Quality metrics in Allen neuropixels publications

Hi there,

I’m interested in how the Allen uses quality metrics to select neurons in its publications. In Siegle et al., 2021, it says " Note that we do not use the default AllenSDK filters in this work, but instead use a receptive field P value of 0.01 as the primary metric for selecting units for analysis.". I assume that this means that the QC metrics are not used.

The Allen sdk offers hardcoded thresholds on three metrics; isi_violations < 0.5; amplitude_cutoff < 0.1; presence_ratio > 0.9. Are there any publications from the Allen that use hardcoded thresholds to select for neurons?


Here’s an example of a publication that used the default thresholds for each of those metrics: Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology | eLife

You’re correct that these filters were not applied in the 2021 Nature paper.