Sharing neurophysiology data from the Allen Brain Observatory
- Allen Institute, United States
Figures
Figure 1
Overview of Allen Brain Observatory Visual Coding datasets.
(a) Target brain regions and example visual stimuli. (b) Standardized rigs for two-photon calcium imaging (left) and Neuropixels electrophysiology (right). (c) Example ΔF/F traces or spike rasters for 100 simultaneously recorded neurons from each modality. Both are extracted during one presentation of a 30 s natural movie. (d) Dataset size after different stages of analysis.
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Figure 1—source data 1
Dataset size after each stage of analysis.
- https://cdn.elifesciences.org/articles/85550/elife-85550-fig1-data1-v1.xlsx
Figure 2
Distributing data from Allen Brain Observatory Visual Coding experiments.
Raw data is acquired and processed at the Allen Institute, combined with metadata (including 3-D neuronal coordinates, stimulus information, eye-tracking data, and running speed) and packaged into NWB files. Each such file is intended to be a complete, self-contained data record for one experimental session in one animal. NWB files are uploaded to three different locations in the cloud: The Amazon Web Services (AWS) Registry of Open Data, the Distributed Archives for Neurophysiology Data Integration (DANDI) repository, and the Allen Institute data warehouse (accessed via the AllenSDK, a Python API for searching for relevant sessions and downloading data). Raw data is also uploaded to the AWS Registry of Open Data. End users can either analyze data in the cloud or download data for local analysis.
Figure 3
Data reuse over time.
Cumulative number of papers or preprints that include novel analysis of Allen Brain Observatory Visual Coding surveys. Triangles indicate the years in which new data was made publicly available. Paper icons indicate the years in which the Allen Institute preprints describing the dataset contents and initial scientific findings were posted.
Additional files
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MDAR checklist
- https://cdn.elifesciences.org/articles/85550/elife-85550-mdarchecklist1-v1.docx
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Source data 1
List of publications using Allen Brain Observatory Visual Coding data as of 2022.
- https://cdn.elifesciences.org/articles/85550/elife-85550-data1-v1.xlsx
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Sharing neurophysiology data from the Allen Brain Observatory
eLife 12:e85550.
https://doi.org/10.7554/eLife.85550
