Import Trackmate XML files in Python as Pandas dataframe.
Project description
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.
Project details
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