A standalone application for analysing time series data, which includes features for processing/labelling/filtering traces and facilitates the detection of hidden states using Hidden Markov Modelling (HMM). It also includes embdedded pre-trained Deep Learning (InceptionTime, DeepLASI) models for classifying/labelling traces.
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.
You can install TraceAnalyser via [GitHub]:
conda create –-name TraceAnalyser python==3.9
conda activate TraceAnalyser
conda install -c anaconda git
conda update --all
pip install git+https://github.com/piedrro/TraceAnalyser.git
python 3.9 requires MATLAB >= 2021b
MATLAB compatibility: https://uk.mathworks.com/support/requirements/python-compatibility.html
pip install matlabengine
This will likely fail due to a MATLAB version issue. Read the traceback, and install the recomended verison. Then try again:
pip install matlabengine==XXXX
To launch a Napari instance:
napari
To launch the Trace Analyser App:
analysis
To launch an ebFRET instance (requires matlab engine installation):
ebFRET
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.
Distributed under the terms of the MIT license, "TraceAnalyser" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.