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Julie-Fabre / bombcell

Automated quality control, curation and neuron classification of spike-sorted electrophysiology data
GNU General Public License v3.0
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Depth relative to probe tip? #79

Closed smattia closed 7 months ago

smattia commented 7 months ago

Hi Julie, bombcell is great! One question - I have been interpreting depth values from 4-shank NP2.0 probes and kilosort (v2.5) as probe tip = 0 (b/c when I record from the bottom of a 4-shank I get depth values from 0-~750 but when recording from an entire shank I get values up to ~2800). I believe the depth values bombcell are the same - so, when you plot the depth in the GUI - does 0 at the top of the plot represent the tip of the probe and depth (increasing downwards) represents further along the probe (but less depth in terms of brain)? Thanks!

Julie-Fabre commented 7 months ago

Hi Stefan,

Thanks for your message!

Bombcell loads the channel positions from kilosort and doesn't reverse the depth-ordering, which means 0 is the top of the probe. The reason we're using the default kilosort ordering is because it's less error-prone when there are many different types of probes (including non-Neuropixels) that can be used.

This was not clear enough, thanks for bringing it up. I'm adding this in the documentation to make it clearer, and changing that GUI plot label.

Cheers, Julie