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env_setup.md

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Setting up the Environment

Create a conda env with napari graph support

conda create -n napari_graph python=3.10 pyqt=5.15.7 # 3.12 and 3.11 not yet supported
conda activate napari_graph
pip install 'git+https://github.com/JoOkuma/napari@napari-graph-2023#egg=napari'
pip install 'git+https://github.com/napari/napari-graph'

Install Motile

conda install -c conda-forge -c funkelab -c gurobi ilpy
pip install git+https://github.com/funkelab/motile.git@1722dabd6e314d349ff50d46fd61abbdd9c17845

Install Traccuracy

pip install 'git+https://github.com/Janelia-Trackathon-2023/traccuracy'

Misc Other Packages

pip install jupytext zarr pre-commit

To run script as notebook

  • run jupyter lab (make sure jupytext extension is enabled)
  • Right click on python script run_motile.py
  • Open with -> jupytext notebook Note: we are using the format "percent script"