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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/
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