The Optogenetics APP



What is the Optogenetics APP?


The Optogenetics APP is a tool to aid an investigator in estimating the required optical power for a given in-vivo experiment involving optogenetics or any other experimental approach that includes light delivery to deep brain areas via optical fibers.


Different brain areas have different optical properties, which determine how light scatters and distributes (and how deeply it penetrates the tissue), once it exits the fiber. The APP has a complete mouse brain atlas included that can be used to determine the optical properties of any brain area in the mouse brain. A user finds the brain areas of choice, marks it on the atlas, then tell the APP what type of optogenetic protein he/she wants to use, as well as the type of optical fiber, desired optical power, and desired protein activation ratio.


Based on these parameters, the APP estimates how far the light will spread in this particular experimental situation (and thus, up to which distance from the fiber tip optogenetic protein activation can be expected). 


For a detailed description of the underlying experimental data, the experimental approach, and an explanation of the optical equations, please see the following peer-reviewed journal article:


Al-Juboori et al:

Light scattering properties differ between different areas of the adult mouse brain.

PlosONE, publication e67626, published July 9, 2013.


Download Manuscript


This manuscript is open access (i.e. can be downloaded free of charge through the link shown above).




How do I get the Optogenetics APP?

 The application is currently available for iOS and Android. 


iOS: Compatible with iPhones, iPads, and certain iPods.:

Download Optogenetics (the demo version) from iTunes

Download Optogenetics Pro (the full version) from iTunes 


Popneuron Limited

3000 Lawrence Street

Suite 50

Denver, CO 80205