MEAlytics

MEAlytics as Python package

Besides the GUI, the MEA analysis tool can also be called as a python library, and has a few functions that can be of use to the user. Let’s walk through an example to fully analyse a MEA file.

Analysing MEA file

Firstly, import the necessary functions:

from CureQ.mea import analyse_wells, get_default_parameters

Next, we define some variables that we later need to pass to the function.

fileadress='C:/mea_data/mea_experiment.h5'
sampling_rate=20000
electrode_amount=12

Then, we retrieve the dictionary containing the default parameters so we can alter the analysis. In this case we turn on multiprocessing to speed up the analysis.

parameters = get_default_parameters()
parameters['use multiprocessing'] = True

Finally, pass all the arguments to the analyse_wells function to initiate the analysis. Because we turned on multiprocessing, we must use and “if __name__ == ‘__main__’: “ guard here. Otherwise, the application will eventually create an infinite number of processes and eventually crash.

if __name__ == '__main__':
    analyse_wells(fileadress=fileadress,
                  sampling_rate=sampling_rate,
                  electrode_amnt=electrode_amount,
                  parameters=parameters
                  )

In the end, it should look like this:

from CureQ.mea import analyse_wells, get_default_parameters

fileadress='C:/mea_data/mea_experiment.h5'
sampling_rate=20000
electrode_amount=12

parameters = get_default_parameters()
parameters['use multiprocessing'] = True

if __name__ == '__main__':
    analyse_wells(fileadress=fileadress,
                  sampling_rate=sampling_rate,
                  electrode_amnt=electrode_amount,
                  parameters=parameters
                  )

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