CLEOSim: Closed Loop, Electrophysiology, and Optogenetics Simulator
Hello there! CLEOSim has the goal of bridging theory and experiment for mesoscale neuroscience, facilitating electrode recording, optogenetic stimulation, and closed-loop experiments (e.g., real-time input and output processing) with the Brian 2 spiking neural network simulator. We hope users will find these components useful for prototyping experiments, innovating methods, and testing observations about a hypotheses in silico, incorporating into spiking neural network models laboratory techniques ranging from passive observation to complex model-based feedback control. CLEOSim also serves as an extensible, modular base for developing additional recording and stimulation modules for Brian simulations.
Closed Loop processing
CLEOSim allows for flexible I/O processing in real time, enabling the simulation of closed-loop experiments such as event-triggered or feedback control. The user can also add latency to closed-loop stimulation to study the effects of computation delays.
CLEOSim provides functions for configuring electrode arrays and placing them in arbitrary locations in the simulation. The user can then specify parameters for probabilistic spike detection or a spike-based LFP approximation developed by Teleńczuk et al., 2020.
By providing an optic fiber-light propagation model, CLEOSim enables users to flexibly add photostimulation to their model. Both a four-state Markov state model of opsin dynamics is available, as well as a minimal proportional current option for compatibility with simple neuron models. Parameters are provided for the common blue light/ChR2 setup.
Just use pip to install:
pip install cleosim
Then head to the overview section of the documentation for a more detailed discussion of motivation, structure, and basic usage.