Open NeuroData

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

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

fs.listdir("s3://open-neurodata")

Description:

This bucket contains multiple neuroimaging datasets (as Neuroglancer Precomputed Volumes) 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 segmentations and meshes.

Contact:

This bucket contains multiple neuroimaging datasets (as Neuroglancer Precomputed Volumes) 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 segmentations and meshes.

Update Frequency:

The dataset may be updated with additional or corrected data on a need-to-update basis.

Managed By:

https://neurodata.io/ocp

Resources:

1. resource:
   • Description: Neuroglancer precomputed volumes in a public bucket
   • ARN: arn:aws:s3:::open-neurodata
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

aws-pds, biology, image processing, neuroimaging, neuroscience, electron microscopy, life sciences, light-sheet microscopy, magnetic resonance imaging, array tomography

Tutorials:

1. tutorial:

   • Title: Download
   • URL: https://neurodata.io/help/download/
   • AuthorName: Benjamin Falk
   • AuthorURL: https://github.com/falkben

2. tutorial:

   • Title: Visualization using Neuroglancer
   • URL: https://neurodata.io/help/visualization/
   • AuthorName: Benjamin Falk
   • AuthorURL: https://github.com/falkben

Tools & Applications:

1. tools & applications:

   • Title: Neuroglancer
   • URL: https://github.com/google/neuroglancer
   • AuthorName: Jeremy Maitin-Shepard
   • AuthorURL: https://github.com/jbms

2. tools & applications:

   • Title: Igneous
   • URL: https://github.com/seung-lab/igneous
   • AuthorName: William Silversmith
   • AuthorURL: https://github.com/william-silversmith

3. tools & applications:

   • Title: CloudVolume
   • URL: https://github.com/seung-lab/cloud-volume
   • AuthorName: William Silversmith
   • AuthorURL: https://github.com/william-silversmith

Publication:

1. publication:

   • Title: A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data
   • URL: https://www.nature.com/articles/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
   • AuthorURL: None

2. publication:

   • Title: To the Cloud! A Grassroots Proposal to Accelerate Brain Science Discovery
   • URL: https://doi.org/10.1016/j.neuron.2016.10.033
   • AuthorName: J. T. Vogelstein, B. Mensh, M. Häusser, N. Spruston, A. C. Evans, K. Kording, K. Amunts, C. Ebell, J. Muller, M. Telefont, S. Hill, S. P. Koushika, C. Calì, P. A. Valdés-Sosa, P. B. Littlewood, C. Koch, S. Saalfeld, A. Kepecs, H. Peng, Y. O. Halchenko, G. Kiar, M. M. Poo, J. B. Poline, M. P. Milham, A. P. Schaffer, R. Gidron, H. Okano, V. D. Calhoun, M. Chun, D. M. Kleissas, R. J. Vogelstein, E. Perlman, R. Burns, R. Huganir, and M. I. Miller
   • AuthorURL: None

3. publication:

   • Title: From cosmos to connectomes: The evolution of data-intensive science
   • URL: https://doi.org/10.1016/j.neuron.2014.08.045
   • AuthorName: R. Burns, J. T. Vogelstein, and A. S. Szalay
   • AuthorURL: None

4. publication:

   • Title: The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience
   • URL: https://arxiv.org/abs/1306.3543
   • AuthorName: R. Burns, W. G. Roncal, D. Kleissas, K. Lillaney, P. Manavalan, E. Perlman, D. R. Berger, D. D. Bock, K. Chung, L. Grosenick, N. Kasthuri, N. C. Weiler, K. Deisseroth, M. Kazhdan, J. Lichtman, R. C. Reid, S. J. Smith, A. S. Szalay, J. T. Vogelstein, and R. J. Vogelstein.
   • AuthorURL: None