ModularImageAnalysis (MIA) is an ImageJ plugin which provides a modular framework for assembling image and object analysis workflows. Detected objects can be transformed, filtered, measured and related. Analysis workflows are batch-enabled by default, allowing easy processing of high-content datasets.

For the full documentation, please go to mianalysis.github.io

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, Bio-Formats, Colour Deconvolution, Correct Bleach, MPICBG, TrackMate, Weka Trainable Segmentation. Required plugins that need installing via the ImageJ updater: MorphoLibJ. Plugins bundled with MIA: Stack Focuser.

A list of bundled dependencies along with their respective licenses can be found here.

Special thanks to all MIA users who have provided vital feedback over the years. In particular, big thanks to Dr. Dominic Alibhai for his many suggestions and ideas.

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.