Distribution of CCF-dorsal-ventral coordinates for VISp units

Technical
1

Hi everyone, I’m currently analyzing some spiking data from the Allen Neuropixels dataset and would like to cross-reference with the depth of each unit, provided as the dorsal-ventral (DV) coordinate registered to the CCF, if I understand correctly.

However, looking at the distribution of DV-coordinates for units labelled as V1/“VISp”, it starts at around 600 μm, while I would have expected it to start at 50-100 μm (or even closer to 0 μm) for units close to the surface. Am I misunderstanding something about the way the CCF system works? Is there some reference value for each session that I have to re-register to?

(The range of DV-coordinates goes from 600 μm to 1800 μm, so that seems reasonable, assuming a cortical thickness of 1000 μm and a non-perpendicular insertion angle.)

Thank you very much for your help!

2

Hi there! The DV coordinates are relative to the top of the CCF volume (which surrounds the whole brain), not the surface of cortex. While many studies report “depth” of units along the axis of probe insertion, in this case we are mapping all units to a global reference frame which has its origin slightly above the brain.

3

Ah, I understand - so to get a crude measure of unit depth (ignoring the fact that the brain surface is not flat), I’d have to at least get the DV coordinate of the brain surface at a given ML-AP coordinate of a unit. But, of course, taking the depth along the perpendicular of a tangent to the brain surface would be much more accurate anyway. Thank you very much!