. Further Information For the latest information on 3DHISTECH products and services, please visit our website at the following URL: http ://www.3dhistech.com Company Address: 29-33 Konkoly-Thege Miklos str 1121 Budapest –...

  • Page 7: Character Formats And Symbols

    Pannoramic SCAN 150 1.14 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: Notes Regarding Operational Safety

    Pannoramic SCAN 150 1.14 User’s Guide Notes Regarding Operational Safety Notes Regarding Operational Safety The Pannoramic SCAN has been designed, manufactured and tested to comply with the standard requirements of DIN EN 61010-1 (IEC 61010-1) and IEC 61010-2-101, Safety Provisions Regarding Electric Measuring &...
  • Page 9 Pannoramic SCAN 150 1.14 User’s Guide Notes Regarding Operational Safety Electric power to the Pannoramic SCAN is supplied via an external mains power Note: supply unit. It allows for operation at line voltages in the range of 100 V to 240 V ±10%, 50/60 Hz, without any extra facilities required for voltage...

  • Page 10: Notes On Warranty

    Notes on Warranty Notes on Warranty 3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic SCAN 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 SCAN 150 1.14 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 12: Product Description

    Pannoramic SCAN 150 1.14 User’s Guide 1 Product Description 1 Product Description 1.1 Product Overview 1.1.1 Intended Use The Pannoramic SCAN is designed to use transmitted light and reflected light fluorescence 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 SCAN 150 1.14 User’s Guide 1 Product Description 1.1.3 Warning and Information Labels The following figure contains the labels used on the Pannoramic SCAN main unit, the external mains power supply unit, and the HXP 120 illuminator. Figure 1 – Warning and information labels May 10, 2010 3DHISTECH Ltd.

  • Page 14: Base Unit

    Pannoramic SCAN 150 1.14 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 15: System Overview

    Pannoramic SCAN 150 1.14 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 system The following figure shows the main parts of the Pannoramic SCAN system.

  • Page 16: Hardware Options

    Pannoramic SCAN 150 1.14 User’s Guide 1 Product Description 4. Mouse 5. Control computer 6. Keyboard 7. Pannoramic SCAN base unit 8. 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 17 Pannoramic SCAN 150 1.14 User’s Guide 1 Product Description Stingray F146C IRF Medical camera 1 CCD camera for normal brightfield application and entry level fluorescent applications. Camera adapters 0.63× adapter 1× adapter Warning! The installation of the cameras in Pannoramic SCAN must be carried out by trained professionals! In any other case the warranty will be automatically voided.

  • Page 18: Control Software

    Pannoramic SCAN 150 1.14 User’s Guide 1 Product Description Pannoramic SCAN Fluorescence Option • Base unit completely equipped with Stingray, Marlin, or Hitachi cameras for – Brightfield scanning, and with AxioCam camera, HXP 120 illuminator, trigger cable and filters for fluorescence scanning Objectives ZEISS Plan-Apochromat 20×/NA 0.8...
  • Page 19 Pannoramic SCAN 150 1.14 User’s Guide 1 Product Description Scan To Server • Pannoramic Viewer software (fully functional) • Optional: Fluorescence slide viewer • TMA module • 3D Reconstruction module • HistoQuant, NuclearQuant, MembraneQuant, FISHQuant, and DensitoQuant modules • ImmunoScreener module •...

  • Page 20: Installation

    Pannoramic SCAN 150 1.14 User’s Guide 2 Installation 2 Installation Warning! The installation of the Pannoramic SCAN 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 21: Connectors And Cables

    Pannoramic SCAN 150 1.14 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 22 Pannoramic SCAN 150 1.14 User’s Guide 2 Installation Video cable (between monitor and control computer) • Power supply cable (between 230V/110V and monitor) • Power supply cable (between 230V/110V and control computer) • Power supply cable (between 230V/110V and power supply unit) •...

  • Page 23: Operating Slides And Magazines

    Pannoramic SCAN 150 1.14 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 all slides and cover slips that meet the following specifications:...

  • Page 24: Affixing Barcode Stickers To Slides

    Pannoramic SCAN 150 1.14 User’s Guide 3 Operating Slides and Magazines Caution! Ensure that no part of the mounted coverslip protrudes from the edges of the slide. Use slides only with completely dried embedding medium. If not so, the coverslip can be shifted that makes slide loading less reliable. Not completely dried embedding might also influence the operation of objectives and other device parts.
  • Page 25 Pannoramic SCAN 150 1.14 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 26: Inserting And Removing Slides

    Broken slide can be removed only by a well-trained person! Only original 3DHISTECH magazines are allowed for use with Pannoramic SCAN! The magazines can contain a maximum of 25 slides.
  • Page 27 Pannoramic SCAN 150 1.14 User’s Guide 3 Operating Slides and Magazines Note: You should insert several slides into a magazine without empty slots. Begin the insertion on position 1 of the magazine. Caution! To insert or remove a filled magazine from the device, or when transporting it without its cover (4), slightly tilt it to its closed side to prevent the slides from accidentally falling out.
  • Page 28 Pannoramic SCAN 150 1.14 User’s Guide 3 Operating Slides and Magazines 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! The input stack can be filled with a maximum of 6 magazines in addition to the one in the magazine loader.

  • Page 29: Software Description

    1. To start the program, double-click on the program icon on the desktop or start it from Start \ Program Files \ 3DHISTECH \ Pannoramic Scanner 2. During start-up, all motors, the preview camera and the scan camera are initialized. After successful initialization, the program displays a Mode selection window.

  • Page 30: Exiting The Software

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Note: It is recommended to use specimens with identical staining for a given batch of magazines in Automatic mode. 4.1.2 Exiting the software To exit the software, click X in the title bar. This turns Mode selection window active again.
  • Page 31 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Caution! To enable barcode reading, you must install Matrox Imaging Library application first. For more information, see the Matrox Imaging Library Installation Guide on the Pannoramic Installation Disk. Before starting the control software, you have to set the barcode settings here. By predefining the barcode type, foreground color (color of the barcode), and other settings, you enable the Read Barcode option when using the control software.
  • Page 32 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 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 33 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 1D barcodes with check digit (CDV) You can select the following 1D barcodes with check digit (CDV): Code 39 • Interleaved 2 of 5 • The check digit is always the last digit of the barcode. It is an additional checking number.

  • Page 34: Image Compensation

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Note: If you give an incorrect number of characters, the system will not be able to read the barcode. Maxicode Dot spacing • You can define the spacing between the dots of the code in pixels. This function only works with Maxicode.
  • Page 35 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Brightfield Compensation Figure 11 – Image compensation Camera Selection The installed active camera is used for Brightfield mode. Objective Selection The installed objective is selected for creating a new compensation image.
  • Page 36 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Optovar Selection If you have selected an optovar for a position in the Microscope Settings window, the optovars for each position are displayed in this field. To select the optovars to be used for creating a new compensation image, check the selection box(es).
  • Page 37 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Figure 12 – Image compensation Camera Selection This field displays the active camera for Fluorescent mode. Objective Selection The objective to be used for creating a new compensation image is shown as selected.
  • Page 38 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Filter Selection If you have selected a filter for a position in the Microscope Settings window, the filters for each position are displayed in this field. Preview Settings If you do not have an empty slide available, you can select those areas with these settings that are not occupied by the specimen, or specks.

  • Page 39: Microscope Settings

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.2.3 Microscope Settings You can define for the software which optovars or filters occupy which turret position. By moving the mouse over the buttons, the software displays information about the setting you are interested in.
  • Page 40 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Camera type The software automatically detects and displays the camera type here. Use manual camera changer Enabling this option allows you to use manual switching between the two cameras. Objective type You can select the type and the magnification level of the objectives.
  • Page 41 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Figure 15 – Camera Rotation tab 2010/ May 10/ 3DHISTECH Ltd. 41(127)
  • Page 42 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Z Difference This function is available only for fluorescence settings; it enables you to set the basic focus differences between the filters. This facilitates more precise focusing during scanning. Figure 16 – Z Difference tab 2010/ May 10/ 3DHISTECH Ltd.
  • Page 43 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Service Figure 17 – 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 44: External Application Call Settings

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.2.4 External Application Call Settings Figure 18 – External Application 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 45: Using Brightfield Manual Mode

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Normal window • Minimized • Maximized • You can test whether the Error Occurred Call settings work by clicking 4.3 Using Brightfield Manual Mode You can use Brightfield Manual 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 46: Routine Work Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 1. Tab panel with scanner functions and settings 2. Scan camera live image display area 3. Preview image recorded by the preview camera 4. Preview image editor toolbar 5. Information area about the digitization progress 4.3.1 Routine work tab...
  • Page 47 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description To return the slide to its magazine, click • To move all magazines to the output stack, click • To enter the slide name To enter the slide name manually, type it into the Slide Name field.

  • Page 48: Scan Options Window

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.3.2 Scan Options window Figure 21 – 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 49 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Scan Settings Focus frequency adjustment is advised when scanning slides with extremely uneven surface. Otherwise, default settings can be used. Fine focus frequency – Adjust the slider to define how many FOVs should be digitized in a •...

  • Page 50: Preview Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description If you enable the Directory function, the virtual slides will be digitized in the specified • folder. You can browse for the folder with the Browse button. If you specify a folder that does not exist, the software will create it.
  • Page 51 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Smaller values result in a more sensitive scanning, meaning that more areas will be digitized, however, this may also include specks or other imperfections of the slide. Greater values result in a less sensitive scanning, but it is possible that some of the smaller specimen areas will not be digitized.

  • Page 52: Preview Area Scanned By Preview Camera

    Pannoramic SCAN 150 1.14 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 53 Pannoramic SCAN 150 1.14 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 54 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Figure 26 – 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 cover slip edges. Select the Use selection box to eliminate those areas.
  • Page 55 Pannoramic SCAN 150 1.14 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 56 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Figure 28 – 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 29 –...
  • Page 57 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Block tab Figure 30 – TMA tool: Block Set the TMA block type in this tab. 4. Select the shape of the TMA spots (Rectangle spots or Circle spots). 5. Enter the number of rows and columns in the Rows and Columns fields or select the appropriate values with the arrows.
  • Page 58 Pannoramic SCAN 150 1.14 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 59: Focus Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Label area To rotate the label area by 180°, select the Rotate image by 180 degree checkbox. Figure 33 – Label area 4.3.5 Focus tab Figure 34 – Focus tab 2010/ May 10/ 3DHISTECH Ltd.
  • Page 60 Pannoramic SCAN 150 1.14 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 61 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Extended focus mode (optional) This determines features of the resulting virtual slide. By choosing this option, the software selects the sharpest image from each focus level for each image field, and combines them into one single image. Therefore those parts that were blurry in auto/manual focus will also be sharp.

  • Page 62: Service Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 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 Opening the protective cover).

  • Page 63: Display Field And Toolbar For Live Images

    Pannoramic SCAN 150 1.14 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 64 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description – Zoom in • – Zoom out • – One pixel on the monitor corresponds to one pixel on the camera • – The live image completely fills the display area •...

  • Page 65: Start Scan

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.3.8 Start Scan To start digitization process, click after checking settings on the Barcodes tab. 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 66 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description To insert and remove slides If you do not want to load all slides, you can specify the first and last slide to be loaded in • the Scan Range by entering the appropriate slide numbers in the selection boxes of First slide and Last slide.

  • Page 67: Barcodes Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.4.2 Barcodes tab Figure 39 – Barcodes tab On this tab you can set identification features and profiles for slides. 2010/ May 10/ 3DHISTECH Ltd. 67(127)
  • Page 68 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Modes in the tab 1. Apply one profile to all slides. One profile is used for all slides in a batch. • Current Profile is the profile that was loaded in Routine work / Scan Profiles.
  • Page 69 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Note: You can separate the character groups with any character you choose, it will not be read by the software. Example for barcode usage Barcode: Folder_Vir_123_prof_n • Folder is the folder for saving •...
  • Page 70 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description The number before M represents the magazine number. The number after M represents the slide position. In this example, the name indicates a slide in magazine 1, position 10. You can also define names for the slides in the table below, by entering names into the column Names / Barcodes.

  • Page 71: Preview Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.4.3 Preview tab Figure 40 – Preview tab The Preview tab offers options for threshold setting and selection of the area to be scanned. The options in Automatic mode are the same as described in Manual mode.

  • Page 72: Focus Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.4.4 Focus tab Figure 41 – Focus tab Focus You can define focus limits by selecting Limit focus range. You can set the upper and lower limits by selecting the desired value in the selection boxes.

  • Page 73: Service Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Figure 42 – Focus level and step size 4.4.5 Service tab Figure 43 – 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 74: Start Scan

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.4.6 Start Scan To start digitization process, click after checking settings in the Barcodes tab. 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 (see Figure 44).
  • Page 75 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description If a running digitization process is interrupted, and you want to continue scanning, click You have two options for resuming depending on current slide position. 1. The canceled slide occupies position 1 in the magazine To resume digitization with the same slide, click Yes.

  • Page 76: Using Fluorescent Manual Mode

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.5 Using Fluorescent Manual Mode 4.5.1 Routine work tab Figure 45 – Routine work tab The Routine work tab provides basic digitization functions. Some features of this tab differs from product to product, these are described in the forthcoming sections.
  • Page 77 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description To insert and remove slides To move the lowest magazine in the input stack to the loading position click • To move the magazine into the output stack, click • To move a selected slide from its magazine to the specimen holder either enter its position •...
  • Page 78 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description To enter the slide name You can enter the slide name manually by typing it into the Slide Name field. • You can also use the barcode as a slide name if a compatible barcode sticker is affixed on •...
  • Page 79 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Figure 46 – Filter properties window Filter name The name of the filter is displayed here. Exposure Settings You can set the Exposure time weight (%) here (displayed under TW in the Filter Selection frame).
  • Page 80 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Digital Gain Note: This is camera-dependent, only working with AxioCam MRm Rev 3. (Index value ranges 0-4) and Hitachi HV-F22CL (Index value ranges 0-2). Enter the Index value by entering it in the box or by selecting the value with the arrow buttons.

  • Page 81: Scan Options

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.5.2 Scan Options Figure 47 – Scan options tab 2010/ May 10/ 3DHISTECH Ltd. 81(127)
  • Page 82 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description These settings determine the resulting quality and storage location of the virtual slide. Image Encoding You can set the image format parameters within this group. JPEG – The quality can be adjusted with the JPEG quality factor slider. Greater •...
  • Page 83 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Do not use extended focus on empty field-of-views – If selected, the extended • focus function will not run on the empty (not containing specimen) field of views. Caution! If the specimen area is barely visible, it is possible that the software will analyze that area as an empty one.
  • Page 84 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Exposure Time Calculate exposure time for each area • Calculate exposure time for full slide • Note: This option is used only if no exposure times were manually predefined. It is recommended to use the second option.

  • Page 85: Preview Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.5.3 Preview tab The Preview tab offers options for threshold setting and selection of the area to be scanned. Figure 48 – Preview tab Use threshold Scan auto thresholded specimen – This automatically detects the specimen in the preview •...
  • Page 86 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Scan area inside the marker – 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. You have to draw a full circle with the pen to enable the detection.

  • Page 87: Preview Area Scanned By Preview Camera

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Scan area dilation Adjust the slider to the desired value to enlarge or decrease the scanned area. The edge is extended discretely by one image field of the camera each time.

  • Page 88: Hardware Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.5.5 Hardware tab Figure 50 – Hardware tab (selected mode: User controlled) 2010/ May 10/ 3DHISTECH Ltd. 88(127)
  • Page 89 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Live You can display a live image of the current specimen in the Live image display field by clicking It will work only if you have selected an area in the preview image with the Position sample.
  • Page 90 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description If you raise the Index value, the exposition time is halved by every step, and the image becomes noisier. Focus To define focus limits, select Limiting the range checkbox. Set the upper and lower limits by selecting the desired value in the selection boxes.

  • Page 91: Service Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description You can accept the current z-value by clicking Set Value. This is recommended for a very flat specimen. If you select the Interpolated focus option, the coarse focus level is calculated from three different focus points of the specimen.
  • Page 92 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Slide Removed Manually Click this button to notify the software that you have removed the slide manually. 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 93: Using Fluorescent Automatic Mode

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.6 Using Fluorescent Automatic Mode 4.6.1 Routine work tab Figure 52 – Routine work tab The Routine work tab provides the following basic digitization functions: 2010/ May 10/ 3DHISTECH Ltd. 93(127)
  • Page 94 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description To insert and remove slides If you do not want to load all the slides, you can specify the first and last slide to be loaded in the Scan Range by entering the appropriate slide numbers in the selection boxes of First slide and Last slide.
  • Page 95 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Stitching channel – This is done on one channel. You can choose whether you want to do • stitching on the focus channel, or on another channel. It is recommended to choose another channel if the focus channel was determined on the basis of exposition time, and it would display less information.
  • Page 96 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Filter name The name of the filter is displayed here. Exposure Settings Exposure time – You can set the fix exposition time here. By selecting the Auto button, the exposition time is set to (the exposition time is calculated by the software).

  • Page 97: Barcodes Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description You can move between the filters by clicking Previous Filter or Next Filter. 4.6.2 Barcodes tab Figure 54 – Barcodes tab On this tab, you can set identification features to the various slides and for assigning profiles.
  • Page 98 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Modes on the tab Apply one profile to all slides • One profile is used for all slides in a batch. • Current Profile is the profile that was loaded in Routine work / Scan Profiles.
  • Page 99 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description Note: You can separate the character groups with any character you choose, it will not be read by the software. Example for barcode usage Barcode: Folder_Vir_123_prof_n • Folder is the folder for saving •...
  • Page 100 Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description The number before M represents the magazine number. The number after M represents the slide position. In this example, the name indicates a slide in magazine 1, position 10. You can also define names for the slides in the table, by entering names into the column Names / Barcodes.

  • Page 101: Preview Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.6.3 Preview tab Figure 55 – Preview tab The Preview tab offers options for threshold setting and selection of the area to be scanned. The options in Automatic mode are the same as described in Manual mode.

  • Page 102: Focus Tab

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 4.6.4 Focus tab Figure 56 – Focus tab Focus You can define focus limits by selecting Limit focus range checkbox. You can set the upper and lower limits by selecting the desired value in the selection boxes.

  • Page 103: Using Profiles

    Pannoramic SCAN 150 1.14 User’s Guide 4 Software Description 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. This slows down digitization process and should be activated only with purpose.
  • Page 104 Pannoramic SCAN 150 1.14 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 105: Troubleshooting And Maintenance

    Pannoramic SCAN 150 1.14 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 106: Cleaning The Device

    Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance Never connect the fiber-optic cable to the device. • Never remove the housing from the device. • 5.1.1 Cleaning the device Before cleaning, switch off the device and pull the plug out.
  • Page 107 Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance The product does not start Power supply is interrupted • 1. Turn the 24V power supply and the control computer on. 2. Check cable connections. Control software has stopped Name of currently selected slide for digitization already exists and is open in Pannoramic •...
  • Page 108 Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance 5. Reattach protective covers. 6. Reconnect 24V power supply and control computer to line power supply. 7. Switch on the 24 V power supply. 8. Switch on the control computer.
  • Page 109 Pannoramic SCAN 150 1.14 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 110: Fluorescent Applications (Optional)

    Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance 5.2.1 Fluorescent Applications (optional) The shutter of the HXP 120 cannot be triggered, in spite of trigger connection through AxioCam MRm Rev3. HXP 120: Shutter is permanently open • Activate shutter remote control with the button at the front of the HXP 120.
  • Page 111 Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance Warning! Avoid leaning over the device when opening it. Figure 58 – Removal of covers Five eccentric screws (3) are located on the bottom face of the baseplate (4). They attach the covers to the baseplate.

  • Page 112: Replacing The Halogen Lamp

    Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance Caution! Make sure that no cables of the scan camera are squeezed as you replace the covers. 5.3.2 Replacing the halogen lamp Figure 59 – Replacing the halogen lamp Warning! Hot surface! Wait for the lamp surface to cool down.

  • Page 113: Replacing Lamp Module (For Fluorescent Option)

    Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance 5. Remove the knurled screws (1) from the heat sink body (6) completely. 6. Turn the lamp mount counter-clockwise (for approximately 45 degrees) until the two clamps (3) are aligned to the hole (5) on the heat sink body.
  • Page 114 Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance Warning! Hot surface! Wait at least twenty minutes to allow the lamp surface to cool down sufficiently. 1. Disconnect power plug (separate all poles from the mains). 2. Unfix screw in lateral cover plate of the lamp housing and remove plate from lamp housing.

  • Page 115: Removing A Slide

    Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance Caution! If Fluorescence scanning option is available, create new compensation images after replacing the bulb in HXP 120. For more information see section 4.2.2 Image Compensation / Fluorescent Compensation. 5.3.4 Removing a slide...
  • Page 116 Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance Figure 61 – Removing a slide 1. Open the protective cover (see section 5.3.1 Opening the protective cover). 2. Push locking lever (1) to the left, and keep the lever in this position.

  • Page 117: Installing And Removing The Filter Module (Fluorescent Option)

    Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance 5.3.5 Installing and Removing the Filter Module (Fluorescent Option) Figure 62 – Installing and removing the filter module 1. Switch the HXP 120 illuminator off. Warning! Crush hazard! Stop the running digitization process before you proceed with filter module installation or removal.

  • Page 118: Removing The Magazine From The Transporting System

    Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance 5. Hold the filter module (3) by its handling pads (one on the right, one on the left (lateral) side of the module) and insert it in forward tilted position from above into the upper spring- loaded clamps (1) at the filter wheel.
  • Page 119 Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance 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. Caution! Check that the magazine is not tilted, so that it rests on both of the horizontal guide rails.

  • Page 120: Transporting Pannoramic Scan

    Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance 5.3.7 Transporting Pannoramic SCAN The following procedure shows how to transport the Pannoramic SCAN. Figure 64 – Transporting handles Caution! Do not use the blue guide rail bar (1) to raise, shift or transport the...
  • Page 121 Pannoramic SCAN 150 1.14 User’s Guide 5 Troubleshooting and Maintenance 3. Turn carrying handles by 90° (B) towards the base unit to secure them. 4. Now you can transport Pannoramic SCAN with the help of another person. 5. After finishing transportation, push carrying handles back into normal position (C).

  • Page 122: Technical Data

    Pannoramic SCAN 150 1.14 User’s Guide 6 Technical Data 6 Technical Data Dimensions (width x depth x height) Base unit approx. 522 mm (W) x 568 mm (D) x 457 mm (H) Base unit without fluorescence option approx. 522 mm (W) x 568 mm (D) x 457 mm (H) 24V 100W power supply approx.
  • Page 123 Pannoramic SCAN 150 1.14 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 124 Pannoramic SCAN 150 1.14 User’s Guide 6 Technical Data Light sources Halogen lamp (transmitted light operation) HAL 12V, 5 W Average service life of halogen lamp 4000h Lamp module for HXP 120 (fluorescent option) 120 W Mercury short arc reflector lamp average service life 2000h The manual describes HXP 120.
  • Page 125 Pannoramic SCAN 150 1.14 User’s Guide 6 Technical Data Scan cameras Stingray F146C IRF Medical camera 1/2” type progressive scan CCD Pixel size 4.65µm x 4.65µm Camera resolution 1388 x 1038 pixel Camera max. speed up to 15 frames per second...
  • Page 126 Pannoramic SCAN 150 1.14 User’s Guide 6 Technical Data Bit-depth 10 bit Pixel resolution with 20× objective and 1× C-mount adapter 0.23µm Connection type CameraLink Control computer, minimum system requirements Operating System Microsoft Windows XP Professional SP3 or Vista Business SP2 32-bit EN/HU Intel Pentium 4, 3 GHz / Intel Pentium Dual Core 2.6 GHz...
  • Page 127 Pannoramic SCAN 150 1.14 User’s Guide Index Index AxioCam..............16, 18, 21, 22, 40, 49, 80, 82, 83, 89, 96, 110, 125 Barcode..2, 3, 18, 24, 25, 26, 30, 31, 32, 33, 34, 47, 65, 67, 68, 69, 70, 74, 78, 97, 98, 99, 100, 124 Brightfield............2, 3, 12, 16, 17, 18, 29, 35, 36, 45, 49, 65, 79, 96, 103...

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