3D maps of human tissues using spatial gene data
Methods to build and annotate tissue atlases using spatial genomic data
['FUNDING_R01'] · J. DAVID GLADSTONE INSTITUTES · NIH-11184228
Researchers are building tools that turn 2D tissue images and spatial gene data into searchable 3D maps to help doctors and scientists understand how cells are arranged in healthy and diseased tissues.
Quick facts
| Phase | ['FUNDING_R01'] |
|---|---|
| Study type | Nih_funding |
| Sex | All |
| Sponsor | J. DAVID GLADSTONE INSTITUTES (nih funded) |
| Locations | 1 site (SAN FRANCISCO, UNITED STATES) |
| Trial ID | NIH-11184228 on ClinicalTrials.gov |
What this research studies
If you donate or allow use of tissue samples, the team will combine 2D slices and spatial genomic data from methods like MERFISH, Slide-seqV2, MIBI, and histology images to recreate tissues in three dimensions. They will align and stitch slices into a 3D coordinate system and link single-cell molecular profiles to locations in the atlas. The atlas will be labeled with landmarks and genomic markers so researchers can query specific spots, regions, or cell types. This work is aimed at making it easier to compare samples and spot disease-related changes in tissue structure.
Who could benefit from this research
Good fit: Adults (21+) who can donate fresh or archived tissue samples or agree to allow their clinical tissue specimens to be used for research are the ideal candidates.
Not a fit: Patients seeking immediate clinical treatment or direct personal benefit are unlikely to gain direct health benefit from participating in this methods-focused research.
Why it matters
Potential benefit: If successful, these 3D tissue atlases could help researchers pinpoint disease-related cell types and environments, which may speed discovery of diagnostics and treatments.
How similar studies have performed: Other spatial genomics and tissue atlas efforts have shown promise, but creating annotated, queryable 3D atlases from varied 2D spatial datasets is a newer and still-developing approach.
Where this research is happening
SAN FRANCISCO, UNITED STATES
- J. DAVID GLADSTONE INSTITUTES — SAN FRANCISCO, UNITED STATES (ACTIVE)
Researchers
- Principal investigator: ENGELHARDT, BARBARA — J. DAVID GLADSTONE INSTITUTES
- Study coordinator: ENGELHARDT, BARBARA
About this research
- This is an active NIH-funded research project — typically early-stage science, not a clinical trial accepting patient enrollment.
- Some NIH-funded labs run parallel clinical studies or seek volunteers for related work. To check, contact the principal investigator or institution listed above.
- For full project details, budget, and progress reports, visit the official NIH RePORTER page below.