For a more detailed explanation of SPOTlight consider looking at our manuscript: > Elosua-Bayes M, Nieto P, Mereu E, Gut I, Heyn H.
SPOTlight: seeded NMF regression to deconvolute
spatial transcriptomics spots with single-cell transcriptomes.
Nucleic Acids Res. 2021;49(9):e50. doi: 10.1093

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1 Introduction

1.1 What is SPOTlight?

SPOTlight is a tool that enables the deconvolution of cell types and cell type proportions present within each capture location comprising mixtures of cells. Originally developed for 10X’s Visium - spatial transcriptomics - technology, it can be used for all technologies returning mixtures of cells.

SPOTlight is based on learning topic profile signatures, by means of an NMFreg model, for each cell type and finding which combination of cell types fits best the spot we want to deconvolute. Find below a graphical abstract visually summarizing the key steps.