napari-moltrack 0.1.9

A user-friendly SMLM analysis platfrom for napari, which includes single molecule localisation, tracking, and analysis features.

napari-moltrack

A user-friendly SMLM analysis platfrom for napari, which includes single molecule localisation, tracking, and analysis features. Based on established python packages such as 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.

Napari-moltrack is also compatible with FRET and ALEX FRET image data, can be used to calculate FRET efficiencies of single molecules/tracks.

Segmentations can be used to exclude regions from 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

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Installation

You can install napari-moltrack via pip:

pip install napari-moltrack

To update napari-moltrack to the latest version, use:

pip install napari-moltrack --upgrade

To install latest development version :

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

BactFit

napari-moltrack integrates BactFit, a package for fitting the shape of rod shaped bacterial cells to an ideal cell model. BactFit allows cell renders and heatmaps to be generated through the transformation of SMLM localisations to an ideal cell model.

BactFit Heatmap

BactFit Cell Render

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.