Light Penetrance in Different Brain Regions

This post explains a further addition to my depth calculator. In this update, I’ve added options to predict optogenetics stimulation depth in different brain regions. I’ve mentioned before about the irrelevance of visible light wavelength compared to the density of brain matter, when calculating depth of light penetrance.

Light scattering measurements

Anyway, I went back to an early paper calculating light scattering in different types of brain tissue (Figure 1)¹. As you can see, absorption of light is irrelevant compared to scattering (note the logarithmic scale). Also, the scattering doesn’t change much across visible wavelengths for grey matter, and not at all for white matter.

So what I’ve done is to take the following estimates for scattering values for each type of brain region:

• Grey matter (blue light): 11.2 (taken from Aravanis et al.²)
• Grey matter (red light): 9
• Thalamus (intermediate scattering): 20
• White matter: 40

Predicting light penetrance

I’ve then plotted the light penetrance using the calculations from Aravanis et al. (also used by Karl Diesseroth) with these different scattering coefficients (Figure 2). Note the logarithmic scale. As I mentioned, shifting to red light makes very little difference to the light penetrance compared with changing the density of brain matter.

In order to make the light scattering relevant to optogenetics stimulation depth for in vivo experiments, I have updated my optogenetics depth calculator to include scattering in different types of brain tissue. Using the new calculator, I have predicted the following effective depths in different brain tissue using my standard parameters:

• Grey matter: 1.57 mm
• Intermediate: 1.24 mm
• White matter: 0.92 mm

As you can see, changing the scattering level of the tissue has a dramatic effect on the effectiveness of your in vivo optogenetic stimulation depth. My suggestion for experiment planning is to use the “intermediate” value as default, and pick one of the others if you have a good idea of your target brain regions.

For example, if you’re working in the cortex, which is heavily “grey”, pick the low scattering value. On the other hand, if you are targeting the brain stem, which is densely “white”, pick the high scattering value. If you want a more accurate predictor of light spread, you need to do more complex modelling.

1. Yaroslavsky et al. Phys Med Biol 47, 2059 (2002) Optical properties of selected native and coagulated human brain tissues in vitro in the visible and near infrared spectral range

2. Aravanis et al. J Neural Eng 4, S143-S156 (2007) An optical neural interface: in vivo control of rodent motor cortex with integrated fiberoptic and optogenetic technology