257-Nicheformer: for Single-Cell and Spatial Omics

Paper Talk · Nov 22, 2025 · 14m

This paper details the introduction and evaluation of Nicheformer, a novel transformer-based foundation model designed for single-cell and spatial omics data analysis. This model is pretrained on SpatialCorpus-110M, a massive collection of over 110 million cells encompassing both dissociated single-cell and spatially resolved transcriptomics data from human and mouse tissues. Nicheformer learns cell representations that encode spatial context, enabling it to perform effectively on spatial-specific downstream tasks, such as spatial composition prediction and spatial label prediction, where…