UnitMatchPy 2.0a0

No project description provided

Unit Match - Python

Run UMPy

To run UMPy standard spike sorting data is needed; channel positions and 2 extractracted raw waveforms for each unit. This can be calculated exteranlly BombCell or using ExtractRawDataDemo.ipynb to extract these waveforms from compressed data (.cbin and .ch) or raw data. There is also a Spike Interface intergrated 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 exrtacting raw waveforms, as there are difference between the methods.

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

The GUI is a optional step to curated and investigate the infomation Unit Match has calculated; for efficent 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, this 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 dependency.

pip install UnitMatchPy