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Particle tracking

napari-trackpy

Plugin to do trackpy particle tracking on microscopy data within napari

License MIT PyPI Python Version tests napari hub

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
  • 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.

Version:

  • 0.3.0

Last updated:

  • 09 November 2023

First released:

  • 07 November 2023

License:

Supported data:

  • Information not submitted

Plugin type:

Save extension:

Save layers:

GitHub activity:

  • Stars: 0
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • numpy
  • magicgui
  • qtpy
  • napari
  • napari-aicsimageio
  • readlif
  • trackpy
  • matplotlib

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