About

Image and object analysis workflow automation plugin for Fiji

Description

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. MIA is developed in the Wolfson Bioimaging Facility at the University of Bristol.

Acknowledgements

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.

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.

Citing MIA

We hope you find MIA useful. If you've used MIA in your research, please cite the following paper:

Cross, S.J., Fisher, J.D.J.R. & Jepson, M.A., "ModularImageAnalysis (MIA): Assembly of modularised image and object analysis workflows in ImageJ", Journal of Microscopy (2023), doi: 110.1111/jmi.13227.

MIA is also archived at Zenodo, which provides a unique DOI for each released version. Zenodo DOIs can be found here.

Publications

MIA has been used in a variety of different analyses, a few published examples of which are listed below. For a more complete list, please go to Publications.

Ongoing development

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.