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.

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.

Citing MIA

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.

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.

Edmunds, G.L., et al., "Adenosine 2A receptor and TIM3 suppress cytolytic killing of tumor cells via cytoskeletal polarization", Communications Biology (2022) 5, doi: 10.1038/s42003-021-02972-8

Kague, E., et al., "3D assessment of intervertebral disc degeneration in zebrafish identifies changes in bone density that prime disc disease", Bone Research (2021) 9, doi: 10.1038/s41413-021-00156-y

McCaughey, J., et al., "ER-to-Golgi trafficking of procollagen in the absence of large carriers", J Cell Biol (2019) 218 929-948, doi: 10.1083/jcb.201806035

Roloff, E.v.L., et al., "Differences in autonomic innervation to the vertebrobasilar arteries in spontaneously hypertensive and Wistar rats", J Physiol (2018) 596 3505-3529, doi: 10.1113/JP275973

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.