Software

    CEM for SPSS

    Authors:  Matthew Blackwell, Stefano Iacus, Gary King, and Giuseppe Porro

    This program is designed to improve the estimation of causal effects via an extremely powerful method of matching that is widely applicable and exceptionally easy to understand and use (if you understand how to draw a histogram, you will understand this method). The program implements the Coarsened Exact Matching (CEM) algorithm described in:

    Astronomical Medicine

    At present, we are using this page only to point to the existing "Astronomical Medicine" software page at the IIC site.  For newer software, check out "Glue," below.

    Project homepage: http://am.iic.harvard.edu/

    IDRISI Software

    Clark Labs: IDRISI Software
    Geospatial technologies for environmental management

    ERDAS Software

    ERDAS 2010 Software: Image and Photogrammetry
    Remote sensing, image-processing and geospatial information management suite

    How To Apply

    Students:

    Undergraduates interested in participating in the Research Scholars Program should check Current Opportunities to find out more about projects currently in need of researchers.  To apply, send a resume and cover letter detailing relevant qualifications and experience to the contact person listed under the project description. 

    Glue

    Glue Logo

    Glue is a Python framework to link visualizations of multiple related datasets. Its goal is to let users easily inter-compare data across several files. 

    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.

    Advanced Video Processing

    Digital video editing and computer graphics have allowed unbridled creativity for professional film makers. However, the software tools and techniques used to accomplish these tasks require expert knowledge and are often slow. With this project, we aim to improve existing video processing tools which currently slow down existing users and block new users from the creative process.

    The Connectome Project

    Colorful dotsWe are interested in the segmentation, visualization and analysis of brain scans in electron and optical microscopy in the multi-terabyte range.

    Sponsored by NSF, NIH and private foundations.

    Team Members: Ray Jones, Seymour Knowles-Barley, Verena Kaynig, Steffen Kirchhoff, Johanna Beyer, Ali Al-Awami, Adi Peleg, Daniel Haehn, Hanspeter Pfister

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