Open 3D Human Organ Atlas lets users explore anatomy in unprecedented detail

An international team of scientists and clinicians has announced the launch of a new open-access 3D portal that allows users to explore intact human organs in unprecedented detail—from the whole organ down to individual cells locally. The Human Organ Atlas, created using a powerful synchrotron imaging method, brings together some of the most detailed 3D images of human organs ever produced. It enables scientists, doctors, educators, students and the wider public to interactively “fly through” organs such as the brain, heart, lungs, kidney and liver, providing a new way of understanding human anatomy and human diseases.

Building on an initial release, the Human Organ Atlas (HOA) is now available in a greatly expanded form and can be accessed directly through a standard web browser, without specialized software. The technology is published in the journal Science Advances.

The Atlas is powered by an advanced imaging method called Hierarchical Phase-Contrast Tomography (HiP-CT), developed at the European Synchrotron (ESRF) in Grenoble, France, by an international team led by University College London (UCL), UK. HiP-CT uses the ESRF’s Extremely Brilliant Source—a new generation of synchrotron source—which is up to 100 billion times brighter than conventional hospital CT scanners.

This allows researchers to scan entire intact ex vivo human organs non-destructively and then zoom in to near-cellular resolution (down to less than one micron, 50 times thinner than the size of a human hair). The technique bridges a century-old gap in medicine between radiology and histology, and represents a major advance in biomedical imaging.

“To create the Human Organ Atlas, we brought together scientists and medics from nine institutes worldwide. This grouping is continuing to expand, helping gain new insights into diseases from osteoarthritis to heart disease and changing how we learn about the human body,” says Peter Lee, Professor at UCL Department of Mechanical Engineering, principal investigator of the HOA beamtime.

“The Human Organ Atlas shows what team science can achieve at its best—we went into this project wanting this data to be used by others and to help further the understanding of human physiology. The Human Organ Atlas is an incredible resource that will continue to grow. I am personally hugely excited to see how the AI community use the Human Organ Atlas in AI foundation models,” says Claire Walsh, Associated Professor at UCL Department of Mechanical Engineering, Director of the Human Organ Atlas Hub.

From COVID-19 to cardiac and gynecological disorders

Initially developed during the COVID-19 pandemic, the method has already led to high-impact publications and scientific advancements, revealing previously unseen microscopic vascular injury in the lungs of patients who died from COVID-19 or reshaping understanding of cardiac disorders. The technology has also been applied to other organs, providing new insights into complex anatomical structures in health and disease, such as pathogenesis of gynecological disorders.

“The virtual 3D histological data derived from Human Organ Atlas hub provide us with valuable insights into the pathogenesis of gynecological disorders. This knowledge is crucial to bridging the current gaps in both understanding and gender disparities,” explains Judith Huirne, Professor of gynecology at Amsterdam UMC medical center.

This Human Organ Atlas portal is the result of more than five years of collaborative effort between many researchers, engineers, clinicians, and infrastructure specialists, united within the Human Organ Atlas Hub, a consortium involving nine institutes across Europe and the United States.

Since its inception, the team has been committed to open science. “From the beginning, we wanted these data to be accessible to everyone and build an open, shared scientific infrastructure at a global scale,” says Paul Tafforeau, ESRF scientist and pioneer of the imaging technique used to create the Human Organ Atlas. “This is a resource for researchers, doctors, educators—but also for anyone curious about how the human body is built.”

“The Human Organ Atlas has in a short while become the gold standard for FAIR data from synchrotrons and is inspiring other communities to do the same,” adds Andy Gotz, ESRF data manager and coordinator of the European Photon and Neutron Open Science Cluster (PANOSC).

A unique tool for AI, medicine and education

To the team’s knowledge, this is the highest-resolution open 3D dataset of intact human organs currently available. The Human Organ Atlas currently provides access to:

• 56 organs, 307 full 3D datasets from 25 donors
• 11 organ types, including brain, heart, lung, kidney, liver, colon, spleen, placenta, uterus, prostate and testis
• Multiscale scans, from whole-organ views down to near-cellular resolution (routinely down to 2 µm, as fine as 0.65 microns for some organs)

The portal has been designed to extend far beyond specialist research laboratories. Each dataset can reach hundreds of gigabytes or even over a terabyte in size. The largest one (a brain) is reaching 14 Tb. To make the data usable worldwide, the portal provides:

• Interactive browser-based visualization (no special software required)
• Downloadable datasets at multiple resolutions
• Tutorials and software tools for analysis
• Regular addition of new data

Beyond advancing anatomical and biomedical research, the Atlas is expected to become a major resource for artificial intelligence. Large, high-quality 3D datasets are rare—limiting the development of advanced medical AI systems. The Human Organ Atlas provides a curated, hierarchical dataset ideally suited for training machine-learning models for segmentation, disease detection and super-resolution analysis.

At the same time, it offers powerful new opportunities for medical education and public engagement with science, allowing anyone to explore the human body out of curiosity.

“Students can explore organs in 3D, scroll through anatomical sections, and zoom into internal tissue detail. It creates an immersive exploratory alternative to classic anatomy diagrams, helping learners build a clearer spatial understanding of complex structures. For both teachers and students, it fundamentally shifts anatomy learning from static description to guided, interactive discovery,” says Alexandre Bellier, Associate professor of anatomy, and head of the Clinical Research Unit of Grenoble Alpes University Hospital.

This is only the beginning. The team plans to expand the collection over the coming years, adding more organs, more samples, and new tools, while growing an open community around the data. The long-term vision is for the atlas to offer access into the inner architecture of the human body and thus, to support research, education, AI development, medical understanding worldwide, and public engagement with science.

“We are opening a new window into the inner architecture of the human body,” says Paul Tafforeau. “After six years of effort, we are still only at the beginning. Currently we work on isolated organs, but in the future, we expect to develop the technique to be able to image complete human bodies with a resolution 10 to 20 times higher than what is possible today. Such data could transform how anatomy is studied and understood.”