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

• In Fiji, run the plugin from Plugins > ModularImageAnalysis (MIA)
• 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 processing view (default view)
• Input files and folders are specified using the "Input control" and Excel file export is configured in the "Output control"

• In Fiji, run the plugin from Plugins > ModularImageAnalysis (MIA)
• 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.