ALLEN CELL EXPLORER
  • About
      Institute
      1. News feed
      2. What we do
      3. Careers
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Cell Catalog quickview
      3. Cell Shorts (documentaries on labs using our cells)
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated methods
      4. Support forum
      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 methods
  • 🔍
      SEARCHBAR

​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

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Read Biophysical Journal article

New article published in Biophysical Journal

Building the next generation of virtual cells to understand cellular biology
We just published a new Biophysical Perspective proposing an ambitious future for Cell Biology in the Biophysical Journal:
"​Cell science has made progress through reductionist approaches, but integrating vast knowledge and making it accessible is challenging. Next-generation virtual cells, which are dynamic 3D models that integrate information from diverse sources including simulations, biophysical models, image-based models, and evidence-based knowledge graphs, could bridge theory and data by integrating diverse information and facilitating collaboration among researchers."
Vertical Divider

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 Nature article
Read our announcement
Try 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.
Read Nature Methods article
Read our announcement

Featured Publications

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Integrated intracellular organization and its variations in human iPS cells
Viana MP, Chen J, Knijnenburg TA, Vasan R, Yan C, Arakaki JE, Bailey M, Berry B, Borensztejn A, Brown EM, Carlson S, Cass JA, Chaudhuri B, Metzler KRC, Coston ME, Crabtree ZJ, Davidson S, DeLizo CM, Dhaka S, Dinh SQ, Do TP, Domingus J, Donovan-Maiye RM, Ferrante AJ, Foster TJ, Frick CL, Fujioka G, Fuqua MA, Gehring JL, Gerbin KA, Grancharova T, Gregor BW, Harrylock L, Haupt A, Hendershott MC, Hookway C, Horwitz AR, Hughes C, Isaac EJ, Johnson GR, Kim B, Leonard AN, Leung W, Lucas JJ, Ludmann SA, Lyons BM, Malik H, McGregor R, Medrash GE, Meharry SL, Mitcham K, Mueller IA, Murphy-Stevens TL, Nath A, Nelson AM, Oluoch SA, Paleologu L, Popiel TA, Riel-Mehan MM, Roberts B, Schaefbauer LM, Schwarzl M, Sherman J, Slaton S, Sluzewski MF, Smith JE, Sul Y, Swain-Bowden MJ, Tang WJ, Thirstrup DJ, Toloudis DT, Tucker AP, Valencia V, Wiegraebe W, Wijeratna T, Yang R, Zaunbrecher RJ, Labitigan RLD, Sanborn AL, Johnson GT, Gunawardane RN, Gaudreault N, Theriot JA, Rafelski SM. Nature, January 4, 2023.
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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.
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​​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.
See More of Our Publications...
​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

The Institute

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Copyright © 2023 Allen Institute. All Rights Reserved.
See more on alleninstitute.org
  • About
      Institute
      1. News feed
      2. What we do
      3. Careers
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Cell Catalog quickview
      3. Cell Shorts (documentaries on labs using our cells)
      Lab methods
      1. Instructional videos for success in the lab
      2. Standard operating procedures (written methods)
      3. Illustrated methods
      4. Support forum
      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 methods
  • 🔍
      SEARCHBAR