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The Allen Integrated Cell launches

The Allen Institute for Cell Science today launched the Allen Integrated Cell, the world’s first predictive and comprehensive 3D model of a live human cell.


2 min read

This new visualization of a large collection of human stem cells will allow researchers around the world to see structures inside a living cell together at the same time, providing a baseline for better understanding healthy cells and for studying human disease models.


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Allen Integrated Cell: A new way to see inside live human cells

Building off last year’s launch of the Allen Cell Explorer, the Allen Integrated Cell comprises two different models that can predict the shape and location of cellular structures. The first, a probabilistic model, emerged from a machine learning approach that accurately predicts the most probable shape and location of structures in a cell based solely on the shape of that cell’s plasma membrane and nucleus.

The second, a label-free model, predicts the location of 3D structures in cells without fluorescent labels. This model is based on another machine learning algorithm created by Allen Institute scientists trained on 3D images of thousands of cells gene edited to express fluorescent protein tags. This model can be used on brightfield microscopy images to visualize many structures inside cells, simultaneously and with high precision.

“All of us have a view of a cell based on what we’ve seen in our biology textbooks and that’s a great starting point, but the fact is, there’s probably no cell in the world that’s ever looked like that,” said Rick Horwitz, Ph.D., Executive Director of the Allen Institute for Cell Science. “The Allen Integrated Cell is the closest thing that I’ve ever seen in science to magic. Now you can see the inner workings of the cell in action in a movie in three dimensions for the first time.”

Learn more in our press release.

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About Allen Institute for Cell Science

The Allen Institute for Cell Science, a division of the Allen Institute, an independent, 501(c)(3) nonprofit medical research organization, is dedicated to understanding and modeling cells: the fundamental units of life. By integrating technologies, approaches, models and data into a common standardized framework, the Allen Institute for Cell Science is creating dynamic, visual models of how genetic information is transformed into cellular behavior, and how the molecules and organelles within each cell interact and function as systems. These predictive models will enable the cell science community to better understand the role of cells in both health and disease. The Allen Institute for Cell Science was launched in 2014 with a contribution from founder and philanthropist, the late Paul G. Allen. The data, tools and models from the Allen Institute for Cell Science are publicly available online at

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