New Software Tool Aims to Help Scientists Better Analyze Complex Spatial Data From Tissues
“Giotto Suite” to streamline the study of tissue biology and disease mechanisms
Illustration depicting the conceptual and flexible integration of spatial datasets across multiple length scales and data modalities in Giotto Suite. Credit: Chen, Chávez-Fuentes, et al., Nature Methods
Researchers at the Icahn School of Medicine at Mount Sinai in New York, Boston Medical Center, and Boston University Chobanian & Avedisian School of Medicine, have developed a software platform to help scientists more easily analyze the molecular structure of tissue in both healthy and disease states. Details on the platform, called Giotto Suite, were reported in the October 1 online issue of Nature Methods [DOI: 10.1038/s41592-025-02817-w].
In recent years, new technologies have made it possible to capture detailed maps of RNA and proteins within intact tissues—a field known as spatial omics. These advances are providing valuable insight into how cells behave and interact in different tissue microenvironments, which is especially important for understanding conditions such as cancer, neurodegenerative diseases, and immune disorders.
“While spatial omics technologies are generating incredibly rich data about the molecular landscape of tissues, the real challenge now lies in analyzing and interpreting that data,” says co-senior corresponding author Guo-Cheng Yuan, PhD, Professor of Genetics and Genomic Sciences, at the Icahn School of Medicine at Mount Sinai. “The biggest obstacle is no longer generating the information—it’s making sense of it. Biologists need tools that can keep pace with the growing complexity and scale of these datasets and help them draw meaningful conclusions. We wanted to create a tool that not only simplifies the analysis process, but also adapts to different types of spatial data and workflows, so researchers can focus on the science rather than the technical hurdles.”
To meet this need, the research teams created Giotto Suite, a suite of modular software tools built in R, a widely used programming language for data analysis. The tool is designed to work with spatial data from any platform and supports a broad range of analyses, including data integration across different types of measurements and resolutions. Its flexible structure also allows users to begin analysis from multiple points, depending on their research needs, say the investigators.
“Many existing tools require users to combine multiple packages to complete a full analysis,” says co-senior corresponding author Ruben Dries, PhD, Assistant Professor of Medicine, Hematology and Medical Oncology at Boston University (BU) Chobanian & Avedisian School of Medicine and Associate Member of the Center for Regenerative Medicine (CReM) at Boston Medical Center and BU. “This tool brings those steps into a single framework, aiming to streamline the process. We also developed it with scalability in mind to accommodate the growing size and complexity of spatial datasets. Our goal was to develop a platform that helps other researchers uncover new insights from their spatial data.”
The researchers cautioned that the current version includes only a subset of available analytical methods, which may not suit every research question. They emphasized, however, that the platform is intended to evolve and that they plan to continue expanding its features, enhancing its interoperability with external software packages, and offering training and support to the research community.
Looking ahead, the researchers plan to apply Giotto Suite in their own studies of cancer and neurodegenerative diseases, while continuing to refine the tool based on feedback from the scientific community. The tool is freely available to researchers at http://giottosuite.com, and the team hopes it will encourage wider use of spatial omics technologies in biomedical research.
The paper is titled “Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem.”
The study’s authors, as listed in the journal, are Jiaji George Chen, Joselyn Cristina Chávez-Fuentes, Matthew O’Brien, Junxiang Xu, Edward Ruiz, Wen Wang, Iqra Amin, Jeffrey Sheridan, Sujung Crystal Shin, Sanjana Varada Hasyagar, Irzam Sarfraz, Pratishtha Guckhool, Adriana Sistig, Veronica Jarzabek, Guo-Cheng Yuan, and Ruben Dries.
This work was supported by the Chan Zuckerberg Initiative’s Essential Open Source Software for Science Program (2022-252544); The Crazy 8 Initiative from the Alex’s Lemonade Stand Foundation for Childhood Cancer; and the National Institutes of Health (NIH) RF1MH128970, RF1MH133703, R01AG066028.
About the Icahn School of Medicine at Mount Sinai
The Icahn School of Medicine at Mount Sinai is internationally renowned for its outstanding 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 academic health systems in the United States, providing care to New York City’s large and diverse patient population.
The Icahn School of Medicine at Mount Sinai offers highly competitive MD, PhD, MD-PhD, and master’s degree programs, with enrollment of more than 1,200 students. It has the largest graduate medical education program in the country, 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 innovative 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 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
About the Mount Sinai Health System
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, more than 400 outpatient practices, more than 600 research and clinical labs, a school of nursing, and a leading school of medicine and graduate education. Mount Sinai advances health for all people, everywhere, by taking on the most complex health care challenges of our time—discovering and applying new scientific learning and knowledge; developing safer, more effective treatments; educating the next generation of medical leaders and innovators; and supporting local communities by delivering high-quality care to all who need it.
Through the integration of its hospitals, labs, and schools, Mount Sinai offers comprehensive health care 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 the five boroughs of New York City, Westchester, Long Island, and Florida. Hospitals within the System are consistently ranked by Newsweek’s® “The World’s Best Smart Hospitals, Best in State Hospitals, World Best Hospitals and Best Specialty Hospitals” and by U.S. News & World Report's® “Best Hospitals” and “Best Children’s Hospitals.” The Mount Sinai Hospital is on the U.S. News & World Report® “Best Hospitals” Honor Roll for 2025-2026.
For more information, visit https://www.mountsinai.org or find Mount Sinai on Facebook, Instagram, LinkedIn, X, and YouTube.