A simple Python tool to convert spike trains to calcium fluorescence-like traces.
spikes2calcium.py- the main function to convert spike trains to calcium-like traces using the method described in Grewe et. al. 2010 (codebase in MATLAB: github.com/HelmchenLab/CalciumSim).utils.py- includes plotting code and spike train generation code for the demo.
import utils
from spikes2calcium import spikes2calcium
# generate spike trains from Poisson distribution
DURATION = 20 # duration of the simulation in s
NUM_NEURONS = 16 # number of neurons to simulate
FRAME_RATE = 24.0 # frame rate of the simulation
FIRING_RATE = 2.0 # firing rate in Hz
spike_trains = utils.generate_spike_trains(firing_rate=FIRING_RATE,
duration=DURATION,
num_neuorns=NUM_NEURONS,
frame_rate=FRAME_RATE)
# convolve spike trains to calcium-like traces
traces = spikes2calcium(spike_trains=spike_trains, frame_rate=FRAME_RATE)
# plot the first 4 neurons
utils.plot_traces(traces=traces,
spike_trains=spike_trains,
frame_rate=FRAME_RATE,
filename='plots/traces.png',
show=False,
close=True)
- Package required:
numpy,matplotlib