Latest Version

OptogenSim: computational tool for Optogenetics light delivery design

Optogenetics is a powerful tool for in in-vivo brain studies due to its unparalleled ability to modulate neural activity  in living tissues and animals. Precise temporal and spatial neuronal control can be achieved through specific cell-type targeting by the use of optogenetic proteins such as channelrhodopsin and optical  stimulation at specific wavelengths.  Given the demonstrated power of this technique, there is now great need to develop improved light delivery strategies that will more accurately stimulate the neurons of interest while reducing the nonspecific effects such as tissue heating or photodamage.

In order to help optimize light delivery strategies, OptogenSIM, a 3D Monte Carlo simulation platform for optogenetic applications, has been developed under an extensive multisite collaboration since August 2012. The development partners in OptogenSIM are: Professor Steven Jacques's Lab[1] at Oregon Health and Science University, the BIST Lab [2]at the University of Wisconsin at Milwaukee, and  the LOCI group at the University of Wisconsin at Madison. OptogenSIM can be used for simulating  light delivery in brain in a wide variety of optogenetic applications. It aims to provide a 3D simulator for predicting light distribution in heterogeneous brain tissue with high resolution, including a voxel-based 3D Monte Carlo tool custom built for optogentics light delivery, generic optical properties  library for different brain tissues, and a 3D mouse brain atlase segmented with SPM-based tool[3,4]. This platform allows for delivering light at any locations of the brain and with commonly used fiber geometries and light source types, taking into account the light wavelength and power, optical fiber diameter and numerical aperture(NA), brain tissue optical properties, light beam type and tissue heterogeneity. 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.  A demonstrated validation of mcxyz vs gold standard MCML can be find at here.

Other rodent brain atlases can also be incorporated into OptogenSIM.  We have tested the simulation on an average 3D mouse brain atlas[5]  and an average 3D rat brain atlas[6] but due to copyright issues for direct distribution of the atlases with our tool,  these atlases have not been included in the current version.

We would like to thank Dr. Helene Benveniste at the Stony Brook University  for providing the permission to incorporate the 3D mouse atlas in OptogenSIM. We also would like to thank Vaibhav D. Phad, a LOCI graduate intern, for discussing and testing the light beam modeling. This simulator was partially sponsored by the University of Wisconsin Intercampus award under grant number UDDS B19-2510 and funding from the Laboratory for Optical and Computational Instrumentation (LOCI).


Main developers:

    Yuming Liu (primary contact)

    Steven Jacques



Standalone version:

1. Make sure the Matlab 2014b MCR is installed properly. The MCR can be freely downloaded from the Mathworks, Inc at Windows64 MCR 2014b or  Mac MCR 2014b.

2.Download the OptogenSIM standalone_for Windows or OptogenSIM standalone for Mac  .Unzip and then run the application “OptogenSIM”((To be noted, before opening ‘OptogenSIM’, if you ever ran the older release, make sure to delete/rename/move the old ‘OSGworking’ folder mentioned in step 3 of the manual, otherwise the new release could not work properly.)):

               In Windows: double click on “OptogenSIM”

               In Mac: right click on “OptogenSIM”(ctrl-click)----->Show Package Contents ----> Contents---->MacOS---->applauncher (right-click and choose open)

 Source-code version:

      Download and unzip source code including the Matlab m-files, data, as well as a distribution of mcxyz.c. Open and run the function “OptogenSIM” to launch the GUI.


Download the quick manual to start.


[1] 3D Monte Carlo code at Steven Jacques's Lab

[2] Optogenetics researches at Ramin Pashaie's BIST Lab

[3] Statistic Parametric Mapping (SPM) software

[4] SPMMOUSE software

[5] Average mouse brain atlas

[6] Average Rat  Brain Atlas

[7] 3D Mouse Brain Atlas


Matlab, C