Allen Cell Explorer: Creating a Dynamic Digital Window Into the Human Cell

Cells are the fundamental units of life. Each cell in our bodies is a microcosm, containing many complex, living, dynamic machines that work together to produce cellular behaviors, which range from basic tasks like moving and dividing to highly specialized ones, like beating in conjunction to pump blood through your heart.

We know a great deal about how many of these cellular machines work, but—and this is a crucial but—we still do not understand how they all work together to perform the many tasks the cell performs at any given moment. Critically, understanding normal cells will greatly help us grasp what goes wrong in cells during disease.

The Allen Cell Explorer was motivated by this need to understand how various components of cells interact to give rise to their behaviors. The result is a one-of-a-kind portal that combines large-scale 3D imaging data, predictive modeling, gene edited cell lines and a growing suite of powerful tools to provide a dynamic digital window into the human cell. We are very excited to launch the Allen Cell Explorer website and share our resources with the global scientific community.

While the Allen Cell Explorer contains numerous tools and features, there are a few in particular that exemplify our approach to studying the cell.

The Integrated Cell Model is the first model to use “deep learning” approaches to predict the organization of human stem cells. Trained on thousands of images of cells, this tool makes predictions about the locations of cellular components based on the location of just a couple of landmark structures. Currently presented in two dimensions, future iterations of the Integrated Cell Model will be available in 3D—you can see a preview of what this will look like on our website now.

Another tool, the 3D Cell Viewer, presents our unique large-scale collection of human stem cells visualized in three dimensions. Users can view and manipulate over 6,000 cells that have been gene-edited with fluorescent tags that light up individual structures of the cell with remarkable clarity. This tool is a valuable entry into discovering the incredible diversity in how cells are structured, even when they are genetic clones.

Guided by the vision of our founder, Paul G. Allen, open science has been a core principle of the Allen Institute for Cell Science from the beginning. The Allen Cell Explorer is our platform to share our models, tools, methods, cell lines and more with researchers around the world. Working as a community, we can apply and expand on these tools to make leaps forward in the field of cell biology, and have great impact on our study of human health and disease.