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3D Histech Pannoramic MIDI II 2.0.5 User Manual

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Pannoramic MIDI II 2.0.5
User's Guide
December 7, 2018
PMII205-Rev1
Rev. 1

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Summary of Contents for 3D Histech Pannoramic MIDI II 2.0.5

  • Page 1 Pannoramic MIDI II 2.0.5 User’s Guide December 7, 2018 PMII205-Rev1 Rev. 1...

  • Page 2: Table Of Contents

    Pannoramic MIDI II 2.0.5 User’s Guide Contents Disclaimer........................5 Declaration Of Conformity....................7 Character Formats and Symbols..................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 MIDI II 2.0.5 User’s Guide 5.1.1 Profile Settings Panel............................45 5.1.2 Microscope Control Panel..........................52 5.1.3 Quick microscope functions...........................62 5.2 Fluorescence Microscope Mode....................64 5.2.1 Profile Settings panel............................64 5.2.2 Microscope Control Panel..........................74 5.2.3 Quick preview functions..........................87 5.2.4 Bottom menu bar of the main window......................90 5.3 Planner mode...........................92...
  • Page 4 Pannoramic MIDI II 2.0.5 User’s Guide Packing the accessories.......................142 Closing the package........................142 Handling of the package......................143 Index........................... 144 December 7, 2018 – Rev. 1 3DHISTECH Ltd. 4(144)

  • Page 5: Disclaimer

    Pannoramic MIDI II 2.0.5 User’s Guide Disclaimer Copyright © 2001-2018 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 II 2.0.5 User’s Guide Further Information For the latest information on 3DHISTECH products and services, please visit our website at the following URL: http ://www.3dhistech.com. Company Address: 3 Öv street 1141 Budapest – HUNGARY December 7, 2018 – Rev. 1 3DHISTECH Ltd.

  • Page 7: Declaration Of Conformity

    Pannoramic MIDI II 2.0.5 User’s Guide Declaration Of Conformity 3DHISTECH Ltd. declares that the product Pannoramic MIDI II slide scanner is designed and produced with consideration of specified requirements according to the IEC 61326-2-6:2005 standard, and conforms to the directives and other standards listed below: IEC 61010-1:2001, “Safety Requirements for Electrical Equipment for Measurement, Control, and...

  • Page 8: Character Formats And Symbols

    Pannoramic MIDI II 2.0.5 User’s Guide 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

    Pannoramic MIDI II 2.0.5 User’s Guide 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 II and in the section 1.1.3 Warning and Information Labels have the following meanings:...
  • Page 10 Pannoramic MIDI II 2.0.5 User’s Guide Electric power to the Pannoramic MIDI II is supplied via an external mains power supply unit. It allows for operation at line voltages in the range of 100 V Note: to 240 V ±10%, 50/60 Hz, without any extra facilities required for voltage transformation.

  • Page 11: Notes On Warranty

    Pannoramic MIDI II 2.0.5 User’s Guide Notes on Warranty 3DHISTECH Ltd. – as the Product Manufacturer – warrants the Pannoramic MIDI 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 minimize damage.

  • Page 12: Terms And Abbreviations

    Pannoramic MIDI II 2.0.5 User’s Guide 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: a dynamic, interactive image that you can manage, save, magnify, zoom, name, evaluate, annotate, mark, comment, send to a colleague electronically for co- operation or advice, and so on.

  • Page 13: Product Description

    Pannoramic MIDI II 2.0.5 User’s Guide 1 Product Description 1 Product Description 1.1 Product Overview 1.1.1 Intended Use The Pannoramic MIDI II is designed to use transmitted light and reflected light fluorescence to digitize biological samples and specimens (histological sections, typically). The target users of the product can work for example, in education, research, industry or medical sectors.
  • Page 14 Pannoramic MIDI II 2.0.5 User’s Guide 1.1.2 Features and Benefits Multiband filter support • FL scanning with a low noise, 16-bit scientific CMOS pco.edge 4.2 camera • New software-aimed flat-field correction compensation method to create homogeneous slide • image 12 slide automatic loading and scanning •...

  • Page 15: Warning And Information Labels

    Pannoramic MIDI II 2.0.5 User’s Guide 1.1.3 Warning and Information Labels 1.1.3 Warning and Information Labels The following figure contains the labels used on the Pannoramic MIDI II main unit, the external mains power supply unit, and the Lumencor SOLA SM II illumination unit.

  • Page 16: Base Unit

    Pannoramic MIDI II 2.0.5 User’s Guide 1.1.4 Base Unit 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. Point Grey Grasshopper 3 or pco.edge 4.2 camera Fluorescent option A 3.

  • Page 17: System Overview

    Pannoramic MIDI II 2.0.5 User’s Guide 1.2 System Overview 1.2 System Overview The standard scope of delivery of the product includes the following hardware and software components. 1.2.1 Pannoramic MIDI II system The following figure shows the main parts of the Pannoramic MIDI II system.

  • Page 18: Hardware Options

    Pannoramic MIDI II 2.0.5 User’s Guide 1.2.2 Hardware Options 1.2.2 Hardware Options Note: The configuration of the control computer and monitor can vary depending on the product order. Cameras Point Grey Grasshopper 3 1 CCD monochrome camera for high-quality sensitive fluorescent applications.
  • Page 19 Pannoramic MIDI II 2.0.5 User’s Guide 1.2.2 Hardware Options Warning! The installation of the cameras in Pannoramic MIDI II must be carried out by trained professionals! 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 20: Control Software

    Pannoramic MIDI II 2.0.5 User’s Guide 1.2.2 Hardware Options Fluorescent Option for Pannoramic MIDI II Fluorescent illumination unit Description Lumencor SOLA SM II Fluorescent illumination unit (can be used with Point Grey Grasshopper 3 camera only) Lumencor SPECTRA 6 Light Engine illumination unit 1.2.3 Control Software...
  • Page 21 Pannoramic MIDI II 2.0.5 User’s Guide 1.2.3 Control Software Pannoramic Viewer software (fully functional) • Optional: CaseCenter • TMA module • 3D Reconstruction module • QuantCenter, HistoQuant, NuclearQuant, MembraneQuant, CISHQuant, FISHQuant, and • DensitoQuant modules TumorBoard module • E-School Encoder •...

  • Page 22: Installation

    Pannoramic MIDI II 2.0.5 User’s Guide 2 Installation 2 Installation Warning! The installation of Pannoramic MIDI II 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: Control Computer Ports

    Pannoramic MIDI II 2.0.5 User’s Guide 2.1 Control computer ports 2.1 Control computer ports The following figure shows the location of the connectors in order to enable easier transportation of the product for a short distance, by disconnecting cables and detaching hardware components from each other.

  • Page 24: Connectors And Cables

    Pannoramic MIDI II 2.0.5 User’s Guide 2.2 Connectors and cables 2.2 Connectors and cables Control – USB (between scanner and control computer) • Preview camera – USB cable (between scanner and control computer) • Point Grey Grasshopper 3 – USB 3.0 cable (between Point Grey Grasshopper 3 camera and •...

  • Page 25: Coupling The Lumencor Spectra 6 Unit With The Scanner

    Pannoramic MIDI II 2.0.5 User’s Guide 2.4 Coupling the Lumencor Spectra 6 unit with the scanner 2.4 Coupling the Lumencor Spectra 6 unit with the scanner To operate the Lumencor Spectra 6 Light Engine fluorescent illumination unit, it has to be attached to the Pannoramic MIDI II base unit, and connected to the camera, and the control computer with cables.

  • Page 26: Power The Scanner On/Off

    Pannoramic MIDI II 2.0.5 User’s Guide 2.5 External power supply unit Figure 6 – 24V external power supply unit 2.6 Power the scanner on/off To turn the scanner on, press down the I side of the rocker switch at the front panel of the 24V external power supply unit (Figure 6 –...

  • Page 27: Preparing Slides And Trays

    Pannoramic MIDI II 2.0.5 User’s Guide 3 Preparing Slides and Trays 3 Preparing Slides and Trays This section demonstrates how to prepare slides and trays. You may use slides and coverslips that meet the following specifications: Slides Coverslips Length 75.0 to 76.0 mm max.
  • Page 28 Pannoramic MIDI II 2.0.5 User’s Guide 3 Preparing Slides and Trays Caution! Do NOT scratch any circular marker onto the glass surface of a slide, use a soft tip pen instead for marking area of interest. 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.

  • Page 29: Affixing Barcode Stickers To Slides

    Pannoramic MIDI II 2.0.5 User’s Guide 3.1 Affixing Barcode Stickers to Slides 3.1 Affixing Barcode Stickers to Slides This section describes how to affix barcode stickers to slides. Barcodes enable virtual slide identification. Figure 7 – Slide with a barcode sticker The label area is recorded by the preview camera, and can be displayed by the control and viewer software.

  • Page 30: Inserting And Removing Slides

    Pannoramic MIDI II 2.0.5 User’s Guide 3.2 Inserting and Removing Slides 3.2 Inserting and Removing Slides To insert slides into a tray Figure 8 – Inserting slides into a tray A tray can contain a maximum of 12 slides. Push a slide (1) into the desired slot (4) of the tray (3) with its barcode end (2) first.
  • Page 31 Pannoramic MIDI II 2.0.5 User’s Guide 3.2 Inserting and Removing Slides 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 32 Pannoramic MIDI II 2.0.5 User’s Guide 3.2 Inserting and Removing Slides Caution! To insert or remove a filled tray from the device, first check tray for incorrectly inserted slides (refer to Figure 9) and always ensure also when moving the tray, slightly tilt it to its closed side to prevent the slides from accidentally falling out.

  • Page 33: Software Description

    Pannoramic MIDI II 2.0.5 User’s Guide 4 Software Description 4 Software Description 4.1 Starting / Exiting Pannoramic MIDI II Software Application 4.1.1 Starting the software To start the program, double-click on the program icon on the desktop or start it from Start \ Program Files \ 3DHISTECH \ Pannoramic Scanner After software initialization the user interface is opened and the mode selection icons are displayed.

  • Page 34: Exiting The Software

    Pannoramic MIDI II 2.0.5 User’s Guide 4.1.2 Exiting the software 4.1.2 Exiting the software To exit the software, Click X at the main window header to close the program. Note, that when exiting the software, the loaded slide will not be automatically unloaded.
  • Page 35 Pannoramic MIDI II 2.0.5 User’s Guide 4.2 Main window functions Slide/tray control Upon clicking the slide icon or entering slide position number at the right side, the slide can be loaded. Unload the slide by clicking Unload next to slide image, and unload the tray by clicking Unload next to the rack image.
  • Page 36 Pannoramic MIDI II 2.0.5 User’s Guide 4.2 Main window functions The following functions are available for you to select from the toolbar: – Fast mode ◦ Live images are displayed with a frequency of at least 10 images per second. If an...
  • Page 37 Pannoramic MIDI II 2.0.5 User’s Guide 4.2 Main window functions Scan Properties By using this function, unique settings can be defined even for each separate scanning. It is included on the profile cards as well, added to the slide in Planner mode.
  • Page 38 Pannoramic MIDI II 2.0.5 User’s Guide 4.2 Main window functions Scan to Server • Server: the drop-down list includes all the saved servers. Click Add new item ... to create ◦ another server connection. Figure 14 – Scan to Server Click Select server profile arrow to show the list of saved server profiles, than click Add new •...
  • Page 39 Pannoramic MIDI II 2.0.5 User’s Guide 4.2 Main window functions After loading server data, user name and password is required to be added for authentication and accessing the server. If connection is successful, a green checkmark is displayed in the window.
  • Page 40 Pannoramic MIDI II 2.0.5 User’s Guide 4.2 Main window functions You can select the following barcode types: 1D barcode types *Code 39 ◦ Code 128 ◦ Code 16K ◦ *Interleaved 2 of 5 ◦ Standard 2 of 5 ◦ IATA 2 of 5 ◦...
  • Page 41 Pannoramic MIDI II 2.0.5 User’s Guide 4.2 Main window functions – Start Scan Scanning of the actual slide or performing the whole previously planned scanning procedure can be initiated. – Stop Scan – Stop actual progress – Take All Preview Figure 17 –...
  • Page 42 Pannoramic MIDI II 2.0.5 User’s Guide 4.2 Main window functions – Open profile Figure 18 – Profile browser window The Profile Browser window containing a list of previously saved profiles is opened. Based on the Illumination type, profiles are grouped into two clusters: Brightfield and Fluorescence. Additional...
  • Page 43 Pannoramic MIDI II 2.0.5 User’s Guide 4.2 Main window functions – Save Profile The selected profile can be saved in this window after typing the profile name into the text field and clicking Save as. – Reset Zoom This function is active only in Live view at 1:1 magnification.

  • Page 44: Scanning Modes And Settings

    Pannoramic MIDI II 2.0.5 User’s Guide 5 Scanning modes and settings 5 Scanning modes and settings After microscope initialization, if FL HW option is provided, you can select from the following two modes: Brightfield scanning mode (see section 5.1 Brightfield Scanning Mode for more information) •...

  • Page 45: Profile Settings Panel

    Pannoramic MIDI II 2.0.5 User’s Guide 5.1.1 Profile Settings Panel 5.1.1 Profile Settings Panel Objective settings This field displays the objective used for scanning. Objective type: 20x; 40x Focus settings for the scan profile Figure 20 – Focus settings for scan profile Limits of the range: You can define focus limits by selecting Limits of the range for focusing.
  • Page 46 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.1 Profile Settings Panel Thresholding: The manually specified value is used for thresholding during scanning. Preview • image of the loaded slide is displayed in the Preview window, and when modifying any of the parameter values, it will have effect on the preview image.
  • Page 47 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.1 Profile Settings Panel Everything within marker ◦ To scan everything within the marked area, check the Everything within marker selection box. Alternatively, click in the preview window to activate this function. Figure 21 – Scan everything within the marked area (selected / not selected) Threshold enhancement •...
  • Page 48 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.1 Profile Settings Panel Caution! It requires lots of time (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 49 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.1 Profile Settings Panel Multilayer mode Select Single layer option if you want to scan a single layer of the slide. • By choosing the Extended focus option, the software selects the sharpest image from each •...
  • Page 50 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.1 Profile Settings Panel Scan Settings These settings cannot be modified when using Pannoramic MIDI II as scanner. Here you can activate the Stop and go scanning mode by which the slide tray stands still during recording the FOV, then it moves on so that the scanner can record the next FOV.
  • Page 51 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.1 Profile Settings Panel 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%. PNG – Lossless compressed image format.

  • Page 52: Microscope Control Panel

    Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel 5.1.2 Microscope Control Panel The Microscope Control panel includes the main control features of the microscope. 5.1.2.1 Preview Window The Preview panel offers options for threshold setting and selection of the area to be scanned.
  • Page 53 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel Preview Type setting determines the type of illumination. In Brightfield mode when using MIDI II, the following preview types are available: Brightfield preview – a normal type of illumination in the microscope for scanning the •...
  • Page 54 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel Warning! Do NOT use Remove coverslip function on TMA slides! The layout of TMA slides may mislead the detecting algorithm. Fill holes inside scanmap : If selected, the holes inside the specimen will also be scanned.
  • Page 55 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel Use marker with threshold : 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.
  • Page 56 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel Preview Toolbar This section is located at the bottom of the preview image. Save scanmap – Click this icon to save the currently selected areas to scanmap. • Position – To position the specimen holder that holds the current slide, click Position •...
  • Page 57 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel Crop – Crop the area of the selected area. • Place Circle – You can select the area to be scanned with the different tools on the • Preview toolbar.
  • Page 58 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel Use selection box restriction – The preview image shows the area that will be digitized • with a red and/or an orange mask. If the Use selection box is enabled, and the crop function is selected, a black frame displayed in the image, and only the area inside the box is scanned.
  • Page 59 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel 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 60 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel Click the button to display barcode label area. To rotate the label area by 180°, click Figure 33 – Barcode label area window – Undo / Redo modification made during specifying the Scanmap. These buttons are inactive when Use threshold function is applied.
  • Page 61 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel 5.1.2.3 Exposure Indicator Activate Exposure indicator function by clicking . Click to calculate exposure time for the actual Live image. In Brightfield mode there is no option for manually setting the values. Exposure time can be displayed in microsecond, millisecond, and also in second.

  • Page 62: Quick Microscope Functions

    Pannoramic MIDI II 2.0.5 User’s Guide 5.1.2 Microscope Control Panel 5.1.2.5 Quick preview functions Use Ctrl+mouse wheel to zoom in or out to the preview area or the Live image. A quick preview function tool pops up by right-clicking to the preview area. It allows a quick access to...
  • Page 63 Pannoramic MIDI II 2.0.5 User’s Guide 5.1.3 Quick microscope functions Autofocus • Live tools • Fast mode ◦ Screenshot ◦ Magnifier ◦ Ruler ◦ Image processor plugins ◦ Add scanmap ◦ Auto exposure • December 7, 2018 – Rev. 1 3DHISTECH Ltd.

  • Page 64: Fluorescence Microscope Mode

    Pannoramic MIDI II 2.0.5 User’s Guide 5.2 Fluorescence Microscope Mode 5.2 Fluorescence Microscope Mode Fluorescence Microscope View consist of three different sections: Profile Settings panel: Profile settings containing parameters used for scanning. • Microscope Control Panel: Live microscope movement functions •...
  • Page 65 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.1 Profile Settings panel E / Z: Multilayer option: Select Extended focus or Z-stack for scanning the required channels • in accordance with the scanning mode set in the profile. Figure 40 – Filter table Objective Settings This field displays the objective used for scanning.
  • Page 66 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.1 Profile Settings panel This will, however, speed up the focusing process. If you deselect the Use fine focus checkbox, the software immediately starts scanning on the basis of the interpolated values, without pre-fine-focusing.
  • Page 67 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.1 Profile Settings panel Pre-scan + high-resolution – creates a High-Resolution fast FL preview image of every ◦ FOV within the selected area (in single layer DAPI, with an illumination time of 20ms) that is displayed in the Profile Wizard window.
  • Page 68 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.1 Profile Settings panel Everything within marker ◦ To scan everything within the marked area, check the Everything within marker selection box. Alternatively, click in the preview window to activate this function. Figure 41 – Scan everything within the marked area (selected / not selected) Threshold enhancement •...
  • Page 69 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.1 Profile Settings panel Caution! It requires lots of time (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 70 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.1 Profile Settings panel Multilayer mode Single layer mode: If none of the filters are selected in the Filters table for multilayer • scanning, this mode is active and can be selected, and Multilayer mode turns inactive.
  • Page 71 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.1 Profile Settings panel Scan settings Change filters after whole slide scanning • To optimize speed, filter change should take place after the digitization of the slide with one channel. Change filters at each field-of-view •...
  • Page 72 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.1 Profile Settings panel Image Correction settings Use Flatfield correction – If this function is active the scanned slide compensates itself with a • special method (light intensity statistical data, not to modify the average intensity of the slide.
  • Page 73 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.1 Profile Settings panel Figure 44 – Image encoding window Compression • BMP – Lossless uncompressed image format, but larger files due to less effective ◦ compression. It is a raw data file. PNG – Lossless compressed image format.

  • Page 74: Microscope Control Panel

    Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel 5.2.2 Microscope Control Panel 5.2.2.1 Preview window Click to open the Preview panel that offers options for threshold setting and selection of the area to be scanned. Figure 45 – Pre-scan preview image Threshold options This section is located at right side of the preview window.
  • Page 75 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Preview Types In FL Microscope mode the following additional preview modes are available: Brightfield preview – a normal type of illumination for scanning. This option is ◦ recommended when scanning in Brightfield mode.
  • Page 76 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Caution! It requires lots of time (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 77 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Manual threshold • Set value manually or calculate value by using the Calculate Threshold function (can be activated only when manual thresholding is selected). This sets the sensitivity of the specimen detection.
  • Page 78 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Dilate mask Adjust the slider to enlarge or decrease the scanned area. To switch to manual mode click the top left corner of the button and the required value can be entered in the box Preview Toolbar This section is located at the bottom of the preview image.
  • Page 79 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Erase • Delete selected areas from the preview image. Deselection is made based on the selected shape from the Preview Toolbar. This area will not be scanned. Figure 48 – Not scanned selection Edit •...
  • Page 80 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Crop • Crop the area of the selected area. Place Circle • You can select the area to be scanned with the different tools on the Preview toolbar. Rectangle tool •...
  • Page 81 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Delete TMA grid by clicking the X at the top right corner, and rotate grid by clicking the icon at the bottom right corner. Enter the number of rows and columns in the Rows and Columns fields or select the appropriate values with the arrows.
  • Page 82 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel The following colors are used in the preview image to demonstrate digitization and selection settings: Figure 52 – Colors in preview image and Label area switching button 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 83 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Marker If Scan area inside the marker is selected in the Preview panel, the preview camera detects the marker pen. The inside areas appear in red color and will be digitized.
  • Page 84 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Click the button to display barcode label area. To rotate the label area by 180°, click Figure 54 – Barcode label area window – Undo / Redo modification made during specifying the Scanmap. These buttons are inactive when Use threshold function is applied.
  • Page 85 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Figure 55 – Focus indicator panel 5.2.2.3 Exposure Indicator Exposure time for the live image can be calculated by using the Calculated Exposure time function . It is available to switch between microsec, millisec, and sec units for the reading of exposure time.
  • Page 86 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.2 Microscope Control Panel Image Intensity Click to open Image intensity panel. An image is defined as a two-dimensional function f(x, y) the amplitude of at any pair of coordinates (x, y) is called the intensity or gray level of the image at that point.

  • Page 87: Quick Preview Functions

    Pannoramic MIDI II 2.0.5 User’s Guide 5.2.3 Quick preview functions 5.2.3 Quick preview functions Use Ctrl + mouse wheel to zoom in or out to the preview area or the Live image. 5.2.3.1 Quick toolbar of preview window Figure 59 – Settings of preview quick toolbar A Quick Toolbar pops up by right clicking any of the control menu items.
  • Page 88 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.3 Quick preview functions 5.2.3.2 Quick Microscope functions A quick microscope functions tool can be displayed upon right-clicking on the background of the main window (outside the preview window). It includes quick-access-buttons to main functions for MIDI II: Figure 60 –...
  • Page 89 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.3 Quick preview functions Microscope mode • Brightfield ◦ Fluorescence ◦ Figure 64 – Microscope mode Live tools • Fast mode ◦ Screenshot ◦ Magnifier ◦ Ruler ◦ Image processor plugins ◦ Use pseudo-color ◦...

  • Page 90: Bottom Menu Bar Of The Main Window

    Pannoramic MIDI II 2.0.5 User’s Guide 5.2.4 Bottom menu bar of the main window 5.2.4 Bottom menu bar of the main window Profile History This function can be activated by clicking in Preferences. During setting scanning profile all of the previously used parameter will be saved automatically.
  • Page 91 Pannoramic MIDI II 2.0.5 User’s Guide 5.2.4 Bottom menu bar of the main window Figure 69 – Profile history tree December 7, 2018 – Rev. 1 3DHISTECH Ltd. 91(144)

  • Page 92: Planner Mode

    Pannoramic MIDI II 2.0.5 User’s Guide 5.3 Planner mode 5.3 Planner mode The whole scanning procedure can be planned in this mode. Assign profiles to slides, modify scan- maps without performing physical loading of slides. In Planner mode not only the scanning of the actually loaded tray can be planned, but also profile assignment to slides of prepared virtual trays is available to be performed.

  • Page 93: General Functions At The Main Menu

    Pannoramic MIDI II 2.0.5 User’s Guide 5.3.1 General functions at the main menu 5.3.1 General functions at the main menu Microscope/Planner selector Horizontal/Vertical selector (Available in Slide view with card mode) Stage Control – Available after initialization, upon clicking the slide icon or entering slide position number at the right side, the slide can be loaded.
  • Page 94 Pannoramic MIDI II 2.0.5 User’s Guide 5.3.1 General functions at the main menu Profile management for all the magazines – The following profile-related tasks applicable for the planner can be performed: Add current profile to all racks • Open profile for all racks •...

  • Page 95: General Functions At The Tray Menu

    Pannoramic MIDI II 2.0.5 User’s Guide 5.3.2 General functions at the tray menu 5.3.2 General functions at the tray menu Rack view mode selector Switch view by clicking this button. Click to add a virtual tray to the planner, and to remove a virtual tray from the planner.

  • Page 96: Slide View With Card

    Pannoramic MIDI II 2.0.5 User’s Guide 5.3.3 General functions at the slide menu By default the Current profile is applied, but you can select another profile by clicking Load profile. Click Add selected profile to apply the selected profile to the slides in the range.
  • Page 97 Pannoramic MIDI II 2.0.5 User’s Guide 5.3.4 Slide view with card Figure 74 – Brightfield profile card and Fluorescence profile card The following information are included in a profile card: Profile name in the top left corner • Profile status is marked with spots of different color: •...
  • Page 98 Pannoramic MIDI II 2.0.5 User’s Guide 5.3.5 Table view mode 5.3.5 Table view mode By clicking each slide will be displayed in a separate row. Click to assign profile to a slide, and to detach a profile from a slide. A slide can have more than one profile assigned to it, and these profiles can either be BF or FL if the scanner is capable to operate in these two scanning modes.

  • Page 99: Card Collection View Mode

    Pannoramic MIDI II 2.0.5 User’s Guide 5.3.6 Card collection view mode 5.3.6 Card collection view mode If you click the button, each of the slide previews are displayed in the window. Add profiles by clicking and detach profiles by clicking .

  • Page 100: Profile And Preview Overview On The Planner

    Pannoramic MIDI II 2.0.5 User’s Guide 5.4 Profile and Preview overview on the Planner 5.4 Profile and Preview overview on the Planner Each of the assigned profiles are checkable and modifiable. The panel at the right side includes all of the profile settings, in coherence with the view type of the Profile Setting panel.

  • Page 101: Progress Features

    Pannoramic MIDI II 2.0.5 User’s Guide 5.5 Progress features 5.5 Progress features The progress is visible both in Microscope and Planner modes whenever there is a running hardware operation or scanning procedure. Progress content can be therefore different depending on the type of the running procedure.

  • Page 102: Settings And Service

    Pannoramic MIDI II 2.0.5 User’s Guide 5.6 Settings and Service 5.6 Settings and Service Activate Settings by clicking and Services by clicking at the right side of the main menu bar. 5.6.1 Settings Activate Settings by clicking at the right side of the main menu bar.
  • Page 103 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.1 Settings Appearance settings View Mode Selector ◦ Text mode ▪ Icon mode ▪ Float Text mode ▪ Float Icon mode ▪ Style selector ◦ Black Jelly ▪ Flat style ▪ Black Jelly light ▪...
  • Page 104 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.1 Settings Live mode Rendered – live image is displayed in an embedded window ◦ External legacy – live image is displayed in an external window ◦ Screenshot folder – Set the folder for storing screenshots by clicking Browse. Otherwise ◦...
  • Page 105 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.1 Settings RGB Light ▪ Relay ▪ Scan Loader ▪ Service ▪ Shutter ▪ Slide Scanner ▪ Stage ▪ Software log ◦ All of the circumstances and states of the slide scanning procedure is saved. LogID is the sequence number of scanning performed on the scanner in use.
  • Page 106 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.1 Settings – Basic settings • On this panel, you can define the swap file location, set shutter auto close time in FL, and set the number of compensation images for preview camera if needed. Click Apply to accept modifications.
  • Page 107 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.1 Settings – Prescan settings • Unlike scan settings in Microscope or Planner mode, Prescan toolbar includes the same settings for pre-scanning but these depend on the hardware / filter settings. December 7, 2018 – Rev. 1 3DHISTECH Ltd.
  • Page 108 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.1 Settings – External application call • Two of the three settings are responsible for opening external applications (.exe or .bat) as defined (for example, CaseViewer software can be opened after scanning is finished).
  • Page 109 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.1 Settings If you define parameters in the Parameters field, it will pass them to the software that it starts. If no parameter is defined, then the parameter will not be passed. The default parameters are the following: For Slide scanning has finished: "<SLIDENAME>"...
  • Page 110 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.1 Settings E-mail • Authentication – User ID and User password are required. • Secure Connection (SSL) – If activated, the messages will be sent through secured • connection. If you have properly set messenger settings, click Save.

  • Page 111: Services

    Pannoramic MIDI II 2.0.5 User’s Guide 5.6.2 Services 5.6.2 Services Activate Service menu by clicking at the right side of the main menu bar. – Service password • Enter password first to enable service settings for modification. – Camera settings •...
  • Page 112 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.2 Services Set Position, Objective type, and Magnification settings of the objective. ◦ Use manual camera changer – Changing the cameras is performed manually. ◦ Prescan objective protection enabled – If activated, slide area near the edges will not be ◦...
  • Page 113 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.2 Services Note: If Lumencor SPECTRA 6 is configured as illumination unit, the corresponding Enable Lumencor hardware trigger option is displayed on the Filter settings form. Stitching overlap – Set the amount how much the FOVs should extend over ◦...
  • Page 114 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.2 Services On this panel you can define which filters occupy which turret positions. Select filter hardware positions from the drop-down list ◦ Move filter wheel to insert position ◦ Enable position ◦ Note: Whenever a selected physical filter is disabled, the filter itself must be removed from the turret.
  • Page 115 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.2 Services – Image compensation • You can use a saved compensation image whenever compensation-related issues occur (deriving from the slide, illumination, staining or embedding medium irregularities). BF cameras field displays the active camera. Currently, there is only one active camera for ◦...
  • Page 116 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.2 Services Note: If you did not set the barcode type correctly, or there is no barcode in the barcode area, the software will display the following error message: “Barcode detection unsuccessful! There might be no barcode present.”...
  • Page 117 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.2 Services Barcode reader library ◦ Select MIL barcode library or Embedded barcode library ▪ General Barcode settings ◦ Inverse barcode color ▪ Activate to invert foreground and background colors of the barcode. Use barcode compensation ▪...
  • Page 118 Pannoramic MIDI II 2.0.5 User’s Guide 5.6.2 Services – Microscope control • Illumination ◦ Condensor covered ▪ Brightfield illumination ▪ Barcode area light ▪ Backlight illumination intensity ▪ Objective guide ◦ Step size ▪ X / Y values or navigation arrows ▪...

  • Page 119: Hosting

    Pannoramic MIDI II 2.0.5 User’s Guide 5.6.2 Services – Slide load tester • Slide loading operation can be checked for each of the slides on the tray. Click Insert tray if the prepared tray is placed onto the feeder plate and pushed in.
  • Page 120 Pannoramic MIDI II 2.0.5 User’s Guide 5.7 Hosting Hosting a teleconsultation session 1. Select Hosting from the microscope mode menu 2. Type in your nickname used during the session 3. Click to start hosting the session 4. The software displays the hosting address and the port number Join teleconsultation as a client 1.

  • Page 121: Using Profiles

    Pannoramic MIDI II 2.0.5 User’s Guide 6 Using Profiles 6 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 122 Pannoramic MIDI II 2.0.5 User’s Guide 6 Using Profiles Fluorescent settings Filter position(s) • Selected focus channel • Selected stitching channel • Flat field correction (ON/OFF) • Intensity statistics • Intensity reducing • Intensity equalization • Sharpening (ON/OFF) • Use of skip empty field-of-views (ON/OFF) •...

  • Page 123: Troubleshooting And Maintenance

    Pannoramic MIDI II 2.0.5 User’s Guide 7 Troubleshooting and Maintenance 7 Troubleshooting and Maintenance 7.1 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 124: Cleaning The Device

    Pannoramic MIDI II 2.0.5 User’s Guide 7 Troubleshooting and Maintenance Lumencor SOLA SM II illumination unit Keep inflammable and combustible materials outside the range of SOLA SM II illumination • unit. Do not expose yourself to the UV radiation of the SOLA SM II illumination unit.

  • Page 125: Troubleshooting

    Pannoramic MIDI II 2.0.5 User’s Guide 7 Troubleshooting and Maintenance 7.2 Troubleshooting This section describes the most common troubleshooting solutions for the Pannoramic MIDI II product. If any problem arises that does not have solution in this manual, contact the service personnel.
  • Page 126 Pannoramic MIDI II 2.0.5 User’s Guide 7 Troubleshooting and Maintenance 7. Switch on the 24 V power supply. 8. Switch on the control computer. 9. Launch control software. Virtual slide is improperly focused almost across its entire surface Focus range enabled •...

  • Page 127: Fluorescent Applications (Optional)

    Pannoramic MIDI II 2.0.5 User’s Guide 7 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 128: Maintenance

    Pannoramic MIDI II 2.0.5 User’s Guide 7 Troubleshooting and Maintenance 7.3 Maintenance This section describes the most common maintenance solutions that can be performed by the user of the product. For maintenance solutions not described in this manual, contact the service personnel.

  • Page 129: Removing A Slide

    Pannoramic MIDI II 2.0.5 User’s Guide 7 Troubleshooting and Maintenance 2. The right half of the cover can be pulled apart only after the FL tray cover is removed. To pull apart the other half, the left side FL tray cover must be removed first.
  • Page 130 Pannoramic MIDI II 2.0.5 User’s Guide 7 Troubleshooting and Maintenance Figure 80 – Removing a slide 1. Push protective covers apart (see section 7.3.1 Opening the protective covers). 2. Move clamp (1) to the left, so the slide could be easily removed.

  • Page 131: Installing And Removing The Filter Module (Fluorescent Option)

    Pannoramic MIDI II 2.0.5 User’s Guide 7 Troubleshooting and Maintenance 7.3.3 Installing and Removing the Filter Module (Fluorescent Option) Figure 81 – Installing and removing the filter module 1. If using an Lumencor SOLA SM II illumination unit, turn it off.

  • Page 132: Transporting Pannoramic Midi Ii

    Pannoramic MIDI II 2.0.5 User’s Guide 7 Troubleshooting and Maintenance 5. Hold the filter module by its handling pads (5) (one on the right, one on the left side of the module) and insert its upper part in forward tilted position under the upper spring-loaded clamps (1).
  • Page 133 Pannoramic MIDI II 2.0.5 User’s Guide 7 Troubleshooting and Maintenance Caution! Do not lift or transport Pannoramic MIDI II by holding its protective covers! Caution! Readjust camera angle if necessary after transporting and reinstalling the Pannoramic MIDI II! December 7, 2018 - Rev. 1 3DHISTECH Ltd.

  • Page 134: Technical Data

    Pannoramic MIDI II 2.0.5 User’s Guide 8 Technical Data 8 Technical Data Dimensions (width x depth x height) Base unit approx. 700 mm (W) x 500 mm (D) x 500 mm (H) Base unit with fluorescence option approx. 700 mm (W) x 500 mm (D) x 500 mm (H) 24V 100W power supply approx.
  • Page 135 Pannoramic MIDI II 2.0.5 User’s Guide 8 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 136 Pannoramic MIDI II 2.0.5 User’s Guide 8 Technical Data Light sources Brightfield illumination PAX-601-3 Precision-Aligned Pulsed Xenon Light Source Average service life 1 x 10 flashes Fluorescent light source 1 (optional) SOLA SM II 365 (5 solid-state sources producing white light) Wavelength range 350–680 nm...
  • Page 137 Pannoramic MIDI II 2.0.5 User’s Guide 8 Technical Data Pixel resolution with 20x objective and 0.63x C-mount adapter 0.27µm Pixel resolution with 20x objective and 1x C-mount adapter 0.17µm Pixel resolution with 40x objective and 0.63x C-mount adapter 0.14µm Pixel resolution with 40x objective and 1x C-mount adapter 0.09µm...

  • Page 138: Appendix - Packaging Instructions

    Pannoramic MIDI II 2.0.5 User’s Guide Appendix – Packaging instructions Appendix – Packaging instructions Figure 1. Preparations 1. Unload the slide from the device by using the scanner software. Remove your slide. 2. Close the scanner software normally. 3. Turn off the scanner with the main switch located on the backside of the device. Disconnect all the cables of the scanner.
  • Page 139 Pannoramic MIDI II 2.0.5 User’s Guide Main parts and their accessories 3. BOX 3 – carton box dedicated for the PC a) PC (placed inside the dedicated foam) b) power cable for PC c) power cable for scanner d) USB cable of the scanner...

  • Page 140: Packaging

    Pannoramic MIDI II 2.0.5 User’s Guide Packaging Packaging The whole system is packed in a big carton box. This is divided into two areas with a vertical carton slab: “Space 1” for accessories (PC, cables, etc.) “Space 2” for BOX 2 (scanner) Figure 2.
  • Page 141 Pannoramic MIDI II 2.0.5 User’s Guide Packaging 1. BOX 2 – scanner box 2. Fixing foams for underneath BOX 2 3. Fixing foams for above BOX 2 4. Bottom part of BOX 1 5. Top of BOX 1 6. BOX 3 7.

  • Page 142: Packing The Midi Ii Scanner

    Pannoramic MIDI II 2.0.5 User’s Guide Packing the MIDI II scanner Packing the MIDI II scanner The most sensitive and most heavy unit is the MIDI II scanner. Please handle it with care, the weight of the device is more than 22 kg.

  • Page 143: Handling Of The Package

    Pannoramic MIDI II 2.0.5 User’s Guide Handling of the package Handling of the package Please be aware to observe the following instructions on Figure 5.: Designation Symbol Explanation The package must always be transported, handled and stored in such a way that the arrows always point upwards.

  • Page 144: Index

    Pannoramic MIDI II 2.0.5 User’s Guide Index Index Barcode......................20, 29, 30, 39, 117, 118 Brightfield......................13, 14, 19, 117, 123 CaseCenter..........................21, 39 Compensation image......................117, 123 Control software..................20, 117, 127, 128, 130, 132 Fluorescent............13, 14, 18, 19, 20, 24, 28, 123, 124, 129, 133, 136 Focus.....................14, 20, 84, 116, 123, 124, 128, 129...

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