Spatial transcriptomics in ovarian biology technologies: computational challenges, and biological insights

In brief: This review synthesizes the technical landscape of current spatial transcriptomic platforms, addresses computational challenges unique to ovarian tissue, and surveys biological discoveries across ovarian development, aging, follicle dynamics, and cancer, providing a practical framework to guide platform selection and analytical strategy in reproductive biology. Abstract: The ovary is a structurally complex organ whose function depends on precisely coordinated interactions among multiple cell types. Spatially resolved transcriptomics (ST) has emerged as a powerful complement to single-cell RNA sequencing (scRNA-seq), enabling gene expression profiling within intact tissue and preserving the spatial context that dissociation-based methods inherently lack. This review provides a comprehensive overview of the major ST platforms, including sequencing-based technologies (Visium, Visium HD, Stereo-seq, and GeoMx) and imaging-based technologies (Xenium, MERSCOPE, and CosMx), with a focus on their distinct technical features, resolution trade-offs, and suitability for ovarian research. We survey 40 published studies applying ST to ovarian biology, spanning atlases, ovarian aging, follicle development and ovulation, and ovarian cancer. We also discuss typical computational analyses as well as their challenges specific to ovary, including cell segmentation of morphologically diverse cell populations, deconvolution of mixed-cell capture spots in sequencing-based platforms, quality control, batch correction, and spatially aware downstream analyses encompassing trajectory inference, cell-cell interaction modeling, gene regulatory network reconstruction, and more. Across these biological contexts, multimodal integration, pairing ST with scRNA-seq, spatial proteomics, or chromatin accessibility profiling, has proven increasingly valuable for resolving the full molecular complexity of ovarian biology. Nevertheless, some challenges persist, and no single platform is universally optimal for all research questions. Thoughtful alignment between biological objectives, tissue scale, and platform capability will be critical for advancing ST from descriptive mapping toward mechanistic and clinically translatable discovery.