(Press-News.org) New York, NY [October 1, 2025]—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
END
Even the United Nations International Year of Glaciers' Preservation has seen further massive melting of glaciers in Switzerland. A winter with little snow was followed by heat waves in June 2025 that saw glaciers nearing the record levels of losses of 2022. Snow reserves from the winter were already depleted in the first half of July, and the ice masses began to melt earlier than had rarely ever been recorded. The cool weather in July provided some relief and prevented an even worse outcome. Nevertheless, almost a further three per cent of the ice volume was lost across Switzerland this year, ...
Researchers from the Institute for Bioengineering of Catalonia (IBEC) and CIBER-BBN, in collaboration with teams from the University of Barcelona (UB) and the Institute of Chemical Research – cicCartuja, University of Seville-CSIC, have discovered that long-distance charge transport between two key proteins in the mitochondrial respiratory chain — cytochrome c and respiratory complex III — is mediated by protons and superoxide ions, which are reactive oxygen species. The study was recently published in the journal Small ...
A newly described fossil reveals that leeches are at least 200 million years older than scientists previously thought, and that their earliest ancestors may have feasted not on blood, but on smaller marine creatures.
“This is the only body fossil we’ve ever found of this entire group,” said Karma Nanglu, a paleontologist with the University of California, Riverside. He collaborated with researchers from the University of Toronto, University of São Paulo, and Ohio State University on a paper describing the fossil, which is now published in PeerJ.
Roughly ...
Rochester, MN, October 1, 2025 – A study evaluating how various shift work patterns contribute to kidney stone risk has revealed that shift workers have a 15% higher risk of developing kidney stones, especially younger workers and those with low levels of manual labor. Body mass index (BMI), fluid intake, and other lifestyle factors play key roles contributing to the occurrence of kidney stones. The findings of the novel study in Mayo Clinic Proceedings, published by Elsevier, indicate that kidney stone prevention efforts should extend to shift workers.
Long-term shift work, identified ...
Demand-responsive transport (DRT) is promoted as an inclusive solution to first- and last-mile mobility challenges, but little is known about the barriers to adoption among people with poor health.
Dr. Haruka Kato, a junior associate professor at Osaka Metropolitan University, examined the factors shaping this population's acceptance and use of DRT in Senboku New Town, Osaka. The study applied the Unified Theory of Acceptance and Use of Technology-3 (UTAUT-3) to assess the opportunities and challenges for using DRT.
The findings reveal that community involvement is a powerful driver of acceptance. The study showed that residents' ...
A research group led by Dr. Shinichi Furuya of the NeuroPiano Institute and Sony Computer Science Laboratories, Inc. announced research findings that for the first time scientifically clarified how pianists’ manipulations of keys alters piano timbre.
Creativity in painting, music, and other arts is underpinned by the ability to create diverse perceptual experiences for audiences. However, whether timbre could actually be changed mid-instrumental performance, and what physical motor skills would be required to do so, remained unclear.
The research group developed a unique sensor system that can measure piano key movements at ...
Bottom Line: In a retrospective study, the 313-SNP breast cancer polygenic risk score (PRS313) blood test could predict future incidents of breast cancer in women diagnosed with ductal carcinoma in situ (DCIS) or lobular carcinoma in situ (LCIS).
Journal in Which the Study was Published: Cancer Epidemiology, Biomarker & Prevention, a journal of the American Association for Cancer Research (AACR)
Author: Jasmine Timbres, clinical information analyst at King’s College London and the study’s lead author, and Elinor J. Sawyer, PhD, the study’s senior author and professor of clinical oncology at King’s College London in the United Kingdom.
Background: ...
Studying a person’s genetic makeup can predict if they will go on to develop invasive breast cancer after abnormal cells have been found in their breast tissue.
For the first time, researchers at King’s College London have shown the connection between a person’s genetic risk score and their risk of developing the disease after irregular cells have been detected.
The research, published in Cancer Epidemiology, Biomarkers & Prevention and funded by Breast Cancer Now, included over 2,000 women in the UK who had been tested for 313 genetic changes, known as a genetic risk score.
These patients had already been diagnosed with either ductal carcinoma in situ (DCIS) ...
Even though many years have passed since the start of the COVID-19 pandemic, the effects of infection with SARS-CoV-2 are not completely understood. This is especially true for Long COVID, a chronic condition that can develop after COVID-19 that causes a variety of lasting symptoms. Among the most common and debilitating of these is cognitive impairment, often referred to as “brain fog,” which affects over 80% of people with Long COVID. Given the hundreds of millions of global cases, Long COVID represents a massive public health and socioeconomic challenge, as it severely ...
People who sleep poorly are more likely than others to have brains that appear older than they actually are. This is according to a comprehensive brain imaging study from Karolinska Institutet, published in the journal eBioMedicine. Increased inflammation in the body may partly explain the association.
Poor sleep has been linked to dementia, but it is unclear whether unhealthy sleep habits contribute to the development of dementia or whether they are rather early symptoms of the disease. In a new study, researchers at Karolinska Institutet have investigated the link between sleep characteristics and how old the brain appears in relation ...
