AllenInstitute / AllenSDK

code for reading and processing Allen Institute for Brain Science data
https://allensdk.readthedocs.io/en/latest/
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Request (Allen Brain Observatory Data): Access to ophys metadata as csv files #2694

Open ehennestad opened 1 year ago

ehennestad commented 1 year ago

The ecephys metadata for the ABO Visual Coding Dataset in the S3 bucket are available as CSV files (i.e sessions.csv, probes.csv), whereas the ophys metadata is available as json (i.e ophys_experiments.json, cell_specimens.json).

As far as I can see, all of these files contain tabular data, and my request would be to also provide the ophys metadata as csv files.

The reason is the following: The json files are large files (especially the cell_specimens.json at ~460 MB), mostly because all the column names are repeated for each row, and the number of rows are large. Additionally, parsing such a large json file takes a while. Having these files available as csv files would speed up both download and parsing/conversion to tabular data for users interested in working with these metadata.