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mianalysis / mia

Modular, object-based analysis for ImageJ/Fiji
GNU General Public License v3.0
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fiji-plugin image-analysis image-processing imagej modular

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Wolfson Bioimaging

About MIA

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

Paper and poster

You can check out the MIA paper here and the latest MIA poster from CBIAS 2022 here

Installation

Via the update site

The latest version of MIA can be installed directly into Fiji via an update site.

  1. Launch the ImageJ Updater from Help > Update...
  2. Click "Manage update sites" and in the window that opens, click "Add update site"
  3. Ensure the following two update sites are ticked:
    • IJPB-plugins
    • ModularImageAnalysis
  4. Close the "Manage update sites" window, then click "Apply changes" in the Updater window

Manually from GitHub

Specific versions of MIA can be downloaded from GitHub and installed into Fiji manually.

Note: If installing MIA manually, the ModularImageAnalysis update site should be disabled from the ImageJ Updater.

  1. Download the desired version of MIA from the Releases page.
  2. Place this .jar file into the /plugins directory of the your Fiji installation.
  3. Install MorphoLibJ using the instructions here

Using MIA

Guides for using MIA can be found here. There are also example workflows in the mia-examples repository (with more to be added over time).

Questions and feedback

If you'd like to ask any questions about MIA, please do so via the image.sc forum using the tag modular-image-analysis.

For reporting bugs, please use our GitHub Issues page.

Contributing

We welcome any contributions to the MIA project. If you'd like to get involved, there are a few ideas on how you could do so in our get involved guide, but any involvement, big or small, would be greatly appreciated.

If you'd like to include the latest version of MIA in your project, you can add the following dependency to your pom.xml file:

<dependency>
    <groupId>io.github.mianalysis</groupId>
    <artifactId>mia-plugin</artifactId>
    <version>1.5.0</version>
</dependency>

Alternatively, if you only want to use a part of MIA (e.g. the quadtree coordinate system), you can find a list of MIA's Maven modules here.

The JavaDocs for MIA are available here.

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 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.

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.