Guides

Using Existing Workflows

Opening, configuring and running pre-prepared workflows distributed as .mia files

Introduction

MIA workflows are distributed as .mia files. These allow the same workflow to be stored and easily shared between different computers. They can be configured to present a small number of key parameters (e.g. input file paths or filter thresholds) to the end user in MIA's processing view while keeping the majority of parameters (those which should remain fixed) accessible only via editing view .

In this guide we will cover loading a pre-prepared workflow file into MIA, setting the accessible parameters, running the workflow and finding the output results.

Loading the workflow

  1. If not already started, launch MIA from the plugins menu at Plugins > ModularImageAnalysis (MIA)
  2. By default, MIA will load into processing view .
    • To make significant edits to a workflow (i.e. changes not possible using the parameters available in "processing view") you can switch to "editing view" by going to View > Switch to editing view.
  3. Click "Load" and select the .mia workflow file
    • Depending on workflow configuration, a number of controls may be visible.
    • Since the visible parameters are determined by the workflow author, please contact them for specific information.

Configuring and running

  1. Typically, although not necessarily, workflows will contain a parameter to set the input file path. To do this, click the box to the right of "Input path" and select either a single file or a folder.
    • Selecting a folder will automatically put MIA into "batch" mode. Here, MIA will iterate over all folders, sequentially processing.
    • If multi-series files (e.g. Leica .lif) are likely to be processed, the workflow author may also have made controls to select input series available.
  2. 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).
  3. Once finished, "Complete" will be displayed in the status panel and all results files will have been saved to their respective locations.
    • Output .xlsx files will be saved in the input directory with the same name as the selected input file/folder.

Saving changes

  1. If changes have been made to the workflow that you'd like to retain for future runs, click "Save" to overwrite the loaded .mia file
    • Alternatively, a new file can be saved by going to File > Save as.