CLEOSim: inject optogenetics, electrodes, and closed-loop control into your Brian simulation!

I’m excited to finally share CLEOSim with the Brian community! CLEO refers to Closed Loop (control), Electrodes, and Optogenetics. I’ve tried to make it as pain-free as possible to add these things to an existing Brian model. The idea is to use this for

  1. prototyping an experiment with Brian before trying it in vivo or
  2. exploring observations/manipulations of a computational model with realistic experimental constraints.

Feel free to reach out with any questions!

CLEOSim: Closed Loop, Electrophysiology, and Optogenetics Simulator — CLEOSim documentation


FYI, it has been rebranded to Cleo. I’m working on a publication now, and in the somewhat near future I’m planning on adding support for a many-to-many light source-opsin relationship