About MIA

MIA is a Fiji plugin which provides a modular framework for assembling image and object analysis pipelines. Detected objects can be transformed, filtered, measured and related. Analysis pipelines 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.

Installation

The latest version of the plugin can be downloaded from the Releases page.
Place this .jar file into the /plugins directory of the your Fiji installation.
MIA requires the "Biomedgroup" and "MorphoLibJ" plugins to be installed.
- For MIA versions before 0.11.0: Launch Fiji's Updater tool and add the "Biomedgroup" and "IJPB-plugins" (possibly listed as "MorphoLibJ") update sites, then restart Fiji.
- For MIA versions 0.11.0 or newer: Start MIA as usual, then click "Yes" when prompted to automatically download the updates.

Getting started

In Fiji, run the plugin from Plugins > Bristol WBIF > Modular Image Analysis
To run an existing analysis workflow

Click "Load" and select the .mia workflow file

Depending on workflow configuration, a number of controls may be visible

When ready, click "Run" to start the analysis

While processing the status panel will display the number of files completed (batch mode) or a summary of the ongoing task (single file mode)

When finished, "Complete" will be displayed in the status panel. Output XLS files will be saved in the input directory.

To create a new workflow

Select View > "Switch to editing view" from the menu bar

Modules are added and removed from the workflow using the "+" and "-" buttons

Module order can be shifted with the arrow buttons

Selecting a module will display its relevant parameters in the right panel

Checkboxes to the right of each module determine if they are visible in the basic view (default view)

Input files and folders are specified using the "Input control" and Excel file export is configured in the "Output control"

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:

Required plugins that need installing via the Fiji updater:

Plugins bundled with MIA:

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

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.

Note

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.