OptogenSIM: A 3D monte carlo simulation platform for light delivery design in optogenetics

Yuming Liu, Steven L. Jacques, Mehdi Azimipour, Jeremy D. Rogers, Ramin Pashaie, Kevin W. Eliceiri

Research output: Contribution to journalArticlepeer-review

47 Scopus citations


Optimizing light delivery for optogenetics is critical in order to accurately stimulate the neurons of interest while reducing nonspecific effects such as tissue heating or photodamage. Light distribution is typically predicted using the assumption of tissue homogeneity, which oversimplifies light transport in heterogeneous brain. Here, we present an open-source 3D simulation platform, OptogenSIM, which eliminates this assumption. This platform integrates a voxel-based 3D Monte Carlo model, generic optical property models of brain tissues, and a well-defined 3D mouse brain tissue atlas. The application of this platform in brain data models demonstrates that brain heterogeneity has moderate to significant impact depending on application conditions. Estimated light density contours can show the region of any specified power density in the 3D brain space and thus can help optimize the light delivery settings, such as the optical fiber position, fiber diameter, fiber numerical aperture, light wavelength and power. OptogenSIM is freely available and can be easily adapted to incorporate additional brain atlases.

Original languageEnglish (US)
Article number250524
Pages (from-to)4859-4870
Number of pages12
JournalBiomedical Optics Express
Issue number12
StatePublished - Nov 16 2015
Externally publishedYes


  • Computation methods
  • Illumination design
  • Light propagation in tissues
  • Modulation techniques

ASJC Scopus subject areas

  • Biotechnology
  • Atomic and Molecular Physics, and Optics


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