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they help us fulfill our mission
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at the interface of data and neuroscience
next generation leaders
fostering emerging leaders in bioscience
research
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science at the scale of greatest impact
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explore our publications
open science
sharing science to speed discovery
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building a blueprint of the brain
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neural dynamics
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creating the ultimate immune system reference
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cell science
unlocking the hidden rules of how cells become organs—and using those rules to build biology's next research frontier
explore cell science
cell science team
Scientist in white coat and purple gloves examining medical test tube in laboratory

Every organ in your body started as a small cluster of identical cells. How those cells knew what to become is still one of science's great mysteries.

A group of stem cells doesn't just grow and expand. The cells self-organize, communicate, and shape themselves into three-dimensional structures that become the tissues and organs of the body. Until now, we've lacked the tools to study this process at the scale and level of detail needed to truly understand it—and then use that knowledge to build something transformative. 

We're building CellScapes: an integrated framework for how cells self-organize by combining imaging, computational modeling, and synthetic biology. Once we understand the rules, we can program them into synthetic tissues that act like miniature organs—giving researchers a new platform to study how cells behave in health, in disease, and in response to medicine.

‍

Microscopic cross-section showing green cells surrounded by purple vascular network on black background
Understanding the rules of how cells become tissues opens an entirely new frontier, where biology becomes programmable and disease interventions become even more precise.

cell science news

video
Simularium: Accelerating discovery by animating insight
Simularium is an innovative online tool designed by the Allen Institute’s Cell Science team that visualizes 4D simulations (animations) of complex...
news
Allen Institute cells blast off into outer space
Researchers from Cedars-Sinai are using Allen Institute cell lines to grow organoids in space, which could help design better drugs for disease
video
What Are the Parts of a Cell?
From mitochondria to endoplasmic reticulum, this educational video explores the major cell organelles and their functions.
We study how cells self-organize by integrating imaging, computational modeling and synthetic biology, revealing fundamental principles in cell biology and laying the groundwork for breakthroughs in diagnosing and treating disease.
Ruwanthi (Ru) Gunawardane
Executive Vice President and Director, Cell Science
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featured publications

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publication / 2025
A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types
Cell
publication / 2025
Enabling global image data sharing in the life sciences
Nature Methods
publication / 2025
Comparing simulations of actin filament compression reveals tradeoff between computational cost and capturing supertwist
microPublication Biology
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Medical scan showing multiple cells with purple and yellow fluorescent markers on black background

access open tools, resources, datasets, and more

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cell science events

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event / April 20–22, 2026
2026 Lake Conference
Join the Allen Institute for Cell Science and Circuit Neuroscience Basel in Seattle, Washington, April 20–22, 2026, for a 3 day conference.
event / September 23 - 25, 2026
Stem Cell & Developmental Biology Early Career Symposium
For the first time, the International Society for Stem Cell Research (ISSCR), the Society for Developmental Biology (SDB), and the Allen Institute for Cell Science (AICS) are collaborating to present a three-day scientific symposium led by early-career scientists.
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cell science scientific advisory council

Bruce R. Conklin
Gladstone Institutes and University of California, San Francisco
Gaudenz Danuser
Institute of Human Biology
Jan Ellenberg
Professor and Director of SciLifeLab
Margaret Gardel
Director of the James Franck Institute
Quincey Justman
Harvard Medical School
Alan Lowe
Director of AI/ML at the Chan Zuckerberg Initiative
Wallace Marshall
University of California, San Francisco
Lucas Pelkmans
University of Zurich
Philip Tagari
Chief Scientific Officer, insitro
Magdalena Zernicka-Goetz
California Institute of Technology
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