This plugin was inspired by TrackMate-Examples, TrackMate-MorpholibJ and TrackMate-StarDist and this preprint by Dimitry Ershov.
- Open a dataset and start TrackMate from the
Plugins > Trackingmenu. - In the 2nd step (Select Detector), choose
CLIJ2 Voronoi Otsu Labeling.
- When configuring the detector, enter
spot-sigmato fine-tune how close objects can be andoutline_sigmato control how precise outlines are. Read more in the [Voronoi-Otsu-Labeling tutorial]
- Wait a moment :-)
- In further processing, it is recommended to filter detected spots by their area.
- Therefore, it might be helpful to change the visualization by adapting the maximum shown area. This makes objects better visible that stick to each other.
- For tracking, the overlap tracker is recommended.
- For visualization, select 'Show tracks local in time'.
CLIJ is developed in the open because we believe in the open source community. See our community guidelines. Feel free to drop feedback or ask questions via image.sc.