BossDB Open Neuroimagery Datasets

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

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

fs.listdir("s3://bossdb-open-data")

Description:

This data ecosystem, Brain Observatory Storage Service & Database (BossDB), contains several neuro-imaging datasets across multiple modalities and scales, ranging from nanoscale (electron microscopy), to microscale (cleared lightsheet microscopy and array tomography), and mesoscale (structural and functional magnetic resonance imaging). Additionally, many of the datasets include dense segmentation and meshes.

Contact:

This data ecosystem, Brain Observatory Storage Service & Database (BossDB), contains several neuro-imaging datasets across multiple modalities and scales, ranging from nanoscale (electron microscopy), to microscale (cleared lightsheet microscopy and array tomography), and mesoscale (structural and functional magnetic resonance imaging). Additionally, many of the datasets include dense segmentation and meshes.

Update Frequency:

New datasets are added as soon as it is available. Minor updates on existing datasets occur sporadically.

Managed By:

https://https://jhuapl.edu

Resources:

1. resource:
   • Description: Large 3D volumes of neuroimaging data and image processing products such as segmentation and reconstructed meshes
   • ARN: arn:aws:s3:::bossdb-open-data
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

aws-pds, life sciences, imaging, neuroscience, neuroimaging, electron microscopy, x-ray tomography, x-ray microtomography, x-ray, magnetic resonance imaging, light-sheet microscopy, calcium imaging, volumetric imaging

Tutorials:

1. tutorial:
   • Title: Data access and download
   • URL: https://bossdb.org/get-started
   • AuthorName: Jordan Matelsky
   • AuthorURL: https://github.com/j6k4m8

Tools & Applications:

1. tools & applications:

   • Title: bossDB
   • URL: https://bossdb.org
   • AuthorName: bossDB Team

2. tools & applications:

   • Title: CloudVolume
   • URL: https://github.com/seung-lab/cloud-volume
   • AuthorName: Seung Lab

Publication:

1. publication:

   • Title: intern: Integrated Toolkit for Extensible and Reproducible Neuroscience
   • URL: https://www.biorxiv.org/content/10.1101/2020.05.15.098707v1
   • AuthorName: Jordan K Matelsky, Luis Rodriguez, Daniel Xenes, Timothy Gion, Robert Hider Jr., Brock Wester, William Gray-Roncal
   • AuthorURL: https://bossdb.org/publications

2. publication:

   • Title: The Block Object Storage Service (bossDB): A Cloud-Native Approach for Petascale Neuroscience Discovery
   • URL: https://doi.org/10.1101/217745v2
   • AuthorName: Robert Hider Jr., Dean M. Kleissas, Derek Pryor, Timothy Gion, Luis Rodriguez, Jordan Matelsky, William Gray-Roncal, Brock Wester
   • AuthorURL: https://bossdb.org/publications

3. publication:

   • Title: A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data
   • URL: https://doi.org/10.1038/s41592-018-0181-1
   • AuthorName: J. T. Vogelstein, E. Perlman, B. Falk, A. Baden, W. Gray Roncal, V. Chandrashekhar, F. Collman, S. Seshamani, J. L. Patsolic, K. Lillaney, M. Kazhdan, R. Hider, D. Pryor, J. Matelsky, T. Gion, P. Manavalan, B. Wester, M. Chevillet, E. T. Trautman, K. Khairy, E. Bridgeford, D. M. Kleissas, D. J. Tward, A. K. Crow, B. Hsueh, M. A. Wright, M. I. Miller, S. J. Smith, R. J. Vogelstein, K. Deisseroth, and R. Burns