What we do!
We develop novel computational methods to study and understand tissue micro-anatomy using spatial-omics data acquired via diverse technologies. Our method has implications in clinical diagnostics and allows for studying the fundamentals of biological systems. Currently, our major focus involves studying diabetic kidney disease in humans.
$14M External Grant Funding
100 100 percent of our graduated Ph.D. students are placed in prominent pharma companies.
Latest works!
We published our work for the community on our cloud-based instance for digital pathology WSI visualization, automated segmentation, and error correction for training a semantic segmentation model. The source code, docker image, and a video overview are freely made available for the community.
Our work integrating deep semantic segmentation and transformer models for disease progression prediction starting from digital image pixels and preserving pixel level spatial relationships between important tissue structures is available online. Great work by Ben Shickel (Assistant Professor, Medicine – Quantitative Health) and Nicholas Lucarelli.
We released FUSION (Functional Unit State Identification in WSIs), a dynamic and interactive visualization tool specialized for spatially resolved molecular-omics and histology images. Example datasets and more information can be found at here. Link to the codes.
join us!
Postdoctoral Associate position available: Job description.
Undergraduate Research Internship available: Job description.
HuBMAP Summer Internship: HuBMAP Website.
NEWS
4/2/2025 Dr. Pinaki Sarder delivered an invited talk at Northwestern University in Chicago on integrating digital pathology and spatial omics for disease outcome prediction.
4/2/2025 The CMIL team, led by Nicholas, Sumanth, and Suhas, conducted a HuBMAP hackathon in Boston, to develop tools for comparing healthy and diseased tissue at the cellular level.
3/19/2025 Dr. Afsari and Dr. Naglah, recipients of the KPMP travel award, presented their research at Gallaudet University in Washington, D.C.
2/19/2025 The CMIL team presented 6 talks and 1 poster at SPIE Medical Imaging 2025 in San Diego. Team members Dr. Afsari, Dr. Mimar, Akshita, Jamie, Hari, Suhas, and Ishaq contributed across a range of topics in computational pathology and medical imaging.
PRESENTATIONS BY OUR STUDENTS
NOVEMBER 3, 2023
ASN Kidney Week 2023
Akshita Gupta presenting her poster at the ASN Kidney Week 2023; Philadelphia, PA.
APRIL 5, 2023
Undergraduate Research Symposium
Our spring break HUBMAP intern, Nick Sherwin, participated in the UF 2023 Spring Undergraduate Research Symposium.
FEBRUARY 22, 2023
Nick’s poster presentation at SPIE 2023
Nick is presenting his and Brandon Ginley’s poster. The poster received an Honorable Mention Poster Award in SPIE Medical Imaging 2023; San Diego, CA.
