Hi, I have a question about the y/z value of the electrodes in the Allen neuropixel dataset; Do they show the depth with respect to the pia? What does positive and negative values mean? I want to find the layer of each cortical recordings. I have checked many sessions but couldn’t find the CCF coordinates to directly extract the layer information. Could you please help me? Thanks, Maryam
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Hi Maryam – the x/y/z values in the electrodes table represent the coordinates of each recording site within the Allen CCF volume. Negative values represent electrodes that are outside this volume (e.g. sticking out above the brain).
However, there is a big caveat that the Y values were accidentally duplicated in the Z column. So if you want the actual 3D CCF coordinates you’ll need to access those via the AllenSDK. See this thread for more info: Neuropixels data - Electrode (X,Y,Z)
The good news is that once you have those coordinates, it’s straightforward to extract cortical layer info for each electrode. This discussion has instructions for how to accomplish that: Cortical Layers using CCFv3 in Neuropixels data - #4 by joshs