Napari PixSeq

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

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.

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

Installation¶

You can install napari-GapSeq2 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.