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Import Trackmate XML files in Python as Pandas dataframe.

Project description

pytrackmate

GitHub Release Test CI Lint CI

Import Trackmate XML files in Python as Pandas dataframe.

Installation 📦

# Pip
pip install pytrackmate

# Conda (mamba and micromamba)
conda install -c conda-forge pytrackmate

# Pixi
pixi add pytrackmate

Usage 🚀

Check the notebook.

fname = "FakeTracks.xml"
spots = trackmate_peak_import(fname)

spots is a dataframe with the following columns:

  • t_stamp
  • t
  • x
  • y
  • z
  • w
  • q
  • spot_id
  • mean_intensity
  • median_intensity
  • min_intensity
  • max_intensity
  • total_intensity
  • std_intensity
  • contrast
  • snr
  • label

Development 🛠️

You need to use pixi.

# Run tests
pixi run -e dev test

# Lint (ruff)
pixi run -e dev lint

# Format code (ruff)
pixi run -e dev format

Release 🚢

The package is released on PyPi and on conda-forge at https://github.com/conda-forge/pytrackmate-feedstock.

To cut a new release:

  • Trigger the release workflow on the main branch.
  • A new GitHub Release will be created with the new version.
  • The new version will be uploaded on PyPi.
  • The conda-forge bot will create a PR to update the feedstock.
  • Once the conda-forge PR merged, the new conda version will be available.

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