Technology-Agnostic Software Streamlines Analysis of Spatial Tissue Data

A team led by researchers at the Icahn School of Medicine at Mount Sinai has created Giotto Suite, a software platform designed to help scientists analyze the molecular structure of tissues in both healthy and disease states. The platform was described in Nature Methods.

Increasingly, spatial omics is being used for studying how cells interact within their environments, especially in the context of cancer, immune disorders, and neurodegenerative diseases. However, interpreting the large and complex datasets produced by these technologies has become a significant challenge.

“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,” noted co-senior author Guo-Cheng Yuan. “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.”

Giotto Suite is built in R, a widely used programming language for data analysis, and offers modular tools that support a variety of spatial data sources. It allows integration across different measurement types and resolutions, giving users flexibility to approach analyses from different starting points. Co-senior author Ruben Dries emphasized the importance of unifying multiple steps into one streamlined framework. “Many existing tools require users to combine multiple packages to complete a full analysis,” Dries said. “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.”

The team acknowledged that the current version of Giotto Suite includes only a subset of available analytical methods, which may not fit every research application. They highlighted their plan to expand its functions, improve connections with external tools, and provide training for the research community. Giotto Suite is freely available online, and the teams plan to apply it to their own research in cancer and neurodegenerative disease while continuing to refine the platform based on user feedback.