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      1. hiPS Cell Structure Overview
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      4. Why endogenous tagging?
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      1. Tools & resources overview
      2. Download cell data (images, genomics, features)
      3. Code repositories & software
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      2. AGAVE 3D pathtrace image viewer
      Web tools
      1. BioFile Finder
      2. Cell Feature Explorer
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      Web tools (con't)
      1. Simularium viewer
      2. Timelapse Feature Explorer
      3. Visual Guide to Human Cells
      4. Vol-E (Web Volume Viewer)
      5. 3D Cell Viewer
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Allen Integrated Cell
      6. └ 3D Probabilistic Modeling
      7. └ Label-free Determination
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      1. Simularium viewer
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      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
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      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. 3D Cell Feature Explorer
      4. 3D Cell Viewer
      5. hiPS cell structure overview
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Allen Institute for Cell Science

Uncovering the design principles of multicellular programs essential for life 
Measure, model, build: steps towards predictive understanding

Launching a new era in cell science

After a decade of pioneering research, we are proud to introduce CellScapes, a bold new initiative to transform how scientists measure, model, and represent cellular behaviors. Over the next ten years, we will generate multimodal and dynamic data and develop cutting-edge tools and frameworks to move beyond static snapshots toward a predictive and intuitive understanding of how cells achieve complex behaviors essential for life. As part of this new initiative, we will engage the scientific community, empowering researchers and educators through our data, tools, and platforms to shape the next generation of cell science. 
Read more about CellScapes
About us
About us
Our tools for open science
Tools for open science
Our publications
Our publications

News and highlights

A new publication in Cell Systems
Unveiling crucial insights into nuclear growth in human iPS cell colonies. By analyzing 3D timelapse data, our Cell Science team has shown how cell lineage and environment shape cellular behavior. 

This timelapse video illuminates the height of nuclei from 4μm (turquoise) to 11μm (fuchsia).
Read publication

Celebrating a decade of discovery
For 10 years, the Allen Institute for Cell Science has been a leader in accelerating advancements in cell biology. By creating groundbreaking tools, resources, and open-access datasets and models, the Institute has empowered researchers and educators to explore and understand cells in new ways. Through its large-scale, interdisciplinary efforts, it has enabled the scientific community to tackle complex biological questions and make discoveries that wouldn’t be possible otherwise.
Explore our past foundational projects

8 new disease cell line collections
We just released 8 disease cell line collections, each containing multiple isogenic control and mutation-carrying clones: 6 cardiomyopathy disease collections (MYH7 gene), 1 skeletal myopathy disease collection (MYH3 gene), and 1 laminopathy disease collection (LMNA/C gene).  
Read release article
Browse our Disease Cell Collections

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Allen Institute for Cell Science is a part of the Allen Institute. The mission of the Allen Institute is to understand the principles that govern life, and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world.
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​Copyright © 2025 Allen Institute. All Rights Reserved.
  • About
      Institute
      1. Our science: CellScapes
      2. Past foundational projects
      3. News feed
      4. About us
      5. Careers
  • Allen Cell Collection
      Order cells & plasmids
      1. Cell Catalog
      2. Disease Collection Cell Catalog
      3. Cell Catalog quickview
      4. Cell video shorts
      Lab methods
      1. Video protocols
      2. Written protocols
      3. Our methodology
      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
      General
      1. Tools & resources overview
      2. Download cell data (images, genomics, features)
      3. Code repositories & software
      Desktop tools
      1. Allen Cell & Structure Segmenter
      2. AGAVE 3D pathtrace image viewer
      Web tools
      1. BioFile Finder
      2. Cell Feature Explorer
      3. Integrated Mitotic Stem Cell
      4. └ Z-stack viewer
      5. └ 3D viewer
      Web tools (con't)
      1. Simularium viewer
      2. Timelapse Feature Explorer
      3. Visual Guide to Human Cells
      4. Vol-E (Web Volume Viewer)
      5. 3D Cell Viewer
  • Analysis & Modeling
      Allen Integrated Cell models
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. └ Z-stack viewer
      4. └ 3D viewer
      5. Allen Integrated Cell
      6. └ 3D Probabilistic Modeling
      7. └ Label-free Determination
      4D biology models
      1. Simularium viewer
      Methodologies
      1. Drug perturbation pilot study
      2. hiPS cells during mitosis
      3. Differentiation into cardiomyocytes
  • Publications
      Articles
      1. Publications
      2. Preprints
      Presentations
      1. Talks & posters
  • Education
      Educational resources
      1. All resources
      2. Teaching materials
      Online tools popular with teachers
      1. Visual Guide to Human Cells
      2. Integrated Mitotic Stem Cell
      3. 3D Cell Feature Explorer
      4. 3D Cell Viewer
      5. hiPS cell structure overview
  • Support
      Questions
      1. FAQs
      2. Forum
      Tutorials for digital tools
      1. Video tutorials
      2. Visual Guide tutorial
      3. AGAVE documentation
      Lab methods
      1. Video protocols
      2. Written protocols
      3. Our methodology
  • 🔍
      SEARCHBAR