Large-scale cell tracking under segmentation uncertainty.

Zebrafish imaged using DaXi whole embryo tracking.

Install conda to avoid conflicts between different packages.

Create a conda environment.

conda create --name tracking -c conda-forge python=3.10 pyqt

And activate it.

ATTENTION: every time you need to run this software you'll have to activate this environment

conda activate tracking

Install the package from github:

pip install git+https://github.com/royerlab/ultrack

Usage examples can be found here, including their environment files and their installation instructions.

The official documentation is available here.

These additional developer documentation are available:

• Parameter configuration schema.
• Intermediate segmentation and tracking SQL database are here.

Installing gurobi and setting up an academic license.

In your existing Conda environment, install Gurobi with the following command:

conda install -c gurobi gurobi

Obtain License: register for an account using your academic email at Gurobi's website. Navigate to the Gurobi's named academic license page, and follow the instructions to get your academic license key.

Activate License: In your Conda environment, run:

grbgetkey YOUR_LICENSE_KEY

Replace YOUR_LICENSE_KEY with the key you received. Follow the prompts to complete activation.

Verify Gurobi's installation by running:

ultrack check_gurobi

Depending on the operating system, the gurobi library might be missing and you need to install it from here.

If you use ultrack in your research, please cite the following paper:

@misc{bragantini2023ucmtracking,
      title={Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps},
      author={Jordão Bragantini and Merlin Lange and Loïc Royer},
      year={2023},
      eprint={2308.04526},
      archivePrefix={arXiv},
      primaryClass={cs.CV}
}

And the respective auxiliary methods (e.g. Cellpose, napari, etc) depending on your usage.