MIA is a Fiji plugin which provides a modular framework for assembling image and object analysis pipelines. Detected objects can be transformed, filtered, measured and related. Analysis pipelines are batch-enabled by default, allowing easy processing of high-content datasets.
MIA is developed in the Wolfson Bioimaging Facility at the University of Bristol.
The plugin makes use of a combination of plugins packaged with Fiji as well as others that can be installed via the updater.
Required plugins pre-packaged with Fiji: AnalyzeSkeleton, Auto Threshold, bUnwarpJ, BioFormats, Colour Deconvolution, Correct Bleach, MPICBG, TrackMate, Weka Trainable Segmentation.
Required plugins that need installing via the Fiji updater: Ridge Detection, MorphoLibJ.
Plugins bundled with MIA: BoneJ legacy plugins, Stack Focuser.
A list of bundled dependencies along with their respective licenses can be found here.
We hope you find MIA useful. If you've used MIA in your research, please cite it using the Zenodo DOI for that version of the plugin. Zenodo DOIs for MIA can be found here.
This plugin is still in development and test coverage is currently incomplete. Please keep an eye on results and add an issue if any problems are encountered.