NucleoView® NC-200™ Software User’s Guide P/N 991-0204 Revision 1.
NucleoView®NC-200™ P/N 991-0204 (English) Revision 1.1 September, 2012 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 991-0204 Rev. 1.
Caution! This software must be operated as described in this User’s Guide and documents referred to herein. Please read the entire guide and referred documents before attempting to use this software.
NucleoView® NC-200™....................................................................................................................................................... 1 User’s Guide ....................................................................................................................................................................... 1 Quick Guide ................................................................................................................................................
Quick Guide 1. Install the NucleoView® NC-200™ software and the NucleoCounter® NC-200™ instrument as described in the documentation on the USB stick containing the NucleoView® NC-200™ software. 2. Start the NucleoView® NC-200™ software by double-clicking NucleoView® NC-200™ icon on the desktop. 3. Wait while the NucleoCounter® NC-200™ instrument initializes (you will hear motors working). When the LED on the instrument turns green the instrument is ready. 4.
Installation Guide Installation Overview Important: You must be logged on as system administrator to install the NucleoView® NC-200™ system components. In a first time installation, you will typically install both the NucleoView® NC-200™ software and one or more sets of NucleoCounter® NC-200™ instrument specific configuration data. This involves installation and activation of various USB drivers on one or more USB ports. To uninstall the software just follow the un-installation procedure.
Select the Open folder to view files option. 6. The root directory contents on the USB stick will be shown. Double click on the Install NucleoView® NC-200™ X.X.X.X file (the version number e.g. 1.0.22.0 will vary depending on your installation) to launch the installation program. NB: It is the .exe file you should double click, not the .bin file. The .exe file also has the installation icon associated in contrast to the icon for the .bin file. 7.
. After a few seconds the ‘Welcome to the NucleoView® NC-200™ Install Wizard’ window will appear. Click Next. 9. On the Prerequisites window you must check the check box to confirm that you have disconnected any NucleoCounter instrument from the PC. Click Next. 991-0204 Rev. 1.
10. On the ‘Ready to install NucleoView® NC-200™’ window you will be given options to install or upgrade the NucleoView® NC-200™ software itself, to install configuration data for specific instrument(s) and to browse for instrument configuration data which are stored elsewhere. Check the options that suites you and click Next. 11. On the License Agreement window read the license agreement, select ‘I accept ...!’ and click Next. 991-0204 Rev. 1.
12. On the ‘Select Additional Tasks’ window check the desired options and click Next. Checking the ‘Associate ChemoMetec Files with the NucleoView application’ will register image files *.cm and protocol files *.cmsx with the NucleoView application for file double click methods. 13. On the ‘Ready to install’ window click Next. The ‘Installing’ window will appear and show progress of extraction and copying of files.
14. On the ‘Window Security’ window click Install. To avoid this window during future software upgrades check the box Always trust software from “IDS Imaging Development Systems GmbH”. 15. On the ‘Window Security’ window click Install. To avoid this window during future software upgrades check the box Always trust software from “MATRIX VISION GmbH”. 16. On the ‘Completing the NucleoView® NC-200™ Install Wizard’ window you may optionally deselect the check box if you don't want to install any instrument.
17. The Install program will now have placed two new icons on your desktop. One is the NucleoCounter® NC-200™ instrument icon used to launch the NucleoView® NC-200™ software, the other is a shortcut to the data folder where NucleoView® NC-200™ stores application data. At this point the NucleoView® NC-200™ software has successfully been installed.
3. You will now see a series of pop-up messages from the Windows operating system informing about driver installations. Among those are: - A USB hub inside the NucleoCounter® NC-200™ instrument - FTDI device driver installed - The camera Due to the intentional and very fast reconfiguration of the camera, you may see an error message from Windows, which can just be ignored. Click Close on any of these pop up messages if needed.
6. When NucleoView detects that the instrument has been disconnected, the icon will again turn red, and you will be prompted to connect the instrument to another USB port on the PC. 7. Repeat the procedure described to install the instrument on the remaining USB ports on the PC. 8. If you are installing more than one instrument on the same PC, you must repeat the USB installation for all instruments on all USB ports, but note that only one instrument must be attached at any time.
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® NC200™ is only able to operate with one instrument at any time. You must never try to operate with more than one instrument as behavior may not be correct.
Main Window Menu Line: See the Menu Line section further below. 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. Zooming may also be achieved by using the + or - buttons. To zoom in on a tablet PC, touch the screen with two fingers and then slide them apart. To zoom out, drag your fingers together.
Volume input fields: Located below the image are the relevant volume controls for the selected application. Right click to change from volumes to parts. Prior to starting an analysis, the volumes or parts used can be edited and the analysis result will have taken into account the entered dilution or concentration of the sample. Upon selecting a protocol, volumes present in the volume input fields are those recommended for the assay.
This button starts the analysis according to the selected application. During the analysis an “Analysis in Progress” image will be displayed. Menu Line File -> Import Package: Imports files into the NucleoView® NC-200™ software. This will typically be a zip-file containing multiple license, protocol and documentation files, or individual *.cmsx, *.cmsu and *.pdf files. File -> Exit: Shuts down the program.
Selecting a Protocol in the Main Window Press the select protocol button 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. Select the protocol which supports the chosen sample unit (media type) and click ‘Select’. If the current installation holds any user adapted protocols, these will be listed indented under their respective master protocols.
Analysis Results When running a protocol the main results (1) will be displayed on the user interface and detailed results will be displayed in the result tab (2). Image File (*.cm), Post Processing File (*.cmpp) and Plot Manager File (*.cmpm) Image Files (*.cm) 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-####-#-*.
Plot Manager File (*.cmpm) Holds a listing of loaded post processing files (*.cmpm) Is placed in the PM files directory under the Results Directory Plot Manager The Plot Manager performs post processing on cell populations and can show results from multiple images in thumbnail sized scatter plots and histograms. 991-0204 Rev. 1.
Browse Analysis Results Buttons Launches the file browser to browse images from a specified date range (day, week, month or year). Return to ‘acquisition mode’ to run a new analysis, when the instrument is connected. File list: Click on a file in the data folder to browse the results of a previously acquired file. The file will be opened and the image will be displayed. Pan and zoom settings are preserved from the previously selected file.
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. A red dot in front of the file name indicates that the file has been modified by a user after it was created.
Report Generator The Report Generator may be launched in several ways; from the File Browser window by right clicking on a file and selecting ‘Add to report’; from the file list in the 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 selected images. Edit the file list using the four buttons in the upper right side of the window.
Image Overlay on the User Interface An image overlay may be enabled with the button in 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 total count are marked with a square. When a large scatter plot or a large histogram is open in the plot manager the cells inside or outside the selected marker or gate respectively, can be marked with the overlay rectangles.
Next Run 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 ID before each sample is run. The sample ID will be used as last part of the image file name for all images shot for the respective protocol. The user may optionally change the operator or the volumes used for the next run sample.
Protocols To perform a certain analysis, you must follow the appropriate protocol. This involves selecting and running the corresponding protocol on the NucleoView® NC-200™ software while following the guidelines in the protocol as described in the Quick Guide section. It requires a license to run a protocol. Via the menu entry View -> License File you can see a list of the installed licenses. Some protocols are user adaptable.
Protocol Adaptation Wizard The Protocol Adaptation Wizard will guide you through adapting different parameters depending on the protocol and saving the adapted protocol as a user adapted protocol. A saved protocol may be locked by a NucleoView® NC-200™ Administrator to prevent further changes. A locked protocol may be unlocked by a NucleoView® NC-200™ Administrator. All lock and unlock events are logged in the adapted protocol file.
Plot Manager The Plot Manager is used for evaluating and the post processing of cell populations found in one or more image files. Post processing results are displayed in thumbnail sized scatter plots and histograms 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' row to all selected rows.
Three types of files may be added to Plot Manager with the following effects: 1. Image files: These are image files (*.cm) on which no data processing, referred to as post processing, has been performed. If no previous post processing has been saved, the new row will only show a row window in the left side of the Plot Manager window. If previous post processing has been saved for this image, this post processing will also be shown in the added row.
Right click also offers an option to copy table contents to clipboard which can be directly pasted into a spreadsheet program. Row Window in Plot Manager The Plot Manager Row Window is used as row header for the post processing of a specific image file. It is always placed in the left side of the Plot Manager window. Row number: The row number is shown in the upper left corner.
File name: The name of the image file is shown with vertical font in the left side of the row window. Check box: Check the check box under the save button if you want the row to be a target for replication of master post processing. Click the ‘add histogram’ button to add a new histogram plot to the rightmost end of this row. Click the ‘add scatter plot’ button to add a new scatter plot to the rightmost end of this row.
Data source indicator: A small colored square in the upper left corner indicates the source of the cell population (see further details in the section Row Window in Plot Manager). Double click: To launch the large histogram plot, double click in the plot area. In the large histogram plot you can define axis parameters, markers and gating settings.
Parameter types: The available parameters depend on the protocol used to generate the *.cm file. Gating Setup: Launches the ‘Gate Configuration’ window, where gating settings can be configured for this plot. New Marker: Creates a new marker. Selected Gate: Edit the selected marker. Move with Arrow Keys Move Left End with Arrow Keys Move Right End with Arrow Keys Copy to Clipboard Delete BMP to Clipboard: Copies the large plot to the clipboard to paste the bitmap image into a preferred program.
Add cells outside marker to image overlay: Same as the inside-option (see above), but for cells outside selected marker. Note: Adding cells to the image overlay is cumulative. Hence if you use this to select both inside and outside cells you may assume that all cells in the image should be marked with an enclosing square. This is however, not always the case. If certain cells have been excluded from the cell population, e.g.
Large Scatter Plot in Plot Manager The large scatter plot is used to set axis parameters, edit polygons and define gating settings. Data source indicator: A small colored square in the upper left corner of the plot area indicates the source of the cell population (see further details in row window). Axis Settings: By clicking on either y-axis or x-axis it is possible to select type of axis, image channel, parameter type and axis limits. Type of axis: Linear, Log or Bi-exponential.
Show Info Copy to Clipboard Delete BMP to Clipboard: Copies the large plot to the clipboard to paste the bitmap image into a preferred program. Cancel: Closes the large plot without saving the changes. OK: Closes the large plot and saves the changes.
Plot Manager Gate Configuration The table in the ‘Gate Configuration’ window is used to configure settings for polygons and marker sets for the plot from which the gate configuration window was launched. The table lists all gates (polygons and markers) which have been defined in the associated row. Note that gates marked as shown will only be shown in the plot, if the conditions for this are fulfilled, i.e. markers are only shown in histogram plots, and polygons are only shown in scatter plots.
Options The options dialog has three tab pages: Folders: The result file folder can be set by the user and the new folder selection can be applied for all users. Please note that changing the result folder location to an network location cause slow reading of the relatively large image files depending on the speed of the network. 21 CFR Part 11: The 21 CFR Part 11 mode can be enabled or disabled by a NucleoView Administrator if the license is present.
21 CFR Part 11 The U.S. Food and Drug Administration has defined regulations for electronic records and electronics signatures in Part 11 of Code of Federal Regulations Title 21, in short here termed 21 CFR Part 11. The NucleoView® NC-200™ application can be set into a restricted mode, so the user via the NucleoView® NC-200™ application itself can not violate the 21 CFR Part 11 regulations.
The NucleoView Admin user have full rights in the NucleoView® NC-200™ application, e.g. the user may switch 21 CFR Part 11 mode on or off, thus breaking the 21 CFR Part 11 compliance. The NucleoViewSuperVisor and NucleoViewUser users have the same rights in the NucleoView® NC-200™ application, and are restricted in their use of the application. Running the NucleoView® NC-200™ application as one of those users makes it impossible to break the 21 CFR Part 11 compliance.
License, Protocol and Documentation Installation Introduction When NucleoView® NC-200™ performs a certain analysis routine (a protocol); this is performed under control of a protocol and documented in a protocol documentation file. To run a given protocol, the corresponding protocol-, license- and documentation-files must have been imported. This is normally performed when the NucleoView® NC-200™ software is installed, but it may also be done any time later as described in the next section.
Maintenance and Backup NucleoView® NC-200™ Software Maintenance A two-channel image taken with NucleoView® NC-200™ is approximately 12 MB in size. Therefore, for example taking 50 images each work day will over a month accumulate approximately 18 GB. The user must hence backup results and free up disc space in good time to ensure trouble free operation. See Image Files for further details about file types and locations. The NucleoView® NC-200™ constantly records all operations in event log files.
How To How to Get Context Sensitive Help While having focus on a control on a specific window, press the button or F1 (not applicable on the main window). This will start on-line help on the relevant page. Online-help will explain about each control on that page starting in upper left corner, working right and then down towards the lower right corner.
Keyboard Shortcuts Image + Zoom in - Zoom out Arrow keys Pan up, down, left or right in displayed image Application Selection F1 Quick selection of protocol attached to favorite F1 button F2 Quick selection of protocol attached to favorite F2 button F3 Quick selection of protocol attached to favorite F3 button Note: Shortcut usability depends on actual focus. 991-0204 Rev. 1.
Trouble Shooting Installation The NucleoView® NC-200™ software or the NucleoCounter® NC-200™ instrument is not installed correctly. NucleoView® NC-200™ Issues (Software) Protocol file is invalid Connection Error 991-0204 Rev. 1.1 The user must be logged on with administrator rights during installation. When connecting the NucleoCounter® NC-200™ instrument to a previously unused USB port, the NucleoView® NC-200™ software may need to reinstall the camera drivers and will prompt the user to do so.
Cassette Issues No cassette is found This may be because either no cassette is in the instrument or the cassette is placed incorrectly. In the latter case, remove the cassette and re-insert it. Non-valid cassette Typically the user has placed an already used cassette in the instrument. Simply replace with an unused cassette which has been correctly loaded. Flow detection error The flow has failed to reach the flow detection point within given time limits.
