A Napari plugin for extracting single molecule sequences from single/multi-channel SMLM microscopy data.
Project description
napari-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.
Formally known as napari-pixseq.
This was built by Dr Piers Turner from the Kapanidis Lab, University of Oxford.
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.
Project details
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