Napari Track Edit

A napari plugin for interactive visualization, navigation, and editing of object tracking results. You can open and edit existing tracking data, manually create new tracking results, or run automatic 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 napari-track-edit. Currently, napari-track-edit requires python >=3.11.

Recommended extras

For better performance, you can install optional extras:

• numba: Speeds up candidate graph construction significantly.

  pip install napari-track-edit[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 napari-track-edit[gurobi]
  

You can install multiple extras at once: pip install napari-track-edit[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 napari-track-edit[gurobi12]  # For Gurobi 12.x licenses
pip install napari-track-edit[gurobi13]  # For Gurobi 13.x licenses

For developers

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 open all widgets via Plugins > Napari Track Edit > Open all widgets.

From here you can:

• load your own Labels or Points data to track with motile,
• load an image to manually track objects,
• or load existing tracking data to explore or edit.

If you would like to see an example first, go to Plugins > Napari Track Edit > Widget - Getting started, and click on one of the two examples, Hela cells (2D) or Mouse embryo (3D), to download and view them:

• Fluo-N2DL-HeLa is a 2D dataset of images and segmentations of HeLa cells from the cell tracking challenge.
• Mouse Embryo Membrane is a 3D dataset of images and segmentations of a membrane labeled developing early mouse embryo (4-26 cells) from Fabrèges et al (2024) available here.

For details, please read the documentation. If you are new to napari-track-edit, you can follow this tutorial to learn the basics.

https://github.com/user-attachments/assets/cd23271d-bbe6-40c2-80cb-8404136a564a

Issues

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