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3DHISTECH Pannoramic 250 FLASH User Manual

1.14 sp1
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Pannoramic 250 FLASH
1.14 SP1
User's Guide
March 30, 2011
Rev. 1

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Summary of Contents for 3DHISTECH Pannoramic 250 FLASH

  • Page 1 Pannoramic 250 FLASH 1.14 SP1 User’s Guide March 30, 2011 Rev. 1...

  • Page 2: Table Of Contents

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide Contents Disclaimer........................5 Character Formats and Symbols..................7 1 Product Description...................... 8 1.1 Product Overview........................8 1.1.1 Intended Use..............................8 1.1.2 Features and Benefits............................8 1.1.3 Main parts of the Base Unit..........................9 1.2 System Overview........................10 1.2.1 Pannoramic 250 FLASH system........................10 1.2.2 Hardware Options............................11...
  • Page 3 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4.3.4 Preview area scanned by preview camera.....................49 4.3.5 Focus tab................................56 4.3.6 Service tab..............................58 4.3.7 Display field and toolbar for live images......................59 4.3.8 Start Scan................................61 4.4 Using Brightfield Automatic Mode..................62 4.4.1 Routine work tab............................62 4.4.2 Barcodes tab..............................64...
  • Page 4 Pannoramic 250 FLASH 1.14 SP1 User’s Guide Index........................... 130 March 30, 2011 3DHISTECH Ltd. 4(130)

  • Page 5: Disclaimer

    IP are the sole properties of the 3DHISTECH Ltd. 3DHISTECH Ltd. is not liable for damage of whatever nature (including, but not limited to, general or specific damage, indirect damage, consequential damage or incidental damage, including the...
  • Page 6 Pannoramic 250 FLASH 1.14 SP1 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 250 FLASH 1.14 SP1 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, pushbuttons 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: Product Description

    1.1 Product Overview 1.1.1 Intended Use Pannoramic 250 FLASH 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 9: Main Parts Of The Base Unit

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product Description Compact design: • Cameras are placed inside the unit • Built-in power supply • Fewer cables • Improved fluorescent scanning mode: • 3 times faster and more silent filter change •...

  • Page 10: System Overview

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

  • Page 11: Hardware Options

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product Description 5. keyboard 6. slide magazine with cover 7. HXP 120 fiber-coupled fluorescent illuminator (optional) 8. Lumencor Spectra illuminator (optional) 1.2.2 Hardware Options The configuration of the control computer and monitor can vary depending on the product order.
  • Page 12 Figure 3 – Camera changer You can fit two cameras into the Pannoramic 250 FLASH 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 13 Objectives Figure 4 – Objective changer You can select two different objectives to be equipped with the Pannoramic 250 FLASH, 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 14 Base Unit options Pannoramic 250 FLASH Base Unit • Pannoramic 250 FLASH Scan Option – base unit equipped with CIS VCC-F52U25CL camera • for Brightfield scanning (no fluorescent accessories included) Pannoramic 250 FLASH Fluorescence Option – base unit completely equipped with CIS VCC- •...

  • Page 15: Control Software

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product Description Fluorescent Options for Pannoramic 250 FLASH Fluorescent unit (internal part) HXP 120 illumination unit Lumencor Spectra 7 Light Engine illumination unit 1.2.3 Control Software Pannoramic Scanner control software • Optional: Fluorescence •...
  • Page 16 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 1 Product Description Pannoramic Viewer software (fully functional) • Optional: Fluorescence slide viewer (built-in with hardware, optional without hardware) • CaseCenter • Pannoramic Viewer TMA module • 3D Reconstruction module • HistoQuant, NuclearQuant, MembraneQuant, FISHQuant, DensitoQuant modules •...

  • Page 17: Installation

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 2 Installation 2 Installation Warning! The installation of Pannoramic 250 FLASH 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 not carried out by professional person.

  • Page 18: Connectors And Cables

    2.3 Mounting the Lumencor Spectra unit To operate the Lumencor Spectra unit, it has to be attached to the Pannoramic 250 FLASH base unit. 1. Switch off the main power supply on the rear panel of the Pannoramic 250 FLASH and disconnect the power cables (see section 1.1.3 Main parts of the Base Unit).
  • Page 19 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 2 Installation 3. Find the mounting hole (1) at the back side of the Pannoramic 250 FLASH unit and rotate the Lumencor unit upside down. Figure 7 – Mounting position 4. Move the lever (1) to the open position, which is to the right when facing the front of the unit (see Figure 8).
  • Page 20 6. Secure the locking lever by moving it to the left (see Figure 9 – Step 2). If the lever stucks at around the center position, apply a bit more pressure to the Lumencor unit. Figure 9 – Mounting the Lumencor unit 7. Close the protective cover of the Pannoramic 250 FLASH. March 30, 2011 3DHISTECH Ltd.

  • Page 21: Operating Slides And Magazines

    Pannoramic 250 FLASH 1.14 SP1 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 22: Affixing Barcode Stickers To Slides

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 3 Operating Slides and Magazines Warning! Do not change correction collar settings on 40x objective, if you need it to be set, contact customer service. 3.2 Affixing Barcode Stickers to Slides This section describes how to affix barcode stickers to slides. Barcodes enable virtual slide identification.

  • Page 23: Inserting And Removing Slides

    3.3.1 Insert slides into a magazine Figure 11 – Inserting slides into a magazine Only original 3DHISTECH magazines are allowed for use with Pannoramic 250 FLASH! 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 24: Insert And Remove Magazines

    3.3.2 Insert and remove magazines Figure 12 – Inserting a magazine Pannoramic 250 FLASH has two pairs of guide rails (5) to manage the loading and unloading of magazines. March 30, 2011 3DHISTECH Ltd.
  • Page 25 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 3 Operating Slides and Magazines Warning! Do not omit to close the protective cover! It must be closed while the microscope is loading and/or scanning! Note: The guide rails have built-in sensors that detect whether there are magazines inserted in the input stack, or whether the output stack is full.
  • Page 26 Pannoramic 250 FLASH 1.14 SP1 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 13 – Gear wheels Note: The input stack can be filled with a maximum of 9 magazines in addition to the one in the magazine loader.

  • Page 27: Opening/Closing The Fl Protective Cover

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 3 Operating Slides and Magazines 3.3.3 Opening/Closing the FL protective cover Figure 14 – Opening the FL protective cover Open the protective cover by moving it upwards and lay it down to the upper cover of the unit, then insert magazines.

  • Page 28: Software Description

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

  • Page 29: Exiting The Software

    Pannoramic 250 FLASH 1.14 SP1 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 30 Pannoramic 250 FLASH 1.14 SP1 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 (color of the barcode), and other settings, you enable the Read Barcode option when using the control software.
  • Page 31 Pannoramic 250 FLASH 1.14 SP1 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 32 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Preprocess Barcode Image You can preprocess the barcode image with the following settings: Sharpen • Gamma modification • Contrast modification • Special Barcode Settings You can change the following special settings: Barcode string length •...

  • Page 33: Image Compensation

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.2.2 Image Compensation You can create a new compensation image when there are compensation errors (deriving from the slide, illumination, staining or embedding medium irregularities) from an empty slide by setting these options.
  • Page 34 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 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. Objective Selection To select the objectives to be used for creating a new compensation image, select the checkbox(es).
  • Page 35 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Note: If you cannot create appropriate compensation images, maybe the compensation slides need to be replaced. To order new Fluorescent Compensation Slides, contact 3DHISTECH Service Support. Camera Selection This field displays the active camera.

  • Page 36: Microscope Settings

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.2.3 Microscope Settings You can define for the software which optovars or filters occupy which turret position. By moving the mouse over the buttons, the software displays information about the setting you are interested in.
  • Page 37 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. Do not modify these settings yourself. March 30, 2011 3DHISTECH Ltd.
  • Page 38 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Figure 20 – Camera Rotation tab March 30, 2011 3DHISTECH Ltd. 38(130)
  • Page 39 Pannoramic 250 FLASH 1.14 SP1 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 21 – Z Difference March 30, 2011 3DHISTECH Ltd.
  • Page 40 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Service Figure 22 – 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 41: External Application Call Settings

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.2.4 External Application Call Settings Figure 23 – External Application Settings These settings open any external application (.exe or .bat) as defined. For example, it might start the Viewer software after finishing scanning, or stop the computer after scanning is finished.

  • Page 42: Using Brightfield Manual Mode

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Minimized • Maximized • You can test whether the Error Occurred Call settings work by clicking 4.3 Using Brightfield Manual Mode You can use Brightfield Manual mode to set the scanning, preview, and image quality settings. You can also set profile settings here, and start scanning in Brightfield Manual mode.

  • Page 43: Routine Work Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 3. Preview image recorded by the preview camera 4. Preview image editor toolbar 5. Information area about the digitization progress 4.3.1 Routine work tab Figure 25 – Routine work tab The Routine work tab provides basic digitization functions.
  • Page 44 Pannoramic 250 FLASH 1.14 SP1 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 45: Scan Options Window

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.3.2 Scan Options window Figure 26 – 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 46: Preview Tab

    Pannoramic 250 FLASH 1.14 SP1 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 47 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Figure 27 – Preview tab Use threshold Brightfield preview – a normal type of illumination in the microscope for scanning the slide. • Darkfield preview – the preview image is created with transmitted Darkfield illumination.
  • Page 48 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Greater values result in a less sensitive scanning, but it is possible that some of the smaller specimen areas will not be digitized. Scan area inside the marker – If the specimen cannot be identified as required for •...

  • Page 49: Preview Area Scanned By Preview Camera

    Pannoramic 250 FLASH 1.14 SP1 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 50 Pannoramic 250 FLASH 1.14 SP1 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 51 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Figure 31 – 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 52 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Ellipse tool • Polygon tool: you can finish the selection process with the polygon tool by • double-clicking with the mouse. TMA tool • To undo your last action, click (maximum of 40 changes).
  • Page 53 Pannoramic 250 FLASH 1.14 SP1 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 tab Figure 34 – TMA tool: Select To create a new TMA object, click New.
  • Page 54 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Set the TMA block type in this tab. 1. Select the shape of the TMA spots (Rectangle spots or Circle spots). 2. Enter the number of rows and columns in the Rows and Columns fields or select the appropriate values with the arrows.
  • Page 55 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Figure 37 – TMA tool Move tab with preview March 30, 2011 3DHISTECH Ltd. 55(130)

  • Page 56: Focus Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Label area To rotate the label area by 180°, select the Rotate image by 180 degree checkbox. Figure 38 – Label area 4.3.5 Focus tab Figure 39 – Focus tab March 30, 2011 3DHISTECH Ltd.
  • Page 57 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Live To display a live image of the current specimen in the Live image display field, click . It will work only if you select an area in the preview image with the Position sample.

  • Page 58: Service Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description You can determine the desired number of focus levels with the Number of 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 59: Display Field And Toolbar For Live Images

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Slide Removed Manually Click this button to notify the software that you have removed the slide manually. Show images during scanning If you select this option, you will be able to see the currently scanned image field during scanning in the live image display field.
  • Page 60 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Figure 42 – Display field and toolbar for live images Toolbar for live images The toolbar is only available for the displayed live image, but not available for camera images during digitization.

  • Page 61: Start Scan

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description – Activates red marking on overexposed pixels • – Recalculates exposure time (useful if too many overexposed pixels were • detected) – Calculates white balance (only for color cameras) •...

  • Page 62: Using Brightfield Automatic Mode

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.4 Using Brightfield Automatic Mode Compared to Manual mode, it has less options in some dialogs, but it has an additional Barcodes tab. 4.4.1 Routine work tab Figure 43 – Routine work tab The Routine work tab provides basic digitization functions.
  • Page 63 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description To save the current profile, click Save. • To select an existing profile from the selection menu, click Load. • You can delete the current profile by clicking Delete. •...

  • Page 64: Barcodes Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.4.2 Barcodes tab Figure 44 – Barcodes tab March 30, 2011 3DHISTECH Ltd. 64(130)
  • Page 65 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description On this tab you can set identification features and profiles for slides. Modes in the tab 1. Apply one profile to all slides. One profile is used for all slides in a batch.
  • Page 66 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Mask: 1-10, 17-19 = PANNORAMIC123 • 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 •...
  • Page 67 Pannoramic 250 FLASH 1.14 SP1 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 68: Preview Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.4.3 Preview tab Figure 45 – 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 69: Focus Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.4.4 Focus tab Figure 46 – 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 70: Service Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Figure 47 – Focus level and step size 4.4.5 Service tab Figure 48 – 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 71: Start Scan

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.4.6 Start Scan To start digitization process, click after checking settings in the Barcodes tab. Caution! Before starting digitization process ensure that you have enough free space on the destination drive. You can check the available free disk space in the last line (Available disk space) of the information area of Current Slide Scan Progress (see Figure 44).
  • Page 72 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description If a running digitization process is interrupted, and you want to continue scanning, click You have two options for resuming depending on current slide position. 1. The canceled slide occupies position 1 in the magazine To resume digitization with the same slide, click Yes.

  • Page 73: Using Fluorescent Manual Mode

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.5 Using Fluorescent Manual Mode 4.5.1 Routine work tab Figure 50 – Routine work tab March 30, 2011 3DHISTECH Ltd. 73(130)
  • Page 74 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description The Routine work tab provides basic digitization functions. Some features of this tab differs from product to product, these are described in the forthcoming sections. To insert and remove slides To move the lowest magazine in the input stack to the loading position click •...
  • Page 75 Pannoramic 250 FLASH 1.14 SP1 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 76 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description For more information on predefining filters, see section 4.2.2. Microscope Settings / Base Settings. To set filter properties, select a filter and click on any of the white boxes next to the filter name.
  • Page 77 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Extended Focus This is the same as in Brightfield mode, but you can set the extended focus for each channel separately. Number of focus levels (displayed under EL in the Filter Selection frame).

  • Page 78: Scan Options

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.5.2 Scan Options Figure 52 – Scan options tab These settings determine the resulting quality and storage location of the virtual slide. March 30, 2011 3DHISTECH Ltd. 78(130)
  • Page 79 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 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 • values result in better quality, but larger files. The default setting is 80%.
  • Page 80 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Caution! If the specimen area is barely visible, it is possible that the software will analyze that area as an empty one. Stitching – By selecting, this function enables seamless stitching of digitized tiles.
  • Page 81 Pannoramic 250 FLASH 1.14 SP1 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.

  • Page 82: Preview Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.5.3 Preview tab The Preview tab offers options for threshold setting and selection of the area to be scanned. Figure 53 – Preview tab Use threshold Brightfield preview – a normal type of illumination in the microscope for scanning the slide.
  • Page 83 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Scan thresholded specimen – 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 84: Preview Area Scanned By Preview Camera

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Scan area dilation Adjust the slider to the desired value to enlarge or decrease the scanned area. The edge is extended discretely by one image field of the camera each time.

  • Page 85: Hardware Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.5.5 Hardware tab Figure 55 – Hardware tab (selected mode: User controlled) March 30, 2011 3DHISTECH Ltd. 85(130)
  • Page 86 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Live You can display a live image of the current specimen in the Live image display field by clicking It will work only if you have selected an area in the preview image with the Position sample.
  • Page 87 Pannoramic 250 FLASH 1.14 SP1 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 88: Service Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description You can accept the current z-value by clicking Set Value. This is recommended for a very flat specimen. If you select the Interpolated focus option, the coarse focus level is calculated from three different focus points of the specimen.
  • Page 89 Pannoramic 250 FLASH 1.14 SP1 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 90: Using Fluorescent Automatic Mode

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.6 Using Fluorescent Automatic Mode 4.6.1 Routine work tab Figure 57 – Routine work tab The Routine work tab provides basic digitization functions. Some features of this tab differs from product to product, these are described in the forthcoming sections.
  • Page 91 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description To insert and remove slides If you do not want to load all the slides, you can specify the first and last slide to be loaded in the Scan Range by entering the appropriate slide numbers in the selection boxes of First slide and Last slide.
  • Page 92 Pannoramic 250 FLASH 1.14 SP1 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 93 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Figure 58 – Filter properties window Filter name The name of the filter is displayed here. Exposure Settings Exposure time – You can set the fix exposition time here. By selecting the Auto button, the exposition time is set to (the exposition time is calculated by the software).
  • Page 94 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Number of focus levels (displayed under EL in the Filter Selection frame). Focus step size (one step = 0.4 μm) (displayed under ES in the Filter Selection frame). For more information about Extended Focus, see section 4.3.5 Focus tab.

  • Page 95: Barcodes Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.6.2 Barcodes tab Figure 59 – Barcodes tab March 30, 2011 3DHISTECH Ltd. 95(130)
  • Page 96 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description On this tab, you can set identification features to the various slides and for assigning profiles. Modes on the tab Apply one profile to all slides • One profile is used for all slides in a batch.
  • Page 97 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Mask: 12-15 = SCAN • Mask: 1-10, 17-19 = PANNORAMIC123 • Note: You can separate the character groups with any character you choose, it will not be read by the software.
  • Page 98 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 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, 1M10) <magazine number>M<slide position>...

  • Page 99: Preview Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.6.3 Preview tab Figure 60 – 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 100: Focus Tab

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.6.4 Focus tab Figure 61 – Focus tab Focus You can define focus limits by selecting Limit focus range checkbox. You can set the upper and lower limits by selecting the desired value in the selection boxes.

  • Page 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 250 FLASH scanner software. Follow these steps to install the ScanToServer application: 1.
  • Page 102 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 3. Click Finish to finalize the installation process of the ScanToServer application. To setup a connection with a designated server, follow the steps below: 1. Click Scan Options on the Routine Work tab panel.
  • Page 103 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 2. Select the Scan to CaseCenter option in the Scan Option window, then click Connect. Figure 64 – 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 104 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 2. The ScanToServer window is displayed. Slide data is displayed in a form for each magazine. Slide data is displayed in a form for • the slides loaded in the tray. If in Manual Mode, only the data of the actually loaded slide can be set (see Figure 66).
  • Page 105 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 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 250 FLASH 1.14 SP1 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 107: Using Profiles

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description 4.8 Using Profiles Note: Saved profile settings cannot be transferred to and used on another control computer. 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 108 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 4 Software Description Use of a fixed scan area • Use selection box (ON/OFF) • Fluorescent settings Filter position(s) • Selected focus channel • Selected stitching channel • Use of skip empty field-of-views (ON/OFF) •...

  • Page 109: Troubleshooting And Maintenance

    Pannoramic 250 FLASH 1.14 SP1 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 250 FLASH 1.14 SP1 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. When the HXP 120 illuminator is switched on: Never look directly into the fiber-optic cable.

  • Page 111: 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 (see section 1.1.3 Main parts of the Base Unit). 8. Switch on the control computer.
  • Page 112 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 5 Troubleshooting and Maintenance Image is black Contact 3DHISTECH Service for support. • 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 113: Fluorescent Applications (Optional)

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 5 Troubleshooting and Maintenance Image is out of focus (in Manual mode) Focus range limit is activated • Deactivate the Limiting focus range option. • Focus range setting is incorrect • Change focus range setting.

  • Page 114: Maintenance

    To perform maintenance work and to interrupt a running digitization procedure because of slide or magazine jamming, the protective cover(s) of the Pannoramic 250 FLASH 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 1.1.3 Main parts of the Base Unit).

  • Page 115: Replacing Fuses Of The Main Power Switch

    Pannoramic 250 FLASH 1.14 SP1 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 1.1.3 Main parts of the Base Unit).

  • Page 116: Replacing Lamp Module (For Fluorescent Option)

    Pannoramic 250 FLASH 1.14 SP1 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 117 Pannoramic 250 FLASH 1.14 SP1 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 76). Figure 76 – 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 118: Removing A Slide

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 5 Troubleshooting and Maintenance 11. Connect power plug. 12. Set hour meter (time counter) to zero. 5.3.4 Removing a slide If a slide got jammed or has suffered breakage during the process of digitization, stop the process and, if possible, move the slide holder to a position where the slide can be easily removed by clicking the Emergency Manual Slide Removal Position button (see section 4.3.6 Service tab).
  • Page 119 7. Turn down the slide loader back into the original position and pull it inwardly (to the Pannoramic 250 FLASH), until the guiding pin connects with the motor block groove again. 8. Press the slide loader down to mechanical stop position, in which the locking lever must engage (1).

  • Page 120: Installing And Removing The Filter Module (Fluorescent Option)

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 5 Troubleshooting and Maintenance 5.3.5 Installing and Removing the Filter Module (Fluorescent Option) Figure 80 – 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 121: Removing A Magazine From The Transporting System

    Pannoramic 250 FLASH 1.14 SP1 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); emission filter (4) 7.
  • Page 122 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 5 Troubleshooting and Maintenance 2. If the magazine is in horizontal position, tilt the upper part of the horizontal magazine drive plate (4) from the magazine loader unit far enough for the driving gear (6) to disengage from the driving worm gear (3).

  • Page 123: Transporting

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide 5 Troubleshooting and Maintenance 5.3.7 Transporting The following procedure shows how to transport Pannoramic 250 FLASH. Figure 82 – Transporting handles Caution! Do not use the protective cover (2) to raise, shift or transport...
  • Page 124 3. Turn carrying handles by 90° (B) towards the base unit to secure them. 4. Now you can transport Pannoramic 250 FLASH with the help of another person. 5. After finishing transportation, push carrying handles back into normal position (C).

  • Page 125: Technical Data

    Pannoramic 250 FLASH 1.14 SP1 User’s Guide Technical Data 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 126 Pannoramic 250 FLASH 1.14 SP1 User’s Guide 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 127 Pannoramic 250 FLASH 1.14 SP1 User’s Guide Technical Data 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 128 Pannoramic 250 FLASH 1.14 SP1 User’s Guide Technical Data Control computer, minimum system requirements Operating System Microsoft Windows Vista Business SP2 EN/HU 64-bit Intel Quad-core processor, 12 MB l2 cache Min: 8 GB DDR2 or DDR3 Recommended: 12 GB DDR3...
  • Page 129 Marker..........................48, 50, 83, 108 Optovar........................34, 36, 44, 63, 109 Pannoramic ............................15 Pannoramic 250 FLASH.2, 8, 10, 12, 13, 14, 15, 17, 18, 19, 20, 23, 24, 102, 112, 115, 116, 120, 123, 124, 125 Pannoramic Scan.........................15, 28 Pannoramic Viewer......................16, 112, 113 Preview..2, 3, 8, 9, 14, 18, 22, 28, 34, 35, 40, 42, 43, 46, 47, 49, 50, 51, 52, 54, 55, 57, 59, 68, 69,...
  • Page 130 Pannoramic 250 FLASH 1.14 SP1 User’s Guide Index Scanner..............2, 8, 15, 18, 25, 28, 34, 42, 48, 83, 102, 107, 112 Scanning..8, 12, 14, 27, 28, 29, 39, 41, 42, 44, 47, 48, 50, 57, 59, 61, 62, 70, 72, 74, 75, 79, 81, 83, 86, 88, 89, 91, 92, 101, 108 ScanToServer.......................46, 81, 102, 103, 105...

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