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 loci_tools.jar and drop it into your MIPAV folder.


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


3. From the command line, compile the plugin with:
   cd mipav/plugins javac -cp /path/to/mipav:/path/to/mipav/loci_tools.jar \ PlugInBioFormatsImporter.java
   where /path/to/mipav is the location of your MIPAV installation.


4. Add loci_tools.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.


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

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