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Fig. 1 | Genome Biology

Fig. 1

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

Fig. 1

The Giotto framework to analyze and visualize spatial expression data. a Schematic representation of the Giotto workflow to analyze and visualize spatial expression data. Giotto Analyzer requires a count matrix and physical coordinates for the corresponding cells. It follows standard scRNAseq processing and analysis steps to identify differentially expressed genes and cell types. In the following step, a spatial grid and neighborhood network is created which is further used to incorporate the spatial information of the single-cell environment and which is used for spatial analysis. b Cell coordinates, annotations, and clustering information are utilized and incorporated in the Giotto Viewer. This interactive viewer allows users to explore the link between cells’ physical positions and their clustering pattern in the expression space (UMAP or tSNE). The addition of raw subcellular transcript coordinates, staining images, or cell segmentation information is also supported. c Overview of the selected broad range of different spatial technologies and datasets which were analyzed and visualized with Giotto. For each dataset the number of features (genes or proteins) and number of cells are shown before filtering. The technologies depicted are sequential fluorescence in situ hybridization plus (seqFISH+), Visium 10X (Visium), Slide-seq, cyclic-ouroboros single-molecule fluorescence in situ hybridization (osmFISH), multiplexed error-robust fluorescent in situ hybridization (merFISH), spatially resolved transcript amplicon readout mapping (STARmap), tissue-based cyclic immunofluorescence (t-CyCIF), Multiplex Ion Beam Imaging (MIBI), and CO-Detection by indexing (CODEX)

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