Example workflows for the modular image and object analysis Fiji plugin, MIA.
These workflows introduce various processes of MIA such as image loading, object segmentation, object measurements, object relationships and visualisation. Each example contains the necessary files to get it running: the example workflow, any raw images required and any example outputs that are generated by the workflow.
For the full MIA documentation, please go to mianalysis.github.io
| Link to example | Example output |
|---|---|
| Introduction to object segmentation |  |
| Object tracking and analysis |  |
| Object relationships and skeletonisation |  |
Each module in these workflows includes a corresponding set of notes summarising the purpose of that module and its configuration. These notes can be viewed by enabling the "Notes" panel ("View > Show notes panel" from the MIA menu) and selecting a module from the list of modules in "editing view".
While these workflows correspond to a specific analysis, the principles covered (i.e. image loading, processing, object detection and measurements) are applicable to most workflows.
Note: Any object outlines in the generated "overlay" images will typically only be visible when opened in ImageJ/Fiji.
The DevelopmentExamples folder includes examples for developers such as template custom modules.
Example workflows are constantly being added. If you have any questions, please contact stephen.cross@bristol.ac.uk.