Invalid_times missing in Neuropixel Visual coding dataset


There seems to be invalid_times not annotated in session 787025148 of the Neuropixel Visual coding dataset, they look like “Gain fluctuations” as described in the white paper, see event 1 and 2 in the following video. You can see the timing of the events in the box up right.

Screen Recording 2021-11-26 at 17.54.36

PS: There are more of these events in this session.


Hi Roberto,

Thanks for reporting this.

This appears to be a different phenomenon than the “gain fluctuations” for two reasons:

  1. This dataset was collected with a different recording system (Neuropixels 3a) than the one that showed the gain fluctuations (Neuropixels 1.0).

  2. Except for one very large event around 3590 s, these artifacts appear to only impact the LFP band. During the gain fluctuations, the AP band gain would temporarily drop to zero, and no spikes would be detected during that interval.

I’m not entirely sure what’s causing the artifacts in this session, but my best guess would be that there is some movement artifact or static discharge that is saturating the LFP band, but not the AP band.

For now, you can set an amplitude threshold to detect these events and exclude the corresponding intervals from analysis. We will work on a systematic way of detecting them across the entire dataset.

Also, please let us know if you find them in any other sessions.


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I found another puzzling thing in session 799864342.
print("regions recorded: ", session.metadata["structure_acronyms"])
regions recorded: ['VISam', nan, 'COAa', 'CA1', 'LP', 'DG', 'VISmma', 'VISp', 'ProS', 'SUB', 'CA3', 'CA2', 'VISl', 'VISal', 'LGd', 'VISrl', 'APN', 'POL']
however COAa is incredibly deep in the brain… and actually when I plot that section of the probe it resides far outside the brain.

This is a result of negative CCF coordinates wrapping around to the bottom of the brain. The units in COAa are artifacts and should be ignored.

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