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Years of Impact

2023 Annual Report

Celebrating Two Decades of Scientific Achievement

20 years ago, the Allen Institute began with an idea to do science differently, to take on some of the biggest, hardest problems in biology through interdisciplinary teamwork, and openly share our science with the world to maximize our impact. Two decades later, big science, team science, and open science remain at the heart of what we do. From brain science, to cell science, to immunology, and beyond, our research is catalyzing new breakthroughs across the globe.  

Not only was 2023 a year to reflect and celebrate, it was also a year of new scientific discovery, achievement, and impact. We launched the Allen Brain Cell Atlas, unifying cell types and anatomy across the whole mouse brain. We welcomed the global scientific community and organized a new bi-annual international conference—the Lake Conferences—showcasing the latest advances in neuroscience. We started a Teacher Academy to train educators on how to use our science in their classrooms. We published landmark studies on the interior design of our cells, the first draft of a whole human brain cell atlas, and the characterization of the aging immune system, just to name a few. At the end of 2023 we celebrated 20 years since the Institute was founded, two decades of impact through open, big and team science, launching our new engagement campaign Allen Impact. 

Today, we face new problems to solve and new mysteries to unravel. Building on 20 years of unwavering commitment and dedication, our team and our global collaborators continue to propel us forward in our quest to understand life and advance health.

A Message From Our CEO

What Makes Us Human?

Detailed cellular maps of the entire human brain reveal clues

Years in the making, researchers from the Allen Institute and a consortium of international scientists and collaborators release the first draft of whole human brain cell atlas, revealing over 3000 cell types and distinct human features that begin to define the contours of our uniqueness as humans. This landmark release was featured in a special issue of Science and builds off  the earlier success and scientific achievements of our mouse brain work, which profiled thousands of cell types and neuronal connections that have been a vital global scientific resource. This first draft of a whole human brain cell atlas lays the crucial groundwork for a complete cell catalogue and rich atlas of all the cells in the human brain, which our scientists and researchers are currently working on as part of the NIH-funded Brain Initiative Cell Atlas Network (BICAN).

The Interior Design of Our Cells

A new way to see how cells organize themselves: A database of 200,000 cell images yielded a bespoke mathematical framework to understand our cellular building blocks. This year, a team at the Allen Institute for Cell Science put numbers on the internal organization of human cells —a biological concept that has to date proven exceptionally difficult to quantify. Their work, published in the journal Nature, also captured details about the rich variation in cell shape even among genetically identical cells grown under identical conditions.

Unraveling the Aging Immune System

Researchers at the Allen Institute for Immunology used TEA-seq, a powerful new method developed by the team, to study how our immune system changes as we age. TEA-seq simultaneously analyzes the gene expression, surface proteins, and chromatin accessibility of individual immune cells. Scientists used TEA-seq to compare T cell populations of healthy children and older adults. They discovered significant molecular changes in a type of T cell that was thought to resist aging and identified a new type of T cell in children that disappears with age. Together, these findings offer new insights that may explain why older people are hit harder by viruses like SARS-CoV-2.

In a separate study, the division’s scientists explored how an overactive inflammatory response could be at the root of many long Covid cases.

A Mysterious Brain Region: The Claustrum

The claustrum is a tiny, sheet-like structure nestled under the cortex, the outermost shell of the brain, that is the most densely connected structure in the brain but whose function still remains mysterious. A pair of studies published this year from scientists in the MindScope Program and the Allen Institute for Brain Science reveal new insights about how the claustrum connects to the rest of the brain; the kinds of neurons that make it up (one of which is studded with receptors for common psychedelic drugs); and how it influences activity in the cortex, the wrinkled, outermost shell of the brain. This year, the MindScope teams transitioned into the Allen Institute for Neural Dynamics and other programs. 


New type of microscope captures stunning views of the brain

Building on technologies originally designed for defect detection in electronics manufacturing, the “ExA-SPIM” microscope is showing scientists the brain as it’s never been seen before. Built by a team of researchers at the Allen Institute for Neural Dynamics, the one-of-a-kind microscope captures views of the entire mouse brain at incredible resolution. The images allow the scientists to view individual neurons and their wiring in the context of the mouse brain’s 80 million other neurons.

Ask anything,

change everything,

Launched this year, Allen Impact is a celebration of the innovative partnerships and collaborations which place our Institution at the vanguard of new knowledge and emerging technologies. Driving our mission to understand life and advance health at pace and scale, and catalyzing solutions to global challenges.

We know that our impact will be enhanced by the creativity and ingenuity of those who engage.

Allen Discovery Center for Neuroimmune Interactions at Icahn School of Medicine at Mount Sinai

The Allen Discovery Center for Neuroimmune Interactions will probe the complex relationship between our brains and immune system—defining, mapping, and understanding the health consequences of interactions between the nervous system and our bodies’ immune cells. The Center will be led by Dr. Brian S. Kim of Mount Sinai and Dr. David Artis of Weill Cornell Medicine who will bring together a multidisciplinary team enabling cutting-edge analytical technologies from neuroscience and from immunology to be applied in new ways to bridge these fields and to catalyze a collaborative scientific research hub that discovers new biology and advances a new therapeutic paradigm in medicine. 

Unveiling the First, Complete Cell-Type Atlas of the Mammalian Brain

In a major milestone for global neuroscience, researchers at the Allen Institute; Harvard; Salk and Broad Institutes; University of California San Diego; and University of California, Berkeley presented the first complete, spatial cell-type atlas of a mammalian brain. The findings, contained within ten studies, were published in a special issue of Nature and reveal stunning cell-type diversity and organizational principles that will play a critical role in understanding the brain in health and disease. The massive body of work represents a complete parts list of the mouse brain and involved the analysis of around 32 million cells, which uncovered around 5300 distinct cell types.

A New Hub for Scientific Discovery

The Seattle Hub for Synthetic Biology is developing advanced technologies for real-time tracking of genetic and molecular changes in millions of cells. This joint effort by the Allen Institute, Chan Zuckerberg Initiative, and the University of Washington aims to understand how such changes can lead to disease, with the ultimate goal of creating interventions that target and repair cellular damage in the earliest stages. The new technology will be based on innovations from the Allen Discovery Center for Cell Lineage Tracing, including the DNA Typewriter and ENGRAM. The center will feature genomic engineering and synthetic biology experts from the Allen Institute and UW, led by UW Medicine researcher Jay Shendure.

Seattle Hub for Synthetic Biology wordmark

Lake Conferences

Debuting a global showcase of neuroscience innovation and research

This year, the Allen Institute helped convene the world’s brightest minds to engage in stimulating forums for discussion and catalyze scientific collaborations in key areas of neuroscience. The Allen Institute and Circuit Neuroscience Basel organized and hosted the Seattle Lake Conference along the beautiful shores of Lake Washington. Held from September 17 to 21, the premier event focused on neural coding and dynamics at the brain-wide level, their implementation in evolved neural circuits, and the impact of artificial intelligence in understanding the brain. The Lake Conferences are jointly organized by Circuit Neuroscience Basel and the Allen Institute, and are held in Switzerland and Seattle.  

Education and Engagement

Supporting users of the Allen Institute’s open science resources in the classroom and lab.  

The Education and Engagement program extends the impact of the Allen Institute’s open science by providing learning opportunities for students, teachers, and researchers. Formally established in late 2022, the program reaches K-12, college, scientific, and public communities in Seattle and across the world. From January through September 2023, we reached:

Teachers look into microscope at Allen Institute Education seminar

Over 100 high school and college educators through our new Teacher Academy professional development program 


Over 500 high school and college students in field trips to the Allen Institute and visits to local high schools 


Over 1000 members of our Seattle community and beyond in two public programs 


Over 1300 scientists through outreach at three scientific conferences and two training workshops onsite at the Allen Institute 

Our Data

Big Science means big data, and the Allen Institute is entering an era of exascale biology with large-scale, ambitious projects that yield rich, robust datasets. 

of data generated in 2023
of data under management

Financial Summary

Allenite Demographics

graph showing increasing employee growth over the last 5 years
Graph showing the number of new allenite employees year over year
graph showing active allenite employees based on race and ethnicity
graph showing age and sex of allenite employees


Board of Directors
Executive Leadership
Advisors and Collaborators

Science Programs at Allen Institute