The article from Nature Methods introducing the Giotto Suite, a comprehensive and modular software package designed for the analysis, integration, and visualization of spatial multiomics data. The core innovation lies in its technology-agnostic data framework, which efficiently handles diverse and complex datasets—including molecular, morphological, and spatial information—across multiple biological scales. The suite offers end-to-end solutions for challenging tasks like data harmonization, multiomics integration (e.g., RNA and protein), and registration of serial tissue sections, while also focusing on scalability and interoperability with other established bioinformatics ecosystems like R/Bioconductor and Python AnnData. Essentially, Giotto Suite establishes a flexible, integrated ecosystem to facilitate advanced spatial data science for researchers.

References:

• Chen J G, Chávez-Fuentes J C, O’Brien M, et al. Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem[J]. Nature Methods, 2025: 1-13.