PixSeq

napari-PixSeq

A Napari plugin for extracting time series traces from Single Molecule Localisation Microsocpy (SMLM) data.

Workflow step:
Image annotation
Image segmentation

License MIT PyPI Python Version napari hub

A Napari plugin for extracting time series traces from single molecule FRET data.

napari-PixSeq uses Picasso (picassosr) as a backend and includes features for aligning image channels/datasets, undrifting images, detecting/fitting localisations and extracting traces, and supports both ALEX and FRET data. Traces can be exported in different formats for downstream analysis.

napari-PixSeq traces can be analysed with TraceAnalyser: https://github.com/piedrro/TraceAnalyser

This is still undergoing development, so some features may not work as expected.

This was built by Dr Piers Turner from the Kapanidis Lab, University of Oxford.


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

Installation

You can install napari-PixSeq via pip:

pip install napari-PixSeq

You can install napari-PixSeq via [GitHub]:

conda create –-name napari-pixseq python==3.9
conda activate napari-pixseq
conda install -c anaconda git
conda update --all

pip install git+https://github.com/piedrro/napari-PixSeq.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 MIT license, "napari-PixSeq" is free and open source software

Issues

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

Version:

  • 1.0.3

Last updated:

  • 21 May 2024

First released:

  • 29 February 2024

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 0
  • 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

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