Mount Sinai Scientists Create AI-Powered Tool to Improve Cancer Tissue Analysis

Scientists at the Icahn School of Medicine at Mount Sinai (New York City) have developed a powerful new computational tool that could transform the way in which cancer tissues are analyzed and help foster more personalized treatments. Published in Nature Biomedical Engineering, the study details MARQO, a next-generation image analysis process that extracts detailed cellular and spatial information from tumor tissue slides with unprecedented accuracy and scalability. 

Developed by a team led by Sacha Gnjatic, Ph.D., professor of Immunology and Immunotherapy at the Icahn School of Medicine, MARQO streamlines the task of analyzing immunohistochemistry (IHC) and immunofluorescence (IF) images, which are produced through staining methods commonly used to detect immune cells and other biomarkers in cancerous tissues. 

In cancer patients, pathologists inspect stained tissue sections under the microscope to determine which cells are present and the way(s) they are arranged. Manually doing this is labor‑intensive and usually limited to small sample areas. 

MARQO tackles this challenge in three key ways: First, while other tools can process entire images, they often require users to chop slides into patches or rely on costly computing clusters. MARQO keeps slides intact and finishes the job in minutes rather than hours, even on standard graphics processing units. Second, MARQO works with a range of common IHC and IF staining technologies, making study‑to‑study comparisons easier and boosting reproducibility. Third, MARQO automatically flags likely positive cells and assigns coordinates and marker intensities, then hands off the final validation to the pathologist, keeping human expertise at the center of the workflow. 

“We designed MARQO to fill a major gap in the field: turning complex whole‑slide images into usable, structured data quickly and consistently,” Dr. Gnjatic said. “By automating the heavy lifting, we let experts focus on interpretation and discovery.” 

While MARQO is currently designed for research use and has not been validated for clinical diagnostics, its compatibility with standard clinical staining methods could enable future applications in pathology labs.  

The research team plans to continue developing MARQO by improving its user interface, adding advanced spatial and neighborhood analysis tools, and expanding its use in high-performance computing environments to support large-scale projects involving millions of digitized tissue slides. 

“This platform could accelerate biomarker discovery, improve how we predict which patients will benefit from specific treatments, and ultimately support the development of more precise cancer diagnostics,” Dr. Gnjatic stated. 

Study co-authors include Mark Buckup (now an M.D./Ph.D. student at University of California San Diego); Edgar Gonzalez-Kozlova, Ph.D., assistant professor of Immunology and Immunotherapy in the Gnjatic Lab; Igor Figueiredo, computer engineer; Pauline Hamon, Ph.D. (now junior faculty in France); and Giorgio Ioannou, senior research assistant and lead on the mIHC imaging platform. 

Study funding was provided by the National Cancer Institute, with seed funding from the Icahn School of Medicine at Mount Sinai. 

The Icahn School of Medicine at Mount Sinai is internationally renowned for its research, educational, and clinical care programs. It is the sole academic partner for the seven member hospitals* of the Mount Sinai Health System, one of the largest U.S. academic health systems, providing care to New York City’s patient population.  The Icahn School of Medicine at Mount Sinai enrolls more than 1,200 students. It has the nation’s largest graduate medical education program, with more than 2,600 clinical residents and fellows training throughout the Health System. Its Graduate School of Biomedical Sciences offers 13 degree-granting programs, conducts basic and translational research, and trains more than 560 postdoctoral research fellows.  

Ranked 11th nationwide in National Institutes of Health (NIH) funding, the Icahn School of Medicine at Mount Sinai is among the 99th percentile in research dollars per investigator, according to the Association of American Medical Colleges.  More than 4,500 scientists, educators, and clinicians work within and across dozens of academic departments and multidisciplinary institutes with an emphasis on translational research and therapeutics. Through Mount Sinai Innovation Partners (MSIP), the Health System facilitates the real-world application and commercialization of medical breakthroughs made at Mount Sinai. 

Mount Sinai Health System is one of the largest academic medical systems in the New York metro area, with 48,000 employees working across seven hospitals, over 400 outpatient practices, more than 600 research and clinical labs, a school of nursing, and a school of medicine and graduate education. Mount Sinai tackles complex healthcare challenges—discovering and applying new scientific learning and knowledge; developing safer, more effective treatments; educating the next generation of medical leaders and innovators; and supporting communities by delivering high-quality care.

Through the integration of its hospitals, labs, and schools, Mount Sinai offers comprehensive healthcare solutions from birth through geriatrics, leveraging innovative approaches such as artificial intelligence and informatics while keeping patients’ medical and emotional needs at the center of all treatment. The Health System includes approximately 9,000 primary and specialty care physicians and 10 free-standing joint-venture centers throughout New York City’s five boroughs, Westchester, Long Island, and Florida.

* Mount Sinai Health System member hospitals: The Mount Sinai Hospital; Mount Sinai Brooklyn; Mount Sinai Morningside; Mount Sinai Queens; Mount Sinai South Nassau; Mount Sinai West; and New York Eye and Ear Infirmary of Mount Sinai.