Feature extraction code for analysis in Gouwens, Sorensen, et al. - Cell, 2020

[gonzalobenegas]

It would be helpful to have access to the code used to extract electrophysiological features for the analysis in the Gouwens, Sorensen, et al. - Cell, 2020 paper. The code availability statement points to the ipfx library but it would be great to have more information about specific scripts, parameters and QC steps.

Additionally, it would be helpful to have direct access to the extracted features besides from the nwb files, similarly to how this portal contains links to both fastqs, bams and gene count matrices.

[tmchartrand]

@gouwens can you help?

[gouwens]

The specific script used is this one: https://github.com/AllenInstitute/ipfx/blob/master/ipfx/bin/run_feature_vector_extraction.py

We run it with basically default parameters - we do use the "LIMS" option because it finds the files and sweep QC information stored in our internal database. We used the lims-passed-except-delta-vm sweep QC option, as well, because some of our earlier Patch-seq experiments used intentionally shortened protocols that did not necessarily have the membrane potential return to zero. But otherwise the sweep QC are as defined in our white paper: http://help.brain-map.org/download/attachments/8323525/CellTypes_Ephys_Overview.pdf?version=2&modificationDate=1508180425883&api=v2

Some extracted electrophysiology features are viewable in the Patch-seq web application: https://knowledge.brain-map.org/data/1HEYEW7GMUKWIQW37BO/specimens/list It is not possible to download the features from the web application yet, but that is something that is planned for a future update.

[gonzalobenegas]

Thanks, this answers my questions!