SAHAAn open research consortium
Spatial Atlas of Human Anatomy
An open, multimodal reference of human tissues at subcellular resolution: matched RNA, protein and histology on the same tissue, across gut and lymphoid organs and circulating blood, in health and selected disease.
Our mission
Every disease starts somewhere in a tissue. To see what goes wrong, we first need a clear, shared picture of what healthy tissue looks like, cell by cell, and we need it to be free for everyone.
SAHA builds that picture. We measure thousands of genes and dozens of proteins in place, on the same tissue section a pathologist reads, and release the results openly so any lab, clinic or student can use them.
About SAHA
SAHA maps how genes, proteins, cells and tissues are organized and interact across the human body, using spatial omics data from donors of varied ages, sexes and ancestries. The goal is a shared reference that improves our understanding of human biology, diagnostics and precision medicine.
Organs
Appendix, bone marrow, colon, ileum, liver, lymph node, pancreas, prostate, rectum and stomach, plus circulating PBMCs. More organs are planned.
Health and disease
Healthy reference tissue, with inflammatory bowel disease, colorectal, pancreatic and prostate cancer as comparators.
Platforms
CosMx RNA (1K–19K-plex) and 64-plex protein, Xenium (377-plex to 5K), with matched H&E, linked to histopathology annotations and clinical metadata.
Open by design
FAIR data in SpatialData format under CC-BY 4.0, analysis code under MIT, and an interactive browser.
Organ coverage
Cells per organ in open release v1, by platform. Hover a bar for exact counts.
| Organ | Donor cores | Acquisitions | Cells | Assays | Tissue states |
|---|
From tissue to open atlas
- Donated tissueHealthy and diseased tissue, given by patients and donors, selected and annotated by pathologists.
- Measured in placeRNA, protein and H&E captured on the same tissue, so every cell keeps its neighbourhood.
- IntegratedCells segmented, typed and matched across platforms and organs into one reference.
- Shared openlyData, code and browsers released free under open licences for anyone to reuse.
Why it matters
A baseline for medicine
Knowing what normal looks like at single-cell resolution helps pathologists and researchers spot the earliest changes in disease.
Diseases side by side
Inflammatory bowel disease and colorectal, pancreatic and prostate cancer profiled with the same methods as healthy tissue, so differences are real, not technical.
Fuel for AI
Matched histology and molecular data teach models to read molecular states from routine H&E slides that every hospital already makes.
Open to all
No paywalls. Students, small labs and hospitals anywhere get the same data as the largest centres.
Milestones
- Spatial omics review in Genome Biology lays out the multimodal approach
- Weill Cornell Medicine and NanoString launch the Spatial Atlas of Human Anatomy
- SAHA presented as a plenary talk at the American Society of Human Genetics
- Spatial Touchstone benchmarking published in Nature Biotechnology
- SAHA atlas preprint posted on bioRxiv
- Release v1: 12.4 million cells across 10 organs, shared with reviewers
- Public release through AWS Open Data, more organs, and the SAHA Explorer browser
SAHA exists because of the patients and donors who gave tissue for research, and their families. We are deeply grateful.
Partners
Academic and research partners
Funding
WCM Englander Institute for Precision Medicine
Industry
Data
Release v1: 126 acquisitions, 12.4 million cells, 10 organs, as SpatialData (zarr v3) objects with full-resolution morphology images, cell segmentation, annotated count and intensity matrices, donor-core assignments and registered H&E. CC-BY 4.0.
Object gallery Request data access
Public download through the AWS Open Data Program and Zenodo opens at publication; until then, request access and we will send instructions. Astronaut PBMC (STAMP) data: preview only, controlled release pending.
Interactive browsers
BioTuring Talk2Data
Browse samples, cell types and gene expression. Free login required; reload the link after signing in.
SAHA Explorer coming soon
Our own deep-zoom browser for H&E, protein and RNA layers on the same tissue.
Code and tools
SAHA on GitHub — github.com/saha-project
All SAHA repositories: paper code, data tooling, integration and phenotyping pipelines.
saha-2026-pub
Analysis code for the atlas paper, by figure, with environment files.
saha-data-access
Data schemas, metadata tables, build and validation scripts, access documentation.
saha-maxfuse
RNA–protein cell matching and integration (MaxFuse).
saha-scimap
Protein marker gating and phenotyping (SCIMAP).
LazySlide
Whole-slide H&E analysis used for SAHA histology (Rendeiro lab, CeMM).
Spatial Touchstone
Cross-platform quality metrics and benchmarking for imaging spatial transcriptomics (Nature Biotechnology 2025).
Publications
- The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs Park J, De Gregorio R, Hissong E, et al. bioRxiv 2025 · in peer review
- Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets Plummer J, Dezem F, Cook D, Park J, et al. Nature Biotechnology 2025 · Spatial Touchstone
- Spatial omics technologies at multimodal and single cell/subcellular level Park J, et al. Genome Biology 2022
How to cite
If you use SAHA data or code, please cite:
Park J, De Gregorio R, Hissong E, et al. The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs. bioRxiv (2025). doi:10.1101/2025.06.16.658716
We will update this to the journal version on publication.
Team
An interdisciplinary collaboration across academia and industry: tissue scientists and pathologists, spatial technology developers, and computational biologists.
Weill Cornell Medicine
Pathology and clinical experts
Collaborators
Industry
Preprint author list (45)
Presentations
Spatial-omics talks and posters on SAHA and related work.
2026
- Multi-Omics 2026Invited speaker · Brisbane, December 2026 (upcoming)
- BIOINFO / GIW ISCB-Asia 2026Invited speaker · November 2026 (upcoming)
- Australasian Genomic Technologies Association (AGTA) Annual Scientific ConferenceInvited speaker
- STOC General Meeting: The Future of Spatial BiologyInvited speaker
- Gordon Research Seminar, Single-Cell Genomics: AI and Machine Learning for Single-Cell and Spatial OmicsInvited speaker
- Nextgen Omics, Spatial & Data USInvited speaker
- DDN Symposium: The Rise of Spatial OmicsInvited speaker
- AGBT General MeetingAbstract-selected speaker
2025
- EMBL Conference: Spatial BiologyInvited speaker
- Human Proteome Organization (HUPO) World CongressAbstract-selected speaker
- American Society of Human GeneticsLightning talk
- American Spatial Biology CongressInvited speaker
- National Society for Histotechnology ConventionKeynote
- 15th International Workshop on Advanced GenomicsInvited speaker
- Complete Molecular Measurement of Human Cells, Organs, and StatesGIST Digital Biology Symposium · invited speaker
- Single-Cell, Multi-Omics Spatial Profiling and Commercial Human SpaceflightNASA Horizons in Biosciences & Informatics Seminar Series · invited speaker
- The Spatial Atlas of Human Anatomy (SAHA): Comprehensive Multi-Omics Spatial Mapping of Human Organ Systems to Improve Precision MedicineAGBT General Meeting · poster
2024
- The SAHA project: Unveiling cellular landscapes of health and diseases and orchestrating a new paradigm in precision medicineAmerican Society of Human Genetics · platform talk
- WCM–NVIDIA AI in Medicine SymposiumSession speaker
- Mapping Health and Disease on Earth and BeyondPrecision Medicine Leaders' Summit, Advances in Single Cell & Spatial Biology · invited speaker
- Mapping Health and Disease on Earth and Beyond: SAHA & Space Omics and Medicine Atlas (SOMA)BioTrac Spatial Biology meeting · invited speaker
- Mapping Health and Disease on Earth and Beyond: SAHA & SOMAFuture of Omics Conference · invited speaker
- Mapping Health and Disease on Earth and Beyond: SAHA and SOMAYoung Scientists Forum for Korea–US Space Medicine Research · invited speaker
- SAHA project: multiscale spatial insights into lung cancer and diseasesUniversity of Cambridge Lung Cancer Workshop · invited speaker
- Mapping Health and Disease on Earth and Beyond: SAHA and SOMAUniversity of Pennsylvania Spatial Biology New Methods Showcase · invited speaker
- The SAHA project: unveiling cellular landscapes and orchestrating a new paradigm in precision medicineAGBT General Meeting · abstract-selected speaker
- SAHA: A Subcellular, Multiscale Spatial Odyssey of Immune and Gastrointestinal Tissues & TumorsAACR Annual Meeting · poster
2023
- The Spatial Atlas of Human Anatomy (SAHA) ProjectSpatial Biology Congress Asia · invited speaker and panelist
- The Spatial Atlas of Human Anatomy: A High-content Spatial Map of the Human BodyAmerican Society of Human Genetics · plenary (abstract-selected)
- The SAHA Project: A High-content Spatial Map of the Human BodyISMB/ECCB · poster
- Spatial omics and multi-omics integrationBumrungrad International Hospital Genetics Seminar Series · invited speaker
2022
- Global Engage Spatial Biology Congress EuropeInvited speaker
- Experimental Biology: Digital Spatial Profiling — Transcriptomics and ProteomicsInvited speaker
News
- SAHA release v1 data available to reviewersOct 2026 · 126 acquisitions, 12.4M cells, 10 organs
- SAHA preprint posted on bioRxivJun 2025 · read the preprint
- Bruker Spatial Biology to announce advances at AGBT 2025Feb 2025
- NanoString launches the CosMx 6,000-plex RNA assayFeb 2024
- Weill Cornell Medicine and NanoString collaborate to create a comprehensive Spatial Atlas of Human AnatomyFeb 2023
Support SAHA
SAHA is an open resource built by many partners. There are several ways to help it grow.
Contribute data
Institutions with spatial omics data on human tissue can join the atlas. See the submission guide.
Partner with us
Technology, pharma and academic partners: co-develop panels, benchmarks and analysis tools.
Fund the atlas
Philanthropic and foundation support sustains open data hosting, new organs and community tools.
Use and cite
Build on the data and code, report issues, and cite the preprint when you do.
What your support makes possible
Free, permanent data hosting
Keeping terabytes of images and cell data online and downloadable at no cost to users.
New organs and donors
Extending the atlas to more tissues and a wider range of ages, sexes and ancestries.
Training and outreach
Workshops, tutorials and early access for students and labs new to spatial biology.
Community tools
Open browsers and analysis software that anyone can use and improve.
Make a gift
Gifts from individuals, foundations and companies directly fund open data and new tissue. Contact us and we will help you give in the way that suits you.
Frequently asked questions
Is SAHA data free to use?
Yes. Data are released under CC-BY 4.0 and code under MIT: reuse them for any purpose, with attribution.
When will the data be publicly downloadable?
Release v1 is shared with reviewers now. Public download through the AWS Open Data Program and Zenodo opens when the atlas paper is published. Until then, request access.
Can my institution contribute data?
Yes. We welcome spatial omics data on human tissue. See the submission guide or write to us.
How is donor privacy protected?
Released data are de-identified. Data with additional consent restrictions, such as the astronaut blood samples, are shared only under controlled access.