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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 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.

Illumination stability & linearity measurement now ​available on protocols.io

The QUAREP-LiMi Working Group has published a first version of the collaborative protocol on Illumination stability & linearity measurement in Protocols.io. 
​In addition to step-by-step instructions, the protocol provides:
  • endorsement (authorship) by 36 people representing research institutions, academia, and industry from around the world.
  • a link to a public database with measurements made by members of the authorship group and to which you can contribute by uploading your own measurements. 
  • a link to a GitHub repository with scripts to automate the measurements with some scopes and power meters.
  • links to tutorial videos.

Featured publications

MOST RECENT
The Simularium Viewer: an interactive online tool for sharing spatiotemporal biological models
Lyons B, Isaac E, Choi NH, Do TP, Domingus J, Iwasa J, Leonard A, Riel-Mehan M, Rodgers E, Schaefbauer L, Toloudis D, Waltner O, Wilhelm L, Johnson GT. Nature Methods, April 4, 2022.
FEATURED
​It’s time to incorporate diversity into our basic science and disease models
Horwitz R, Riley EA, Millan MT, Gunawardane RN. Nature Cell Biology, November 29, 2021.
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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