pytrackmate

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.