Giotto: a toolbox for integrative analysis and visualization of spatial expression data.
IF: 17.906
Cited by: 249


Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spatial data analysis and visualization. The analysis module provides end-to-end analysis by implementing a wide range of algorithms for characterizing tissue composition, spatial expression patterns, and cellular interactions. Furthermore, single-cell RNAseq data can be integrated for spatial cell-type enrichment analysis. The visualization module allows users to interactively visualize analysis outputs and imaging features. To demonstrate its general applicability, we apply Giotto to a wide range of datasets encompassing diverse technologies and platforms.


Spatial Transcriptomics

MeSH terms

Computational Biology
Data Analysis
Gene Expression Profiling
Image Processing, Computer-Assisted
In Situ Hybridization
Organ Specificity
Spatial Analysis


Dries, Ruben
Zhu, Qian
Dong, Rui
Eng, Chee-Huat Linus
Li, Huipeng
Liu, Kan
Fu, Yuntian
Zhao, Tianxiao
Sarkar, Arpan
Bao, Feng
George, Rani E
Pierson, Nico
Cai, Long
Yuan, Guo-Cheng

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