3D Histech Pannoramic SCAN 150 1.18 User Manual
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3D Histech Pannoramic SCAN 150 1.18 User Manual

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Pannoramic SCAN 150
1.18
User's Guide
April 3, 2014
Rev. 1
PS1.18-UG-EN-Rev1

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Summary of Contents for 3D Histech Pannoramic SCAN 150 1.18

  • Page 1 Pannoramic SCAN 150 1.18 User’s Guide April 3, 2014 Rev. 1 PS1.18-UG-EN-Rev1...

  • Page 2: Table Of Contents

    Pannoramic SCAN 150 1.18 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 1.18 User’s Guide 4.3.2 Scan Options window.............................49 4.3.3 Preview panel..............................51 4.3.4 Preview area scanned by preview camera.....................54 4.3.5 Focus panel..............................60 4.3.6 Service panel..............................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 panel............................65...
  • Page 4 Pannoramic SCAN 150 1.18 User’s Guide Index........................... 131 April 3, 2014 - Rev. 1 3DHISTECH Ltd. 4(131)

  • Page 5: Disclaimer

    Pannoramic SCAN 150 1.18 User’s Guide Disclaimer Copyright © 2001-2014 3DHISTECH Ltd. All rights reserved. Intellectual property related to the 3DHISTECH products are as follows: EP 1,789,831; US 7,663,078; EP 2,024,772; JP 2009-512685; US 12/301,781; EP 1,644,767; JP 2007- 516451; US7,327,515; EP 1,994,398; JP 2008-557835; US 12/281,566; U0700210; US 6,246,785;...
  • Page 6 Pannoramic SCAN 150 1.18 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 1.18 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 1.18 User’s Guide Character Formats and Symbols Declaration of Conformity 3DHISTECH Ltd. declares that the product Pannoramic SCAN 150 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

    Pannoramic SCAN 150 1.18 User’s Guide Notes Regarding Operational Safety 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 section 1.1.3 Warning and Information Labels have the following meanings:...
  • Page 10 Pannoramic SCAN 150 1.18 User’s Guide Notes Regarding Operational Safety Remember to unplug the power cord before you open the Pannoramic SCAN 150 or replace a fuse! Disconnect plug! Only connect external devices that are safety extra low voltage rated to the Warning! instrument to avoid the risk of electrical shock.

  • Page 11: Notes On Warranty

    Pannoramic SCAN 150 1.18 User’s Guide 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 1.18 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

    Pannoramic SCAN 150 1.18 User’s Guide 1 Product Description 1 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 (histological sections, typically). The target users of the product can work for example, in education, research, industrial, or medical sectors.
  • Page 14 Pannoramic SCAN 150 1.18 User’s Guide 1 Product Description Software-aimed flat-field correction compensation method to create homogenous slide • image 150 slide automatic loading and scanning • Improved permanent autofocus • 3MP camera for barcode reading and preview image •...

  • Page 15: Warning And Information Labels

    Pannoramic SCAN 150 1.18 User’s Guide 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 illumination unit.

  • Page 16: Base Unit

    Pannoramic SCAN 150 1.18 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 17: System Overview

    Pannoramic SCAN 150 1.18 User’s Guide 1 Product Description Fluorescence option – B • 8. Lumencor Spectra 6 Light Engine (fiber-coupled illumination unit, use with pco.edge 4.2 camera only) 9. Illumination adapter (optional, use with pco.edge 4.2 camera only) 10. Fiber optic cable 1.2 System Overview...

  • Page 18: Hardware Options

    Pannoramic SCAN 150 1.18 User’s Guide 1 Product Description 1. HXP 120 fiber-coupled illumination unit (optional) 2. 24 V external power supply unit 3. Lumencor Spectra 6 Light Engine (optional) 4. Monitor 5. Mouse 6. Control computer 7. Keyboard 8. Pannoramic SCAN 150 base unit 9.
  • Page 19 Pannoramic SCAN 150 1.18 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 1.6× adapter Warning! The installation of the cameras in Pannoramic SCAN 150 must be carried out by trained professionals, otherwise the warranty will be automatically voided.
  • Page 20 Pannoramic SCAN 150 1.18 User’s Guide 1 Product Description Pannoramic SCAN 150 Basic Mixed Option – Base unit completely equipped with Stingray or • CIS VCC-FC60FR19CL cameras for Brightfield scanning; with AxioCam camera and HXP 120 illumination unit, trigger cable and filters for fluorescence scanning Pannoramic SCAN 150 Advanced Mixed Option –...

  • Page 21: Control Software

    Pannoramic SCAN 150 1.18 User’s Guide 1 Product Description 1.2.3 Control Software Pannoramic Scanner control software Optional: Fluorescence • Extended focus • Z-stack • Barcode reader (licensed feature) • Pannoramic Viewer software (fully functional) Optional: CaseCenter • TMA module •...

  • Page 22: Installation

    Pannoramic SCAN 150 1.17 User’s Guide 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 23: Connectors And Cables

    Pannoramic SCAN 150 1.17 User’s Guide 2 Installation 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. 4x USB port 10. 2x USB port 11. Network port 12.

  • Page 24: Coupling The Lumencor Spectra 6 Unit With The Scanner

    Pannoramic SCAN 150 1.17 User’s Guide 2 Installation Power supply cable (between 230V/110V and CIS camera) • Power supply cable (between 230V/110V and pco.edge 4.2 camera) • Optical cable (between HXP 120 fluorescent illumination unit or Lumencor Spectra 6 Light •...

  • Page 25: Operating Slides And Magazines

    Pannoramic SCAN 150 1.18 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 slides and coverslips that meet the following specifications:...

  • Page 26: Affixing Barcode Stickers To Slides

    Pannoramic SCAN 150 1.18 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. Note: FISH fluorescent signals become more easily detectable for the...

  • Page 27: Inserting And Removing Slides

    Pannoramic SCAN 150 1.18 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 28 Pannoramic SCAN 150 1.18 User’s Guide 3 Operating Slides and Magazines Caution! Incorrect slide insertion may break the glass. Always make sure that slides are correctly inserted in the magazine. The edge of the broken area of the slide is sharp and its removal can lead to injury and contagion! Broken slide can be removed only by a well-trained person! The magazines can contain a maximum of 25 slides.
  • Page 29 Pannoramic SCAN 150 1.18 User’s Guide 3 Operating Slides and Magazines To insert and remove magazines Figure 8 – Inserting a magazine 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! 1.
  • Page 30 Pannoramic SCAN 150 1.18 User’s Guide 3 Operating Slides and Magazines Caution! Make sure that the magazines are not misplaced, because it can cause serious damages in the feeding mechanism. Note: The input stack can be filled with a maximum of 6 magazines in addition to the one in the magazine loader.

  • Page 31: Software Description

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4 Software Description 4.1 Starting / Exiting Pannoramic Scanner Software 4.1.1 Starting the software For the scanning software you can choose from different scanning modes at the startup of the program.

  • Page 32: Exiting The Software

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.1.2 Exiting the software If you close a mode or one of the options window the Mode selection window turns active again. To exit the software, click X in the title bar of the Mode selection window, and the magazine(s) on the input stack can be unloaded to the output stack automatically if clicking Yes in the appearing message box.
  • Page 33 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Figure 12 – Barcode settings Functions To move the lowest magazine in the input stack to the loading position click • To move the magazine into the output stack, click •...
  • Page 34 Pannoramic SCAN 150 1.18 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 35: Image Compensation

    Pannoramic SCAN 150 1.18 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 36 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Brightfield Compensation Figure 13 – Brightfield compensation Camera Selection This field displays the active camera. Currently, there is only one active camera for Brightfield mode. Objective Selection This field displays the objective used for scanning.
  • Page 37 Pannoramic SCAN 150 1.18 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 38: Microscope Settings

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.2.3 Microscope Settings By moving the mouse cursor over the buttons, the software displays information about the setting you are interested in. Base Settings Figure 15 – Base Settings panel Objective type You can select the type and the magnification level of the objectives.
  • Page 39 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Note: If Lumencor is configured as illumination unit, the corresponding Enable Lumencor hardware trigger option is displayed on the form. The function Enable HXP 120 fluorescent light source shutter is available only for AxioCam MRm Rev 3. The AxioCam and the HXP 120 must be connected by a trigger cable to enable this function.
  • Page 40 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Camera Rotation Figure 17 – Camera Rotation panel 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, and do not modify these settings yourself.
  • Page 41 Pannoramic SCAN 150 1.18 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 18 – Z Difference panel April 3, 2014 - Rev.

  • Page 42: Event Call Settings

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Service Figure 19 – Service panel This panel contains control and maintenance functions. Emergency Manual Slide Removal Position The specimen holder will be moved to a position where the slide can be removed manually after opening the cover (see section 5.3.1 Removing the protective cover).
  • Page 43 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Two of the three settings are responsible for opening external applications (.exe or .bat) as defined. For example, Pannoramic Viewer software can be opened after finishing scanning, or the computer can be turned off after scanning is finished. You can define external application call settings for the...
  • Page 44 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description First click Setup to display the Messenger Setup window, in which you can dedicate an e-mail server through which the software sends e-mails to the selected recipients. Figure 21 – Messenger Setup window In the Messenger Setup window the following parameters can be set: Message Type –...
  • Page 45 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description If you have properly set messenger settings, click OK, then click Users in the Message Call • section of the Event Call Settings window to address functions to the recipients (that can be selected under the Send Message when: field).

  • Page 46: Using Brightfield Manual Mode

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 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 47: Routine Work Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.3.1 Routine work panel Figure 24 – Routine work panel The Routine work panel 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 48 Pannoramic SCAN 150 1.18 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 49: Scan Options Window

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.3.2 Scan Options window Figure 25 – Scan options window These settings will determine the quality and storage location of the virtual slide. You can choose the following predefined image formats (and a subsequent custom option) from the...
  • Page 50 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Accordingly, further adjustments can be made, except if PNG or BMP image format is selected. Figure 26 – Image encoding window JPEG – The quality can be adjusted with the JPEG quality factor slider. Greater ◦...

  • Page 51: Preview Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Select the Scan To CaseCenter function to scan directly to CaseCenter server. For • information on how to use the ScanToServer application, see section 4.7 Scan To Server. If you enable the Directory function, the virtual slides will be digitized in the specified •...
  • Page 52 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Important! Make sure that the detection result is acceptable for you. Otherwise set the threshold value manually or append missing areas with the help of Scanned function located at the preview toolbar. For more information see section 4.3.4 Preview area scanned by preview camera –...
  • Page 53 Pannoramic SCAN 150 1.18 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. Depending on the threshold level, it is possible that the edges of the coverslip are detected as areas to be digitized.

  • Page 54: Preview Area Scanned By Preview Camera

    Pannoramic SCAN 150 1.18 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 55 Pannoramic SCAN 150 1.18 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 56 Pannoramic SCAN 150 1.18 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 57 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description TMA tool TMA tool is used for selecting TMA spots on TMA slides. You can set the selection settings on the following four tabs: Select panel Figure 34 – TMA tool: Select To create a new TMA object, click New.
  • Page 58 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Set the type of TMA block on this panel. 1. Select the shape of the TMA spots (Rectangle spots or Circle spots). 2. Enter the number of rows and columns in the Rows and Columns fields or select the appropriate values with the arrows.
  • Page 59 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Figure 37 – TMA tool Move panel with preview April 3, 2014 - Rev. 1 3DHISTECH Ltd. 59(131)

  • Page 60: Focus Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Label area To rotate the label area by 180°, select the Rotate image by 180 degrees checkbox. Figure 38 – Label area 4.3.5 Focus panel Figure 39 – Focus panel April 3, 2014 - Rev. 1 3DHISTECH Ltd.
  • Page 61 Pannoramic SCAN 150 1.18 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. To display a live image during scanning, select Show images during scanning in the Service panel.

  • Page 62: Service Panel

    Pannoramic SCAN 150 1.18 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 63: Display Field And Toolbar For Live Images

    Pannoramic SCAN 150 1.18 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 1.18 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 65: Start Scan

    Pannoramic SCAN 150 1.18 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 66 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description The Routine work panel provides basic digitization functions. To insert and remove slides In Automatic mode a preloaded magazine has to be placed into the main unit. This magazine • is the first one, irrespectively of the total number of magazines (1-6) to be loaded. Click to load the magazine.

  • Page 67: Barcodes Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.4.2 Barcodes panel Figure 44 – Barcodes panel Identification features and profiles for slides can be set on this panel. April 3, 2014 - Rev. 1 3DHISTECH Ltd. 67(131)
  • Page 68 Pannoramic SCAN 150 1.18 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 69 Pannoramic SCAN 150 1.18 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 1.18 User’s Guide 4 Software Description 4. Generate name if no name was defined By choosing this option, a name is generated automatically in the following format if no name was defined and there is no barcode: (for example, <magazine number>M<slide position>...

  • Page 71: Preview Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.4.3 Preview panel Figure 45 – Preview panel The Preview panel 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 Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.4.4 Focus panel Figure 46 – Focus panel 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 Panel

    Pannoramic SCAN 150 1.18 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 74: Start Scan

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.4.6 Start Scan To start digitization process, click after checking settings in the Barcodes panel. 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 49).

  • Page 75: Using Fluorescent Manual Mode

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.5 Using Fluorescent Manual Mode 4.5.1 Routine work panel Figure 50 – Routine work panel The Routine work panel provides basic digitization functions. April 3, 2014 - Rev. 1 3DHISTECH Ltd.
  • Page 76 Pannoramic SCAN 150 1.18 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 77 Pannoramic SCAN 150 1.18 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 78 Pannoramic SCAN 150 1.18 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 79 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Digital Gain Note: This function is camera-dependent, when working with AxioCam MRm Rev3, the Index value ranges from 0 to 4, and when using pco.edge 4.2 camera, the value ranges from 0 to 6.

  • Page 80: Scan Options

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.5.2 Scan Options Figure 53 – Scan options panel 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.
  • Page 81 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Select an item from the Image quality drop-down list. There are four predefined quality types, and a custom settings option on the list: Excellent (JPEG XR: 90) • Good (JPEG XR: 80) •...
  • Page 82 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Scan Settings Focus frequency – This value determines how many field of views will pass before • the sample is refocused. This value should be selected depending on the unevenness and size of the specimen.
  • Page 83 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Multi Filter Change Mode This is for a multi-channel digitization. To optimize speed, filter change should take place after the digitization of the slide with one channel. Filters should be changed for each field of view if very precise colocalization is required, but consider that this option is more time consuming.

  • Page 84: Preview Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.5.3 Preview panel The Preview panel offers options for threshold setting and selection of the area to be scanned. Figure 55 – Preview panel Use threshold Scan specimen with auto threshold – This automatically detects the specimen in the •...
  • Page 85 Pannoramic SCAN 150 1.18 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. 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.
  • Page 86 Pannoramic SCAN 150 1.18 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. Warning! Do not use Remove coverslip function on TMA slides! The layout of TMA slides may mislead the detecting algorithm.

  • Page 87: Hardware Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.5.4 Hardware panel Figure 57 – Hardware panel (selected mode: User controlled) April 3, 2014 - Rev. 1 3DHISTECH Ltd. 87(131)
  • Page 88 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Live Click to display a live image of the current specimen in the Live image display field. This option has no effect on a running digitization process where no live image is displayed.
  • Page 89 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description You can enter the Index value by typing it in the box or by selecting the value with the arrow buttons. If you raise the Index value, the exposition time is halved by every step, and the image becomes noisier.

  • Page 90: Service Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description If you deselect the Use fine focus checkbox, the software immediately starts scanning on the basis of the interpolated values, without pre-fine-focusing. Manual Exposure By selecting the Use manual exposure times, you can determine the exposure times. The values are typically set on Auto, meaning that the exposure times are determined automatically.

  • Page 91: Using Fluorescent Automatic Mode

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.6 Using Fluorescent Automatic Mode 4.6.1 Routine work panel Figure 59 – Routine work panel The Routine work panel provides some 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 92 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description button is active if there is no magazine loaded in the input feed. Click this button to load the magazine. If you do not want to load all the slides, you can specify the first and last slide to be loaded in •...
  • Page 93 Pannoramic SCAN 150 1.18 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 1.18 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 1.18 User’s Guide 4 Software Description Multilayer Settings By clicking the the Multilayer Settings window is displayed. The containing settings are the same as in Brightfield mode, but you can select extended focus or Z-stack value for the specific channel.

  • Page 96: Barcodes Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 4.6.2 Barcodes panel Figure 62 – Barcodes panel On this panel, you can set identification features to the various slides and for assigning profiles. April 3, 2014 - Rev. 1 3DHISTECH Ltd.
  • Page 97 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Modes on the panel 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 1.18 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 Panel

    Pannoramic SCAN 150 1.18 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 Panel

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description The Preview panel 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

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description This panel contains control and maintenance functions. Emergency Manual Slide Removal Position The specimen holder will be moved to a position where the slide can be removed manually after opening the cover (see section 5.3.1 Removing the protective cover).
  • Page 102 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description 2. Select the Scan to CaseCenter option in the Scan Option window, then click the Connect button. Figure 67 – Scan to CaseCenter option 3. Type in or select the server address from the Connect to: drop-down menu, and give the User name and password.
  • Page 103 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Slide settings in the Scan To Server window 1. In the Routine work panel, click the button. 2. The Scan To Server window is displayed. Slide data is displayed in a form for each magazine. If in Manual Mode, only the data of •...
  • Page 104 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description To scan slides within a defined range, first give the number of the starting (First • slide) and the final slide (Last slide). For example, if you want to scan slides to server from 3-14, type: First slide: 3;...
  • Page 105 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Select a folder where the slide will be scanned to. After clicking the Folder drop- • down list, a path will be displayed in which the destination folder can be selected.

  • Page 106: Using Profiles

    Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Click Done when finished or Cancel to quit the Scan To Server window. If you save • the form, slides will be scanned to server according to the data recorded in the form after you start scanning.
  • Page 107 Pannoramic SCAN 150 1.18 User’s Guide 4 Software Description Use of scan everything within marked area (ON/OFF) • Remove coverslip function (ON/OFF) • Filling of holes (ON/OFF) • Use of removing specks according to the set value (ON/OFF) • Use saved scan area •...

  • Page 108: Troubleshooting And Maintenance

    Pannoramic SCAN 150 1.18 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 109: Cleaning The Device

    Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance HXP 120 illumination unit Keep inflammable and combustible materials outside the range of HXP 120 illumination unit. • Do not expose yourself to the UV radiation of the HXP 120 illumination unit.

  • Page 110: Troubleshooting

    Pannoramic SCAN 150 1.18 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 111 Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance 4. Remove magazine manually (see section 5.3.6 Removing the 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 112 Pannoramic SCAN 150 1.18 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 113: Fluorescent Applications (Optional)

    Pannoramic SCAN 150 1.18 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 114: Maintenance

    Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance 5.3 Maintenance This section describes the most common maintenance solutions that can be performed by the user of the product. For maintenance solutions not described in this manual, contact the service personnel.

  • Page 115: Replacing The Halogen Lamp

    Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance Caution! Use caution to prevent contact between the safety rails and the scan camera as you take cover off. 3. Turn eccentric screw at the front of the base plate by 90° anticlockwise and use both hands to carefully raise and take cover (2) off.
  • Page 116 Pannoramic SCAN 150 1.18 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 117: Replacing Lamp Module (For Fluorescent Option)

    Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance 5.3.3 Replacing Lamp Module (for Fluorescent Option) 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. Accordingly, the module is fully operational after lamp replacement.
  • Page 118 Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance 3. Press plug securing latches inward (1) then disconnect plug of the lamp module (2) (see Figure 78). Figure 78 – Disconnect plug 4. Loosen pressure bolt with the lever (1) and by keeping the lever pressed, remove lamp module (2) (see Figure 79).

  • Page 119: Removing A Slide

    Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance Caution! Incorrect handling may considerably reduce the lamp module’s useful life. Hold it by the ceramic part in all cases! Never touch the lamp’s glass surface or the inside surface of the reflector. Skin oil is harmful to these parts.
  • Page 120 Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance Figure 81 – Removing the slide loader Figure 82 – Removing a slide 1. Open the protective cover (see section 5.3.1 Removing the protective covers). 2. Push locking lever (1) to the left, and keep the lever in this position.

  • Page 121: Installing And Removing The Filter Module (Fluorescent Option)

    Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance Caution! If the slide is broken, make sure to remove all pieces completely from the device. The edge of the broken area of the slide is sharp and it can lead...
  • Page 122 Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance 2. Pull protective cover halves apart or remove the right part completely (see section 5.3.1 Removing the protective covers). 3. Select the desired filter in the corresponding software window (see section 4.2.3 Microscope Settings / Filter Settings).

  • Page 123: Removing The Magazine From The Transporting System

    Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance 5.3.6 Removing the magazine from the transporting system Figure 84 – Removing a magazine 1. Remove the protective covers (see section 5.3.1 Removing the protective covers). 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.

  • Page 124: Transporting Pannoramic Scan 150

    Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance 3. Push the magazine on the guide rails (2-3) to the left or to the right to remove it from the transporting system. 4. If the magazine is tilted because of twisted tappets (1), first restore the tappets to their initial position.
  • Page 125 Pannoramic SCAN 150 1.18 User’s Guide 5 Troubleshooting and Maintenance Note: The base unit has four carrying handles for transporting. Two or four people can carry the base unit using these carrying handles. To determine the appropriate number of transporter people, observe the laws of your country regarding load carrying capacity limitations.

  • Page 126: Technical Data

    Pannoramic SCAN 150 1.17 User’s Guide 6 Technical Data 6 Technical Data Dimensions (width x depth x height) Base unit approx. 740 mm (W) x 530 mm (D) x 450 mm (H) Base unit without fluorescence option approx. 740 mm (W) x 530 mm (D) x 450 mm (H) 24V 100W power supply approx.
  • Page 127 Pannoramic SCAN 150 1.17 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 Radio interference suppression in accordance with EN 55011 class B...
  • Page 128 Pannoramic SCAN 150 1.17 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 Lumencor light source SPECTRA 6 Light Engine...
  • Page 129 Pannoramic SCAN 150 1.17 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 Bit-depth 8 bit / 14 bit (16 bit in High SNR mode) Pixel resolution with 20×...
  • Page 130 Pannoramic SCAN 150 1.17 User’s Guide 6 Technical Data Bit-depth 16 bit Pixel resolution with 20x objective and 1x C-mount adapter 0.325µm Cooling Peltier with forced air (fan) Connection type Dual Camera Link Full (10 taps, 85MHz) Control computer, minimum system requirements Operating System Microsoft Windows 7 Professional SP1 64-bit EN 2x Intel Xeon processor (6-core) 12 MB l2 cache...
  • Page 131 Pannoramic SCAN 150 1.18 User’s Guide Index Index AxioCam..............18, 19, 20, 23, 24, 39, 79, 81, 82, 88, 94, 113, 129 Barcode....21, 26, 27, 28, 32, 33, 34, 35, 48, 65, 67, 68, 69, 70, 74, 77, 96, 97, 98, 104, 128 Brightfield..............13, 18, 19, 20, 31, 36, 38, 46, 50, 65, 79, 95, 106...

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