Bringing TrackMate in the era of machine-learning and deep-learning

TrackMate is an automated tracking software used to analyze bioimages and distributed as a Fiji plugin. Here we introduce a new version of TrackMate rewritten to improve performance and usability, and integrating several popular machine and deep learning algorithms to improve versatility. We illustrate how these new components can be used to efficiently track objects from brightfield and fluorescence microscopy images across a wide range of bio-imaging experiments. Object tracking is an essential image analysis technique used across biosciences to quantify dynamic processes. In life sciences, tracking is used for instance to track single particles, sub-cellular organelles, bacteria, cells, and whole animals.