https://github.com/hadim/pytrackmate
Import Trackmate XML files in Python as Pandas dataframe
https://github.com/hadim/pytrackmate
Last synced: about 1 year ago
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Import Trackmate XML files in Python as Pandas dataframe
- Host: GitHub
- URL: https://github.com/hadim/pytrackmate
- Owner: hadim
- License: mit
- Created: 2018-04-26T16:24:45.000Z (about 8 years ago)
- Default Branch: main
- Last Pushed: 2025-03-01T18:47:12.000Z (over 1 year ago)
- Last Synced: 2025-05-07T08:17:16.095Z (about 1 year ago)
- Language: Jupyter Notebook
- Homepage:
- Size: 391 KB
- Stars: 9
- Watchers: 3
- Forks: 6
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.rst
- License: LICENSE
- Authors: AUTHORS.rst
Awesome Lists containing this project
README
# pytrackmate
[pypi-badge]: https://img.shields.io/pypi/v/pytrackmate
[release-badge]: https://img.shields.io/github/v/release/hadim/pytrackmate?logo=github
[test-badge]: https://github.com/hadim/pytrackmate/actions/workflows/test.yaml/badge.svg?branch=main
[lint-badge]: https://github.com/hadim/pytrackmate/actions/workflows/lint.yaml/badge.svg?branch=main
[![PyPI - Version][pypi-badge]](https://pypi.org/project/pytrackmate/)
[![GitHub Release][release-badge]](https://github.com/hadim/pytrackmate/releases)
[![Test CI][test-badge]](https://github.com/hadim/pytrackmate/actions/workflows/test.yaml)
[![Lint CI][lint-badge]](https://github.com/hadim/pytrackmate/actions/workflows/lint.yaml)
Import [Trackmate](https://imagej.net/TrackMate) XML files in Python as Pandas dataframe.
## Installation 📦
```bash
# Pip
pip install pytrackmate
# Conda (mamba and micromamba)
conda install -c conda-forge pytrackmate
# Pixi
pixi add pytrackmate
```
## Usage 🚀
Check the [notebook](notebooks/Trackmate.ipynb).
```python
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](https://pixi.sh).
```bash
# 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](https://pypi.org/project/pytrackmate/) and on conda-forge at .
To cut a new release:
- Trigger [the `release` workflow on the main branch](https://github.com/hadim/pytrackmate/actions/workflows/release.yaml).
- 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](https://github.com/conda-forge/pytrackmate-feedstock).
- Once the conda-forge PR merged, the new conda version will be available.