Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits
Fig 7
Computing extracellular field potential in BMTK.
A simulation using a version of the V1 model (Fig 6) with a white full-field flash stimulus is illustrated. The BioNet module of BMTK was used to run the simulation and compute the extracellular potential at multiple virtual electrode locations along the cortical depth; consequently, the potential was used to obtain the Local Field Potential and Current Source Density (CSD). Top row: LFP from example simulation and example mouse. The LFPs are found from averaging over 5 trials in the simulation and 75 trials in the experiments. Middle row: Corresponding CSDs for the LFPs in top row. The CSD is estimated using the delta-source iCSD method [51] assuming a column diameter of 0.8 mm for the simulation (the diameter of the core with biophysically detailed neurons in the model) and 1.6 mm for the experiment (roughly in accordance with the diameter of mouse V1). Bottom row: firing rates for the excitatory (“E”) and inhibitory (“I”) populations in each layer (2/3, 4, 5, and 6). Black: experiment mean. Gray: experiment standard deviation. Blue: simulation mean. Simulation rates are averaged over all neurons in a population and 5 trials. Experimental data are averaged over all neurons of the given type recorded from 47 mice, 75 trials each.