ALLEN CELL EXPLORER
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      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 and 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
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  • Education
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      1. All resources
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      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
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      1. Video tutorials
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News feed

For general news from the Allen Institute for Cell Science, visit alleninstitute.org

Celebrating a decade of discovery

5/14/2025

 
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

We are at Cell Bio 2024!

12/1/2024

 
Picture
When: Dec 14 - 18, 2024
Where: San Diego, California

Visit exhibit hall booth #313 to meet researchers, educators, and recruiting staff from the Allen Institute for Cell Science and learn about our open science resources & career opportunities. Explore our datasets, visualization tools, software, and human iPS cell lines available on the Allen Cell Explorer.
Our talks & posters
Conference Website

New disease cell line collections launched

6/4/2024

 
We just released 8 disease cell line collections, each containing multiple isogenic control and mutation-carrying clones:
  • 6 cardiomyopathy disease collections, each with a different point mutation in the MYH7 gene
  • 1 skeletal myopathy disease collection with point mutation in the MYH3 gene
  • 1 laminopathy disease collection has a mutation in the LMNA/C gene associated with progeria
These cell lines will be valuable tools to further our understanding of the fundamental mechanisms which underly these disease phenotypes and enable relevant pharmacological discoveries to treat them. This monumental one-time release of the 8 disease cell line collections with a total of 37 clones is comparable in magnitude to the 58 cell lines in the Allen Cell Catalog, which were released over the last 8 years.
Read release article
Browse Disease Cell Line Collection

New perspective published in Cell

5/23/2024

 
Establishing a conceptual framework for holistic cell states and state transitions
Picture
"Cell states were traditionally defined by how they looked, where they were located, and what functions they performed. In this post-genomic era, the field is largely focused on a molecular view of cell state. Moving forward, we anticipate that the observables used to define cell states will evolve again as single-cell imaging and analytics are advancing at a breakneck pace via the collection of large-scale, systematic cell image datasets and the application of quantitative image-based data science methods. This is, therefore, a key moment in the arc of cell biological research to develop approaches that integrate the spatiotemporal observables of the physical structure and organization of the cell with molecular observables toward the concept of a holistic cell state. In this perspective, we propose a conceptual framework for holistic cell states and state transitions that is data-driven, practical, and useful to enable integrative analyses and modeling across many data types."

Register for TEMTIA 11

4/2/2024

 
We are excited to host the 11th EMT International Association  (TEMTIA 11) meeting at the Allen Institute in Seattle, Washington, USA, on November 12-15, 2024.
Picture
Event Details
Register
Abstract Submission
The epithelial to mesenchymal transition (EMT) is a cell state change during which cells transition from stationary to migratory behavior. Associated with normal development but also a characteristic of many cancers, EMT includes complex changes across multiple cell characteristics and is consistently and universally difficult to define. At this year’s TEMTIA, we will leverage the diversity of the field, convening experts across contexts, perspectives, and scales of study to address this challenge. Scientific sessions will be organized with common themes such as: data integration, microscopy in EMT, modeling of state changes, and more.
​​
To recognize the seminal contributions of Dr. Elizabeth Hay to the EMT field, TEMTIA will present the Betty Hay award of AU$1000.00 to a young female scientist. To apply for the fellowship or for more information, visit the Event Details page.

​Talk/poster abstract submission deadline: 
May 31, 2024
​Please contact [email protected] for any questions.

Allen Institute for Cell Science at BPS 2024

1/15/2024

 
Picture
Meet scientists from the Allen Institute for Cell Science, learn about our open resources and updates on our scientific researches, talk to our recruiting team about career opportunities, and more at the 2023 Annual Meeting of the Biophysical Society (BPS).

Date: February 10-14, 2024
Location: Philadelphia, Pennsylvania
​Booth #301

Our Posters & Talks Schedule
Conference Website

Happy Holidays 2023!

12/20/2023

 
Happy Holidays from all of us at the Allen Institute for Cell Science!
A tinsel wreath decorated with hiPSCs and the message “Happy Holidays”

Allen Institute for Cell Science at Cell Bio 2023

11/15/2023

 
Picture
Meet scientists from the Allen Institute for Cell Science, learn about our open resources and updates on our scientific researches, talk to our recruiting team about career opportunities, and more at the Cell Bio 2023 - the annual meeting of the American Society for Cell Biology.

Date: Jun 14 - 17, 2023
Location: Boston, Massachusetts
Poster & Talk Abstracts

New video tutorial for our online Cell Catalog!

8/25/2023

 
​Explore our collection of fluorescently tagged human induced pluripotent stem cell lines as part of the Allen Cell Collection. These cell lines target key cellular structures and they are openly available to support your research. In this video tutorial, Allen Institute for Cell Science intern Rennie Dupar walks you through the cell lines, supporting data and images, and important resources.

Visit our webpage Digital tool tutorials with videos for more video tutorials!

Allen Institute for Cell Science at ISSCR 2023!

6/14/2023

 
Allen Institute for Cell Science at ISSCR
Our poster schedule
Meet scientists from the Allen Institute for Cell Science, learn about our open resources and updates on our scientific researches, talk to our recruiting team about career opportunities, and more at the 2023 Annual Meeting of the International Society for Stem Cell Research (ISSCR).

Date: Jun 14 - 17, 2023
Location: Boston, Massachusetts
Conference website
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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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  • 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 and 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