Morphological determinants of action potential dynamics in substantia nigra (Moubarak et al 2022)

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This model allows to simulate pacemaking activity in 37 fully reconstructed neurons. Calcium and sodium conductances vary by 11 increments in the Axon bearing dendrite part to simulate a 11*11*37 models. For each model Action potential (AP) properties are measured : frequency, amplitude, Threshold, Half duration, max first and second derivative. AP and conductances traces are then saved in a csv file.
1 . Moubarak E, Inglebert Y, Tell F, Goaillard J-M (2022) Morphological determinants of cell-to-cell variations in action potential in substantia nigra dopaminergic neurons J Neurosci
Model Information (Click on a link to find other models with that property)
Model Type: Axon; Dendrite; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Basal ganglia;
Cell Type(s): Dopaminergic substantia nigra neuron;
Channel(s): I Potassium; I Na,t; I Sodium; Ca pump; I A; I K,Ca; IK Skca; I h;
Gap Junctions:
Simulation Environment: NEURON;
Model Concept(s): Active Dendrites; Action Potential Initiation; Action Potentials; Dendritic Action Potentials;
Implementer(s): Tell, Fabien [fabien.tell at];
Search NeuronDB for information about:  I Na,t; I A; I h; I K,Ca; I Sodium; I Potassium; Ca pump; IK Skca;
This model was used to generate data from Figures 3-5 and 7-8 of the article.

Date_cell_*.hoc (ex : 04_02_2014_C2.hoc) files described the realistic morphology of 37 DA neurons. They also contain the conductances for each compartment. Conductances units are in pS/µm².

init_*.hoc files are files of initialization (dt, time of simulation, graph, etc.). They load Date_cell_*.hoc files and then launch the simulation and the analysis.

mod files are based on the equation described in Table 1.

Variable_G.hoc file is called by init_*.hoc and allows automatic changing conductances in several compartments. This file also records membrane potential and its derivative. It also records somatic conductances.

Freq.hoc calculates the spike frequency after some spikes have been generated and save the trace corresponding to the first spike of the data chunk from which the frequency was analyzed. Here you can specify the number of spikes you want to skip, the number of spikes you want to measure the frequency from and the amount of time before and after the spike you want to record.

1/ If the the amount of time before and after the spike you want to record is longer than the inter-spike interval, the program will analyze two spikes as one and the data will be wrong.
2/ If the number of spike generated during the simulation is less than the number of spikes skipped plus the number of spikes kept, no measurement will occur. So increase the time window.

Soma_analysis computes the spike characteristics at the soma and write them into a file. Here you set the threshold for the first derivative.
We compared the automatic analysis with « hand-made analysis » on action potential sweeps generated by the program. Except for very complex action potentials (large initial segment effect or quasi action potentials), the results are similar. So if you found outliers data points, check the corresponding sweep. launches the compilation of mod files and the simulation on linux computer. It doesn't not work on windows. To use it on windows, you need to load the init_* files one by one or to write your own bat file. You also need to compile mod files first.

As you will note, the above script launches Neuron for each cell and quit it when the analyis of the cell is complete. It means that for each cell the hoc files describing the topology, morphology and biophysics are loaded on a fresh (new) start of NEURON. In doing so, every previous neuron properties will be destroyed preventing potential problems with changes in topology. In addtion, it may help doing parallelization since each cell could be launched independently.

"data" directory is needed to put the files generated by the program, otherwise they are written in the present one.

On a recent computer (Intel® Xeon(R) CPU E5-2637 v4 @ 3.50GHz × 14) and under linux, simulation runs take around 500 seconds each for a dt of 0.02 ms and 1000 seconds for a dt of 0.01 ms (the one used in the study) for a simulated duration of 8000 ms. Since we use all CPU to launch 14 cells at the same time, the total time was reduced accordingly.

We apologize in advance for any unseen errors. Please let us know.

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