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convert calcium trace to spikes

Project description

Deconvolve calcium imaging data to spikes. A wrapper around Chenkov and McColgan so it’s easier to use their model and weights. Assuming you have a imageJ roi measurement csv file, and a known sample_rate of your two photon recording:

import numpy as np
from ca2spike import deconvolve
calcium_data = np.genfromtxt(file_path, delimiter=',')[1:, 1::4].T
spike_data, timestamps, new_sample_rate = deconvolve(data, sample_rate)

Here the new sample rate is just a rounded int, coz otherwise your analysis experience will suck.

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