ALLEN CELL EXPLORER
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  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Cell Catalog quickview
      3. Cell Shorts (documentaries on labs using our cells)
      4. Support forum
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
      About our hiPS cells
      1. hiPS Cell Structure Overview
      2. Visual Guide to Human Cells
      3. Cell structure observations
      4. Why endogenous tagging?
      5. Differentiation into cardiomyocytes
      6. Genomics
      7. Download cell data (images, genomics, features)
  • Data & Digital Tools
      Online image analysis
      1. Cell Feature Explorer (plotting & 3D viewer)
      2. 3D cell viewer (pre2018)
      3. Deep cell zoom (216,016 cells)
      Online modeling viewers
      1. Visual Guide to Human Cells
      2. Simularium (4D visual analysis)
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      6. Allen Integrated Cell viewer
      7. Label-free examples viewer
      8. 3D probabilistic model viewer
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Data & code
      1. Download cell data (images, genomics, features)
      2. Code repositories & software
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Overview
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Label-free Determination
      6. └ 3D viewer
      7. 3D Probabilistic Modeling
      8. └ 3D viewer
      9. Visual Guide to Human Cells
      4D biology models
      1. Simularium (online 4D viewer)
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. All journal publications
      2. Preprints (biorxiv, arxiv)
      Posters
      1. Select posters
  • Education
      Education resources
      1. All Resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. Cell Feature Explorer (interactive plotting & 3D viewer)
      4. 3D cell viewer (pre2018 data)
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Digital tool tutorials with videos
      2. Visual Guide tutorial
      3. AGAVE user guide
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
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​ALLEN INSTITUTE FOR CELL SCIENCE

​Allen Cell Explorer

We're hiring scientists & engineers
Available jobs
​Welcome to the Allen Cell Explorer where you can access an unprecedented view into the organizational diversity of human stem cells through open data, tools, cell lines, plasmids, and models developed by the Allen Institute for Cell Science. All our scientific resources are openly available to support the cell biology community and accelerate discovery in human health and disease.

Highlights

New article published in Nature

Integrated intracellular organization and its variations in human iPS cells
Database of 200,000 cell images yields new mathematical framework to understand our cellular building blocks.
Read our story
Read Nature article
Try the Simularium Viewer

New article published in Nature Methods

The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models
The Simularium Viewer makes it easy to share and interrogate interactive 3D visualizations of biological simulation trajectories and related plots directly in a web browser. ​Its primary goal is to facilitate collaborations among experimental and computational biologists by removing major challenges to sharing, accessing, and comparing simulation results.
Nature Methods article
Interview article

Publications

MOST RECENT
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The dawn of interoperating spatial models in cell biology​
Iwasa JH, Lyons B, Johnson GT. Elsevier, December 2022.
Read
FEATURED
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​It’s time to incorporate diversity into our basic science and disease models
Horwitz R, Riley EA, Millan MT, Gunawardane RN. Nature Cell Biology, November 29, 2021.
Read
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A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes
Grancharova T, Gerbin KA, Rosenberg AB, Roco CM, Arakaki JE, DeLizo CM, Dinh SQ, Donovan-Maiye RM, Hirano M, Nelson AM, Tang J, Theriot JA, Yan C, Menon V, Palecek SP, Seelig G, Gunawardane RN. Scientific Reports, August 04, 2021.
Read
Picture
​Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes
Gerbin KA, Grancharova T, Donovan-Maiye RM, Hendershott MC, Anderson HG, Brown JM, Chen J, Dinh SQ, Gehring JL, Johnson GR, , Lee H, Nath A, Nelson AM, Sluzewski MF, Viana MP, Yan C, Zaunbrecher RJ, Cordes Metzler KR, Gaudreault N, Knijnenburg T, Rafelski SM, Theriot JA, Gunawardane RN. Cell Systems, June 16, 2021.
Read
MORE...
​We study the human cell holistically. To understand and predict cell behaviors, we develop and image high quality human induced pluripotent stem (hiPS) cell lines with genome editing to illuminate over 40 key cellular structures. This live cell imaging, together with image analysis, visualization tools and computational models enable novel interpretations of cell behavior by us and researchers around the globe.

Cells & plasmids for your lab

​We have created a series of gene edited human iPSCs that we use as the foundation for our image data, and that we share with the larger scientific community.
Cell Catalog
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Obtain cell lines & plasmids for your lab​; quality control details
Genomics
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​Explore & download genomics & transcriptomics data
Standard operating procedures
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Step-by-step protocols to culture & image gene-edited hiPSCs successfully
Instructional videos
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Instructional videos provided to ensure success in your lab

Featured digital tools

AGAVE 3D desktop image viewer
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View multi-channel images using cinematographic rendering 
Cell Feature Explorer
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Access & interact with our public 3D image datasets & feature measurements online
Allen Cell & Structure Segmenter
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Perform 3D segmentations of intracellular structures
Data & code
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Access data & code developed at the institute

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Copyright © 2023 Allen Institute. All Rights Reserved.
cellscience.alleninstitute.org
  • About
      Institute
      1. News feed
      2. What we do
      3. Publications
      4. Allen Institute | allenInstitute.org
      5. Careers
      Site
      1. Home page
      2. Site updates
      3. Archived content
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Cell Catalog quickview
      3. Cell Shorts (documentaries on labs using our cells)
      4. Support forum
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
      About our hiPS cells
      1. hiPS Cell Structure Overview
      2. Visual Guide to Human Cells
      3. Cell structure observations
      4. Why endogenous tagging?
      5. Differentiation into cardiomyocytes
      6. Genomics
      7. Download cell data (images, genomics, features)
  • Data & Digital Tools
      Online image analysis
      1. Cell Feature Explorer (plotting & 3D viewer)
      2. 3D cell viewer (pre2018)
      3. Deep cell zoom (216,016 cells)
      Online modeling viewers
      1. Visual Guide to Human Cells
      2. Simularium (4D visual analysis)
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      6. Allen Integrated Cell viewer
      7. Label-free examples viewer
      8. 3D probabilistic model viewer
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Data & code
      1. Download cell data (images, genomics, features)
      2. Code repositories & software
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Overview
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Label-free Determination
      6. └ 3D viewer
      7. 3D Probabilistic Modeling
      8. └ 3D viewer
      9. Visual Guide to Human Cells
      4D biology models
      1. Simularium (online 4D viewer)
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. All journal publications
      2. Preprints (biorxiv, arxiv)
      Posters
      1. Select posters
  • Education
      Education resources
      1. All Resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. Cell Feature Explorer (interactive plotting & 3D viewer)
      4. 3D cell viewer (pre2018 data)
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Digital tool tutorials with videos
      2. Visual Guide tutorial
      3. AGAVE user guide
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated overviews
  • 🔍
      SEARCHBAR