Abstract The recent development of optogenetic tools, to manipulate neuronal activity using light, provides opportunities for novel brain-machine interface (BMI) control systems for treating neurological conditions. An issue of critical importance, therefore, is how well light penetrates through brain tissue. We took two different approaches to estimate light penetration through rodent brain tissue. The first employed so-called “nucleated patches” from cells expressing the light-activated membrane channel, channelrhodopsin (ChR2). By recording light-activated currents, we used these nucleated patches as extremely sensitive, microscopic, biological light-meters, to measure light penetration through 300-700µm thick slices of rodent neocortical tissue. The nucleated patch method indicates that the effective illumination drops off with increasing tissue thickness, corresponding to a space constant of 317µm (95% confidence interval between 248-441µm). We compared this with measurements taken from directly visualizing the illumination of brain tissue, orthogonal to the direction of the light. This yielded a contour map of reduced illumination with distance, which along the direction of light delivery, had a space constant, τ 453µm. This yields a lower extinction coefficient, µ e (the reciprocal of τ , ∼3mm -1 ) than previous estimates, implying better light penetration from LED sources than these earlier studies suggest.

Characterization of light penetration through brain tissue, for optogenetic stimulation