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Practical Guide to Cell Segmentation, Domain Identification and Cell Type Annotation in Single-Cell Spatial Transcriptomics (Visium HD)
A hands-on tutorial covering cell segmentation with SOPA (StarDist + ProSeg), spatial domain identification with Novae (with batch correction on the fly), and cell type annotation using 1) reference-based methods, deconvolution on 8 µm bins with RCTD-py and FlashDeconv, plus CellTypist on segmented cells using a scRNA-seq reference, and 2) reference-free annotation with Enrichmap gene set signatures (with built-in batch correction and spatial smoothing), on a Visium HD colorectal cancer dataset.
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Cancer subtyping using cNMF and literature markers
An example of usage of cNMF to identify cancer subtypes