main.ipynb simulate the growth and dynamics of a 2D neuronal culture. fluo_from_binar_spikes.m convert the binar spikes generated by main.ipynb in calcium fluorescence traces.

remark: a folder ./RESULTS/ must be created in the main directory to save files (or modify the codes according to your data folder)

The dynamics of each neuron follows Izhikevich’s integrate-and-fire model, with the addition of a pre-synaptic depression dynamics accounts for neurotransmitter depletion following repetitive firing

references: Abante, Piga et al (2024) "Autoregressive variational autoencoder uncovers underlying physics of neural firing and connectivity" Orlandi et al. (2013) "Noise focusing and the emergence of coherent activity in neuronal cultures" Izhikevich (2003) "Simple model of spiking neurons" Alvarez-Lacalle, and Moses (2009) "Slow and fast pulses in 1-D cultures of excitatory neurons"