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Allen Institute
Open Science Tools
Allen Institute
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We share what we do openly with the world

At the Allen Institute, we believe shared understanding accelerates new discoveries and nurtures breakthroughs.

Explore our open data portals

Serving the scientific community is at the center of our mission to expand our understanding of human health and disease.

Allen Mouse Brain Atlas Gene Expression

Allen Brain Map

We publicly release comprehensive, large-scale datasets that investigate the mammalian brain.
Visit Brain Map
Image showing human cell variance

Allen Cell Explorer

Learn more about our open data, cell lines, software tools, models, plasmids, and more.
Visit Explorer

Human Immune System Explorer

A portal for exploring data and resources from studies of the human immune system in health and disease.
Explore HISE

Featured Resources

Whole mouse brain image showing spatial location of transcriptomic-defined cell types

Allen Brain Cell Atlas

The Allen Brain Cell (ABC) Atlas provides a platform for visualizing multimodal single cell data across the mammalian brain.

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The Allen Cell & Structure Segmenter is a Python-based open source toolkit developed for 3D segmentation of intracellular structures in fluorescence microscope images.

Seattle Alzheimer’s Disease Brain Cell Atlas

A cell-by-cell map of regions of the human brain in aging and dementia that aims to uncover the cellular and molecular roots of Alzheimer’s disease.

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The Allen Cell & Structure Segmenter is a Python-based open source toolkit developed for 3D segmentation of intracellular structures in fluorescence microscope images.

Cell and Structure Segmenter

The Allen Cell & Structure Segmenter is a Python-based open source toolkit developed for 3D segmentation of intracellular structures in fluorescence microscope images.

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Morphology reconstructions of neurons

MICrONS Explorer

This data portal includes electron microscopy-based reconstructions of cortical circuitry from mouse visual cortex.

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Image from the Allen Cell Collection of human iPS cells expressing Tubulin

Allen Cell Collection

The Allen Cell Collection contains over 50 high quality fluorescently tagged human iPS cell lines that illuminate key cellular structures

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    Education and Training 

    Learn how to use our data and resources to support your research by attending in-person, and virtual trainings and workshops.

    Events and Training

    We also provide educators with resources to inspire and engage the next generation of scientists. Our educational resources help students use our open data and tools to support independent research, scientific thinking, and analysis skills.

    Educator Resources