Software

OpenMIMS Data Analysis Software

OpenMIMS is an ImageJ plugin. It can run on any system running ImageJ.

ImageJ Installation:

  • Download OpenMIMS.zip (contains jar files, documentation and source code).
  • Extract the contents to the ImageJ 'plugins' folder. **NOTE: Overwrite any previous versions of the jar files contained in the zip file that may already exist in the 'plugins' folder.
  • Restart ImageJ.

Fiji Installation

Requirements:

  • ImageJ 1.43u (or higher).
  • Java 1.6 (or higher).

Documentation:

Test Data:

  • SampleData1 (4 masses, single plane, 2.1Mb) im
  • SampleData2 (90M) zip

After installing, launch ImageJ and under the Plugins menu, select the Open MIMS Image. This will open the plugin. Files can then be opened either using File>Open MIMS Image or by dragging and dropping a file over the graphical interface.

If you are having issues opening images try opening the sample data file. If you are unable to open the sample than the problem most likely resides in the installation process. Make sure to overwrite/delete all previous versions of any .jar files that may exist in your 'plugins' directory. If you are able to open sample data but not your own images, please contact us with any error report that may have been generated at the following email address:

nrimssoftware@partners.org

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Access the Read-only SVN Source Code Repository

To check out a local copy of the OpenMIMS repository, use the following command:

            > svn checkout https://zoomwhee.mgh.harvard.edu/svn_devel/OpenMIMS

Access the Source Code through NetBeans

Alternatively, users may perform a check-out of the OpenMIMS project from within the Netbeans IDE by clicking the

     Team>>Subversion>>Checkout 

menu item and entering the following web address into the Repository field:

NetBeans screen 1
Click Next and fill in the appropriate fields for your system:
NetBeans screen 2
Click Finish. At this point you should be able to run the project and the OpenMIMS GUI should appear. You can test the plugin using the test data provided above.