How to configure and run tracking

This guide shows you how to set up a tracker and run it on your segmented data.

Reference keys: tracking, cell population

Prerequisite: You must have segmented masks for the population of interest.

Configure the tracker

  1. Navigate to the Tracking module in the main processing panel.

  2. Click the Settings button to open the configuration window.

  3. Select a Tracker:

    • Choose bTrack (default) for complex behaviors (division, apoptosis) and crowded scenes. It uses a Bayesian approach with motion prediction.

    • Choose trackpy for simple particle tracking (Brownian motion).

  4. Add Features (Optional): Click Add features to calculate morphological (e.g., area) or intensity features during tracking. Enable :term:`Haralick Texture Features` if you need texture analysis (computationally expensive).

  5. Configure Post-Processing (Optional): Enable options to filter short tracks, fill gaps, or extrapolate positions.

  6. Click Save to apply your settings.

For a detailed explanation of every parameter, see the Tracking Settings Reference.

Run tracking

  1. In the Tracking module control panel, check the TRACK box.

  2. Ensure you have selected the wells/positions you wish to process.

  3. Click Submit.

Celldetective will load the segmentation masks, run the selected tracker, compute the requested features, and save the results as trajectories_targets.csv (or _effectors) in the output/tables folder of each position.

Visualize tracks

  1. Select a single position in the file list.

  2. Click the Eye button in the Tracking module.

  3. Napari will open with the following layers:

    • image: Raw microscopy data.

    • segmentation: Labeled cell masks (color-coded by ID).

    • tracks: Trajectory lines connecting cell positions over time.

    • points: Centroids of detected cells.