The Optogenetics APP
What is the Optogenetics APP?
The Optogenetics APP is a tool which aids an investigator in calculating the required optical power for 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 very different optical properties, which determine how light scatters and distributes, once it exits the optical fiber. To accurately determine the amount of light required for a given experimental design, knowledge about the specific scattering properties of the brain region, the wavelength of the light and specific opsin to be used, as well as the properties of the optical fiber are required. Once a user inputs these parameters, the app calculates the maximal depth at which effective excitation of the opsin can be achieved. The penetration depth is plotted as a function of optical power (mW), such that a user can see how light scatters in the brain tissue under the specific circumstances.
This first release includes a number of input parameters, as well the two most popular opsins, Channelrhodopsin and Halorhodopsin (1st generation). Scattering coefficients for eight different regions of the adult mouse brain are included, and the calculator assumes that blue light (453 nm) is used.
Future releases will include additional opsins, additional wavelengths, and a brain atlas that includes scattering coefficients for any brain region of the adult mouse brain.
For the scientific basis of this calculator as well as additional information, please see:
Saif Al-Juboori, Anna Dondzillo, Elizabeth Stubblefield, Gidon Felsen, Achim Klug and Tim Lei:
Light scattering properties differ between different areas of the adult mouse brain. Under review.
How do I get the Optogenetics APP?
The application is currently available for iOS only. It is compatible with iPhones, iPads, and certain iPods.
Versions for Android and web browsers will be coming shortly!