Hello is there a notebook somewhere that can be used to make a figure showing the trajectory of probes through the brain for the visual behaviour neuropixels dataset?
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This notebook shows an example of how to plot probe trajectories for the Visual Coding Neuropixels dataset, but it should work for Visual Behavior as well:
https://allensdk.readthedocs.io/en/latest/_static/examples/nb/ecephys_lfp_analysis.html
Note that the probe tracks are quite straight in the original brains, but they become curved after warping to the CCF.
@joshs That tutorial is not really what I’m looking for. I want to make somethign like this…
Figure 1A from Nitzan, Noam, et al. “Brain-wide interactions during hippocampal sharp wave ripples.” Proceedings of the National Academy of Sciences 119.20 (2022): e2200931119.
I guess you could use cell 9 from the tutorial you posted to get the images to the left of the brain, but how could I plot a mouse brain with a region highlighted and color coded coordinates? Are there any packages from the ABI that allow you to render mouse brains for figures like that?
Do you think it’s possible to remap the ccf of the channels to layers of CA1 like the striatum radiatum or the pyramidal layer? How accurate would that be? I have a way of getting cortical layer out using the 10um Allen Mouse Brain Map, but it doesn’t label the CA1 layers.
Currently I identify pyramidal layers by looking for the channels in CA1 with the highest high frequency power (150-250hz) on a probe. It seems to correspond to the channels with high numbers of units on them, I tried using that as a way as well but some probes have so few cells on them its hard to use that as a way of identifying the pyramidal layer.
Those figures were made using brainrender. You’ll have to check out their docs page for more info on how to insert probes (or cell locations) into the scene.
For mapping cells to the layers of CA1, I would recommend looking at features of the LFP (such as relative theta phase) that indicate depth within that structure. If there are probes with very few cells in hippocampus it probably means that they are mostly going through white matter tracts. In that case it will be difficult to map them to specific CA1 layers.
Ah ok so I should be checking the number of cells per probe across each recording as well.
Yeah, each probe takes a slightly different trajectory through hippocampus, and there will likely be some that do not pass through the pyramidal layer at all.
CA1 seems to have very few clusters in general though so sometimes its hard to judge. Ifigured it’s because of the sparse firing of those clusters. Still though I will check that before loading probes.