Allen Cell Imaging Collections

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/allen-cell-imaging-collections-dataset")

fs.listdir("s3://allencell")

Description:

This bucket contains multiple datasets (as Quilt packages) created by the Allen Institute for Cell Science (AICS). The imaging data in this bucket contains either of the following:

1. field of view images from glass plates
2. cell membrane, DNA, and structure segmentations
3. cell membrane, DNA and structure contours
4. machine learning imaging predictions of the previously listed modalities.

In addition, many of the datasets include CSVs that contain feature sets related to that data.

Contact:

This bucket contains multiple datasets (as Quilt packages) created by the Allen Institute for Cell Science (AICS). The imaging data in this bucket contains either of the following:

1. field of view images from glass plates
2. cell membrane, DNA, and structure segmentations
3. cell membrane, DNA and structure contours
4. machine learning imaging predictions of the previously listed modalities.

In addition, many of the datasets include CSVs that contain feature sets related to that data.

Update Frequency:

Biweekly

Managed By:

https://www.allencell.org

Resources:

1. resource:
   • Description: Data files in a public bucket
   • ARN: arn:aws:s3:::allencell
   • Region: us-east-1
   • Type: S3 Bucket

Tags:

aws-pds, life sciences, biology, cell imaging, cell biology, microscopy, image processing, machine learning, Homo sapiens

Tutorials:

1. tutorial:

   • Title: Download and train label-free models
   • URL: https://github.com/AllenCellModeling/pytorch_fnet/blob/master/examples/download_and_train.py
   • AuthorName: Greg Johnson
   • AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/staff-profiles/greg-johnson/

2. tutorial:

   • Title: Integrating single-cell sequencing and nuclear imaging data
   • URL: https://drive.google.com/file/d/1nuiYOurmbic7rZeHPen_M3fDbsN7n5Ws/view?usp=sharing
   • AuthorName: Chengxiang Qiu and William Noble
   • AuthorURL: https://noble.gs.washington.edu/

Tools & Applications:

1. tools & applications:

   • Title: Allen Cell Feature Explorer
   • URL: https://cfe.allencell.org/
   • AuthorName: Allen Institute for Cell Science
   • AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/

2. tools & applications:

   • Title: Allen Cell Structure Segmenter
   • URL: https://www.allencell.org/segmenter.html
   • AuthorName: Jianxu Chen, Liya Ding, Matheus P. Viana, Melissa C. Hendershott, Ruian Yang, Irina A. Mueller, Susanne M. Rafelski
   • AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/

3. tools & applications:

   • Title: Pytorch 3D Integrated Cell
   • URL: github.com/AllenCellModeling/pytorch_integrated_cell
   • AuthorName: Gregory R. Johnson, Rory M. Donovan-Maiye, Mary M. Maleckar
   • AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/

4. tools & applications:

   • Title: AICS Volume Viewer
   • URL: https://github.com/AllenInstitute/volume-viewer
   • AuthorName: Dan Toloudis
   • AuthorURL: https://alleninstitute.org/what-we-do/cell-science/about/team/staff-profiles/daniel-toloudis/

5. tools & applications:

   • Title: Visual Guide to Human Cells
   • URL: https://www.allencell.org/visual-guide-to-human-cells.html
   • AuthorName: Allen Institute for Cell Science
   • AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/

6. tools & applications:

   • Title: AICSImageIO
   • URL: https://github.com/AllenCellModeling/aicsimageio
   • AuthorName: Matthew Bowden, Jackson Brown, Jamie Sherman, Dan Toloudis
   • AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/

7. tools & applications:

   • Title: Integrated Mitotic Stem Cell
   • URL: https://imsc.allencell.org
   • AuthorName: Allen Institute for Cell Science
   • AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/

Publication:

1. publication:

   • Title: Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy
   • URL: https://www.nature.com/articles/s41592-018-0111-2
   • AuthorName: Chawin Ounkomol, Sharmishtaa Seshamani, Mary M. Maleckar, Forrest Collman & Gregory R. Johnson
   • AuthorURL: https://alleninstitute.org/about/team/

2. publication:

   • Title: Robust integrated intracellular organization of the human iPS cell: where, how much, and how variable?
   • URL: https://www.biorxiv.org/content/10.1101/2020.12.08.415562v1
   • AuthorName: Matheus P. Viana, Jianxu Chen*, Theo A. Knijnenburg*, Ritvik Vasan*, Calysta Yan*... Allen Institute for Cell Science... Graham T. Johnson, Ruwanthi N. Gunawardane, Nathalie Gaudreault, Julie A. Theriot, Susanne M. Rafelski
   • AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/