Products & Tools

The Allen Cell Explorer 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 create a dynamic digital window into the human cell.

We are creating the visualizations of the inner architecture of the cell based on real data, providing major, new insights into what human cells look like and replacing imagined cartoons with data-driven, dynamic representations. Seeing how the organization of human cells changes as they grow, differentiate, and respond to drugs will enable researchers to ask new questions and make better predictions about health and disease.

Community engagement and open science are central values of the Allen Institute for Cell Science. In addition to our continuing, active community engagement on assays, cell lines and other activities, we will also make our engineered lines, reagents, data, methods, algorithms, models and analyses publicly available.


Integrated Cell Model

The Integrated Cell Model uses “deep learning” approaches to predict the organization of human stem cells. Trained on thousands of images of cells, this computational tool makes predictions about the locations of cellular components based on the location of a couple of landmark structures. Currently presented in two dimensions, future iterations of the Integrated Cell Model will be available in 3D.  

3D Cell Viewer

The 3D Cell Viewer presents our unique large-scale collection of human stem cells visualized in three dimensions. Gene edited cells are marked with fluorescent tags that make individual structures in the cell glow with remarkable clarity. Users can view and manipulate thousands of cells and appreciate the large diversity of cells, even from the same clonal line.

Cell Catalog, featuring Allen Cell Collection and Allen Plasmid Collection

We share and distribute the gene edited lines we create through the Allen Cell Collection at the Coriell Institute, and provide extensive documentation and quality control information through our own Cell Catalog.

We also share and distribute the plasmids we use to create our gene edited lines through Addgene, so that researchers can create similarly precise tags for individual structures in virtually any human cell.

Research Updates

As we uncover interesting and helpful observations about cells, we present them in our Research Updates, as a first glimpse for exploration and hypothesis.


As part of our open science model, we share our methods and protocols for everything we create so others can recreate our results and drive their own experiments forward.