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.

Example Functionalities

Analysis and visualization of large-scale spatial transcriptomic and proteomic datasets.

Fig.A Visualization in both expression (top) and physical (bottom) space of the cell types identified by Giotto Analyzer in the pre-optic hypothalamic merFISH dataset, which consists of 12 slices from the same 3D sample (distance unit = 1 μm). Fig.B Heatmap showing the marker genes for the identified cell populations in Fig.A, Fig.C Visualization in both expression and physical space of two representative slices within the z-orientation (100 μm and 400 μm). Fig.D, Fig.E Overlay of gene expression in both expression and physical space for the selected slices in Fig.C, Fig.F.

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