Allen Mouse Brain Atlas

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

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

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

Description:

The Allen Mouse Brain Atlas is a genome-scale collection of cellular resolution gene expression profiles using in situ hybridization (ISH). Highly methodical data production methods and comprehensive anatomical coverage via dense, uniformly spaced sampling facilitate data consistency and comparability across >20,000 genes. The use of an inbred mouse strain with minimal animal-to-animal variance allows one to treat the brain essentially as a complex but highly reproducible three-dimensional tissue array. The entire Allen Mouse Brain Atlas dataset and associated tools are available through an unrestricted web-based viewing application (http://mouse.brain-map.org). The collection of > 650,000 images have been made available in this Open Data bucket to enable efficient access and analysis of the this dataset.

Contact:

The Allen Mouse Brain Atlas is a genome-scale collection of cellular resolution gene expression profiles using in situ hybridization (ISH). Highly methodical data production methods and comprehensive anatomical coverage via dense, uniformly spaced sampling facilitate data consistency and comparability across >20,000 genes. The use of an inbred mouse strain with minimal animal-to-animal variance allows one to treat the brain essentially as a complex but highly reproducible three-dimensional tissue array. The entire Allen Mouse Brain Atlas dataset and associated tools are available through an unrestricted web-based viewing application (http://mouse.brain-map.org). The collection of > 650,000 images have been made available in this Open Data bucket to enable efficient access and analysis of the this dataset.

Update Frequency:

Never

Managed By:

http://www.alleninstitute.org/

Resources:

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

Tags:

aws-pds, biology, genetic, gene expression, imaging, neurobiology, image processing, life sciences, transcriptomics, Mus musculus

Tutorials:

1. tutorial:
   • Title: Accessing Allen Mouse Brain Atlas data
   • URL: https://github.com/AllenInstitute/open_dataset_tools/blob/main/example_notebooks/Accessing_Allen_Mouse_Brain_Atlas_Data.ipynb
   • AuthorName: Allen Institute for Brain Science
   • AuthorURL: www.alleninstitute.org

Tools & Applications:

1. tools & applications:
   • Title: Allen Mouse Brain Atlas
   • URL: https://mouse.brain-map.org
   • AuthorName: Allen Institute for Brain Science
   • AuthorURL: www.alleninstitute.org

Publication:

1. publication:
   • Title: Genome-wide atlas of gene expression in the adult mouse brain
   • URL: http://www.nature.com/articles/nature05453
   • AuthorName: Ed Lein, et al.
   • AuthorURL: www.alleninstitute.org