Optogenetics is a tool which aids an investigator in calculating 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, once it exits the optical fiber. To estimate the amount of light required for a given experimental design, knowledge about the specific scattering properties of the brain region of choice, the specific opsin to be used, and the properties of the optical fiber are required. Once a user inputs these parameters into the APP, it calculates the maximal depth at which excitation of the opsin can be expected. 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.
Version 2 supports 17 different opsins and a complete light scattering brain atlas for the adult mouse that allows a user to look up the brain area of his/her choice, and read the specific scattering coefficient for this particular area.
For the scientific basis of this calculator, please see Al-Juboori, Dondzillo, Stubblefield, Felsen, Lei, and Klug: Light scattering properties vary across different regions of the adult mouse brain. PlosONE, in press.
For a user manual and additional information, please see www.optogeneticsapp.com.
A Pro and a Lite version are available. The two versions are identical with the exception that the Pro version includes a complete brain atlas consisting of 43 images / plates, while the atlas Lite version only has 5 plates.