molSEEQ

A Napari plugin for extracting single molecule sequences from single/multi-channel SMLM microscopy data.

Compatible with both ALEX and FRET data. All functions are parallelised/GPU accelerated where possible to increase performance. Multiple datasets can be loaded and processed in parallel.

napari-molseeq 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-molseeq 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.

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Installation¶

You can install napari-molseeq via pip:

pip install napari-molseeq

You can install napari-molseeq via [GitHub]:

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

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

Issues¶

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