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3D Histech Pannoramic MIDI 1.15 User Manual

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Pannoramic MIDI
1.15
User's Guide
March 13, 2012
Rev. 1

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  • Page 1 Pannoramic MIDI 1.15 User’s Guide March 13, 2012 Rev. 1...

  • Page 2: Table Of Contents

    Pannoramic MIDI 1.15 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 1.1.3 Warning and Information Labels........................14...
  • Page 3 Pannoramic MIDI 1.15 User’s Guide 4.3.2 Scan Options window.............................48 4.3.3 Preview tab..............................50 4.3.4 Preview area scanned by preview camera.....................53 4.3.5 Focus tab................................59 4.3.6 Service tab..............................61 4.3.7 Display field and toolbar for live images......................62 4.3.8 Start scan................................63 4.4 Using Brightfield Automatic Mode..................64 4.4.1 Routine work tab............................64...
  • Page 4 Pannoramic MIDI 1.15 User’s Guide Index........................... 131 March 13, 2012 - Rev 1 3DHISTECH Ltd. 4(131)

  • Page 5: Disclaimer

    Pannoramic MIDI 1.15 User’s Guide Disclaimer Copyright © 2001-2012 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 1.15 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 1.15 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 1.15 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

    Pannoramic MIDI 1.15 User’s Guide Character Formats and Symbols 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 Pannoramic MIDI 1.15 User’s Guide Character Formats and Symbols Remember to unplug the power cord before you open the Pannoramic MIDI Disconnect plug! base unit or replace a fuse! Use only electric fuses which are rated for the specified nominal current. You Warning! are prohibited from using makeshift fuses or short-circuiting of a fuse holder.

  • Page 11: Notes On Warranty

    Pannoramic MIDI 1.15 User’s Guide 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.

  • Page 12: Terms And Abbreviations

    Pannoramic MIDI 1.15 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

    Pannoramic MIDI 1.15 User’s Guide 1 Product Description 1 Product Description 1.1 Product Overview 1.1.1 Intended Use The Pannoramic MIDI 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 14: Warning And Information Labels

    Pannoramic MIDI 1.15 User’s Guide 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 illuminator. Figure 1 – Warning and information labels March 13, 2012 - Rev 1 3DHISTECH Ltd.

  • Page 15: Base Unit

    Pannoramic MIDI 1.15 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. CIS VCC-F52U25CL scan camera 4.

  • Page 16: Pannoramic Midi System

    Pannoramic MIDI 1.15 User’s Guide 1 Product Description 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. HXP 120 fiber-coupled illuminator (option) 2. 24 V power supply 3.

  • Page 17: Hardware Options

    Pannoramic MIDI 1.15 User’s Guide 1 Product Description 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 18 Pannoramic MIDI 1.15 User’s Guide 1 Product Description Camera adapters 0.63× adapter 1× adapter Warning! The installation of the cameras in Pannoramic MIDI 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 19: Control Software

    Pannoramic MIDI 1.15 User’s Guide 1 Product Description Fluorescent Option for Pannoramic MIDI Fluorescent unit (internal part) HXP 120 Fluorescent illumination unit (can be used with AxioCam MRm Rev3 only) Lumencor Spectra 7 Light Engine illumination unit (can be used with pco.edge camera only)
  • Page 20 Pannoramic MIDI 1.15 User’s Guide 1 Product Description Pannoramic Viewer software (fully functional) • Optional: CaseCenter • Pannoramic Viewer TMA module • 3D Reconstruction module • HistoQuant, NuclearQuant, MembraneQuant, FISHQuant, and DensitoQuant modules • ImmunoScreener module • E-School Encoder •...

  • Page 21: Installation

    Pannoramic MIDI 1.15 User’s Guide 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 22: Connectors And Cables

    Pannoramic MIDI 1.15 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 23 Pannoramic MIDI 1.15 User’s Guide 2 Installation Video cable (between monitor and control computer) • Power supply cable (between 230V/110V and monitor) • Power supply cable (between 230V/110V and control computer) • Power supply cable (between 230V/110V and power supply unit) •...

  • Page 24: Operating Slides And Trays

    Pannoramic MIDI 1.15 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 can use all slides and coverslips that meet the following specifications:...

  • Page 25: Affixing Barcode Stickers To Slides

    Pannoramic MIDI 1.15 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. Warning! Ensure that no part of the mounted coverslip protrudes from the edges of the slide.
  • Page 26 Pannoramic MIDI 1.15 User’s Guide 3 Operating Slides and Trays The label area is recorded by the preview camera, and can be displayed by the control and viewer software. To affix barcode stickers to slides, do the following: 1. Peel off the barcode sticker (2) from the roll.

  • Page 27: Inserting And Removing Slides

    Pannoramic MIDI 1.15 User’s Guide 3 Operating Slides and Trays 3.3 Inserting and Removing Slides To insert slides into a tray 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...
  • Page 28 Pannoramic MIDI 1.15 User’s Guide 3 Operating Slides and Trays To insert and remove trays Figure 7 – Inserting a tray 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 29: Software Description

    Pannoramic MIDI 1.15 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 30: Exiting The Software

    Pannoramic MIDI 1.15 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 31 Pannoramic MIDI 1.15 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 ( black or white – the color of the barcode), and other settings, you enable the Read Barcode option when using the control software.
  • Page 32 Pannoramic MIDI 1.15 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 33: Image Compensation

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description Foreground Color You can select the following foreground color of the barcode area: Black • White • Barcode Image Compensation Click Use barcode compensation image to use the previously created compensation image for scanning the label area.
  • Page 34 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Brightfield Compensation Figure 11 – Brightfield Compensation 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.
  • Page 35 Pannoramic MIDI 1.15 User’s Guide 4 Software Description 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. Therefore, the scanner will not use those areas for the creation of the compensation images.
  • Page 36 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Figure 12 – Fluorescent Compensation March 13, 2012 - Rev 1 3DHISTECH Ltd. 36(131)
  • Page 37 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Camera Selection This field displays the active camera. Filter Selection for Live Image Select the filter you want to use for displaying the Live image. Live You can display a live image of the current specimen in the Live image display field by clicking .

  • Page 38: Microscope Settings

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description By clicking Advanced Options button you can set the maximum exposition time used for creating the compensation image. To create the compensation image(s), click . Click the Stop button to interrupt the process.
  • Page 39 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Base Settings Figure 14 – Base settings Objective type You can select the type and the magnification level of the objective. March 13, 2012 - Rev 1 3DHISTECH Ltd. 39(131)
  • Page 40 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Camera type The software automatically detects and displays the camera type set in the Pos. 1 box upon clicking the Test and Apply Camera Settings button. If Pannoramic MIDI features a manual camera changer, activate the Use manual camera changer option first, then set the appropriate cameras both for Brightfield and Fluorescent (Pos.
  • Page 41 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Figure 15 – Camera rotation March 13, 2012 - Rev 1 3DHISTECH Ltd. 41(131)
  • Page 42 Pannoramic MIDI 1.15 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 16 – Z Difference tab March 13, 2012 - Rev 1 3DHISTECH Ltd.

  • Page 43: External Application Call Settings

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description Service Figure 17 – 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 44: Using Brightfield Manual Mode

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 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. You can define external application call settings for the following cases: Scan Finished Call •...
  • Page 45 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Figure 19 – Main window of control software 1. Tab panel with scanner functions and settings 2. Scan camera live image display area 3. Preview image recorded by the preview camera 4. Preview image editor toolbar 5.

  • Page 46: Routine Work Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.3.1 Routine work tab Figure 20 – Routine work tab The Routine work tab 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 47 Pannoramic MIDI 1.15 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 48: Scan Options Window

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.3.2 Scan Options window Figure 21 – 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 49 Pannoramic MIDI 1.15 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 50: Preview Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.3.3 Preview tab The Preview tab offers options for threshold setting and selection of the area to be scanned. Figure 22 – Preview tab Use threshold Scan specimen with auto threshold – This automatically detects the specimen in the preview •...
  • Page 51 Pannoramic MIDI 1.15 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 52 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Figure 24 – 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 53: Preview Area Scanned By Preview Camera

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description To save a new mask, click Save. It will display a drop-down menu. Select whether to save preview mask or TMA grid. To load a mask, click Load. It will display a drop-down menu. Select whether to load preview mask or TMA grid.
  • Page 54 Pannoramic MIDI 1.15 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 55 Pannoramic MIDI 1.15 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 56 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Figure 28 – Not scanned selection 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 29 –...
  • Page 57 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Block tab Figure 30 – TMA tool: Block 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 58 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Move tab The Move tab 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 59: Focus Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description Label area To rotate the label area by 180°, select the Rotate image by 180 degree checkbox. Figure 33 – Label area 4.3.5 Focus tab Figure 34 – Focus tab March 13, 2012 - Rev 1 3DHISTECH Ltd.
  • Page 60 Pannoramic MIDI 1.15 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 61: Service Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description Figure 35 – 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 62: Display Field And Toolbar For Live Images

    Pannoramic MIDI 1.15 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 63: Start Scan

    Pannoramic MIDI 1.15 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 64: Using Brightfield Automatic Mode

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description Caution! Before starting digitization process ensure that you have enough free space on the destination drive. You can check the available free disk space in the last line (Available disk space) of the information area of Current Slide Scan Progress.
  • Page 65 Pannoramic MIDI 1.15 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 66: Barcodes Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.4.2 Barcodes tab Figure 39 – Barcodes tab March 13, 2012 - Rev 1 3DHISTECH Ltd. 66(131)
  • Page 67 Pannoramic MIDI 1.15 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 68 Pannoramic MIDI 1.15 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 69 Pannoramic MIDI 1.15 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 70: Preview Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.4.3 Preview tab Figure 40 – 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 71: Focus Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.4.4 Focus tab Figure 41 – 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. This is useful if focusing was not targeted on the specimen, but on a spot on the coverslip.

  • Page 72: Service Tab

    Pannoramic MIDI 1.15 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 73: Start Scan

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.4.6 Start scan To start digitization process, click after checking settings on 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 74: Using Fluorescent Manual Mode

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.5 Using Fluorescent Manual Mode 4.5.1 Routine work tab Figure 45 – Routine work tab panel The Routine work panel provides basic digitization functions. March 13, 2012 - Rev 1 3DHISTECH Ltd.
  • Page 75 Pannoramic MIDI 1.15 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 76 Pannoramic MIDI 1.15 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 77 Pannoramic MIDI 1.15 User’s Guide 4 Software Description To set filter properties, select a filter and click on any of the white boxes of the TW and DG columns next to the filter name. This displays the Filter Properties window.
  • Page 78 Pannoramic MIDI 1.15 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 from 0 to 6. Enter the Index value by entering it in the box or by selecting the value with the arrow buttons.

  • Page 79: Scan Options

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.5.2 Scan Options Figure 48 – Scan options tab March 13, 2012 - Rev 1 3DHISTECH Ltd. 79(131)
  • Page 80 Pannoramic MIDI 1.15 User’s Guide 4 Software Description 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. JPEG – The quality can be adjusted with the JPEG quality factor slider. Greater •...
  • Page 81 Pannoramic MIDI 1.15 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. Do not use multilayer mode on empty field-of-views – If selected, the •...
  • Page 82 Pannoramic MIDI 1.15 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 83: Preview Tab

    Pannoramic MIDI 1.15 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 49 – Preview tab Use threshold Scan specimen with auto threshold – This automatically detects the specimen in the •...
  • Page 84 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Scan area inside the marker – If the specimen cannot be identified as required for • digitization, (for example, weak contrast), it can help to encircle completely the specimen with a black marker pen.
  • Page 85 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Fill holes in scan area – If selected, the holes inside the specimen will also be scanned. Often these holes contain small sample objects that otherwise would not be scanned. Remove specks – If selected, the scanner does not digitize objects smaller than the predetermined size.

  • Page 86: Hardware Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.5.4 Hardware tab Figure 51 – Hardware tab (selected mode: User controlled) March 13, 2012 - Rev 1 3DHISTECH Ltd. 86(131)
  • Page 87 Pannoramic MIDI 1.15 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 88 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Digital Gain Note: This is camera-dependent, when working with AxioCam MRm Rev 3 camera the Index value ranges from 0 to 4, and when using pco.edge the value ranges from 0 to 6.
  • Page 89 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Manual Focus By selecting the Use manual focus box, you can preset the coarse focus value. By activating the Coarse focus function, the lower limit value is set to -200, and the upper limit value is set to +200 of the current focus value.

  • Page 90: Service Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.5.5 Service tab Figure 52 – 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 91: Using Fluorescent Automatic Mode

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.6 Using Fluorescent Automatic Mode 4.6.1 Routine work tab Figure 53 – Routine work tab panel The Routine work tab panel provides some basic digitization functions. March 13, 2012 - Rev 1 3DHISTECH Ltd.
  • Page 92 Pannoramic MIDI 1.15 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 93 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Filter Settings Focus channel – Choose a filter that you want to focus with. It is recommended to choose a • filter that is related to the staining that stained the most of the specimen, or where the exposition time is low.
  • Page 94 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Filter name The name of the filter is displayed here. Exposure Settings Exposure time – You can set the fix exposition time here. By selecting the Auto button, the exposition time is set to (the exposition time is calculated by <AUTO>...
  • Page 95 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Fluorescent compensation Use saved compensation image. Compensation images can be created for those filters, for which compensation images are created previously. To create compensation image, see section 4.2.2 Image Compensation / Fluorescent Compensation.

  • Page 96: Barcodes Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.6.2 Barcodes tab Figure 56 – Barcodes tab On this tab, you can set identification features to the various slides and for assigning profiles. March 13, 2012 - Rev 1 3DHISTECH Ltd.
  • Page 97 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Modes on the tab 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 98 Pannoramic MIDI 1.15 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 99 Pannoramic MIDI 1.15 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 100: Preview Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.6.3 Preview tab Figure 57 – 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 101: Focus Tab

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.6.4 Focus tab Figure 58 – 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 102: Scan To Server

    Pannoramic MIDI 1.15 User’s Guide 4 Software Description 4.7 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 MIDI scanner software.
  • Page 103 Pannoramic MIDI 1.15 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 104 Pannoramic MIDI 1.15 User’s Guide 4 Software Description 2. Select the Scan to CaseCenter option in the Scan Option window, then click Connect. Figure 61 – Scan to CaseCenter option 3. Type in or select the server address from the Connect to: drop-down list, then give the user name and password.
  • Page 105 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Slide settings in the CaseCenter window 1. In the Routine work tab panel, click the button. 2. The CaseCenter window opens. Slide data is displayed in a form for the slides loaded in the tray. If in Manual Mode, •...
  • Page 106 Pannoramic MIDI 1.15 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 1-12, type: First slide: 1;...
  • Page 107 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Figure 66 – Folder selection Fill in the Case and Block fields in case you do not use masks, or select an item from • the drop-down list. With the Multi fill option the selected slides will be given the same input data to •...

  • Page 108: Using Profiles

    Pannoramic MIDI 1.15 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 109 Pannoramic MIDI 1.15 User’s Guide 4 Software Description Fluorescent settings Filter position(s) • Selected focus channel • Selected stitching channel • Use of skip empty field-of-views (ON/OFF) • Do not use extended focus on empty field-of-views (ON/OFF) • Selected image bit depth •...

  • Page 110: Troubleshooting And Maintenance

    Pannoramic MIDI 1.15 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 111: Cleaning The Device

    Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance When the HXP 120 illuminator 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 112: Troubleshooting

    Pannoramic MIDI 1.15 User’s Guide 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.
  • Page 113 Pannoramic MIDI 1.15 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 114: Fluorescent Applications (Optional)

    Pannoramic MIDI 1.15 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 115: Maintenance

    Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance The switching of the Lumencor cannot be triggered, in spite of trigger connection through the camera. Contact 3DHISTECH Service for support. • No suitable exposure time can be found. Signal is too weak.
  • Page 116 Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance Note: To improve access to special points you can remove the covers completely. Figure 67 – 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 117: Replacing The Halogen Lamp

    Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance Caution! Make sure that no cables are squeezed as you replace the cover(s). This refers in particular to the cable(s) of the scan camera. 5.3.2 Replacing the halogen lamp Figure 68 – Replacing the halogen lamp Warning! Hot surface! Wait for the lamp surface to cool down.

  • Page 118: Replacing Lamp Module (For Fluorescent Option)

    Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance 3. Open the cover (see section 5.3.1 Opening the protective covers). 4. Hold the lamp mount (2) with your hand. 5. Remove the knurled screws (1) from the heat sink body (6) completely.
  • Page 119 Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance Warning! Hot surface! Wait at least twenty minutes to allow the lamp surface to cool down sufficiently. 1. Disconnect power plug (separate all poles from the mains). 2. Unfix screws of lateral cover plate and remove it from the unit housing (see Figure 69).
  • Page 120 Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance Figure 71 – Removing the lamp module 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 72).

  • Page 121: Removing A Slide

    Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance 10. Screw the lateral cover-plate down to the housing. 11. Connect power plug. 12. Set hour meter (time counter) to zero. Caution! If Fluorescence scanning option is available, create new compensation images after replacing the bulb in HXP 120.

  • Page 122: Installing And Removing The Filter Module (Fluorescent Option)

    Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance 1. Push protective covers apart (see section 5.3.1 Removing the protective covers). 2. Position the slide (2). 3. Remove the slide carefully. Caution! If the slide is broken, make sure to remove all pieces completely from the device.
  • Page 123 Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance Warning! Crush hazard! Stop the running digitization process before you proceed with filter module installation or removal. 2. Pull the pair of the protective cover halves apart or remove the right part completely (see section 5.3.1 Removing the protective covers), but do not switch the main unit off.

  • Page 124: Transporting Pannoramic Midi

    Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance 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. You can find the weight data of the base unit in section 6.
  • Page 125 Pannoramic MIDI 1.15 User’s Guide 5 Troubleshooting and Maintenance Caution! Readjust camera angle if necessary after transporting and reinstalling the Pannoramic MIDI! Caution! If Fluorescence scanning option is available, create new compensation images after transporting and reinstalling the Pannoramic MIDI! For more information see section 4.2.2 Image Compensation /...

  • Page 126: Technical Data

    Pannoramic MIDI 1.15 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 without fluorescence option approx. 522 mm (W) x 568 mm (D) x 457 mm (H) 24V 100W power supply approx.
  • Page 127 Pannoramic MIDI 1.15 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 128 Pannoramic MIDI 1.15 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 129 Pannoramic MIDI 1.15 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 130 Pannoramic MIDI 1.15 User’s Guide 6 Technical Data Bit-depth 16 bit Pixel resolution with 20x objective and 1x C-mount adapter 0.22µm Cooling Peltier with forced air (fan) Connection type dual Camera Link (full, 10 taps) Control computer, minimum system requirements...
  • Page 131 Pannoramic MIDI 1.15 User’s Guide Index Index AxioCam............17, 18, 19, 22, 23, 40, 49, 78, 80, 81, 88, 94, 114, 129 Barcode..2, 3, 13, 19, 25, 26, 27, 30, 31, 32, 33, 47, 64, 66, 67, 68, 69, 73, 76, 96, 97, 98, 99, 106, Brightfield..............2, 3, 13, 17, 18, 29, 34, 40, 44, 49, 64, 78, 95, 108...

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