Cortical Layers using CCFv3 in Neuropixels data


I have a quick question about the Neuropixels dataset. I was thinking of analyzing some layer-specific things in the Neuropixels data (especially in layer 6b). The units are only labelled with a cortical region, but no layer - in order to assign them a layer I’ve used the ccfv3 coordinates of the units where available and the annotation matrix with reference space key ‘annotation/ccf_2017’.
This works fine and is very easy, however I’ve noticed that some units then end up in another (adjacent) cortical area than they were originally prescribed to (i.e. their original ‘ecephys_structure_acronym’). This just made me wonder: how trustworthy is this method? Has anyone tried this before (I haven’t found anything that similar in the forum…)? Is it possible to extract the layer information of these units?
I’m happy to post any code.

Thank you for any help!!


Jean-Philippe Dufour

Hi Jean-Philippe,

Glad you were able to figure out the layer assignments! This is the same method we used to assign layers in Siegle, Jia et al. (2021) Nature.

The reason for the discrepancy in the area labels is that the cortical area determined from our retinotopic mapping procedure takes precedence over the area extracted from the CCF coordinates. Because the precise cortical area boundaries can vary from mouse to mouse, we register the probe insertion image to each mouse’s individual cortical surface map in order to recover the actual area that was recorded. If the exact area of origin is ambiguous, the cells are labeled VIS. We chose to call the area label the ecephys_structure_acronym in order to indicate that it may differ from the expected structure acronym at a particular location in the CCF.