Publication Date
9-1-2025
Journal
Trends in Genetics
DOI
10.1016/j.tig.2025.05.002
PMID
40461389
PMCID
PMC12486146
PubMedCentral® Posted Date
9-1-2026
PubMedCentral® Full Text Version
Author MSS
Abstract
Spatial transcriptomics (ST) enables systematic profiling of whole-transcriptome gene expression in tissues while preserving spatial context. Recent advances in sequencing- and imaging-based ST technologies have ushered in the era of microscopic-resolution ST (μST), allowing transcriptome mapping at cellular and even subcellular scales with unprecedented precision. Despite these advances, μST faces substantial challenges, including sparse transcript discovery per submicron (or micron)-sized spatial units and data fragmentation across platforms, hindering integration and analysis. There is also a growing demand for scalable, segmentation-free, and universally applicable analysis methods, as well as strategies for 3D mapping, multi-omics integration, and artificial intelligence (AI)-driven spatial analysis. In this review, we highlight recent breakthroughs, outline key challenges, and discuss emerging experimental and computational solutions shaping the future of μST.
Keywords
Humans, Transcriptome, Gene Expression Profiling, Genomics, Artificial Intelligence, Animals, Computational Biology
Published Open-Access
yes
Recommended Citation
Si, Yichen; Lee, Joo Sang; Jun, Goo; et al., "Spatial Omics Enters the Microscopic Realm: Opportunities and Challenges" (2025). Faculty, Staff and Students Publications. 7897.
https://digitalcommons.library.tmc.edu/baylor_docs/7897