Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits
Fig 8
Simulation of optogenetic perturbations using BMTK.
The point-neuron version of the V1 model (Fig 6) is used here for illustration. Perturbations are achieved by injecting positive or negative current into cells. (A) Raster plots from 3-second simulations (stimulus: 0.5 s gray followed by 2.5 s of a drifting grating). Simulations without perturbation, with complete silencing of all Layer 6 excitatory cells (E6), and activation of all E6 cells (current equal to 0.5 of the rheobase of each neuron at rest is injected) are illustrated. The perturbation here is applied throughout the course of simulation. (B) Summary of silencing individual cell classes in the V1 model, for the same visual stimulus as in (A). The cell classes listed along the horizontal axis are silenced one by one, and the effect on each cell class (listed along the vertical axis) is characterized using the Optogenetic Modulation Index (OMI; see Main text), averaged over 10 trials and over all cells in the class. The entries “allHtr3a”, “allPvalb”, and “allSst” refer to simulations where, e.g., the Sst class of neurons was silenced in all layers (“allSst”). (C) Activation of Layer 6 excitatory or Pvalb inhibitory neurons, for the same visual stimulus as in (A). Different amplitudes of perturbations are sampled. OMI is computed as in (B), and is shown for 3 select cell classes. Due to inter-laminar projections of Layer 6 Pvalb interneurons to upper layers, activation of either Layer 6 excitatory or Layer 6 inhibitory Pvalb cells leads to the suppression of activity in Layer 4.