modeldbrepository / 267589

Decorrelation in the developing visual thalamus (Tikidji-Hamburyan et al, accepted)

Synaptic and circuit mechanisms prevent detrimentally precise correlation in the developing mammalian visual system

by Ruben A. Tikidji-Hamburyan, Gubbi Govindaiah, William Guido, Matthew T. Colonnese

eLife 2023; 12:e84333. DOI: https://doi.org/10.7554/eLife.84333.

Required software

For any simulation in this record, one needs Python(version 3.9.9 and higher) and libraries cython, numpy, scipy and matplotlib.

$pip3 install --user numpy scipy matplotlib cython

Additional libraries:

Figure 1	NEURON, pyabf and inspyred
Figure 2,4,5	NEURON, h5py, and neurodsp

To install all libraries for all scripts, use a single command

$pip3 install --user numpy scipy matplotlib cython NEURON pyabf inspyred h5py neurodsp brian2

Files, directories, and models in this record

File or directory	Description
TC-fitting	Fitting procedure and associated files for Figure 1 in the manuscript
dLGN-network	Thalamic network at P7-P10 for Figures 2, 4, and 5 in the manuscript
experimentaldata	an example of a neuron recording and mask file for the optimization as well as Maccione et al. 2014 recording from waverepo repository on GitHub
P07-selected-checked-gmin-20220921.json	A reduced, fully validated, and human-evaluated database of 286 models of thalamocortical neurons in visual LGN at P7-P10, enough to reproduce any results in the manuscript