UnitMatchPy 2.16

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Unit Match - Python

Run UMPy

To run UMPy standard spike sorting data is needed; channel positions and 2 extracted raw waveforms for each unit. This can be calculated externally BombCell or using extract_raw_demo.ipynb to extract these waveforms from compressed data (.cbin and .ch) or raw data. There is also a Spike Interface integrated notebook UMPy_spike_interface_demo.ipynb which uses spike interface to get this data. Be careful not to mix and match the different ways of extracting raw waveforms, as there are difference between the methods.

There are to example notebooks for running UMPy UMPy_example.ipynb and UMPy_example_detailed.ipynb. These notebooks will guide you through running Unit Match all you need to supply is paths to the data. UMPy_example.ipynb is recommended to use first as it is simpler, however UMPy_example_detailed.ipynb may be useful in unique cases as it is more modular.

The GUI is a optional step to curated and investigate the information Unit Match has calculated; for efficient usage of the GUI please look at GUI_Reference_Guide.md in the Demo Notebooks folder.

Dependencies

This version relies on many core python packages: numpy, scipy, JobLib, pandas, tkinter and matplotlib. All of these libaries come with a Anaconda version of python. For extracting raw data, the library mtscomp is needed, and can be installed by pip install mtscomp.

Installation

After creating an python environment

conda create --name UnitMatch python 
conda activate UnitMatch

You can install UnitMatchPy with pip. It will automatically install all the dependencies.

pip install UnitMatchPy