allen-cell-imaging-collections.yaml

Name: Allen Cell Imaging Collections
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.
Documentation: https://open.quiltdata.com/b/allencell
Contact: jacksonb@alleninstitute.org
ManagedBy: "[Allen Institute for Cell Science](https://www.allencell.org)"
UpdateFrequency: Biweekly
Tags:
  - biology
  - cell imaging
  - microscopy
  - image processing
  - machine learning
License: https://www.allencell.org/terms-of-use.html
Resources:
  - Description: Data files in a public bucket
    ARN: arn:aws:s3:::allencell
    Region: us-east-1
    Type: S3 Bucket
DataAtWork:
  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/
    - 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/
    - 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/
    - 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/
    - 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/
    - 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/
    - 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/
  Tutorials:
    - 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/
    - 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/
  Publications:
    - 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/