molSEEQ

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

Piers Turner

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.

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.

Version:

1.0.8

Last updated:

2025-07-06

First released:

2024-07-25

License:

Supported data:

Information not submitted

Plugin type:

Widget

Open extension:

Save extension:

Python versions supported:

Operating system:

Information not submitted

Requirements:

napari[all]==0.5.0
numpy
magicgui
qtpy
scipy
pyqtgraph
picassosr==0.7.3
pandas
matplotlib>=3.7.0
scipy
opencv-python
tqdm
originpro
pyqt5-tools
trackpy
shapely
astropy
mat4py
tox; extra == "testing"
pytest; extra == "testing"
pytest-cov; extra == "testing"
pytest-qt; extra == "testing"
napari; extra == "testing"
pyqt5; extra == "testing"