Project Overview

How do cells work? To answer this question, we first need to understand what they look like.

At the Allen Institute for Cell Science, we are using cutting-edge technologies to grow, modify and microscopically observe thousands of cells to gain a clear understanding of the internal architecture of cells as a first step towards deeply understanding how cells work. 

Our Workflow


Our research program is built on a pipeline of cutting edge technologies, modified and brought to an industrial scale.

Our process is tightly integrated as cells are gene edited, assayed, imaged, modeled, and presented to the community through the Allen Cell Explorer: a tool to organize, view and interrogate our cell image data and models. Our teams work closely together to ensure that the data we collect are of the highest possible quality, and that the images, analyses and models we generate are useful to the scientific community.

Gene Editing Stem Cells


In order to image specific parts of the cell, most researchers use a technique that involves flooding the cell with a glowing protein that binds to the part of the cell they are interested in imaging.

The Allen Institute for Cell Science is taking a new approach, creating gene edited cell lines that express a glowing protein at the precise location of the tagged part of the cell. This powerful method allows our scientists to observe the individual parts of the cell with amazing clarity and precision.


For our studies, we use human induced pluripotent stem cells (hiPSCs). Working with human cells means our work is much more reproducible and relevant to human disease and regeneration, and stem cells can be differentiated into many kinds of specialized cells.

Quality Control


Our cells undergo a rigorous quality control process to assess the health of the cells and their colonies to ensure the cells are behaving normally even after the gene tag is introduced. We also ensure that they can successfully differentiate into specialized cell types.

Large-Scale Imaging


After ensuring the quality of our cells, we capture images and videos of thousands of cells through a large-scale automation process.

Image Analysis and Modeling



Using cutting-edge tools like deep learning and artificial intelligence, our teams develop methods to analyze the images to make sense of the cells’ structures, activities and organization, as well as changes during growth and differentiation and responses to known drugs and mutations. We then use the generated data to build models to learn and predict those same properties.

Our efforts culminate in the Allen Cell Explorer—a data portal for the visualization and interrogation tools, dynamic 3D images and models of cell behavior.