napari-moltrack

napari-moltrack

Single molecule tracking package for Napari

License BSD-3 PyPI Python Version tests codecov napari hub

A Napari plugin for single molecule localisation and tracking based on Picasso, GPUfit and Trackpy. This plugin was designed to detect/track single molecules inside cells, but can be used for any other SMLM/tracking application.

All functions are parallelised/GPU accelerated where possible to increase performance. Multiple datasets can be loaded and processed in parallel.

Single molecule localisations can be filtered by their properties (e.g. photons, width, etc.) and can be rendered as a super resolution image.

Segmentations can be used to exclude regions froHm single molecule localisation and tracking. Segmentations can be added automatically using Cellpose or can be added manually. Includes tools for editing/modifying segmentations at a sub-pixel resolution.

Compatible with both single and multi channel .tif and .fits files.

napari-moltrack was written by Piers Turner, Kapanidis Group, University of Oxford....

https://www.physics.ox.ac.uk/research/group/gene-machines


This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install napari-moltrack via pip:

pip install napari-moltrack

To install latest development version :

pip install git+https://github.com/piedrro/napari-moltrack.git

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-moltrack" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

Version:

  • 0.0.23

Last updated:

  • 21 June 2024

First released:

  • 30 May 2024

License:

Supported data:

  • Information not submitted

Plugin type:

  • Information not submitted

GitHub activity:

  • Stars: 1
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • napari[all]
  • numpy
  • magicgui
  • qtpy
  • scipy
  • pyqtgraph
  • picassosr
  • pandas
  • matplotlib
  • opencv-python
  • tqdm
  • originpro
  • pyqt5-tools
  • torch
  • cellpose>=3.0.1
  • omnipose
  • trackpy
  • shapely
  • astropy