Motile Tracker

An application for interactive tracking with motile. The full documentation of the plugin can be found here.

Motile is a library that makes it easy to solve tracking problems using optimization by framing the task as an Integer Linear Program (ILP). See the motile documentation for more details on the concepts and method.

Installation

Users can download and install an executable application from the github release, or install from pypi in the environment of their choice (e.g. venv, conda) with the command pip install motile-tracker. Currently, the motile_tracker requires python >=3.11.

Recommended extras

For better performance, you can install optional extras:

• numba: Speeds up candidate graph construction significantly.

  pip install motile-tracker[numba]
  

• gurobi: Uses the Gurobi solver instead of the default open-source solver. Gurobi is much faster but requires a license (free for academics).

  pip install motile-tracker[gurobi]
  

You can install multiple extras at once: pip install motile-tracker[numba,gurobi]

Gurobi license version mismatch

If you have a Gurobi license and encounter an error about license version mismatch, you may need to install a specific version of gurobipy that matches your license. Use one of the version-specific extras:

pip install motile-tracker[gurobi12]  # For Gurobi 12.x licenses
pip install motile-tracker[gurobi13]  # For Gurobi 13.x licenses

Developers can clone the GitHub repository and then use uv to install and run the code. See the developer guide in DEVELOPER.md for more information.

Usage

Start napari and call the main widget via Plugins > Motile > Motile Main Widget. 2D+time and 3D+time sample data can be loaded via File > Open Sample > Motile. You can track objects in napari Labels or Points layers. For details, please read the documentation.

If you are new to using motile-tracker, you can follow this tutorial to learn the basics.

Package the application into an executable and create the installer

Tagging any branch will automatically trigger the deploy.yml workflow, which pushes the tagged version to PyPi and creates a github release; draft release if the tag contains "-dev", pre-release if the tag contains "-rc' or a full release otherwise. In case of a draft or pre release, when the user updates the release notes and promotes it to a published release, github will trigger make_bundle_app.yml workflow which will create the Linux, Mac and Windows installer and will upload them as release artifacts to github.

Issues

If you encounter any problems, please file an issue along with a detailed description.