Mapping where different cells sit in tissues using images and single-cell gene data
Integrative analysis of spatial transcriptomics with histology images and single cells
This project links routine tissue microscope images with detailed single-cell gene data to learn which cells are where in tissues and how they relate to disease.
Quick facts
| Grant type | R01 grant |
|---|---|
| Study type | NIH-funded research |
| Funding institution | University of Pennsylvania NIH-funded |
| Lab location | 1 site (Philadelphia, United States) |
| Project ID | NIH-11169850 on NIH RePORTER |
What this research studies
Researchers are using gene reads from individual cells (single-cell RNA sequencing) together with spatial gene maps and standard H&E tissue images to learn how cell types are arranged inside tissues. They will develop computer methods that match single-cell profiles to locations on tissue images and to the sparser spatial transcriptomics spots. Because full spatial gene maps are costly, the team aims to use the cheaper H&E images plus single-cell data to predict fine-grained spatial information more broadly. This work is meant to reveal where disease-related cells are and how they interact inside affected tissue.
Who could benefit from this research
Good fit: Ideal participants are people willing to donate surgical or biopsy tissue samples or who allow their existing clinical tissue samples to be used for research.
Not a fit: Patients who do not donate tissue or whose conditions are unrelated to the tissues under study are unlikely to receive direct benefit from this project.
Why it matters
Potential benefit: If successful, this could help doctors pinpoint disease-driving cell types in tissue and support more precise diagnoses and targeted therapies in the future.
How similar studies have performed: Related methods have shown promise in labs, but integrating routine H&E images, single-cell data, and spatial maps at scale remains a fairly new and developing approach.
Where this research is happening
Philadelphia, United States
- University of Pennsylvania — Philadelphia, United States (Active)
Researchers
- Principal investigator: Li, Mingyao — University of Pennsylvania
- Study coordinator: Li, Mingyao
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.