# napari-trackpy
[](https://github.com/rhoitink/napari-trackpy/raw/main/LICENSE)
[](https://pypi.org/project/napari-trackpy)
[](https://python.org)
[](https://github.com/rhoitink/napari-trackpy/actions)
[](https://napari-hub.org/plugins/napari-trackpy)
Plugin to do [trackpy] particle tracking on 3D microscopy data within [napari]. Currently only tracking of XYZ data is implemented.
## Installation
You can install `napari-trackpy` via [pip]:
pip install napari-trackpy
To install latest development version :
pip install git+https://github.com/rhoitink/napari-trackpy.git
## How to use this plugin?
* Load your XYZ data (using [napari-aicsimageio])
* Make sure to split channels into different layers, such that the layer only contains 3D (XYZ) data
* Open the widget for the tracking plugin via `Plugins` > `XYZ particle tracking`
* Optimize the tracking settings for your dataset, for an extensive description of the settings, visit [this tutorial](http://soft-matter.github.io/trackpy/dev/tutorial/tracking-3d.html)
* Save your tracking data into the `.xyz` file format using `Ctrl`+`S` (on the points layer) or via the menu `File` > `Save Selected Layer(s)...`
## Contributing
Contributions are very welcome. Tests can be run with [tox].
## License
Distributed under the terms of the [MIT] license,
"napari-trackpy" is free and open source software
## Issues
If you encounter any problems, please [file an issue] along with a detailed description.
[napari]: https://github.com/napari/napari
[trackpy]: https://github.com/soft-matter/trackpy
[napari-aicsimageio]: https://github.com/AllenCellModeling/napari-aicsimageio
[MIT]: http://opensource.org/licenses/MIT
[file an issue]: https://github.com/rhoitink/napari-trackpy/issues
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
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