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​Welcome to the Allen Cell Explorer where you can access an unprecedented view into the organizational diversity of human stem cells through open data, tools, cell lines, plasmids, and models developed by the Allen Institute for Cell Science. All our scientific resources are openly available to support the cell biology community and accelerate discovery in human health and disease.

Highlights

New article published in Biophysical Journal

Building the next generation of virtual cells to understand cellular biology
We just published a new Biophysical Perspective proposing an ambitious future for Cell Biology in the Biophysical Journal:
"​Cell science has made progress through reductionist approaches, but integrating vast knowledge and making it accessible is challenging. Next-generation virtual cells, which are dynamic 3D models that integrate information from diverse sources including simulations, biophysical models, image-based models, and evidence-based knowledge graphs, could bridge theory and data by integrating diverse information and facilitating collaboration among researchers."
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New article published in Nature

Integrated intracellular organization and its variations in human iPS cells
Database of 200,000 cell images yields new mathematical framework to understand our cellular building blocks.

New article published in Nature Methods

The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models
The Simularium Viewer makes it easy to share and interrogate interactive 3D visualizations of biological simulation trajectories and related plots directly in a web browser. ​Its primary goal is to facilitate collaborations among experimental and computational biologists by removing major challenges to sharing, accessing, and comparing simulation results.

Publications

FEATURED
Integrated intracellular organization and its variations in human iPS cells
Viana MP, Chen J, Knijnenburg TA, Vasan R, Yan C, Arakaki JE, Bailey M, Berry B, Borensztejn A, Brown EM, Carlson S, Cass JA, Chaudhuri B, Metzler KRC, Coston ME, Crabtree ZJ, Davidson S, DeLizo CM, Dhaka S, Dinh SQ, Do TP, Domingus J, Donovan-Maiye RM, Ferrante AJ, Foster TJ, Frick CL, Fujioka G, Fuqua MA, Gehring JL, Gerbin KA, Grancharova T, Gregor BW, Harrylock L, Haupt A, Hendershott MC, Hookway C, Horwitz AR, Hughes C, Isaac EJ, Johnson GR, Kim B, Leonard AN, Leung W, Lucas JJ, Ludmann SA, Lyons BM, Malik H, McGregor R, Medrash GE, Meharry SL, Mitcham K, Mueller IA, Murphy-Stevens TL, Nath A, Nelson AM, Oluoch SA, Paleologu L, Popiel TA, Riel-Mehan MM, Roberts B, Schaefbauer LM, Schwarzl M, Sherman J, Slaton S, Sluzewski MF, Smith JE, Sul Y, Swain-Bowden MJ, Tang WJ, Thirstrup DJ, Toloudis DT, Tucker AP, Valencia V, Wiegraebe W, Wijeratna T, Yang R, Zaunbrecher RJ, Labitigan RLD, Sanborn AL, Johnson GT, Gunawardane RN, Gaudreault N, Theriot JA, Rafelski SM. Nature, January 4, 2023.
A comprehensive analysis of gene expression changes in a high replicate and open-source dataset of differentiating hiPSC-derived cardiomyocytes
Grancharova T, Gerbin KA, Rosenberg AB, Roco CM, Arakaki JE, DeLizo CM, Dinh SQ, Donovan-Maiye RM, Hirano M, Nelson AM, Tang J, Theriot JA, Yan C, Menon V, Palecek SP, Seelig G, Gunawardane RN. Scientific Reports, August 04, 2021.
​Cell states beyond transcriptomics: Integrating structural organization and gene expression in hiPSC-derived cardiomyocytes
Gerbin KA, Grancharova T, Donovan-Maiye RM, Hendershott MC, Anderson HG, Brown JM, Chen J, Dinh SQ, Gehring JL, Johnson GR, , Lee H, Nath A, Nelson AM, Sluzewski MF, Viana MP, Yan C, Zaunbrecher RJ, Cordes Metzler KR, Gaudreault N, Knijnenburg T, Rafelski SM, Theriot JA, Gunawardane RN. Cell Systems, June 16, 2021.
MORE...
​We study the human cell holistically. To understand and predict cell behaviors, we develop and image high quality human induced pluripotent stem (hiPS) cell lines with genome editing to illuminate over 40 key cellular structures. This live cell imaging, together with image analysis, visualization tools and computational models enable novel interpretations of cell behavior by us and researchers around the globe.

Cells & plasmids for your lab

​We have created a series of gene edited human iPSCs that we use as the foundation for our image data, and that we share with the larger scientific community.
Obtain cell lines & plasmids for your lab​; quality control details
​Explore & download genomics & transcriptomics data
Step-by-step protocols to culture & image gene-edited hiPSCs successfully
Instructional videos provided to ensure success in your lab

Featured digital tools

View multi-channel images using cinematographic rendering 
Access & interact with our public 3D image datasets & feature measurements online
Perform 3D segmentations of intracellular structures
Access data & code developed at the institute
Our diversity, equity & inclusion commitment
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