Allen Brain Observatory - Visual Coding AWS Public Data Set

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/allen-brain-observatory-dataset")

fs.listdir("s3://allen-brain-observatory")

Description:

The Allen Brain Observatory – Visual Coding is a large-scale, standardized survey of physiological activity across the mouse visual cortex, hippocampus, and thalamus. It includes datasets collected with both two-photon imaging and Neuropixels probes, two complementary techniques for measuring the activity of neurons in vivo. The two-photon imaging dataset features visually evoked calcium responses from GCaMP6-expressing neurons in a range of cortical layers, visual areas, and Cre lines. The Neuropixels dataset features spiking activity from distributed cortical and subcortical brain regions, collected under analogous conditions to the two-photon imaging experiments. We hope that experimentalists and modelers will use these comprehensive, open datasets as a testbed for theories of visual information processing.

Contact:

The Allen Brain Observatory – Visual Coding is a large-scale, standardized survey of physiological activity across the mouse visual cortex, hippocampus, and thalamus. It includes datasets collected with both two-photon imaging and Neuropixels probes, two complementary techniques for measuring the activity of neurons in vivo. The two-photon imaging dataset features visually evoked calcium responses from GCaMP6-expressing neurons in a range of cortical layers, visual areas, and Cre lines. The Neuropixels dataset features spiking activity from distributed cortical and subcortical brain regions, collected under analogous conditions to the two-photon imaging experiments. We hope that experimentalists and modelers will use these comprehensive, open datasets as a testbed for theories of visual information processing.

Update Frequency:

Annually

Managed By:

http://www.alleninstitute.org/

Resources:

1. resource:

   • Description: Project data files in a public bucket
   • ARN: arn:aws:s3:::allen-brain-observatory
   • Region: us-west-2
   • Type: S3 Bucket

2. resource:

   • Description: SageMaker launch template with s3fs bucket mounts
   • ARN: arn:aws:s3:::allen-brain-observatory-templates
   • Region: us-west-2
   • Type: S3 Bucket

Tags:

aws-pds, neurobiology, neuroimaging, image processing, imaging, life sciences, signal processing, electrophysiology, Mus musculus

Tutorials:

1. tutorial:
   • Title: Use the Allen Brain Observatory – Visual Coding on AWS
   • URL: https://github.com/AllenInstitute/AllenSDK/wiki/Use-the-Allen-Brain-Observatory-%E2%80%93-Visual-Coding-on-AWS
   • AuthorName: Nika Keller, David Feng
   • AuthorURL: https://twitter.com/AllenInstitute