petersaj
commented
1 year ago Hi Ela - this happens in a few places in the CCF: there are some places that only have a parent label, presumably because there was ambiguity in how that region should be labeled, I'm not sure if it's documented. For example, here's a slice with red showing areas that are just labeled "thalamus":
Whether to exclude them I guess depends on your analysis and whether you've got other electrophysiological landmarks or signatures to use for assigning regions.
If you're picking up spikes in fiber tracts, do the waveforms look axonal (e.g. upward-going, like Fig S2B in this paper https://www.sciencedirect.com/science/article/pii/S0896627314003614#app2)? If not, seems more likely that the probe isn't actually in the fiber bundle in that spot.
Hey Andy, our lab has been using your code for a few months now. I discovered that sometimes my units are assigned to "fiber tracts", "thalamus", and "root". I have read about the way Allen Institute 3d brain is organized. It looks like these are "parent structures". For example, "root" is a bigger name for: gray matter, fiber tracts, and ventricular systems. My guess is that parent names have their position somewhere in the 3d atlas. And if my probe "hits" this spot, units will be called as a parent structure. Have you noticed that? In your opinion, should they be excluded from the analysis? Also, I don't know if neurons in gray matter and fiber tracts behave the same way as in "normal" brain structures and if they can be sorted confidently using kilosort. I'd appreciate your advice. Kind regards, Ela