Giotto: a toolbox for integrative analysis and visualization of spatial expression data

Genome Biol. 2021 Mar 8;22(1):78. doi: 10.1186/s13059-021-02286-2.


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computational Biology / methods*
  • Data Analysis
  • Gene Expression Profiling / methods*
  • Image Processing, Computer-Assisted
  • Immunohistochemistry / methods
  • In Situ Hybridization* / methods
  • Organ Specificity / genetics
  • Software*
  • Spatial Analysis
  • Transcriptome

Associated data

  • Dryad/10.5061/dryad.8t8s248