Computational simulation model of the early visual system
DESCRIPTION
This framework uses four core functions to run a leaky integrate-and-fire neuron model simulation of (at this moment) monkey V1 and V2. Work is underway to widen its applicability. The four functions are:
- runBuildConnectivity.m
- runBuildStimulation.m 3a) runSimulation.m AND 3b) runSimulationIndInp.m
- runSimBatchAggregator.m
The program runBuildConnectivity.m (1) creates a .mat file containing the synaptic connectivity and simulation parameters. It in turn uses the subfunction buildConnectivity() to create the actual connectivity matrix. You can set the simulation parameters and model connectivity by editing the fields of the sConnParams structure in this file. See the function buildConnectivity() for more information. This function effectively creates the "anatomy" of your model network, which you can then use to run a simulation.
The second script that is required to run the simulation is runBuildStimulation (2), which creates the input that will feed into the network through a simplified retina/LGN filter layer. This function can create visual stimuli in retinal degrees, just as you would for an actual visual neuroscience experiment.
The main workhorse is accessed through runSimulation.m (3a) or runSimulationIndInp.m (3b). These functions use string-based inputs with parameter delimited by commas so compiled version can also be started from the command line. The difference between the two functions is that (3a) will simulate a single retina, which means that shared noise will propagate to cortex and induce information-limiting correlations. If you want to remove this source of shared fluctuations, you will have to use (3b). The drawback of (3b) is that simulating independent inputs for all V1 cells is computationally very intensive, so it will noticeably slow down the simulation speed.
Finally, if you run the simulation on a cluster with independent workers in a massively parallel manner, you can use runSimBatchAggregator.m (4) to combine the separate simulation runs from a single connectivity structure into one data file. See the runSimBatchAggregator.m file for more information.
VERSION HISTORY
V0.9.0.20190204 These functions were written by Jorrit Montijn in Alexandre Pouget's lab in Geneva, over the course of 2016-2018.
V0.9.1.20190212 Started to update help functions and rename functions to things that are more concise, and/or make more sense [by JM].