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Cell segmentation and tracking

Overview

In this example, we demonstrate how to use microSAM1 with napari in combination with the TrackMate2 Fiji plugin to track cell migration. The dataset consists of time-lapse fluorescence images of MDA-MB-231 cells expressing an ERK activity reporter, acquired using a widefield fluorescence microscope3.

We use the DAPI staining channel as a reference for cell tracking. microSAM is employed to segment the cell nuclei, and the resulting labeled nuclei are subsequently used as input for tracking cell trajectories with TrackMate in Fiji. Between these steps, several preprocessing operations are performed, including splitting and merging image channels.

Visualize and split the channels

dataset -> use fiji

Segment nuclei with micro-SAM

Adjust the setting for automatic segmentation.

segment the cells.

export the resulting mask (annotation) as an image

in fiji, merge the resulting mask with the original 2 channels image

Track cells with trackmate

adjust trackmate settings

visualize results

Acknowledge

Resources

  1. Archit, A., Freckmann, L., Nair, S. et al. Segment Anything for Microscopy. Nat Methods 22, 579–591 (2025). https://doi.org/10.1038/s41592-024-02580-4 ↩

  2. Ershov, D., Phan, MS., Pylvänäinen, J.W. et al. TrackMate 7: integrating state-of-the-art segmentation algorithms into tracking pipelines. Nat Methods 19, 829–832 (2022). https://doi.org/10.1038/s41592-022-01507-1 ↩

  3. Jean-Yves Tinevez, & Joanna W. Pylvänäinen. (2021). Cell migration with ERK signalling [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5205955 ↩