Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem.

Area of Science:

• Spatial omics
• Genomics
• Bioinformatics

Background:

• Spatial omics technologies map tissue architecture and gene regulation.
• These technologies generate vast, multi-scale data, posing integration challenges.
• Efficiently harmonizing diverse spatial omics datasets is crucial for biological discovery.

Purpose of the Study:

• To present Giotto Suite, an integrated, open-source toolbox for spatial omics data analysis.
• To provide a technology-agnostic framework for representing and integrating diverse spatial omics data.
• To enable scalable, flexible, and end-to-end solutions for spatial multi-omic data analysis and visualization.

Main Methods:

• Developed Giotto Suite, a modular R-based software package.
• Created a technology-agnostic data framework for spatial omics data.
• Integrated molecular, morphology, spatial, and annotated feature information.
• Built interoperable interfaces for genomics and spatial data science.

Main Results:

• Giotto Suite allows representation and integration of diverse spatial omics data at any resolution.
• The suite provides scalable solutions for data analysis, integration, and visualization.
• Demonstrated flexible, multi-scale, multi-omic data analysis workflows.

Conclusions:

• Giotto Suite offers a comprehensive ecosystem for spatial multi-omic data analysis.
• The open-source nature and interoperable interfaces foster custom pipeline development.
• Facilitates deeper mechanistic insights into biological processes and diseases through integrated spatial omics data.