TrackMate

Fiji plugin for detecting and tracking objects (cells, foci, single molecules) across time-lapse images.

Overview

TrackMate splits tracking into two stages: first detect objects in each frame, then link detections into tracks. Both stages offer multiple algorithms, so the same plugin covers use cases from nuclear tracking to single-molecule analysis.

Key features

• Multiple detectors: LoG/DoG spot detection, thresholding, label-image import, StarDist, Cellpose, ilastik
• Multiple trackers: LAP, Kalman, nearest-neighbour, overlap-based
• Interactive track editing and filtering
• Scriptable in Jython/Groovy for reproducible pipelines
• TrackMate Batcher for running the same settings over many files without scripting

Installation

TrackMate ships with Fiji — no separate install needed. Detector extensions (StarDist, Cellpose, ilastik) are enabled via their respective update sites; see the plugin pages linked above.

Saving and loading results

• Results save as an XML file containing detections, tracks, and the source image reference.
• Reopen via Plugins > Tracking > Load a TrackMate file.

Tip

To project existing tracks onto a different image (e.g. a registered version), open the XML in a text editor and edit the image filename reference before loading.

Official documentation

• TrackMate plugin page
• Getting started
• Scripting guide

Learning resources

Written

• TrackMate tutorials index — covers detectors, trackers, and analysis workflows.
• TrackMate Batcher + SPT metrics — run the same pipeline on multiple movies without scripting.