Mapping where genes are active inside tissues to find individual cells and their neighbors
Computational methods for in situ spatial transcriptomics
['FUNDING_OTHER'] · DUKE UNIVERSITY · NIH-11142446
This project builds computer tools to pinpoint RNA molecules and define individual cells in tissue images so scientists can better see how cells are arranged in healthy and diseased tissue.
Quick facts
| Phase | ['FUNDING_OTHER'] |
|---|---|
| Study type | Nih_funding |
| Sex | All |
| Sponsor | DUKE UNIVERSITY (nih funded) |
| Locations | 1 site (DURHAM, UNITED STATES) |
| Trial ID | NIH-11142446 on ClinicalTrials.gov |
What this research studies
Researchers will create new computer methods that combine the exact locations of RNA molecules with tissue images to draw accurate cell boundaries. They will train and refine these methods using modern machine-learning algorithms, including transformer-based image segmentation. The team will produce a manually annotated benchmark dataset from real in situ spatial transcriptomics data across different tissues and disease contexts to test performance. They will also develop ways to group cells and name cell types by combining gene activity with cell shape and local cell density.
Who could benefit from this research
Good fit: Patients whose biopsy or surgical tissue samples (for example tumor, inflammatory, or organ tissue) are shared with the research team or participating biobanks would be the most relevant contributors.
Not a fit: People seeking an immediate therapy or direct clinical benefit should not expect direct treatment from this computational methods project.
Why it matters
Potential benefit: If successful, these tools could help scientists and clinicians understand disease mechanisms at single-cell resolution and improve diagnosis and treatment targets.
How similar studies have performed: Related computational approaches for spatial transcriptomics have shown promise, but this project aims to advance segmentation accuracy and provide new benchmark data that are currently limited.
Where this research is happening
DURHAM, UNITED STATES
- DUKE UNIVERSITY — DURHAM, UNITED STATES (ACTIVE)
Researchers
- Principal investigator: JI, ZHICHENG — DUKE UNIVERSITY
- Study coordinator: JI, ZHICHENG
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.