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3D Histech Pannoramic SCAN 150 User Manual

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Pannoramic SCAN 150
1.15
User's Guide
March 13, 2012
Rev. 1

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Summary of Contents for 3D Histech Pannoramic SCAN 150

  • Page 1 Pannoramic SCAN 150 1.15 User’s Guide March 13, 2012 Rev. 1...

  • Page 2: Table Of Contents

    Pannoramic SCAN 150 1.15 User’s Guide Contents Disclaimer........................5 Character Formats and Symbols..................7 Declaration Of Conformity....................8 Notes Regarding Operational Safety................9 Notes on Warranty......................11 Terms and Abbreviations....................12 1 Product Description....................13 1.1 Product Overview........................13 1.1.1 Intended Use..............................13 1.1.2 Features and Benefits.............................13...
  • Page 3 Pannoramic SCAN 150 1.15 User’s Guide 4.3.2 Scan Options window.............................50 4.3.3 Preview tab..............................52 4.3.4 Preview area scanned by preview camera.....................55 4.3.5 Focus tab................................61 4.3.6 Service tab..............................63 4.3.7 Display field and toolbar for live images......................64 4.3.8 Start Scan................................66 4.4 Using Brightfield Automatic Mode..................66 4.4.1 Routine work tab............................66...
  • Page 4 Pannoramic SCAN 150 1.15 User’s Guide Index........................... 132 March 13, 2012 - Rev. 1 3DHISTECH Ltd. 4(132)

  • Page 5: Disclaimer

    Pannoramic SCAN 150 1.15 User’s Guide Disclaimer Copyright © 2001-2012 3DHISTECH Ltd. All rights reserved. Intellectual property related to the 3DHISTECH products are as follows: EP 1,789,831; US 7,663,078; EP 2,024,772; JP 2009-512685; US 12/301,781; EP 1,644,767; JP 2007- 516451; US7,327,515; EP 1,994,398; JP 2008-557835; US 12/281,566; U0700210; US 6,246,785;...
  • Page 6 Pannoramic SCAN 150 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 7: Character Formats And Symbols

    Pannoramic SCAN 150 1.15 User’s Guide Character Formats and Symbols Character Formats and Symbols Example Words or characters that appear on the screen. These include field names, screen and window titles, pushbutton and menu names, paths or options. Keys on the keyboard. For example, function keys (such as F11) or the Ctrl+M key combination.

  • Page 8: Declaration Of Conformity

    Pannoramic SCAN 150 1.15 User’s Guide Character Formats and Symbols Declaration Of Conformity 3DHISTECH Ltd. declares that the product Pannoramic MIDI 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 9: Notes Regarding Operational Safety

    The below section of this User’s Guide contains information and warnings of a kind that must be followed by owner/operator personnel. Warning and advisory symbols which are used on the base unit of the Pannoramic SCAN 150 and in the section 1.1.3 Warning and Information Labels have the following meanings:...
  • Page 10 Please note that the digitizing process has to be interrupted and the insert moved via software to the output position before removing the insert. A defective Pannoramic SCAN 150 is not classified as domestic waste. It must be Warning! properly disposed in accordance with currently valid legal requirements.

  • Page 11: Notes On Warranty

    Notes on Warranty Notes on Warranty 3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic SCAN 150 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 12: Terms And Abbreviations

    Pannoramic SCAN 150 1.15 User’s Guide Terms and Abbreviations Terms and Abbreviations Comma Separated Value Field of View Numerical Aperture Virtual Slide / Slide A digital image of a thin glass plate on which specimens are mounted for microscopic study:...

  • Page 13: Product Description

    1.1 Product Overview 1.1.1 Intended Use The Pannoramic SCAN 150 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 14: Warning And Information Labels

    1 Product Description 1.1.3 Warning and Information Labels The following figure contains the labels used on the Pannoramic SCAN 150 main unit, the external mains power supply unit, and the HXP 120 illuminator. Figure 1 – Warning and information labels March 13, 2012 - Rev.

  • Page 15: Base Unit

    Pannoramic SCAN 150 1.15 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 16: System Overview

    The standard scope of delivery of the product includes the following hardware and software components. 1.2.1 Pannoramic SCAN 150 system The following figure shows the main parts of the Pannoramic SCAN 150 system. Figure 3 – Pannoramic SCAN 150 system overview 1. HXP 120 fiber-coupled illuminator (option) 2.

  • Page 17: Hardware Options

    Pannoramic SCAN 150 1.15 User’s Guide 1 Product Description 6. Keyboard 7. Pannoramic SCAN 150 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 18 Base Unit options Pannoramic SCAN 150 Basic Scan Option / Fast Option – Base unit equipped with Stingray or • CIS cameras for Brightfield scanning (no fluorescent accessories included) Pannoramic SCAN 150 Basic Fluorescence Option –...

  • Page 19: Control Software

    Pannoramic SCAN 150 1.15 User’s Guide 1 Product Description Objectives Carl Zeiss Plan-Apochromat 20×/NA 0.8 • Carl Zeiss Plan-Apochromat 40× Corr/NA 0.95 • Fluorescent Options for Pannoramic SCAN 150 Fluorescent unit (internal part) HXP 120 Fluorescent illumination unit (can be used with AxioCam...
  • Page 20 Pannoramic SCAN 150 1.15 User’s Guide 1 Product Description Z-stack • Barcode reader (licensed feature) • Scan To Server • Pannoramic Viewer software (fully functional) Optional: CaseCenter • Pannoramic Viewer TMA module • 3D Reconstruction module • HistoQuant, NuclearQuant, MembraneQuant, FISHQuant, and DensitoQuant modules •...

  • Page 21: Installation

    2 Installation 2 Installation Warning! The installation of the Pannoramic SCAN 150 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 22: Connectors And Cables

    Pannoramic SCAN 150 1.14 SP1 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 23 Pannoramic SCAN 150 1.14 SP1 User’s Guide 2 Installation pco.edge – a pair of CameraLink cables (between pco.edge camera and control computer) • Video cable (between monitor and control computer) • Power supply cable (between 230V/110V and monitor) • Power supply cable (between 230V/110V and control computer) •...

  • Page 24: Operating Slides And Magazines

    Pannoramic SCAN 150 1.15 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 25: Affixing Barcode Stickers To Slides

    Pannoramic SCAN 150 1.15 User’s Guide 3 Operating Slides and Magazines Note: The distance between slide edges and the edges of the mounted coverslip should be 1-2 mm, and they should be parallel with each other. Caution! Ensure that no part of the mounted coverslip protrudes from the edges of the slide.
  • Page 26 Pannoramic SCAN 150 1.15 User’s Guide 3 Operating Slides and Magazines The label area is recorded by the preview camera, and can be displayed by the control and viewer software. To affix barcode stickers to slides, do the following: 1. Peel off the barcode sticker (2) from the roll.

  • Page 27: 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 150! The magazines can contain a maximum of 25 slides.
  • Page 28 Pannoramic SCAN 150 1.15 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 29 Pannoramic SCAN 150 1.15 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 30: Software Description

    Pannoramic SCAN 150 1.15 User’s Guide 3 Operating Slides and Magazines Figure 8 – Misplaced magazine Note: The input stack can be filled with a maximum of 6 magazines in addition to the one in the magazine loader. Caution! Do not place magazines into the output stack (3) or remove magazines with already digitized slides from there during the digitization process.

  • Page 31: Exiting The Software

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 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. Figure 9 – Mode selection window The selection window displays two Brightfield or Fluorescent scan modes depending on the...

  • Page 32: Options

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description When exiting Manual mode, it automatically unloads the slide. When closing the Mode selection window, it automatically unloads magazine. Scanning process ends with the slide out. 4.2 Options The Options menu can be activated from the main menu of the Mode selection window.
  • Page 33 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Before starting the control software, you have to set the barcode settings here. 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 34 Pannoramic SCAN 150 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 35: Image Compensation

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Foreground Color You can select the following foreground color of the barcode area: Black • White • Barcode Image Compensation Click Use barcode compensation image to use the previously created compensation image for scanning the label area.
  • Page 36 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Brightfield Compensation Figure 12 – Brightfield compensation Camera Selection This field displays the active camera. Currently, there is only one active camera for Brightfield mode and one active camera for Fluorescent mode.
  • Page 37 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Objective Selection This field displays the objective used for scanning. 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 38 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Figure 13 – Fluorescent compensation 2012. March 13. 3DHISTECH Ltd. 38(132)
  • Page 39 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Camera Selection This field displays the active camera. Filter Selection for Live Image Select the filter you want to use for displaying the Live image. Live You can display a live image of the current specimen in the Live image display field by clicking .

  • Page 40: Microscope Settings

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description By clicking Advanced Options button you can set the maximum exposition time used for creating the compensation image. To create the compensation image(s), click . Click the Stop button to interrupt the process.
  • Page 41 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Base Settings Figure 15 – Base Settings tab Objective type You can select the type and the magnification level of the objectives. 2012. March 13. 3DHISTECH Ltd. 41(132)
  • Page 42 The software automatically detects and displays the camera type set in the Pos. 1 box upon clicking the Test and Apply Camera Settings button. If Pannoramic SCAN 150 features a manual camera changer, activate the Use manual camera changer option, then set the appropriate cameras both for Brightfield and Fluorescent (Pos.1 and Pos.2) scanning modes.
  • Page 43 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Figure 16 – Camera Rotation tab 2012. March 13. 3DHISTECH Ltd. 43(132)
  • Page 44 Pannoramic SCAN 150 1.15 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 17 – Z Difference tab 2012.

  • Page 45: External Application Call Settings

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Service Figure 18 – 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 46: Using Brightfield Manual Mode

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 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. You can define external application call settings for the following cases: Scan Finished Call •...
  • Page 47 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Figure 20 – Main window of control software 1. Tab panel with scanner functions and settings 2. Scan camera live image display area 3. Preview image recorded by the preview camera 4.

  • Page 48: Routine Work Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 4.3.1 Routine work tab Figure 21 – Routine work tab The Routine work tab provides basic digitization functions. Features are described in the forthcoming section. To insert and remove slides To move the lowest magazine in the input stack to the loading position click •...
  • Page 49 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description To enter the slide name To enter the slide name manually, type 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 50: Scan Options Window

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 4.3.2 Scan Options window Figure 22 – 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 51 Pannoramic SCAN 150 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 52: Preview Tab

    Pannoramic SCAN 150 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 23 – Preview tab Use threshold Scan specimen with auto threshold – This automatically detects the specimen in the preview •...
  • Page 53 Pannoramic SCAN 150 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 54 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Figure 25 – 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 55: Preview Area Scanned By Preview Camera

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description To save a new mask, click Save. It will display a drop-down menu. Select whether to save preview mask or TMA grid. To load a mask, click Load. It will display a drop-down menu. Select whether to load preview mask or TMA grid.
  • Page 56 Pannoramic SCAN 150 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 57 Pannoramic SCAN 150 1.15 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 58 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Figure 29 – 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 30 –...
  • Page 59 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Block tab Figure 31 – 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 60 Pannoramic SCAN 150 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 61: Focus Tab

    Pannoramic SCAN 150 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 34 – Label area 4.3.5 Focus tab Figure 35 – Focus tab 2012. March 13.
  • Page 62 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Live To display a live image of the current specimen, click This function works only if you select an area in the preview image with the Position sample. This option has no effect on a running digitization process where no live image is displayed.

  • Page 63: Service Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description With the Z-stack method separate layers are created and stored, and can be opened with • Pannoramic Viewer. The Z-stack slide contains the extended focus layer. Both for Extended focus and Z-Stack scanning methods, you can determine the desired number of focus levels with the Focus levels selection box.

  • Page 64: Display Field And Toolbar For Live Images

    Pannoramic SCAN 150 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 65 Pannoramic SCAN 150 1.15 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 66: Start Scan

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 4.3.8 Start Scan To start digitization process, click 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 67 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description The Routine work panel provides basic digitization functions. Some features of this tab differs from product to product, these are described in the forthcoming sections. To insert and remove slides In Automatic mode a preloaded magazine has to be placed into the main unit. This magazine is the •...

  • Page 68: Barcodes Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 4.4.2 Barcodes tab Figure 40 – Barcodes tab Identification features and profiles for slides can be set on this panel. 2012. March 13. 3DHISTECH Ltd. 68(132)
  • Page 69 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Features on the panel 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 70 Pannoramic SCAN 150 1.15 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 71 Pannoramic SCAN 150 1.15 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 72: Preview Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 4.4.3 Preview tab Figure 41 – 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 73: Focus Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 4.4.4 Focus tab Figure 42 – 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 74: Service Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Both for Extended focus and Z-Stack scanning methods, you can determine the desired • number of focus levels with the Focus levels selection box. The current focus value is the starting point. If you set 5 for example, one current, two focus levels above and below FOVs are captured.

  • Page 75: Start Scan

    Pannoramic SCAN 150 1.15 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 45).

  • Page 76: Using Fluorescent Manual Mode

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 4.5 Using Fluorescent Manual Mode 4.5.1 Routine work tab Figure 46 – Routine work tab The Routine work panel provides basic digitization functions. 2012. March 13. 3DHISTECH Ltd. 76(132)
  • Page 77 Pannoramic SCAN 150 1.15 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 1.15 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 1.15 User’s Guide 4 Software Description To set filter properties, select a filter and click on any of the white boxes of the TW and DG columns next to the filter name. This displays the Filter Properties window.
  • Page 80 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Digital Gain Note: This is camera-dependent, when working with AxioCam MRm Rev 3. the Index value ranges from 0 to 4, and with pco.edge from 0 to 6. 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 1.15 User’s Guide 4 Software Description 4.5.2 Scan Options Figure 49 – Scan options tab 2012. March 13. 3DHISTECH Ltd. 81(132)
  • Page 82 Pannoramic SCAN 150 1.15 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 1.15 User’s Guide 4 Software Description Do not use multilayer mode on empty field-of-views – If selected, the • extended focus or the Z-stack function will not run on the empty (not containing specimen) field of views.

  • Page 84: Preview Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Digital slide destination This 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.
  • Page 85 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Use threshold Scan specimen with auto threshold – This automatically detects the specimen in the • preview image. Scan specimen with user set threshold – This sets the sensitivity of the specimen detection.
  • Page 86 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description General threshold options Remove coverslip – If selected, the edges of the coverslip are not detected as specimen to be scanned. Fill holes in scan area – If selected, the holes inside the specimen will also be scanned.

  • Page 87: Hardware Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 4.5.4 Hardware tab Figure 52 – Hardware tab (selected mode: User controlled) 2012. March 13. 3DHISTECH Ltd. 87(132)
  • Page 88 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Live You can display a live image of the current specimen by clicking This option has no effect on a running digitization process where no live image is displayed. To display a live image during scanning, select Show images during scanning on the Service tab.
  • Page 89 Pannoramic SCAN 150 1.15 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 90: Service Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description If you select the Interpolated focus option, the coarse focus level is calculated from three different focus points of the specimen. Carry out a manual focusing sequence in the preview image on those three points. Set the correct focus value of the desired preview position by clicking Set.

  • Page 91: Using Fluorescent Automatic Mode

    Pannoramic SCAN 150 1.15 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 92 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description The Routine work tab panel provides the following basic digitization functions: To insert and remove slides In Automatic mode a preloaded magazine has to be placed into the main unit. This magazine •...
  • Page 93 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Filter Settings Focus channel – Choose a filter that you want to focus with. It is recommended to choose a • filter that is related to the staining that stained the most of the specimen, or where the exposition time is low.
  • Page 94 Pannoramic SCAN 150 1.15 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 <AUTO>...
  • Page 95 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Fluorescent compensation Use saved compensation image. Compensation images can be created for those filters, for which compensation images are created previously. To create compensation image, see section 4.2.2 Image compensation / Fluorescent compensation.

  • Page 96: Barcodes Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 4.6.2 Barcodes tab Figure 57 – Barcodes tab On this tab, you can set identification features to the various slides and for assigning profiles. 2012. March 13. 3DHISTECH Ltd. 96(132)
  • Page 97 Pannoramic SCAN 150 1.15 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. You •...
  • Page 98 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Example for barcode usage Barcode: Folder_Vir_123_prof_n • Folder is the folder for saving • Vir is the name of the virtual slide • 123_prof_n is the profile name • The barcode control will then look like the following: •...

  • Page 99: Preview Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Load Names and Profiles from File • You can import previously saved names and assigned profiles by clicking Save Names and Profiles to File • By clicking the button, you can save the entered names and assigned profiles.

  • Page 100: Focus Tab

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 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. In Automatic mode you cannot change the threshold values (it will use the threshold values that were set previously in the Manual mode), and when activating the Use selection box option, the area cannot be set.

  • Page 101: 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 SCAN 150 scanner software. Follow these steps to install the ScanToServer application: 1.
  • Page 102 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 2. Accept the License Agreement, then click Install to continue. 3. Click Finish to finalize the installation process of the ScanToServer application. 2012. March 13. 3DHISTECH Ltd. 102(132)
  • Page 103 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description To setup a connection with a designated server, follow the steps below: 1. Click Scan Options on the Routine Work tab panel. Figure 61 – Scan Options button 2. Select the Scan to CaseCenter option in the Scan Option window, then click the Connect button.
  • Page 104 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description 3. Type in or select the server address from the Connect to: drop-down menu, and give the User name and password. Activate the Secure connection option to enable HTTPS connection. Click Connect when finished.
  • Page 105 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Figure 65 – CaseCenter window in Automatic Mode Give the number of the starting (First slide) and the final slide (Last slide) to be • scanned in the appropriate field. For example, if you want to scan slides to server from 3-14, type: First slide: 3;...
  • Page 106 Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description Figure 66 – Profile selection Profiles 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 107: Using Profiles

    Pannoramic SCAN 150 1.15 User’s Guide 4 Software Description If modification is done to the folder tree in the CaseCenter server, click Update Tree • to refresh the tree view. Click Done when finished or Cancel to quit the CaseCenter window. If you save the •...
  • Page 108 Pannoramic SCAN 150 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 • Use of scan everything within marked area (ON/OFF) •...

  • Page 109: Troubleshooting And Maintenance

    Pannoramic SCAN 150 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 110: Cleaning The Device

    Pannoramic SCAN 150 1.15 User’s Guide 5 Troubleshooting and Maintenance HXP 120 illuminator Keep inflammable and combustible materials outside the range of HXP 120 illuminator. • Do not expose yourself to the UV radiation of the HXP 120 illuminator. •...

  • Page 111: Troubleshooting

    Pannoramic SCAN 150 1.15 User’s Guide 5 Troubleshooting and Maintenance 5.2 Troubleshooting This section describes the most common troubleshooting solutions for the Pannoramic SCAN 150 product. If any problem arises that does not have solution in this manual, contact the service personnel.
  • Page 112 Pannoramic SCAN 150 1.15 User’s Guide 5 Troubleshooting and Maintenance 4. Remove magazine manually (see section 5.3.7 Removing a Magazine from the Transporting System). If a jammed magazine cannot be removed, contact service personnel. 5. Reattach protective covers. 6. Reconnect 24V power supply and control computer to line power supply.
  • Page 113 Pannoramic SCAN 150 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 114: Fluorescent Applications (Optional)

    Pannoramic SCAN 150 1.15 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 115: Maintenance

    Pannoramic SCAN 150 need to be opened in order to eliminate the problem. Before removing the covers, exit the control software, switch off the 24 V power supply and disconnect the power cables.

  • Page 116: Replacing The Halogen Lamp

    Pannoramic SCAN 150 1.15 User’s Guide 5 Troubleshooting and Maintenance Caution! Use caution to prevent contact between the safety rails (5) and the scan camera as you take cover (1) off. 3. Turn eccentric screw at the front of the baseplate by 90° anticlockwise and use both hands to carefully raise and take cover (2) off.
  • Page 117 Pannoramic SCAN 150 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 118: Replacing Lamp Module (For Fluorescent Option)

    Pannoramic SCAN 150 1.15 User’s Guide 5 Troubleshooting and Maintenance 5.3.3 Replacing Lamp Module (for Fluorescent Option) NOTE: This section recites some extracts from the HXP 120 operating manual. For detailed information, especially instructions regarding safety, consult that manual. Also, no alignment is required for the lamp module.
  • Page 119 Pannoramic SCAN 150 1.15 User’s Guide 5 Troubleshooting and Maintenance 4. Loosen pressure bolt with the lever (1) and by keeping the lever pressed, remove lamp module (2) (see Figure 72). Figure 72 – Removing the lamp module 5. Carefully retrieve the new lamp module from its transporting container. Hold the lamp module only by its ceramic part.

  • Page 120: Removing A Slide

    Pannoramic SCAN 150 1.15 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 121 Pannoramic SCAN 150 1.15 User’s Guide 5 Troubleshooting and Maintenance Figure 75 – 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 122: Installing And Removing The Filter Module (Fluorescent Option)

    Pannoramic SCAN 150 1.15 User’s Guide 5 Troubleshooting and Maintenance 5.3.5 Installing and Removing the Filter Module (Fluorescent Option) Figure 76 – 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 123: Removing The Magazine From The Transporting System

    Pannoramic SCAN 150 1.15 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 124 Note: Any manipulation performed on a mechanical component (for example transporting system) by the user must be followed by a complete Pannoramic SCAN 150 initialization routine (software restart). March 13, 2012 - Rev. 1 3DHISTECH Ltd. 124(132)

  • Page 125: Transporting Pannoramic Scan 150

    Pannoramic SCAN 150 1.15 User’s Guide 5 Troubleshooting and Maintenance 5.3.7 Transporting Pannoramic SCAN 150 The following procedure shows how to transport the Pannoramic SCAN 150. Figure 78 – Transporting handles Caution! Do not use the blue guide rail bar (1) to raise, shift or transport the...
  • Page 126 3. Turn carrying handles by 90° (B) towards the base unit to secure them. 4. Now you can transport Pannoramic SCAN 150 with the help of another person. 5. After finishing transportation, push carrying handles back into normal position (C).

  • Page 127: Technical Data

    Pannoramic SCAN 150 SP1 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 128 Pannoramic SCAN 150 SP1 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 129 Pannoramic SCAN 150 SP1 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...
  • Page 130 Pannoramic SCAN 150 SP1 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 131 Pannoramic SCAN 150 SP1 1.14 User’s Guide 6 Technical Data Bit-depth 16 bit Pixel resolution with 20x objective and 1x C-mount adapter 0.22µm Cooling Peltier with forced air (fan) Connection type dual Camera Link (full, 10 taps) Control computer, minimum system requirements...
  • Page 132 Marker..........................53, 56, 85, 108 Pannoramic MIDI..........................8 Pannoramic SCAN 150..2, 3, 9, 10, 11, 13, 14, 16, 17, 18, 19, 21, 27, 42, 101, 111, 115, 124, 125, Pannoramic Viewer.......................20, 63, 74, 113 Preview. .3, 22, 26, 31, 37, 39, 46, 47, 52, 54, 55, 56, 57, 60, 62, 72, 75, 84, 85, 86, 90, 99, 100, 129 RGB..............................65...

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