Tracking

The Tracking module links segmented cells across frames to create trajectories. This allows you to analyze cell motility, lineage, and dynamic behaviors.

Overview

After segmentation, individual cell detections exist independently in each frame. Tracking connects these detections across time to form trajectories, assigning a persistent identity to each cell. This is essential for any time-resolved analysis — measuring speed, detecting events such as division or death, and studying interactions between populations.

Available trackers

Celldetective integrates two tracking algorithms:

bTrack [1] (default) — a Bayesian tracker that uses Kalman filters and cell features to predict motion. It handles complex behaviors such as division and apoptosis, and is the recommended choice for crowded scenes.
trackpy — a Crocker–Grier particle tracker well-suited for simple Brownian motion.

Both trackers produce a table of cell positions, identities, and (optionally) morphological or intensity features per frame. Results are saved as a CSV file (trajectories_<population>.csv) in the output/tables folder of each position.

Post-processing

After tracking, optional post-processing can be applied to clean up results:

Filter out short tracks.
Interpolate gaps (missing detections within a track).
Extrapolate positions backwards or forwards to the movie boundaries.

Interpolated and extrapolated rows have a position but no mask: their class_id, the label of the cell’s mask in the segmentation, is left empty rather than interpolated, so that no mask is invented for them.

These options are configured in the tracking settings and applied automatically after tracking. The same options can also be tuned interactively in the napari track-correction viewer (pre-filled from your tracking configuration) and applied on export, letting you preview their effect on the tracks before committing – see How to correct a single-cell track.

For a full list of post-processing and tracker parameters, see the Tracking Settings Reference.

How-to guides

Task	Guide
Configure a tracker and run it on your data	how-to
Correct a tracking error	how-to