Workflow from Scientific Research

Spotiphy workflow. Spotiphy requires three types of input data: scRNA-seq data, spot-level sequencing-based ST data and high-resolution histological images. The workflow consists of five major steps. (1) Reference construction. scRNA-seq data are used to select top marker genes and generate a signature reference for all cell types. (2) Segmentation. The histological image is used to count the number of nuclei in each spot. (3) Generative modeling. ST data are used to generate cell-type proportions and iscRNA data. (4) Imputation. Gaussian processes are used to impute cell-type proportions and iscRNA data for cells located outside the transcriptomic spots. (5) Transformation. The results of steps 3 and 4 are merged to produce a pseudo-single-cell-resolved whole-transcriptome image.

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