A key challenge of analyzing data from high-resolution spatial profiling technologies is to
suitably represent the features of cellular neighborhoods or niches. Here we introduce the …

The rapid growth of large-scale spatial gene expression data demands efficient and reliable
computational tools to extract major trends of gene expression in their native spatial context …

Multiplex immunofluorescence (mIF) assays multiple protein biomarkers on a single tissue
section. Recently, high-plex CODEX (co-detection by indexing) systems enable …

The growth of large-scale spatial gene expression data requires new computational tools to
extract major trends in gene expression in their native spatial context. Here, we describe an …

In many data-driven applications, higher-order relationships among multiple objects are
essential in capturing complex interactions. Hypergraphs, which generalize graphs by …

Background Multiplexed immunofluorescence (mIF) methods image dozens of molecules at
subcellular resolution and whole-slide scale, allowing detailed characterization of tumor …

Abstract Development and homeostasis in multicellular systems both require exquisite
control over spatial molecular pattern formation and maintenance. Advances in spatially …

Background Multiplexed immunofluorescence imaging is a powerful spatial biology tool that
can produce rich marker expression data at single-cell resolution and whole-slide scales …

The rapid development of deep learning methods has transformed concepts and pipelines
in the analysis of large-scale data cohorts. In parallel, datasets of unprecedented size and …