The Challenge of Cell Segmentation in Spatially Resolved Transcriptomics

Abstract

Spatially resolved transcriptomics (SRT) is transforming how we study tissues by measuring gene expression in cells in their spatial context. However, the field lacks robust methodological guidance on one of its most fundamental analytical steps: how to accurately segment cells and assign spatially localized transcripts to them. Major technical challenges include sparse molecular signals, transcript displacement, complex cellular morphologies, and the projection of three-dimensional tissue architecture onto two-dimensional imaging planes. These challenges make segmentation a major source of uncertainty, with errors that can propagate through downstream analyses and ultimately lead to misleading biological interpretations. Here, we argue that segmentation should be treated as a central unresolved problem in spatial omics rather than a routine preprocessing step. We review current approaches, highlight key methodological limitations, including the lack of appropriate metrics and gold-standard benchmarks, and propose a community-driven path forward. Establishing shared evaluation frameworks, scalable benchmark datasets, and transparent reporting standards will be essential for transforming SRT into a robust and reproducible foundation for biological discovery and clinical translation.