TrackMate is a Fiji tool for tracking cells and organelles in time-lapse fluorescence microscopy images. It was designed with user-friendliness and extensibility in mind. Its ultimate goal is to serve as a platform for users to implement an analysis pipeline or their own tracking algorithm, within a convenient UI.

This webinar will be a presentation of TrackMate and its story, and a live demo of some if its less well-known features. TrackMate capabilities and limitations will be discussed. We will also introduce how to extend TrackMate, and some extensions including contributions by others. Finally, we will discuss the future of TrackMate and briefly introduce Mastodon.

1. Using TrackMate to track cells and organelles. – Why does TrackMate exist? – Core TrackMate features. – Brief live demo.

2. Some discreet features of TrackMate. – Interoperability. – Less well-known features.

3. Scripting and extending TrackMate. – Scripting in Jython inside Fiji. – TrackMate Java extension mechanism.

4. Some TrackMate extensions.

5. The future of TrackMate.

6. Q&A.