MIA: Modular Image Analysis

MIA is a Fiji 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-house at the Wolfson Bioimaging Facility, in response to the needs of our users.


  • Workflows can be automated from initial image loading through processing, object detection, measurement extraction, visualisation, and data exporting.
  • Near 200 modules integrated with key Fiji plugins such as BioFormats, TrackMate and Weka Trainable Segmentation.
  • Workflows are, by default, compatible with batch processing multiple files within a single folder.
  • Designed for compatibility with spatially-calibrated 5D images, yielding image and object measurements in both pixel and physical units.
  • Compatible with many proprietary imaging formats such as Leica .lif and Zeiss .czi via Fiji’s BioFormats plugin.
  • Functionality can be extended via integration with Fiji’s scripting interface or with Java classes that extend the core MIA framework


  • Easy to install and run as a Fiji plugin. This also provides MIA access to all other plugins currently available to Fiji.
  • Open source and free to download, so can be installed on multiple computers.
  • Developed within the Bioimaging Facility, so support can be provided by the creators. Similarly, functionality can be added as required for specific projects.


  • Specific versions of MIA can be cited via Zenodo


Additional information

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