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allen-cell-imaging-collections.yaml
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allen-cell-imaging-collections.yaml
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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. The types of data included in this bucket are listed below:
1) Field of view or cropped images of cells
2) Segmentations of structures in the images (e.g., boundaries of cells, DNA, other intracellular structures, etc.)
3) Processed versions of the above images and segmentations
4) Machine learning predictions and labels of the data listed above
5) Models trained on the previously listed data
6) Additional supporting non-image data related to the above listed data types (e.g., gene expression data, whole genome sequencing data, features derived from the images or model predictions, metadata)
7) Simulation, analysis, and visualization data of in silico cell structures, cells, and cell populations
External funding:
The generation of some datasets was supported by the National Human Genome Research Institute of the National Institutes under Award Number UM1HG011593. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Documentation: https://open.quiltdata.com/b/allencell
Contact: [email protected]
ManagedBy: "[Allen Institute for Cell Science](https://www.allencell.org)"
UpdateFrequency: Biweekly
Tags:
- aws-pds
- life sciences
- biology
- cell imaging
- cell biology
- microscopy
- image processing
- machine learning
- Homo sapiens
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: Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories
URL: https://doi.org/10.1101/2024.06.28.601071
AuthorName: Julie C. Dixon*, Christopher L. Frick*, Chantelle L. Leveille*, Philip Garrison, Peyton A. Lee, Saurabh S. Mogre, Benjamin Morris, Nivedita Nivedita, Ritvik Vasan, Jianxu Chen, Cameron L. Fraser, Clare R. Gamlin, Leigh K. Harris, Melissa C. Hendershott, Graham T. Johnson, Kyle N. Klein, Sandra A. Oluoch, Derek J. Thirstrup, M. Filip Sluzewski, Lyndsay Wilhelm, Ruian Yang, Daniel M. Toloudis, Matheus P. Viana, Julie A. Theriot & Susanne M. Rafelski
AuthorURL: https://alleninstitute.org/about/team/
- Title: Interpretable representation learning for 3D multi-piece intracellular structures using point clouds
URL: https://doi.org/10.1101/2024.07.25.605164
AuthorName: Ritvik Vasan, Alexandra J. Ferrante, Antoine Borensztejn, Christopher L. Frick, Nathalie Gaudreault, Saurabh S. Mogre, Benjamin Morris, Guilherme G. Pires, Susanne M. Rafelski, Julie A. Theriot & Matheus P. Viana
AuthorURL: https://alleninstitute.org/about/team/
- Title: 4D hybrid model interrogates agent-level rules and parameters driving hiPS cell colony dynamics
URL: https://doi.org/10.1101/2024.08.12.607546
AuthorName: Jessica S. Yu, Blair Lyons, Susanne Rafelski, Julie A. Theriot, Neda Bagheri & Graham T. Johnson
AuthorURL: https://alleninstitute.org/about/team/
- Title: A human induced pluripotent stem (hiPS) cell model for the holistic study of epithelial to mesenchymal transitions (EMTs)
URL: https://doi.org/10.1101/2024.08.16.608353
AuthorName: Caroline Hookway*, Antoine Borensztejn*, Leigh K. Harris*, Sara Carlson, Gokhan Dalgin, Suraj Mishra, Nivedita Nivedita, Ellen M. Adams, Tiffany Barszczewski, Julie C. Dixon, Jacqueline H. Edmonds, Erik A. Ehlers, Alexandra J. Ferrante, Margaret A. Fuqua, Philip Garrison, Janani Gopalan, Benjamin W. Gregor, Maxwell J. Hedayati, Kyle N. Klein, Chantelle L. Leveille, Sean L. Meharry, Haley S. Morris, Gouthamrajan Nadarajan, Sandra A. Oluoch, Serge E. Parent, Amber Phan, Brock Roberts, Emmanuel E. Sanchez, M. Filip Sluzewski, Lev S. Snyder, Derek J. Thirstrup, John Paul Thottam, Julia R. Torvi, Gaea Turman, Matheus P. Viana, Lyndsay Wilhelm, Chamari S. Wijesooriya, Jie Yao, Julie A. Theriot, Susanne M. Rafelski & Ruwanthi N. Gunawardane
AuthorURL: https://alleninstitute.org/about/team/
- Title: Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy
URL: https://doi.org/10.1038/s41592-018-0111-2
AuthorName: Chawin Ounkomol, Sharmishtaa Seshamani, Mary M. Maleckar, Forrest Collman & Gregory R. Johnson
AuthorURL: https://alleninstitute.org/about/team/
- Title: Integrated intracellular organization and its variations in human iPS cells
URL: https://doi.org/10.1038/s41586-022-05563-7
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/
- Title: Automated human induced pluripotent stem cell culture and sample preparation for 3D live-cell microscopy
URL: https://doi.org/10.1038/s41596-023-00912-w
AuthorName: Benjamin W. Gregor*, Mackenzie E. Coston*, Ellen M. Adams, Joy Arakaki, Antoine Borensztejn, Thao P. Do, Margaret A. Fuqua, Amanda Haupt, Melissa C. Hendershott, Winnie Leung, Irina A. Mueller, Aditya Nath, Angelique M. Nelson, Susanne M. Rafelski, Emmanuel E. Sanchez, Madison J. Swain-Bowden, W. Joyce Tang, Derek J. Thirstrup, Winfried Wiegraebe, Brian P. Whitney, Calysta Yan, Ruwanthi N. Gunawardane & Nathalie Gaudreault
AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/
- Title: "Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes"
URL: https://doi.org/10.1016/j.cels.2021.05.001
AuthorName: Kaytlyn A. Gerbin*, Tanya Grancharova*, Rory M. Donovan-Maiye*, Melissa C. Hendershott*, Helen G. Anderson, Jackson M. Brown, Jianxu Chen, Stephanie Q. Dinh, Jamie L. Gehring, Gregory R. Johnson, HyeonWoo Lee, Aditya Nath, Angelique M. Nelson, M. Filip Sluzewski, Matheus P. Viana, Calysta Yan, Rebecca J. Zaunbrecher, Kimberly R. Cordes Metzler, Nathalie Gaudreault, Theo A. Knijnenburg, Susanne M. Rafelski, Julie A. Theriot & Ruwanthi N. Gunawardane
AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/
- Title: A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes
URL: https://doi.org/10.1038/s41598-021-94732-1
AuthorName: Tanya Grancharova*, Kaytlyn A. Gerbin*, Alexander B. Rosenberg, Charles M. Roco, Joy E.Arakaki , Colette M. DeLizo, Stephanie Q. Dinh, Rory M. Donovan-Maiye, Matthew Hirano, Angelique M. Nelson, Joyce Tang, Julie A. Theriot, Calysta Yan, Vilas Menon, Sean P. Palecek, Georg Seelig & Ruwanthi N. Gunawardane
AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/
- Title: A deep generative model of 3D single-cell organization
URL: https://doi.org/10.1371/journal.pcbi.1009155
AuthorName: Rory M. Donovan-Maiye, Jackson M. Brown, Caleb K. Chan, Liya Ding, Calysta Yan, Nathalie Gaudreault, Julie A. Theriot, Mary M. Maleckar, Theo A. Knijnenburg & Gregory R. Johnson
AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/
- Title: Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization
URL: https://doi.org/10.1091/mbc.e17-03-0209
AuthorName: Brock Roberts*, Amanda Haupt*, Andrew Tucker, Tanya Grancharova, Joy Arakaki, Margaret A. Fuqua, Angelique Nelson, Caroline Hookway, Susan A. Ludmann, Irina A. Mueller, Ruian Yang, Rick Horwitz, Susanne M. Rafelski & Ruwanthi N. Gunawardane
AuthorURL: https://www.alleninstitute.org/what-we-do/cell-science/about/team/