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3D Histech Pannoramic MIDI User Manual

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Pannoramic MIDI
1.18
User's Guide
November 20, 2013
Rev. 1
PM1.18-UG-Rev1

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Summary of Contents for 3D Histech Pannoramic MIDI

  • Page 1 Pannoramic MIDI 1.18 User’s Guide November 20, 2013 Rev. 1 PM1.18-UG-Rev1...

  • Page 2: Table Of Contents

    3.1 Preparing Slides and Trays.......................25 3.2 Affixing Barcode Stickers to Slides...................26 3.3 Inserting and Removing Slides....................27 4 Software Description....................30 4.1 Starting / Exiting Pannoramic MIDI Software Application............30 4.1.1 Starting the software............................30 4.1.2 Exiting the software............................31 4.2 Options.............................31 4.2.1 Barcode Settings.............................31 4.2.2 Image Compensation.............................34...
  • Page 3 Pannoramic MIDI 1.18 User’s Guide 4.3.2 Scan Options window.............................47 4.3.3 Preview panel..............................49 4.3.4 Preview area scanned by preview camera.....................52 4.3.5 Focus panel..............................58 4.3.6 Service panel..............................60 4.3.7 Display field and toolbar for live images......................61 4.3.8 Start scan................................63 4.4 Using Brightfield Automatic Mode..................63 4.4.1 Routine work panel............................63...
  • Page 4 Pannoramic MIDI 1.18 User’s Guide Index........................... 127 April 3, 2014 - Rev 1 3DHISTECH Ltd. 4(127)

  • Page 5: Disclaimer

    Pannoramic MIDI 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 MIDI 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: Declaration Of Conformity

    Pannoramic MIDI 1.18 User’s Guide Declaration Of Conformity 3DHISTECH Ltd. declares that the product Pannoramic MIDI slide scanner is designed and produced with consideration of specified requirements according to the ISO 13485:2003 and IEC 61326-2- 6:2005 standards, and conforms to the directives and other standards listed below: IEC 61010-1:2001 (ed.

  • Page 8: Character Formats And Symbols

    Pannoramic MIDI 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, 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 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 MIDI and in the section 1.1.3 Warning and Information Labels have the following meanings:...
  • Page 10 Please note that the digitizing process has to be interrupted and the insert moved via software to the output position before removing the insert. A defective Pannoramic MIDI is not classified as domestic waste. It must be Warning! properly disposed in accordance with currently valid legal requirements.

  • Page 11: Notes On Warranty

    Character Formats and Symbols Notes on Warranty 3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic MIDI 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 minimize damage. On receiving...

  • Page 12: Terms And Abbreviations

    Pannoramic MIDI 1.18 User’s Guide Character Formats and Symbols Terms and Abbreviations Comma Separated Value Field of View Numerical Aperture Virtual Slide / Slide A digital image of a thin glass plate on which specimens are mounted for microscopic study:...

  • Page 13: Product Description

    1.1.2 Features and Benefits The Pannoramic MIDI offers world class brightfield and fluorescent whole slide scanning on up to 9 channels. An outstanding 0.12 µm/pixel (in Brightfield) and 0.16 µm/pixel (in Fluorescent) resolution is achieved with the 40×/0.95 NA (equivalent to 80×...
  • Page 14 Focus algorithm finds the focus which is most appealing to the human eye • Pannoramic MIDI is an optimal choice for customers who want to scan in brightfield and in fluorescent mode where the quantity of scanned slides will be regularly over 10 slides per day. It has the best price/performance ratio with a reliable loading/scanning mechanism.

  • Page 15: Warning And Information Labels

    1 Product Description 1.1.3 Warning and Information Labels The following figure contains the labels used on the Pannoramic MIDI main unit, the external mains power supply unit, and the HXP 120 illumination unit. Figure 1 – Warning and information labels April 3, 2014 - Rev 1 3DHISTECH Ltd.

  • Page 16: Base Unit

    Pannoramic MIDI 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 covers 2. Slide tray 3. Manual camera changer 4.

  • Page 17: System Overview

    The standard scope of delivery of the product includes the following hardware and software components. 1.2.1 Pannoramic MIDI system The following figure shows the main parts of the Pannoramic MIDI system. Figure 3 – Pannoramic MIDI system overview 1. Lumencor SPECTRA 6 Light Engine illumination unit (option) 2.

  • Page 18: Hardware Options

    Pannoramic MIDI 1.18 User’s Guide 1 Product Description 8. Keyboard 9. Slide tray 1.2.2 Hardware Options Note: 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 Base Unit options Pannoramic MIDI Basic Scan Option / Fast Option – base unit equipped with Stingray or CIS • cameras for Brightfield scanning (no fluorescent accessories included) Pannoramic MIDI Basic Fluorescence Option –...
  • Page 20 Pannoramic MIDI 1.18 User’s Guide 1 Product Description Pannoramic MIDI Basic Mixed Option – base unit completely equipped with Stingray or CIS • VCC-FC60FR19CL camera for Brightfield scanning; with AxioCam camera and HXP 120 illumination unit, trigger cable and filters for fluorescence scanning Pannoramic MIDI Advanced Mixed Option –...

  • Page 21: Control Software

    Pannoramic MIDI 1.18 User’s Guide 1 Product Description Lumencor SPECTRA 6 Light Engine illumination unit (can be used with pco.edge 4.2 camera only) 1.2.3 Control Software Pannoramic Scanner control software • Optional: Fluorescence • Extended focus • Z-stack • Barcode reader (licensed feature) •...

  • Page 22: Installation

    2 Installation 2 Installation Warning! The installation of Pannoramic MIDI 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 MIDI 1.17 User’s Guide 2 Installation 1. Status display 2. DVD drive (RW) 3. Power on/off button 4. Earphone and microphone 3.5mm Jack ports 5. 2x USB port 6. Power supply connector 7. PS/2 mouse port 8. PS/2 keyboard port 9.

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

    Pannoramic MIDI 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 Trays

    Pannoramic MIDI 1.18 User’s Guide 3 Operating Slides and Trays 3 Operating Slides and Trays 3.1 Preparing Slides and Trays This section demonstrates how to prepare slides and trays. You may use slides and coverslips that meet the following specifications:...

  • Page 26: Affixing Barcode Stickers To Slides

    Pannoramic MIDI 1.18 User’s Guide 3 Operating Slides and Trays 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 MIDI 1.18 User’s Guide 3 Operating Slides and Trays 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 MIDI 1.18 User’s Guide 3 Operating Slides and Trays Caution! Incorrect slide insertion may break the glass. Always make sure that slides are correctly inserted in the tray. The edge of the broken area of the slide is sharp and its removal can lead to injury and contagion!
  • Page 29 Pannoramic MIDI 1.18 User’s Guide 3 Operating Slides and Trays Caution! To insert or remove a filled tray from the device, or when transporting it, slightly tilt it to its closed side to prevent the slides from accidentally falling out.

  • Page 30: Software Description

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

  • Page 31: Exiting The Software

    Pannoramic MIDI 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.
  • Page 32 Pannoramic MIDI 1.18 User’s Guide 4 Software Description Barcode settings can be modified in the Barcode Settings window. By predefining 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 33 Pannoramic MIDI 1.18 User’s Guide 4 Software Description EAN 8 • EAN 13 • UPC-A • 2D Barcode Types You can select the following 2D barcode types: Data Matrix • PDF417 • MicroPDF417 • Maxicode • QR code • 1D barcodes with check digit (CDV)

  • Page 34: Image Compensation

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.2.2 Image Compensation You can use a saved compensation image whenever compensation-related issues occur (deriving from the slide, illumination, staining or embedding medium irregularities). To set compensation parameters properly, follow the instructions below.
  • Page 35 Pannoramic MIDI 1.18 User’s Guide 4 Software Description 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. Preview Settings There might be specks or minor etches on the surface of the compensation slide that require modifying the threshold settings.

  • Page 36: Microscope Settings

    You can select the type and the magnification level of the objective. Camera type If Pannoramic MIDI features a manual camera changer, first activate the Use manual camera changer option, then set the appropriate camera types both for Brightfield and Fluorescent scanning modes in Pos.
  • Page 37 Pannoramic MIDI 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 38 Pannoramic MIDI 1.18 User’s Guide 4 Software Description Camera Rotation Figure 16 – Camera rotation 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.
  • Page 39 Pannoramic MIDI 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 17 – Z Difference panel April 3, 2014 - Rev 1 3DHISTECH Ltd.

  • Page 40: Event Call Settings

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description Service Figure 18 – Service panel This panel contains control and maintenance functions. Emergency Manual Slide Removal Position The slide 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...
  • Page 41 Pannoramic MIDI 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 42 Pannoramic MIDI 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 20 – Messenger Setup window In the Messenger Setup window the following parameters can be set: Message Type –...
  • Page 43 Pannoramic MIDI 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 44: Using Brightfield Manual Mode

    Pannoramic MIDI 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. Manual mode is perfect for digitizing slides that require unique settings, or single slides.

  • Page 45: Routine Work Panel

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.3.1 Routine work panel Figure 23 – 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 a slide to the loading position, click the number of the slide that you want to load •...
  • Page 46 Pannoramic MIDI 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 47: Scan Options Window

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.3.2 Scan Options window Figure 24 – Scan Options window These settings will determine the resulting quality and storage location of the virtual slide. You can choose the following predefined image formats (and a subsequent custom option) from the...
  • Page 48 Pannoramic MIDI 1.18 User’s Guide 4 Software Description Accordingly, further adjustments can be made, except if PNG or BMP image format is selected. Figure 25 – Image encoding window JPEG – The quality can be adjusted with the JPEG quality factor slider. Greater ◦...

  • Page 49: Preview Panel

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description The Scanned slide destination field determines where to digitize the virtual slides. Select the Scan To CaseCenter function to scan directly to a dedicated CaseCenter server. • For information on how to use the ScanToServer application, see section 4.
  • Page 50 Pannoramic MIDI 1.18 User’s Guide 4 Software Description Use threshold Scan specimen with auto threshold – This automatically detects the specimen in the preview • image. 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.
  • Page 51 Pannoramic MIDI 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 52: Preview Area Scanned By Preview Camera

    Pannoramic MIDI 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 53 Pannoramic MIDI 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 54 Pannoramic MIDI 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 55 Pannoramic MIDI 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 33 – TMA tool: Select To create a new TMA object, click New.
  • Page 56 Pannoramic MIDI 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 57 Pannoramic MIDI 1.18 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 58: Focus Panel

    Pannoramic MIDI 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 37 – Label area 4.3.5 Focus panel Figure 38 – Focus panel April 3, 2014 - Rev 1 3DHISTECH Ltd.
  • Page 59 Pannoramic MIDI 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 60: Service Panel

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description Figure 39 – Focus level and step size 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 61: Display Field And Toolbar For Live Images

    Pannoramic MIDI 1.18 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 62 Pannoramic MIDI 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 63: Start Scan

    Pannoramic MIDI 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 Scan Progress information area.
  • Page 64 Pannoramic MIDI 1.18 User’s Guide 4 Software Description The Routine work panel provides basic digitization functions. To insert and remove slides To load the tray, click . The system checks the positions for slides during the loading • process. If you do not want to load all slides, you can specify the first and last slide to be loaded in •...

  • Page 65: Barcodes Panel

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.4.2 Barcodes panel Figure 43 – Barcodes panel April 3, 2014 - Rev 1 3DHISTECH Ltd. 65(127)
  • Page 66 Pannoramic MIDI 1.18 User’s Guide 4 Software Description Identification features and profiles for slides can be set on this panel. Features on the panel 1. Apply one profile to all slides One profile is used for all slides in a batch.
  • Page 67 Pannoramic MIDI 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 68 Pannoramic MIDI 1.18 User’s Guide 4 Software Description 1M does not change, the number after 1M represents the slide position. In this example, the name indicates a slide in position 10. You can also define names for the slides in the table below, by entering names into the column Names / Barcodes.

  • Page 69: Preview Panel

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.4.3 Preview panel Figure 44 – 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 70: Focus Panel

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.4.4 Focus panel Figure 45 – 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 71: Service Panel

    Pannoramic MIDI 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 72: Start Scan

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.4.6 Start scan To start digitization process, click after checking settings on 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 48).

  • Page 73: Using Fluorescent Manual Mode

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.5 Using Fluorescent Manual Mode 4.5.1 Routine work panel Figure 49 – Routine work panel The Routine work panel provides basic digitization functions. April 3, 2014 - Rev 1 3DHISTECH Ltd. 73(127)
  • Page 74 Pannoramic MIDI 1.18 User’s Guide 4 Software Description To insert and remove slides To move a slide to the loading position, click the number of the slide that you want to load • To load a slide from the tray to the specimen holder, click .
  • Page 75 Pannoramic MIDI 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 76 Pannoramic MIDI 1.18 User’s Guide 4 Software Description Figure 50 – Filter properties window Filter name The name of the filter is displayed here. Exposure Settings You can set the Exposure time weight (%) here (displayed under TW in the Channel Settings frame).
  • Page 77 Pannoramic MIDI 1.18 User’s Guide 4 Software Description Digital Gain Note: This is camera-dependent, with AxioCam MRm Rev 3 the index value ranges from 0 to 4, and with pco.edge 4.2 from 0 to 6. Enter the Index value by entering it in the box or by selecting the value with the arrow buttons.

  • Page 78: Scan Options

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.5.2 Scan Options Figure 52 – 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 79 Pannoramic MIDI 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 80 Pannoramic MIDI 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 81 Pannoramic MIDI 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 82: Preview Panel

    Pannoramic MIDI 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 54 – Preview panel Use threshold Scan specimen with auto threshold – This automatically detects the specimen in the •...
  • Page 83 Pannoramic MIDI 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.
  • Page 84 Pannoramic MIDI 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 85: Hardware Panel

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.5.4 Hardware panel Figure 56 – Hardware panel (selected mode: User controlled) April 3, 2014 - Rev 1 3DHISTECH Ltd. 85(127)
  • Page 86 Pannoramic MIDI 1.18 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 This option has no effect on a running digitization process where no live image is displayed.
  • Page 87 Pannoramic MIDI 1.18 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 88: Service Panel

    Pannoramic MIDI 1.18 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 on Auto, meaning that the exposure times are determined automatically. After selecting the corresponding filter and activating the live image, you can preset an exposure time in the Exposure value field.

  • Page 89: Using Fluorescent Automatic Mode

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.6 Using Fluorescent Automatic Mode 4.6.1 Routine work panel Figure 58 – Routine work panel The Routine work panel provides some basic digitization functions. April 3, 2014 - Rev 1 3DHISTECH Ltd.
  • Page 90 Pannoramic MIDI 1.18 User’s Guide 4 Software Description To insert and remove slides To load the tray, click . The system checks the positions for slides during the loading • process. If you do not want to load all slides, you can specify the first and last slide to be loaded in •...
  • Page 91 Pannoramic MIDI 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 92 Pannoramic MIDI 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 93 Pannoramic MIDI 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 94: Barcodes Panel

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.6.2 Barcodes panel Figure 61 – 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 95 Pannoramic MIDI 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.
  • Page 96 Pannoramic MIDI 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 97 Pannoramic MIDI 1.18 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) <tray number>M<slide position>...

  • Page 98: Preview Panel

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.6.3 Preview panel Figure 62 – 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 99: Focus Panel

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.6.4 Focus panel Figure 63 – Focus panel 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 100: Scan To Server

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.7 Scan To Server The ScanToServer function is available for you to scan directly to a dedicated CaseCenter server. To setup a connection with a designated server, follow the steps below: 1. Click Scan Options on the Routine Work panel.
  • Page 101 Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4. Click the Connect button in the Scan Options window to connect to the server. If the connection is established the server status will be modified from Not connected to Connected. Click OK to close the Scan Options window.
  • Page 102 Pannoramic MIDI 1.18 User’s Guide 4 Software Description Figure 70 – Scan To Server window in Automatic Mode Give the number of the starting (First slide) and the final slide (Last slide) to be • scanned in the appropriate field. For example, if you want to scan slides to server from 1-12, type: First slide: 1;...
  • Page 103 Pannoramic MIDI 1.18 User’s Guide 4 Software Description Figure 71 – Scan To Server window in Automatic Mode Profiles can be added by selecting a list entry from the Profile drop-down list. • Select a folder where the slide will be scanned to. After clicking the Folder drop- •...
  • Page 104 Pannoramic MIDI 1.18 User’s Guide 4 Software Description If modification is done to the folder tree of the CaseCenter server while the Scan To • Server window is open, click Update Tree to refresh the tree view. Server side barcode parsing option can be selected if CaseCenter is connected with •...

  • Page 105: Using Profiles

    Pannoramic MIDI 1.18 User’s Guide 4 Software Description 4.8 Using Profiles Note: Saved profile settings cannot be transferred to and used on another control computer and if using a different type of 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 106 Pannoramic MIDI 1.18 User’s Guide 4 Software Description Fluorescent settings Filter position(s) • Selected focus channel • Selected stitching channel • Flat field correction (ON/OFF) • Sharpening (ON/OFF) • Use of skip empty field-of-views (ON/OFF) • Do not use extended focus on empty field-of-views (ON/OFF) •...

  • Page 107: Troubleshooting And Maintenance

    Pannoramic MIDI 1.17 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 108: Cleaning The Device

    Pannoramic MIDI 1.17 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 109: Troubleshooting

    5 Troubleshooting and Maintenance 5.2 Troubleshooting This section describes the most common troubleshooting solutions for the Pannoramic MIDI product. If any problem arises that does not have solution in this manual, contact the service personnel. The product does not start Power supply is interrupted •...
  • Page 110 Pannoramic MIDI 1.17 User’s Guide 5 Troubleshooting and Maintenance 8. Switch on the control computer. 9. Launch control software. Illumination error! Probably the lamp has burned out. Please turn off the scanner and check the lamp! Halogen lamp is defective •...

  • Page 111: Fluorescent Applications (Optional)

    Pannoramic MIDI 1.17 User’s Guide 5 Troubleshooting and Maintenance Slide is often positioned incorrectly Guiding fault in transport system • Contact 3DHISTECH Service for support. ◦ Digitization process is extremely slow Extended focusing option is activated • Deactivate the Extended focusing option if not required.

  • Page 112: Maintenance

    To replace the halogen lamp, (or to perform other maintenance work) and to interrupt a running digitization procedure because of slide or tray jamming, the protective covers of the Pannoramic MIDI need to be opened in order to eliminate the problem.
  • Page 113 Pannoramic MIDI 1.17 User’s Guide 5 Troubleshooting and Maintenance Figure 75 – Removal of covers The protective cover is composed of two halves locked to each other. Locate the hole (1) at the front of the right half of the cover (2): 1.

  • Page 114: Replacing The Halogen Lamp

    Pannoramic MIDI 1.17 User’s Guide 5 Troubleshooting and Maintenance 5.3.2 Replacing the halogen lamp Figure 76 – Replacing the halogen lamp Warning! Hot surface! Wait for the lamp surface to cool down. Keep a cool-down time of approximately 15 minutes.

  • Page 115: Replacing Lamp Module (For Fluorescent Option)

    Pannoramic MIDI 1.17 User’s Guide 5 Troubleshooting and Maintenance 8. First, remove the defective bulb (4) from the lamp mount, then insert a new bulb into its mount. Warning! Do not touch the bulb with your bare fingers! Use a dry, clean, lint-free cloth or gloves when inserting the bulb into the mount.
  • Page 116 Pannoramic MIDI 1.17 User’s Guide 5 Troubleshooting and Maintenance Figure 77 – Removing the lateral cover of the HXP 120 3. Press plug securing latches inward (1) then disconnect plug of the lamp module (2) (see Figure 78). Figure 78 – Disconnect plug 4.

  • Page 117: Removing A Slide

    Pannoramic MIDI 1.17 User’s Guide 5 Troubleshooting and Maintenance 5. Carefully retrieve the new lamp module from its transporting container. Hold the lamp module only by its ceramic part. 6. Insert the new lamp module. Make sure that the groove (1) in the contact surface of the lamp captures the corresponding pin of the lamp mount (see Figure 80).
  • Page 118 Pannoramic MIDI 1.17 User’s Guide 5 Troubleshooting and Maintenance Warning! Crush hazard! Before you remove a jammed slide, cancel the running digitization process, terminate the software session and turn the power off. Any manipulation performed on a mechanical component must be followed by a complete device initialization routine (software restart).

  • Page 119: Installing And Removing The Filter Module (Fluorescent Option)

    Pannoramic MIDI 1.17 User’s Guide 5 Troubleshooting and Maintenance 5.3.5 Installing and Removing the Filter Module (Fluorescent Option) Figure 82 – Installing and removing the filter module 1. If using an HXP 120 illumination unit, turn it off. Warning! Crush hazard! Stop the running digitization process before you proceed with filter module installation or removal.

  • Page 120: Transporting Pannoramic Midi

    9. If an HXP 120 illumination unit is used, turn it on again (consider the cooling time possibly required). 5.3.6 Transporting Pannoramic MIDI The following procedure shows how to transport Pannoramic MIDI. Note: The base unit does not have carrying handles for transporting. Two people can carry the base unit by holding it by its base plate.
  • Page 121 3. Transport Pannoramic MIDI with the help of another person. 4. After finishing transportation, reestablish cable connections. Caution! Do not lift or transport Pannoramic MIDI by holding its protective covers! Caution! Readjust camera angle if necessary after transporting and reinstalling the Pannoramic MIDI! April 3, 2014 - Rev.

  • Page 122: Technical Data

    Pannoramic MIDI 1.17 User’s Guide 6 Technical Data 6 Technical Data Dimensions (width x depth x height) Base unit approx. 418 mm (W) x 517 mm (D) x 418 mm (H) Base unit with fluorescence option approx. 418 mm (W) x 568 mm (D) x 457 mm (H) 24V 100W power supply approx.
  • Page 123 Pannoramic MIDI 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...
  • Page 124 Pannoramic MIDI 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 Average service life of Mercury short arc reflector lamp...
  • Page 125 Pannoramic MIDI 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...
  • Page 126 Pannoramic MIDI 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...
  • Page 127 Lumencor..................13, 19, 20, 24, 86, 107, 112, 124 Lumencor SPECTRA 6 Light Engine...................21, 124 Marker..........................50, 53, 83, 105 Pannoramic MIDI.....7, 9, 10, 11, 13, 14, 15, 17, 19, 20, 22, 28, 30, 36, 109, 112, 120, 121 Pannoramic SCAN 150........................24 Pannoramic Viewer.......................21, 60, 71, 110 Pco.edge............................125...

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