The MIPAV (Medical Image Processing, Analysis, and Visualization) application—developed at the Center for Information Technology at the National Institutes of Health—enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy. You can use Bio-Formats as a plugin for MIPAV to read images in the formats it supports.


Follow these steps to install the Bio-Formats plugin for MIPAV:

  1. Download bioformats_package.jar and drop it into your MIPAV folder.

  2. Download the plugin source code into your user mipav/plugins folder.

  3. From the command line, compile the plugin with:

    cd mipav/plugins
    javac -cp $MIPAV:$MIPAV/bioformats\_package.jar \\
  4. where $MIPAV is the location of your MIPAV installation.

  5. Add bioformats_package.jar to MIPAV’s class path:

    • How to do so depends on your platform.

    • E.g., in Mac OS X, edit the mipav.app/Contents/Info.plist file.

  6. Run MIPAV and a new “BioFormatsImporter - read image” menu item will appear in the Plugins > File submenu.

See the readme file for more information.

To upgrade, just overwrite the old bioformats_package.jar with the latest one. You may want to download the latest version of MIPAV first, to take advantage of new features and bug-fixes.