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TrackMate

https://imagej.net/plugins/trackmate/ Getting started: https://imagej.net/plugins/trackmate/tutorials/getting-started

Fiji plugin to track objects e.g. cells, foci or single-molecules.

Basically consists of two steps. First segmentation/detection of objects then apply a tracking algorithm on this.

Segmentation of objects can be done through different methods e.g. spot detector, on a binary image, Stardist (nuclei), Cellpose, ilastik. For tracking also different algorithms are available.

Scriptable in Fiji. https://imagej.net/plugins/trackmate/scripting/scripting

Also tools available to apply same analysis on multiple images without writing a script. Trackmate batcher: https://forum.image.sc/t/new-version-of-the-trackmate-helper-v1-2-1-with-a-batcher-and-the-spt-metrics/68180

Saving TrackMate projects

  • TrackMate results can be saved as XML files containing all tracking data
  • You can open this again in Fiji via Plugins->Tracking->Load a TrackMate file
  • Trick for projecting tracks onto a different image: You can open the XML file in a text editor, then search for the image filename reference and modify it

Key points to discuss:

  • Integration with OMERO: How to store and retrieve TrackMate results in OMERO
  • Batch processing: Methods for applying the same tracking parameters across multiple images
  • Script examples: Basic Jython/Groovy scripts for automating TrackMate analysis
  • Export options: Different ways to export tracking results (CSV, ROIs, visualizations)
  • TrackMate parameters: Explanation of key tracking settings and when to adjust them