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.

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.