Database of conductance-based models of thalamocortical neurons

The current database contains only models of thalamocortical relay neurons (TC) in the mouse visual thalamus (dorsal lateral geniculate nucleus) recorded at postnatal day 7 (P7).

Software

The model of TC neuron is implemented in NEURON simulator.

pip3 install --user neuron

Preparations

All necessary NEURON modules are located in mods directory and borrowed from Iavarone et al. (2019). You must compile them before any simulation.

nrnivmodl mods

The basic model

Even adult TC neurons are relatively electrically compact (Sherman and Guillery, 2004; Bloomfield and Sherman, 1989). Developing TC neurons have shorter and thicker processes (Charalambakis et al., 2019; El-Danaf et al., 2015). That allows the usage of a conductance-based ”pen-and-ball” two-compartment model with a single segment for the somatodendritic compartment and a multisegment compartment for an axon. The model is implemented as a single class in cell.py.

The database

The current database P07-selected-checked-gmin.json (last updated 2022-09-21) contains fully validated and human-evaluated 286 sets of model parameters.

Try a neuron model in the database

To try neurons in the database in the standard current-clamp protocol, you can run cell.py with at least two command line arguments: name of the database file and neuron ID. The third optional command line argument will be interpreted as the amplitude value of the current-clamp protocol. Note cell.py does not read initial conditions for steady-state from the database, and therefore transient dynamics are expected.

Examples

python cell.py P07-selected-checked-gmin.json 2 0.1	python cell.py P07-selected-checked-gmin.json 280 0.1

Citation

Please use DOI: 10.5281/zenodo.7312024 as the reference for the database.