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.
Creating a new workflow
In Fiji, run the plugin from Plugins > Bristol WBIF > Modular Image Analysis
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"
Using an existing workflow
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.