DOI: 10.5281/zenodo.17495139
title: Dataset to the publication: Rózsa, T., Cagnol, R., Antolík, J. Iso-orientation bias of layer 2/3 connections unifies spontaneous, visually and optogenetically driven V1 dynamics

description: This dataset contains simulation data sufficient to reproduce the main results (Figures 2-6) of the publication: Rózsa, T., Cagnol, R., Antolík, J. "Iso-orientation bias of layer 2/3 connections unifies spontaneous, visually and optogenetically driven V1 dynamics". The dataset is contains three different types of data: LFP signal recordings, spike times, and associated metadata (LFP site positions, neuron positions, and stimulation patterns). Metadata and LFP signals are stored as continuous numpy arrays, while spike times are stored as ragged numpy arrays, as the number of spikes across neurons in a single recording is variable. All spike times are recorded from the same layer 2/3 excitatory population of 38150 neurons, except for the file opto_center_stimulation_l23_inhibitory_spikes.npy, where we record from layer 2/3 inhibitory neurons. All LFP data refers to the same 100x100 grid of electrodes recording from excitatory populations in layer 4 or layer 2/3.

Here we describe the files in the dataset:



lfp_data_x.npy: x coordinates of the 100x100 electrode grid, centered on (0,0). Used in Figure 2.

lfp_data_y.npy: y coordinates of the 100x100 electrode grid, centered on (0,0). Used in Figure 2.

lfp_data_l4.npy: raw unfiltered synthetic LFP signal generated by layer 4, recorded by a grid of 100x100 electrodes for 20s of spontaneous activity with sampling rate of 1ms. Dimensions: (100,100,20160). Used in Figure 2.

lfp_data_l23.npy: raw unfiltered synthetic LFP signal generated by layer 2/3, recorded by a grid of 100x100 electrodes for 20s of spontaneous activity with sampling rate of 1ms. Dimensions: (100,100,20160). Used in Figure 2.

lfp_data_l23_nobias.npy: raw unfiltered synthetic LFP signal generated by layer 2/3 in the configuration where iso-orientation bias is absent in horizontal connectivity, recorded by a grid of 100x100 electrodes for 20s of spontaneous activity with sampling rate of 1ms. Dimensions: (100,100,20160). Used in Figure 2.

spiking_neuron_positions_mm_x.npy: x coordinates of recorded spiking neurons in a 4x4mm area, centered on (0,0). Dimensions: (38150). Used in all Figures.

spiking_neuron_positions_mm_y.npy: y coordinates of recorded spiking neurons in a 4x4mm area, centered on (0,0). Dimensions: (38150). Used in all Figures.

spontaneous_activity_120s_l23_spikes.npy: Spike times recorded during 120s of spontaneous activity, from layer 2/3 neurons in a 4x4mm area, centered on (0,0). Dimensions: (38150, number_of_spikes). Used in all Figures. 

spontaneous_activity_120s_no_orientation_bias_l23_spikes.npy: Spike times recorded from the model version with no iso-orientation bias for layer 2/3 long-range connections during 120s of spontaneous activity, from layer 2/3 neurons in a 4x4mm area, centered on (0,0). Dimensions: (38150, number_of_spikes). Used in Figures 2,3,4.

drifting_gratings_l23_spikes.npy: Spike times recorded during 10 trials of 2s stimulation with sinusoidal drifting gratings of 8 orientations, from layer 2/3 neurons in a 4x4mm area, centered on (0,0). Dimensions: (8, 10, 38150, number_of_spikes). Used in Figure 3.

opto_fullfield_l23_spikes.npy: Spike times recorded during 40 trials of 4s fullfield optogenetic stimulation (1s rest, 1s stimulation, 2s rest), from layer 2/3 neurons in a 4x4mm area, centered on (0,0). Dimensions: (40, 38150, number_of_spikes). Used in Figure 4.

opto_fullfield_no_orientation_bias_l23_spikes.npy: Spike times recorded from the model version with no iso-orientation bias for layer 2/3 long-range connections during 40 trials of 4s fullfield optogenetic stimulation (1s rest, 1s stimulation, 2s rest), from layer 2/3 neurons in a 4x4mm area, centered on (0,0). Dimensions: (40, 38150, number_of_spikes). Used in Figure 4.

endogenous_stimulation_patterns.npy: 8 different endogenous stimulation patterns used for optogenetic stimulation, covering an area of 4x4mm, centered on (0,0). Dimensions: (8,100,100). Used in Figures 4,5.

surrogate_stimulation_patterns.npy: 8 different surrogate stimulation patterns used for optogenetic stimulation, covering an area of 4x4mm, centered on (0,0). Dimensions: (8,100,100). Used in Figures 4,5.

opto_endogenous_l23_spikes.npy: Spike times recorded during 5 trials of 4s optogenetic stimulation (1s rest, 1s stimulation, 2s rest) with 8 different endogenous stimulation patterns, from layer 2/3 neurons in a 4x4mm area, centered on (0,0). Dimensions: (8, 5, 38150, number_of_spikes). Used in Figures 4,5.

opto_endogenous_no_orientation_bias_l23_spikes.npy: Spike times recorded from the model version with no iso-orientation bias for layer 2/3 long-range connections during 5 trials of 4s optogenetic stimulation (1s rest, 1s stimulation, 2s rest) with 8 different endogenous stimulation patterns, from layer 2/3 neurons in a 4x4mm area, centered on (0,0). Dimensions: (8, 5, 38150, number_of_spikes). Used in Figures 4,5.

opto_surrogate_l23_spikes.npy: Spike times recorded during 5 trials of 4s optogenetic stimulation (1s rest, 1s stimulation, 2s rest) with 8 different surrogate stimulation patterns, from layer 2/3 neurons in a 4x4mm area, centered on (0,0). Dimensions: (8, 5, 38150, number_of_spikes). Used in Figures 4,5.

opto_center_stimulation_l23_excitatory_spikes: Spike times recorded during 10 trials of 4s optogenetic stimulation (1s rest, 1s stimulation, 2s rest) in a circular area centered at (0,0) of 6 different radii (50, 100, 150, 200, 250, 300 μm), from layer 2/3 excitatory neurons in a 4x4mm area, centered on (0,0). Dimensions: (6, 10, 38150, number_of_spikes). Used in Figure 6.

opto_center_stimulation_l23_inhibitory_spikes: Spike times recorded during 10 trials of 4s optogenetic stimulation (1s rest, 1s stimulation, 2s rest) in a circular area centered at (0,0) of 6 different radii (50, 100, 150, 200, 250, 300 μm), from layer 2/3 inhibitory neurons in a 4x4mm area, centered on (0,0). Dimensions: (6, 10, 18626, number_of_spikes). Used in Figure 6.