ChemoMetec NC-250 User Manual
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ChemoMetec NC-250 User Manual

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NucleoView NC-250™ Software
User's Guide
P/N 991-0252
Revision 1.6

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  • Page 1 NucleoView NC-250™ Software User’s Guide P/N 991-0252 Revision 1.6...
  • Page 2 NucleoView NC-250™ P/N 991-0252 (English) Revision 1.6 June, 2016 ChemoMetec A/S Gydevang 43, DK-3450 Allerod, Denmark Telephone: (+45) 48 13 10 20, Fax: (+45) 48 13 10 21 Internet: www.chemometec.com, E-mail: sales@chemometec.com 991-0252 Rev. 1.6 June 2016...
  • Page 3 NC-250™ serial number and have it available when contacting ChemoMetec A/S for support. The NucleoCounter NC-250™ serial number is found on the label affixed to the rear side of the instrument. The version number of the NucleoView NC-250™ software shall also be noted, this can be found on the Help – About menu item in the NucleoView NC-250™ software.

  • Page 4: Table Of Contents

    Table of contents Quick Guide ......................................5 Installation Guide ..................................... 6 Installation Overview ..................................... 6 Minimum Computer Requirements and Preparations before Installation ..................... 6 Installing the NucleoView™ Software and NucleoCounter® Instrument ......................6 Installing Licenses and Protocols .................................. 15 Software Upgrade ......................................15 Installing a new NucleoCounter®...

  • Page 5: Quick Guide

    2. Start the NucleoView NC-250™ software by double-clicking NucleoView NC-250™ icon on the desktop. 3. Wait while the NucleoCounter® NC-250™ instrument initializes. The slide tray can be heard aligning during this process. When the LED on the instrument turns green, the instrument is ready.

  • Page 6: Installation Guide

    Important: You must be logged on as system administrator to install the NucleoView NC-250™ system components. In a first time installation, you will typically install both the NucleoView NC-250™ software and one or more sets of NucleoCounter® NC-250™ instrument specific configuration data. This involves installation and activation of various USB drivers on one or more USB ports.
  • Page 7 5. Windows will detect the USB stick and present an AutoPlay window if AutoPlay is enabled. Select the Open folder to view files option. If AutoPlay is not enabled open the contents of the USB stick via Windows Explorer. 6. The directory contents on the USB stick will be shown. Double-click on the Install NucleoView NC- 250™...
  • Page 8 8. After a few seconds the ‘Welcome to the NucleoView NC-250™ Install Wizard’ window will appear. Click ‘Next’. 9. On the Prerequisites window you must check the check box to confirm that you have disconnected all NucleoCounter® instruments from the PC.
  • Page 9 10. On the ‘Ready to install NucleoView NC-250™’ window you will be given options to install or upgrade the NucleoView NC-250™ software itself, to install configuration data for specific instrument(s) and to browse for instrument configuration data which are stored elsewhere. Check the appropriate options and click ‘Next’.
  • Page 10 12. On the ‘Select Additional Tasks’ window check the desired options and click ‘Next’. Checking the ‘Associate ChemoMetec Files with the NucleoView application’ will associate the image files *.cm and protocol files *.cmsx with the NucleoView application making it possible to open the files directly by double-clicking.
  • Page 11 14. On the ‘Window Security’ window click Install. Installation of FTDI CDM divers may appear. Select ‘Extract’ on the FTDI CDM Drivers window. Select ‘Next’ on the Device Driver Installation Wizard window. Select ’I accept this agreement’ and click ’Next’. 991-0252 Rev.
  • Page 12 Click ‘Finished’. 17. On the ‘Completing the NucleoView NC-250™ Install Wizard’ window you may select the option to restart the PC later. The Software requires a restart of the PC to operate correctly. Make sure to login with the same user after restart.
  • Page 13 Note: Depending on file versions and previous install history, a reboot of the computer may be requested before the NucleoView NC-250™ program is launched. If a reboot is needed, it is essential that you log on using the same administrator user as used during the above installation.
  • Page 14 4. NucleoView NC-250™ will display a message box stating successful installation of the instrument, and recommends that you continue installing this instrument on the remaining USB ports on the PC.

  • Page 15: Installing Licenses And Protocols

    You will also be given the option to browse for and select instrument data stored elsewhere. IMPORTANT: You may install multiple instruments on the same PC, but be aware that NucleoView NC-250™ 991-0252 Rev. 1.6...

  • Page 16: Uninstall Nucleoview™ Software

    Uninstall NucleoView™ Software Either uninstall via Add/Remove Programs in the Control Panel, or run the un-installer via the ChemoMetec ->NucleoView NC-250™->Uninstall NucleoView NC-250™ in the Start Menu. This may be required if you wish to downgrade to an earlier version of NucleoView NC-250™.

  • Page 17: Installation Qualification (Iq Test)

    Installation Qualification (IQ Test) 1. Start the NucleoView NC-250™ software by double-clicking the icon on the desktop. 2. Wait while the NucleoCounter® NC-250™ initialize. During this time, the motors may be heard positioning. 3. Click the button (just below the F3 button in the right side of the main window) to launch the Select Protocol window.

  • Page 18: Operation Qualification (Oq Test)

    Operation Qualification (OQ Test) 1. Start the NucleoView NC-250™ software by double-clicking the icon on the desktop. 2. Wait while the NC-250™ instrument is initializing. During this time, the motors may be heard positioning. 3. Click the button (just below the F3 button in the right side of the main window) to launch the Select Protocol window.

  • Page 19: Performance Qualification (Pq Test)

    1. Check that you have a 912-3003 NC Test Kit 3 (Slides, beads). 2. Start the NucleoView NC-250™ software by double-clicking the icon on the desktop. 3. Wait while the NC-250™ instrument is initializing. During this time, the motors may be heard positioning. 4. Click the button to launch the Select Protocol window.

  • Page 20: Main Window

    Main Window Menu Line: See the Menu Line section below for a more detailed description of content. Image Tab Page: If a file is selected, the image is shown on the left hand side of the main window. Zooming in and out on the image may be done by using the scroll wheel with the mouse pointer inside the image area.
  • Page 21 2. Channel color buttons. Colors assigned to each channel. Click on a channel color field to enable/disable the display of the respective channel. 3. Overlay control. After an analysis is successfully completed, the ‘overlay’ button is enabled. Left-click on this button to enable or disable the display of an Image Overlay, highlighting the cells included in the analysis.

  • Page 22: Menu Line

    This button allows the user to export the results for the shown files as a CSV file. Menu Line File -> Import Package: Imports files into the NucleoView NC-250™ software. This will typically be a zip-file containing license, protocol and documentation files, or individual *.cmsx, *.cmsu and *.pdf files.
  • Page 23 License, Protocol and Documentation Installation for more details. View -> Application Log: Opens the NucleoView log file window. This file may be useful for ChemoMetec if support is needed. Help -> Software Users Guide: Opens this NucleoView NC-250™ software user’s guide.

  • Page 24: Selecting A Protocol

    Selecting a Protocol Press the ‘select protocol’ button (placed just below the F3 button in the right side of the Main window) to open the Select Protocol window: Select type of ‘Organism’, type of ‘Analysis’ and preferred ‘Media Types’ to see which protocols are available for this in the current installation.

  • Page 25: Analysis Results

    Hold all primary analysis data (picture, instrument ID, settings, protocol used etc.)  Have up to 3 channels per image  Use a ChemoMetec proprietary file format with extension cm  Are named yyyymmdd-####-#-*.cm (year-month-day-number)-(chamber)-(sample ID).cm  Are placed in Today’s Directory named yyyymmdd (year-month-day) ...
  • Page 26 Post Processing File (*.cmpp)  Holds post processing results for a specific *.cm image file corresponding to one row in a Plot Manager  Has the same file name as its corresponding image file (*.cm file), but with extension ‘cmpp’ ...

  • Page 27: Browse Results

    Browse Results Buttons In the upper right corner launches the File Browser to browse images from a specified date range (day, week, month or year). Marks the row for the selected file for which the image and extended results are displayed. Click on this button to select the file acquired in this chamber.
  • Page 28  Pan and zoom settings are preserved from the previously selected file. The extended results for the selected file will be shown in the result tab page. Furthermore, the protocol, media type, sample ID, operator and volumes will be shown for the selected file. ...

  • Page 29: File Browser

    File Browser Select a date, a week, a month or a year on the left side of the File Browser. The right side is then populated with all images from the selected period. The first column lists file names, and the following columns list further properties of each file.

  • Page 30: File Properties

    File Properties The file properties window contains three or four tab pages:  General with the file name and the sample ID. The sample ID can be edited after an analysis has been completed. In the Log field the user can optionally enter comments about the image file that will be logged in the file.

  • Page 31: Report Generator

    Report Generator The Report Generator may be launched in several ways; from the File Browser window by right-clicking on one or more selected files and selecting ‘Add to report’; from the Browse File list in the main user interface right-clicking on a file and selecting ‘Add to report’; or via the menu entry ‘Tools->Report Generator’. It is used to generate a report for the files added to the Report Generator.

  • Page 32: Image Scaling

    Image Scaling When an image is presented on the screen, the color intensity (pixel intensity values) will by default be shown with automatic scaling and automated estimation of the background. For each channel, pixel values will be depicted in the range 0 to 255 in color intensity. The automatic scaling and the automated estimation of the background can simultaneously be turned off by clicking Auto Scale and the automated estimation of the background can be turned off by clicking Auto Bkg, when Auto Scale is enabled.

  • Page 33: Image Overlay

    Image Overlay An image overlay may be enabled with the button near the right bottom corner of the image. It performs two kinds of cell marking on the displayed image:  When an analysis is completed successfully, cells that are included in the analysis are marked with a square.

  • Page 34: Next Analysis

    Next Analysis When a run is completed, the main result is displayed at the bottom right of the user interface and detailed results are displayed in the result tab page. Input fields: The user may optionally enter sample IDs for each chamber. The sample ID will be used as last part of the image file name for all image files shot for the respective protocol.

  • Page 35: Protocols

    Protocols To perform a particular analysis, the appropriate protocol must be used. This involves selecting and running the corresponding protocol on the NucleoView NC-250™ software while following the guidelines in the protocol as described in the Quick Guide section. Each instrument requires a unique license to run a protocol. Via the menu entry View -> License File you can see a list of the installed Licenses.

  • Page 36: Protocol Adaptation Wizard

    Protocol Adaptation Wizard The Protocol Adaptation Wizard will guide you through adapting different parameters and saving the adapted protocol as a user adapted protocol. A saved protocol may be locked by the user to prevent further changes. A locked protocol can be unlocked again to overwrite with new user adaptations. A new adapted protocol, based on a locked protocol, can be saved by choosing the save as function.

  • Page 37: Plot Manager

    Plot Manager The Plot Manager is used for evaluation and post processing of cell populations found in one or more image files. Results are displayed in scatter plots, histograms and table plots arranged in rows and columns, where each row comprises results for one particular image file. The Plot Manager is specifically suited for batch processing of several image files as it can replicate processing from one ‘Master’...

  • Page 38: Layout Editing

    There are two ‘save’ buttons in the Plot Manager. The ‘save’ button exists for each row and is placed in Row window in the left part of the row. This button saves the post processing data i.e. gates, polygon, quadrants and graphs associated with the individual sample. The second type of ‘save’ button at the top of the window is always present (beside the button) and saves the current Plot Manager contents to a *.cmpm file placed in a PM Files folder.

  • Page 39: Plot Statistics

    Plot Statistics The Statistics window lists detailed gating statistics for all visible polygons and markers. The above image shows all the available sub-columns. Right-click on a column header to edit which sub- columns to display. If several different alias names has been set for a gate the gate alias name presented in the statistics will be for the first row with an alias name.
  • Page 40 Row number: The row number is shown in the upper left corner. Data source indicator: The data source of the cell population in this row is shown with a small colored square to the left of the ‘save’ button: 1. Grey: Indicates that the cell population has been loaded from data embedded in the image file, i.e. data which was obtained when the image was originally acquired and analyzed by running a protocol.

  • Page 41: Histogram Plot In Plot Manager

     Show Hidden Rows: Toggles between showing and hiding rows marked as hidden.  Properties: Displays the File Properties dialog for the file corresponding to the selected row. Histogram Plot in Plot Manager The histogram plot is used to plot a user selectable parameter together with user defined marker sets which marks, gates and counts cell populations.

  • Page 42: Large Histogram Plot In Plot Manager

    Large Histogram Plot in Plot Manager The large histogram plot is used to set axis parameters, edit marker sets, define gating settings and add overlay histograms. 1. Axis Settings: By clicking on the x-axis it is possible to select type of axis, image channel, parameter type and axis limits.
  • Page 43 6. Cancel: Closes the large plot without saving the changes. OK: Closes the large plot and saves the changes. 7. Line type and colors: These may be set with the controls in the upper right corner of the plot window after an additional histogram has been overlaid to an existing histogram. 8.

  • Page 44: Scatter Plot In Plot Manager

    population, e.g. all non-single cells, then these are not part of the histogram, and therefore will not be included in the selected cells list. Editing a Marker: A marker can be moved when the mouse curser is above the marker and is marked with the move symbol .

  • Page 45: Large Scatter Plot In Plot Manager

    Large Scatter Plot in Plot Manager The large scatter plot is used to set axis parameters, add or edit polygons and quadrants and define gating settings. 1. Axis Settings: By clicking on either the y-axis or x-axis it is possible to select type of axis scale, image channel, parameter type and axis limits.
  • Page 46 2. Gating Setup: Launches the Gate Configuration window, where gating settings can be configured for this plot. 3. New Polygon: Creates a new polygon. Click in the plot area to add points in the polygon. Click in the gray area around the plot to delete the last point in the polygon. Click on the starting point to close the polygon.
  • Page 47  Show Info About Selected Gate: Displays a new window with information of how many cells are outside and inside the gate in each image. Depending on the state of the large scatter plot, some of the above options may be dimmed or be replaced with an alternative option.

  • Page 48: Large Table Plot In Plot Manager

    Click the ‘delete plot’ button to remove a plot from the row. This will leave an empty area in which you may, via right-click, insert another plot or simply delete the area. Double-click: To launch the Large Table Plot double-click in the plot area. Right-click: Shows the context menu offering the following options: ...
  • Page 49  Insert Formula …: Selecting Insert formula writes a = that indicates that a number or a calculation will be written in the selected table cell. Subsequently, “Insert value …” can be selected to insert a gate parameter or a protocol variable. Selecting gate parameter guides in steps to select the desired gate and parameter like % of plot or mean for the x-axis parameter.

  • Page 50: Plot Manager Gate Configuration

     Insert Row Above: Inserts a new row above the selected row.  Insert Row Below: Inserts a new row below the selected row.  Delete Row: Deletes the selected row. Editing a table: The table can be moved when the mouse curser is above the lines of the table and is marked with the move symbol .
  • Page 51 To disable the showing of a gate click to remove the checkmark in the show column. Gate configuration:  Disable: This option disables gating for the selected gate.  Include: This option results in display of all events inside the selected gate. ...

  • Page 52: Export Data

    Export Data In the menu line File->Export Data cell data may be exported to file formats which are compatible with third party software such as FCS Express. Format Specification: Select export format FCS for export according to ISAC ‘Data File Standard for Flow Cytometry, Version FCS3.0’...

  • Page 53: Pdf Report

    PDF Report In the menu line File->Create PDF Report data may be saved to a PDF file for the selected file. The PDF report functionality is also available by right clicking on a file in the file list in the main window. The report file name can be set and the location where to save the PDF file can be selected.

  • Page 54: Options

    PDF reports will be saved can be set and the folder selection can be applied for all users. The default folder for saving PDF report is in the NucleoView NC-250 folder on the desktop in the subfolder \results\PDF reports.
  • Page 55 Saved PDF reports will be named with the same file name as the cm file name with a pdf extension and can be selected to be automatically opened. The PDF can be printed to the default printer if one is installed.

  • Page 56: Cfr Part 11

    Part 11 of Code of Federal Regulations Title 21, in short here termed 21 CFR Part 11. The NucleoView NC-250™ application can be set into a restricted mode, so the user via the NucleoView NC- 250™ application itself can not violate the 21 CFR Part 11 regulations. This means that on a computer system that is 21 CFR Part 11 compatible, it is possible to keep the compliancy even after installation and use of the NucleoView NC-250™...

  • Page 57: Approval

    Event Log The event logs created by the NucleoView NC-250™ application are always stored in the current results folder. Changing this folder will create a new event log file in the newly set results folder.

  • Page 58: License, Protocol And Documentation Installation

    To run a given protocol, the corresponding protocol-, license- and documentation-files must have been imported. This is normally performed when the NucleoView NC-250™ software is installed, but it may also be done any time later as described in the next section.

  • Page 59: Maintenance And Backup

    Maintenance and Backup NucleoView™ Software Maintenance A two-channel image taken in an A8 slide with NucleoView NC-250™ is approximately 15 MB in size. Therefore, for example performing 50 viability and cell count assays each work day will over a month accumulate approximately 16 GB.

  • Page 60: How To

    How to Verify Correct Operation of the NucleoCounter® Instrument after Transportation The NucleoCounter® NC-250™ Instrument is a very robust device which handles shipping well, provided it is packaged correctly in the original shipping box. In case of extreme physical stress, it may however suffer internal damage and/or misalignment.

  • Page 61: Keyboard Shortcuts

    Keyboard Shortcuts Image Zoom in Zoom out Arrow keys Pan up, down, left or right in displayed image Application Selection Quick selection of protocol attached to favorite F1 button Quick selection of protocol attached to favorite F2 button Quick selection of protocol attached to favorite F3 button Note: Shortcut usability depends on actual focus.

  • Page 62: Trouble Shooting

    Connection Error The NucleoCounter® NC-250™ instrument icon in the upper left corner of the main window stays red after NucleoView NC-250™ has been launched, i.e. the NucleoView NC-250™ software does not connect to the instrument. This may be caused by an error in the USB connection.
  • Page 63 This warning may be shown when a program such as a virus Sharing violation on cm files protection program is scanning the cm file while NucleoView is trying to access the same file. In virus protection programs disable scanning of the ChemoMetec folder: C:\Users\Public\Documents\ChemoMetec. 991-0252 Rev. 1.6 June 2016...
  • Page 64 NucleoView NC-250™ software has been terminated in an standby inappropriate way while the tray was ejected. Restart NucleoView NC-250™ and the tray is automatically inserted. The instrument gives An actuator motor might be blocked. abnormal sounds Inspect that the sample tray movement has not been blocked by any external objects, then check that there is no internal blocking, e.g.

  • Page 65: Appendix A: Description Of Changes From Latest Revision

    Appendix A: Description of changes from latest revision This chapter describes changes from latest revision of this User’s guide. New: Changes:  Front Page Revision 1.6  Page 2 Revision 1.6 June 2016  Minimum Computer Requirements and Preparations before Installation (Page 6) Operating System: Windows 7, Windows 8.1 or Windows 10.

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