CureQ 1.0.4

Library for analyzing MEA files.

CureQ

This is the repository of the CureQ consortium.
This repository contains a library with functions for analyzing MEA files.
This repository is maintained by the Amsterdam University of Applied Sciences (AUMC).
For more information about the analysis or how to use the library, check out the "CureQ MEA-analysis library User Guide.pdf" file.
For more information about the CureQ project, visit https://cureq.nl/

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Install the library

First, make sure you have installed a version of python on your machine, all python releases can be found here: https://www.python.org/downloads/
Secondly, make sure you have installed a package manager, like pip or conda.
Next, open a terminal and navigate to your home folder.

Install library with pip

Install the MEA analyzer with the following command when you are using Pip:

pip install CureQ 

Install library with conda

Install the MEA analyzer with the following command when you are using Conda:

conda install CureQ::CureQ

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Library usage

Now you can try the CureQ library functions in your Python environment.
Import the function you need, call this function and watch how the pipeline analyzes your MEA file!

Example for analyzing all MEA wells

from CureQ.mea import analyse_well               # Library function for analyzing wells

file_path = 'path/to/your/mea_file.h5'           # Path to your MEA file
hertz = 20000                                    # Sampling frequency of MEA system
electrodes = 12                                  # Electrode amount per well

# Analyzes all wells in the MEA file
if __name__=='__main__':
   analyse_well(fileadress=file_path, hertz=hertz, electrode_amnt=electrodes)

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Example visualisations of the MEA analysis pipeline

Spike detection

Single burst detection

Network burst detection