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3D Histech Pannoramic 250 FLASH II User Manual

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Pannoramic 250 FLASH II
1.18.1
User's Guide
May 29, 2014
Rev. 1

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Summary of Contents for 3D Histech Pannoramic 250 FLASH II

  • Page 1 Pannoramic 250 FLASH II 1.18.1 User’s Guide May 29, 2014 Rev. 1...

  • Page 2: Table Of Contents

    Pannoramic 250 FLASH II 1.18.1 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 250 FLASH II 1.18.1 User’s Guide 4.2.3 Microscope Settings............................43 4.2.4 Event Call Settings............................48 4.3 Using Brightfield Manual Mode....................50 4.3.1 Routine work panel............................52 4.3.2 Scan Options window.............................54 4.3.3 Preview panel..............................57 4.3.4 Preview area scanned by preview camera.....................60 4.3.5 Focus panel..............................66 4.3.6 Service panel..............................68...
  • Page 4 Pannoramic 250 FLASH II 1.18.1 User’s Guide 5.3.5 Installing and Removing the Filter Module (Fluorescent Option)..............127 5.3.6 Removing a Magazine from the Transporting System..................128 5.3.7 Transporting..............................130 6 Technical Data......................132 Index........................... 136 May 29, 2014 – Rev. 1 3DHISTECH Ltd.

  • Page 5: Disclaimer

    Pannoramic 250 FLASH II 1.18.1 User’s Guide Disclaimer Copyright © 2001-2014 3DHISTECH Ltd. All rights reserved. Intellectual property related to the 3DHISTECH products are as follows: EP 1,789,831; US 7,663,078; EP 2,024,772; JP 2009-512685; US 12/301,781; EP 1,644,767; JP 2007- 516451;...
  • Page 6 Pannoramic 250 FLASH II 1.18.1 User’s Guide THE SOFTWARE IS PROVIDED “AS IS” AND WITHOUT WARRANTY OF ANY KIND, EXPRESSED, IMPLIED OR OTHERWISE, INCLUDING WITHOUT LIMITATION, ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. IN NO EVENT SHALL SAM LEFFLER OR SILICON GRAPHICS BE LIABLE FOR ANY SPECIAL, INCIDENTAL,...

  • Page 7: Character Formats And Symbols

    Pannoramic 250 FLASH II 1.18.1 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, push-buttons 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

    Declaration of Conformity Declaration of Conformity 3DHISTECH Ltd. declares that the product Pannoramic 250 FLASH II 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 250 FLASH II and in the section 1.1.3 Warning and Information Labels have the following meanings:...
  • Page 10 Caution! influences to a maximum possible degree. During periods of non-use, the Pannoramic 250 FLASH II must be protected with a dust cover. Check that power is turned off before you put the cover on. There is crush hazard in the movement area of the slide insert during operation.

  • Page 11: Notes On Warranty

    Notes Regarding Operational Safety Notes on Warranty 3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic 250 FLASH II 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 250 FLASH II 1.18.1 User’s Guide Notes Regarding Operational Safety Terms and Abbreviations Comma Separated Value Field of View Numerical Aperture Photobleaching A phenomenon that leads to a dramatic loss of fluorescence emission intensity (a fluorophore permanently loses the ability to fluoresce) due to photon-induced chemical damage and covalent modification, therefore fluorescent signals cannot be properly detected.

  • Page 13: Product Description

    1.1.2 Features and Benefits The Pannoramic 250 FLASH II offers world class brightfield and fluorescent whole slide scanning on up to 9 channels. An outstanding 0.19 µm/pixel (in Brightfield) and 0.16 µm/pixel (in Fluorescent) resolution is achieved with a 40×/0.95 NA (equivalent to 52×...
  • Page 14 Pannoramic 250 FLASH II 1.18.1 User’s Guide 1 Product Description Fluorescent scanning mode: • High-end fluorescent illumination device – Lumencor Spectra Light Engine 6 • 3 times faster and more silent filter change • Multiband filter support • FL scanning with a low noise, 16-bit scientific CMOS pco.edge 4.2 camera •...

  • Page 15: Warning And Information Labels

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 1 Product Description 1.1.3 Warning and Information Labels The following figure contains the labels used on the Pannoramic 250 FLASH II main unit and the HXP 120 fluorescent illumination unit. Figure 1 – Warning and information labels May 29, 2014 –...

  • Page 16: Main Parts Of The Base Unit

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 1 Product Description 1.1.4 Main parts of the Base Unit The following figures show the main parts of the base unit. Figure 2 – Main parts of base unit 1. Protective FL cover 2.

  • Page 17: System Overview

    The standard scope of delivery of the product includes the following hardware and software components. 1.2.1 Pannoramic 250 FLASH II system The following figure shows the main parts of the Pannoramic 250 FLASH II system. Figure 3 – Pannoramic 250 FLASH II system overview 1. Pannoramic 250 FLASH II base unit 2.

  • Page 18: Hardware Options

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 1 Product Description 1.2.2 Hardware Options The configuration of the control computer and monitor can vary depending on the product order. Cameras AxioCam MRm Rev 3 1 CCD scientific, cooled, monochrome camera for high quality, sensitive fluorescent applications.
  • Page 19 Motorized camera changer Figure 4 – Motorized camera changer You can fit two cameras into the Pannoramic 250 FLASH II on the first adapter (1) (fluorescent position) and the second adapter (2) (brightfield position) at the same time. They are set and switched by the software automatically, without any human assistance.
  • Page 20 Objectives Figure 5 – Objective changer You can select two different objectives to be equipped with the Pannoramic 250 FLASH II, the first objective (1) and the second objective (2). 20x/NA 0.80 and 40x/NA 0.95 objectives can be used. You can change between the objectives with one click.
  • Page 21 FOVs. Base Unit options Pannoramic 250 FLASH II Basic Brightfield Option – base unit equipped with CIS VCC- • FC60FR19CL camera for Brightfield scanning (no fluorescent accessories included) Pannoramic 250 FLASH II Basic Fluorescence Option –...

  • Page 22: Control Software

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 1 Product Description Fluorescent Options for Pannoramic 250 FLASH II Fluorescent unit (internal part) HXP 120 illumination unit (can be used only with AxioCam MRm Rev3 camera) Lumencor Spectra 6 Light Engine illumination unit (can be used only with pco.edge 4.2 camera)
  • Page 23 Pannoramic 250 FLASH II 1.18.1 User’s Guide 1 Product Description Pannoramic Viewer software (fully functional) • Optional: CaseCenter • Pannoramic Viewer TMA module • 3D Reconstruction module • QuantCenter, HistoQuant, NuclearQuant, MembraneQuant, FISHQuant, CISHQuant, and • DensitoQuant modules TumorBoard module •...

  • Page 24: Installation

    Pannoramic 250 FLASH II 1.18.1.1 User’s Guide 2 Installation 2 Installation Warning! The installation of Pannoramic 250 FLASH II must be carried out by trained professionals! In any other case the warranty will be automatically voided. Supplier/Distributor is not liable for any damages caused by an installation that is not carried out by a professional person.

  • Page 25: Connectors And Cables

    Power supply cable (between 230V/110V and monitor) • Power supply cable (between 230V/110V and control computer) • Power supply cable (between 230V/110V and Pannoramic 250 FLASH II main unit) • Optical cable (between HXP 120 fluorescent illumination unit and scanner) •...

  • Page 26: Mounting The Lumencor Spectra Unit

    (see section 1.1.4 Main parts of the Base Unit). 2. Open protective cover (see section 5.3.1 Opening the protective cover). 3. Find the mounting hole (1) at the back side of the Pannoramic 250 FLASH II unit and rotate the Lumencor unit (2) upside down.
  • Page 27 Lumencor unit. Figure 10 – Mounting the Lumencor unit 7. Close the protective cover of the Pannoramic 250 FLASH II. 8. Connect power supply cables both of the scanner and the illumination unit.
  • Page 28 Pannoramic 250 FLASH II 1.18.1.1 User’s Guide 2 Installation Figure 11 – Lumencor Spectra 6 LE connecting ports May 29, 2014 – Rev. 1 3DHISTECH Ltd. 28(137)

  • Page 29: Operating Slides And Magazines

    Pannoramic 250 FLASH II 1.18.1 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 30: Affixing Barcode Stickers To Slides

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 3 Operating Slides and Magazines Note: Fluorescent signals become more easily detectable for the scanner, therefore resulting in a brighter and better image, by treating the slide with a formula that prevents rapid photobleaching of fluorescent reagents (e.g.

  • Page 31: Inserting And Removing Slides

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 3 Operating Slides and Magazines Caution! Ensure that a marginal space of 1-2 mm remains on all sides between the sticker and the label area outer limits. It is vital for barcode identification.

  • Page 32: Insert And Remove Magazines

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 3 Operating Slides and Magazines Only original 3DHISTECH P250 magazines are allowed for use with Pannoramic 250 FLASH II! The magazines can contain a maximum of 25 slides. Push slide (1) into the magazine (3) with its barcode end (2) first. The symbols on the side of •...
  • Page 33 Pannoramic 250 FLASH II 1.18.1 User’s Guide 3 Operating Slides and Magazines Pannoramic 250 FLASH II has two pairs of guide rails (5) to manage the loading and unloading of magazines. Warning! Do not omit to close the protective cover! It must be closed while the...
  • Page 34 Pannoramic 250 FLASH II 1.18.1 User’s Guide 3 Operating Slides and Magazines 3. Slide down the magazine on the input guide rails until it rests on the gear wheels (6) or magazines. Figure 15 – Gear wheels Caution! Make sure that the magazines are properly placed between the rails, because it can cause serious damages in the feeding mechanism.

  • Page 35: Opening/Closing The Fl Protective Cover

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 3 Operating Slides and Magazines Caution! Do not place magazines into the output stack (4) or remove magazines with already digitized slides from there during the digitization process. Only remove magazines from the output stack when you have finished digitization of all slides.

  • Page 36: Software Description

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4 Software Description 4.1 Starting / Exiting the Pannoramic Scanner Software 4.1.1 Starting the software For the scan software you can choose from different scanning modes at the startup of the program.

  • Page 37: Exiting The Software

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description The camera changer changes the cameras according to the settings in the Microscope Settings options depending on the selected scan modes. It changes to the camera defined for Brightfield scanning if Brightfield scan mode is selected, whereas it changes to the camera defined for fluorescent scanning if Fluorescent scan mode is selected.

  • Page 38: Barcode Settings

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.2.1 Barcode Settings Figure 20 – Barcode settings Barcode settings can be modified in this window. By predefining the barcode type, foreground color (black or white – the color of the barcode), and other settings, you enable the Read Barcode option when using the control software.
  • Page 39 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Functions 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 40: Image Compensation

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description MicroPDF417 • Maxicode • QR code • 1D barcodes with check digit (CDV) You can select the following 1D barcodes with check digit (CDV): Code 39 • Interleaved 2 of 5 •...
  • Page 41 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Brightfield compensation Figure 21 – Image compensation Camera Selection This field displays the active camera. Currently, there is only one active camera for Brightfield mode. Objective Selection To select the objectives to be used for creating a new compensation image, select the checkbox(es).
  • Page 42 Pannoramic 250 FLASH II 1.18.1 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 43: Microscope Settings

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.2.3 Microscope Settings By moving the mouse over the buttons, the software displays information about the setting you are interested in. Base Settings Figure 23 – Base Settings panel Objective type You can select the type and the magnification level of the objectives.
  • Page 44 Pannoramic 250 FLASH II 1.18.1 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. Filter Settings Figure 24 – Filter Settings panel On this panel you can define which filters occupy which turret positions.
  • Page 45 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Camera Rotation Figure 25 – 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 3DHISTECH service support.
  • Page 46 Pannoramic 250 FLASH II 1.18.1 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 26 – Z Difference panel May 29, 2014 –...
  • Page 47 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Service Figure 27 – 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 Opening the protective cover).

  • Page 48: Event Call Settings

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.2.4 Event Call Settings Figure 28 – Event Call Settings window Two of the three settings are responsible for opening external applications (.exe or .bat) as defined (for example, Pannoramic Viewer software can be opened after scanning is finished). You can define...
  • Page 49 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Run defines the window mode that the external application will start in. The following window modes can be set: Normal window • Minimized • Maximized • You can test whether the Scanning Error Occurred settings work by clicking .

  • Page 50: Using Brightfield Manual Mode

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description There are 2 feedback messages that come up after sending the e-mail: “An e-mail has been sent to the recipient.” ◦ “An error has been occurred. The e-mail could not be sent.” - Check parameters then retry.
  • Page 51 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Figure 31 – Main window of control software 1. Panel with scanner functions and setting 2. Scan camera live image display area 3. Preview image recorded by the preview camera 4.

  • Page 52: Routine Work Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.3.1 Routine work panel Figure 32 – 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 53 Pannoramic 250 FLASH II 1.18.1 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 54: Scan Options Window

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.3.2 Scan Options window Figure 33 – Scan options window These settings will determine the resulting quality and storage location of the virtual slide. You can choose from the following predefined image formats (and a subsequent custom option) from...
  • Page 55 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Figure 34 – Image encoding window JPEG – The quality can be adjusted with the JPEG quality factor slider. ◦ Greater values result in better quality, but larger files. The default setting is 80%.
  • Page 56 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Brightfield Compensation The Use saved compensation image function enables to use previously recorded reference images for all slides. Use this function when the slide is completely covered by the specimen (for example, blood smear) thereby making compensation image capture impossible.

  • Page 57: Preview Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.3.3 Preview panel The Preview panel offers options for threshold setting and selection of the area to be scanned. Figure 35 – Preview panel Use threshold Brightfield preview – a normal type of illumination in the microscope for scanning the slide.
  • Page 58 Pannoramic 250 FLASH II 1.18.1 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 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 59 Pannoramic 250 FLASH II 1.18.1 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 60: Preview Area Scanned By Preview Camera

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Use saved scan area This function is useful if the slides contain areas of interest that cannot be detected by the preview camera. This function along with saving profiles helps to scan all slides with the most adequate settings.
  • Page 61 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Areas that will be scanned These areas are digitized on the basis of user settings (for example, Fill holes in scan area) and not detected by the selected threshold value.
  • Page 62 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description You can select the area to be scanned with the different tools on the toolbar: Square tool • Ellipse tool • Polygon tool: you can finish the selection process with the polygon tool by •...
  • Page 63 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description TMA tool TMA tool is used for selecting TMA spots on TMA slides. You can set the selection settings on the following four tabs: Select panel Figure 42 – TMA tool: Select To create a new TMA object, click New.
  • Page 64 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Set the TMA block type in 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 65 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Move panel The Move panel 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 66: Focus Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Label area To rotate the label area by 180°, select the Rotate image by 180 degrees checkbox. Figure 46 – Label area 4.3.5 Focus panel Figure 47 – Focus panel May 29, 2014 –...
  • Page 67 Pannoramic 250 FLASH II 1.18.1 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. Focus To define focus limits, select Limit focus range. Set the upper and lower limits by selecting the desired value in the selection boxes.

  • Page 68: Service Panel

    Pannoramic 250 FLASH II 1.18.1 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 69: Display Field And Toolbar For Live Images

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.3.7 Display field and toolbar for live images The display field for live images displays images of the scan camera. The live image is displayed if no current digitization process is running.
  • Page 70 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Toolbar for live images The toolbar is only available for the displayed live image, but not available for camera images during digitization. – Zoom in • – Zoom out •...

  • Page 71: Start Scan

    Pannoramic 250 FLASH II 1.18.1 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 72 Pannoramic 250 FLASH II 1.18.1 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 •...

  • Page 73: Barcodes Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.4.2 Barcodes panel Figure 52 – Barcodes panel May 29, 2014 – Rev. 1 3DHISTECH Ltd. 73(137)
  • Page 74 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description On this panel you can set identification features and profiles for slides as follows: Features 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.
  • Page 75 Pannoramic 250 FLASH II 1.18.1 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 76 Pannoramic 250 FLASH II 1.18.1 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 77: Preview Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.4.3 Preview panel Figure 53 – 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 78: Focus Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.4.4 Focus panel Figure 54 – 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. This is useful if focusing was not targeted on the specimen, but on a spot on the coverslip.

  • Page 79: Service Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description With the Z-stack method separate layers are created and stored, and can be opened with • Pannoramic Viewer. A Z-stack slide includes extended focus layers. Both for Extended focus and Z-Stack scanning methods, you can determine the desired •...

  • Page 80: Start Scan

    Pannoramic 250 FLASH II 1.18.1 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 57).

  • Page 81: Using Fluorescent Manual Mode

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.5 Using Fluorescent Manual Mode 4.5.1 Routine work panel Figure 58 – Routine work panel May 29, 2014 – Rev. 1 3DHISTECH Ltd. 81(137)
  • Page 82 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description The Routine work panel provides the following basic digitization functions: To insert and remove slides To move the lowest magazine in the input stack to the loading position click •...
  • Page 83 Pannoramic 250 FLASH II 1.18.1 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 84 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description For more information on predefining filters, see section 4.2.3 Microscope Settings / Filter Settings. To set filter properties, select a filter and click on any of the white boxes in TW and DG columns next to the filter name.
  • Page 85 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Digital Gain Note: This is camera-dependent, when working with AxioCam MRm Rev 3 camera the Index value ranges from 0 to 4, and in case using the pco.edge 4.2 camera, the value ranges from 0 to 6.

  • Page 86: Scan Options

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.5.2 Scan Options Figure 61 – 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 87 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Low (JPEG XR: 30) • Custom... • If choosing this option, the Image encoding window is displayed on which you can select from different image formats. Accordingly, further adjustments can be made, except in case PNG or BMP is selected.
  • Page 88 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Maximum exposure time – A limit value can be set to determine that the exposure • time cannot be longer than the time of focusing and calculation of exposure. This is necessary because the exposure time would be too long when taking image of an empty field of view.
  • Page 89 Pannoramic 250 FLASH II 1.18.1 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 90: Preview Panel

    Pannoramic 250 FLASH II 1.18.1 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 63 – Preview panel May 29, 2014 – Rev. 1 3DHISTECH Ltd.
  • Page 91 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Use threshold Brightfield preview – a normal type of illumination in the microscope for scanning the slide. • This option is not recommended in Fluorescent manual mode. Darkfield preview – the preview image is created with transmitted Darkfield illumination.
  • Page 92 Pannoramic 250 FLASH II 1.18.1 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 93 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Fill holes in scan area – If selected, the holes inside the specimen will also be scanned. • Often these holes contain small sample objects that otherwise would not be scanned.

  • Page 94: Hardware Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.5.4 Hardware panel Figure 66 – Hardware panel (selected mode: User controlled) Live Click to display a live image of the current specimen in the Live image display field. May 29, 2014 – Rev. 1 3DHISTECH Ltd.
  • Page 95 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 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 panel.
  • Page 96 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 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. This is useful if Auto Focus does not find the focus on the specimen, but on the coverslip.

  • Page 97: Service Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Manual Exposure By selecting the Use manual exposure times, you can determine the exposure times. The values are typically set to Auto, meaning that the exposure times are determined automatically. After selecting the corresponding filter and activating the live image, you can preset the Exposure value.

  • Page 98: Using Fluorescent Automatic Mode

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.6 Using Fluorescent Automatic Mode 4.6.1 Routine work panel Figure 68 – Routine work panel The Routine work panel provides some basic digitization functions. May 29, 2014 – Rev. 1 3DHISTECH Ltd.
  • Page 99 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 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 (1-10) to be loaded.
  • Page 100 Pannoramic 250 FLASH II 1.18.1 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 101 Pannoramic 250 FLASH II 1.18.1 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 <AUTO>...
  • Page 102 Pannoramic 250 FLASH II 1.18.1 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 103: Barcodes Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.6.2 Barcodes panel Figure 71 – Barcodes panel On this panel, you can set identification features to the various slides and for assigning profiles. May 29, 2014 – Rev. 1 3DHISTECH Ltd.
  • Page 104 Pannoramic 250 FLASH II 1.18.1 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.
  • Page 105 Pannoramic 250 FLASH II 1.18.1 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 106: Preview Panel

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Save Names and Profiles to File • By clicking the button, you can save the entered names and assigned profiles. You can define a name before saving. The information will be saved in a CSV format: 1;<slide position>,<slide name>,<profile name>...

  • Page 107: Focus Panel

    Pannoramic 250 FLASH II 1.18.1 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 108: Scan To Server

    Pannoramic 250 FLASH II 1.18.1 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 Opening the protective cover).
  • Page 109 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 2. Select the Scan to CaseCenter option in the Scan Option window, then click Connect. Figure 76 – 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 110 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4. If the connection is established the server status will be modified from Not connected to Connected. Click OK to close the Scan Options window. Figure 78 – Connected to server Slide settings in the Scan To Server window 1.
  • Page 111 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description When in Automatic Mode, the form contains 25 rows for all the slots per magazine • (Figure 80). To additional magazines click Add+ panel next to the Magazine 01 panel.
  • Page 112 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description The barcode '1234567890', and a mask '1-3' result that the first three characters of the barcode will be displayed and set as slide name (123). Case and Block fields can be set this way as well, if necessary.
  • Page 113 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description With the Multi fill option the selected slides will be given the same input data to • their specific fields. Profile, Folder, Case, and Block fields can be auto-filled this way by clicking the drop-down lists at the Multi fill section at the bottom of the window.

  • Page 114: Using Profiles

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description 4.8 Using Profiles Note: Saved profile settings cannot be applied if using a different type of Pannoramic scanner. If you want to scan a group of slides, it is advised to save your settings previously in a profile and continue scanning in Automatic mode.
  • Page 115 Pannoramic 250 FLASH II 1.18.1 User’s Guide 4 Software Description Use of removing specks according to the set value (ON/OFF) • Use saved scan area • Use selection box (ON/OFF) • Fluorescent settings Filter position(s) • Selected focus channel •...

  • Page 116: Troubleshooting And Maintenance

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 5 Troubleshooting and Maintenance 5 Troubleshooting and Maintenance 5.1 Safety Information Check cables, plugs and connections before operation, and if defective or cannot be replaced, contact 3DHISTECH Service for support. Check whether the device is compatible with your local line voltage. It can operate at line voltages 100V to 240V and 50/60 Hz.

  • Page 117: Cleaning The Device

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 5 Troubleshooting and Maintenance When the HXP 120 illumination unit is switched on: • Never look directly into the fiber-optic cable. ◦ Never remove the fiber-optic cable from the device. ◦ Never connect the fiber-optic cable to the device.

  • Page 118: Troubleshooting

    6. Reconnect power supply cable of the base unit and the control computer to line power supply. 7. Switch on the power supply of the Pannoramic 250 FLASH II (see section 1.1.4 Main parts of the Base Unit). 8. Switch on the control computer.
  • Page 119 Pannoramic 250 FLASH II 1.18.1 User’s Guide 5 Troubleshooting and Maintenance Virtual slide is improperly focused almost across its entire surface Focus range enabled • Disable Limiting focus range. • Poor image quality Imaging error (for example, chromatic aberrations) •...

  • Page 120: Fluorescent Applications (Optional)

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 5 Troubleshooting and Maintenance Focus range setting is incorrect • Change focus range setting. • All individual images show a shading effect Algorithm failed to find empty image fields • Capture a reference image with a blank slide (see section 4.2.2 Image •...

  • Page 121: Maintenance

    To perform maintenance work and when slide or magazine jamming occurs, the protective cover(s) of the Pannoramic 250 FLASH II need to be opened in order to eliminate the problem. Before opening the cover, exit the control software, switch off the main power supply and disconnect the power cables (see section 1.1.4 Main parts of the Base Unit).

  • Page 122: Replacing Fuses Of The Main Power Switch

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 5 Troubleshooting and Maintenance 5.3.2 Replacing fuses of the main power switch 1. Switch off the main power supply and disconnect the power cable (see section 1.1.4 Main parts of the Base Unit).

  • Page 123: Replacing The Hxp 120 Lamp Module (For Fluorescent Option)

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 5 Troubleshooting and Maintenance 5.3.3 Replacing the HXP 120 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.
  • Page 124 Pannoramic 250 FLASH II 1.18.1 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 91). Figure 91 – 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 125: Removing A Jammed Or Broken Slide

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 5 Troubleshooting and Maintenance 10. Connect power plug. 11. Set hour meter (time counter) to zero. 5.3.4 Removing a jammed or broken slide If a slide got jammed or has suffered breakage during the process of digitization, stop the process and, if possible, move the slide holder to a position where the slide can be easily removed by clicking the Emergency Manual Slide Removal Position button (see section 4.3.6 Service panel).
  • Page 126 7. Turn down the slide loader (2) back into the original position and pull it inwardly (to the Pannoramic 250 FLASH II), until the guiding pin connects with the motor block groove again. 8. Press the slide loader (2) down to mechanical stop position, in which the locking lever must engage (1).

  • Page 127: Installing And Removing The Filter Module (Fluorescent Option)

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 5 Troubleshooting and Maintenance 5.3.5 Installing and Removing the Filter Module (Fluorescent Option) Figure 95 – Installing and removing the filter module 1. If using an HXP 120 illumination unit, turn it off.

  • Page 128: Removing A Magazine From The Transporting System

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 5 Troubleshooting and Maintenance 6. Press the filter module down, until it safely connects to the bottom spring-loaded clamps (2) of the filter wheel. Mounting position of the filters: excitation filter (5) and emission filter (4) 7.
  • Page 129 Note: Any manipulation performed on a mechanical component (for example, transporting system) by the user must be followed by a complete Pannoramic 250 FLASH II initialization routine (software restart). May 29, 2014 – Rev. 1 3DHISTECH Ltd.

  • Page 130: Transporting

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 5 Troubleshooting and Maintenance 5.3.7 Transporting The following procedure shows how to transport Pannoramic 250 FLASH II. Figure 97 – Transporting handles Caution! Do not use the FL protective cover (2) to raise, shift or transport Pannoramic 250 FLASH II! May 29, 2014 –...
  • Page 131 3. Turn carrying handles by 90° (B) towards the base unit to secure them. 4. Now you can transport Pannoramic 250 FLASH II with the help of another person. 5. After finishing transportation, push carrying handles back into normal position (C).

  • Page 132: Technical Data

    Pannoramic 250 FLASH II 1.18.1 User’s Guide 6 Technical Data 6 Technical Data Dimensions (width × depth × height) Base unit approx. 68×95×55 cm Base unit without fluorescence option approx. 68×69×55 cm Weight Base unit approx. 46 kg Base unit with fluorescent option Approx.
  • Page 133 Pannoramic 250 FLASH II 1.18.1 User’s Guide 6 Technical Data Operating data Intended site closed room facilities Electrical protection class Internal protection degree IP 20 Electrical safety in compliance with DIN EN 61010-1:2001, DIN EN 61010-2- 101:2002 (IEC 61010-1:2001, IEC 61010-2-101:2002)
  • Page 134 Pannoramic 250 FLASH II 1.18.1 User’s Guide 6 Technical Data Code128 (UCC/EAN128) (ASCII encoding) • EAN8 (Numeric encoding) • EAN13 (Numeric encoding) • UPC-A (Numeric encoding) • DataMatrix (Numeric encoding, Alpha encoding, AlphanumericPunc encoding, • AlphaNumeric encoding, ASCII encoding, IS08 encoding) Maxicode (Encoding mode 2, 3, 4, 5, 6) •...
  • Page 135 Pannoramic 250 FLASH II 1.18.1 User’s Guide 6 Technical Data CIS VCC-FC60FR19CL camera Global Shutter Type CMOS (Diagonal 15.930mm) Pixel size 5.5µm × 5.5µm Camera resolution 2048(H) × 2048(V) pixel Frame rates 17fps / 34fps / 68fps / 135fps Bit-depth...

  • Page 136: Index

    Lumencor..............14, 17, 21, 22, 25, 26, 27, 44, 95, 116, 120, 133 Marker..........................58, 61, 92, 114 Pannoramic 250 FLASH II..8, 9, 10, 11, 13, 15, 17, 19, 20, 21, 22, 24, 25, 26, 27, 32, 33, 118, 121, 122, 126, 129, 130, 131 Pannoramic Viewer.......................23, 68, 79, 119...
  • Page 137 Pannoramic 250 FLASH II 1.18.1 User’s Guide Index ScanToServer........................56, 89, 108 May 29, 2014 – Rev. 1 3DHISTECH Ltd. 137(137)

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