fiji-trackmate-20260601

Trackmate is a powerful tool for tracking and analyzing cells and particles in time-lapse acquisitions. It integrates now multiple advanced segmentation algorithms via a series of plugins. This container provides those additional tools with support for GPU computing, including: - spotiflow - cellpose 3 - cellpose 4 (SAM-based) - YOLO - trackastra

You can find more information in the general Trackmate documentation and in the specific pages for segementation extensions.

Please refer to the VIBE documentation for more information.

Requirements

• Apptainer

Build Instructions

To build the container, run the following command in the terminal:

apptainer build fiji-trackmate-20260601.sif build.def

Run Instructions

This container runs by default napari with:

apptainer run --nv fiji-trackmate-20260601.sif