Cell Organelle Segmentation in Electron Microscopy (COSEM) on AWS

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

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

fs.listdir("s3://janelia-cosem-datasets")

Description:

High resolution images of subcellular structures.

Contact:

High resolution images of subcellular structures.

Update Frequency:

New datasets and derived data are added as soon as they are available.

Managed By:

https://www.janelia.org/

Resources:

1. resource:

   • Description: Raw FIB-SEM datasets and derived data.
   • ARN: arn:aws:s3:::janelia-cosem-datasets
   • Region: us-east-1
   • Type: S3 Bucket

2. resource:

   • Description: Machine learning models for organelle prediction.
   • ARN: arn:aws:s3:::janelia-cosem-networks
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

aws-pds, cell biology, computer vision, electron microscopy, life sciences, imaging, organelle

Publication:

1. publication:

   • Title: Enhanced FIB-SEM systems for large-volume 3D imaging
   • URL: https://elifesciences.org/articles/25916
   • AuthorName: C. Shan Xu, Kenneth J. Hayworth, Zhiyuan Lu, Patricia Grob, Ahmed M. Hassan, José G. García-Cerdán, Krishna K. Niyogi, Eva Nogales, Richard J. Weinberg, Harald F. Hess.

2. publication:

   • Title: Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells.
   • URL: https://science.sciencemag.org/content/367/6475/eaaz5357
   • AuthorName: David P. Hoffman, Gleb Shtengel, C. Shan Xu, Kirby R. Campbell, Melanie Freeman, Lei Wang, Daniel E. Milkie, H. Amalia Pasolli, Nirmala Iyer, John A. Bogovic, Daniel R. Stabley, Abbas Shirinifard, Song Pang, David Peale, Kathy Schaefer, Wim Pomp, Chi-Lun Chang, Jennifer Lippincott-Schwartz, Tom Kirchhausen1, David J. Solecki, Eric Betzig, Harald F. Hess

3. publication:

   • Title: Whole-cell organelle segmentation in volume electron microscopy
   • URL: https://www.nature.com/articles/s41586-021-03977-3
   • AuthorName: Lisa Heinrich, Davis Bennett, David Ackerman, Woohyun Park, Jon Bogovic, Nils Eckstein, et al.