A practical guide for choosing an optimal spatial transcriptomics technology from seven major commercially available options

BMC Genomics. 2025 Jan 20;26(1):47. doi: 10.1186/s12864-025-11235-3.

Abstract

Spatial transcriptomics technology enables the mapping of gene expression within tissues, allowing researchers to visualize the spatial distribution of RNA molecules and gain insights into cellular organization, interactions, and functions in their native environments. A variety of spatial technologies are now commercially available, each offering distinct technical parameters such as cellular resolution, detection sensitivity, gene coverage, and throughput. This wide range of options can make it challenges or create confusion for researchers to select the most appropriate platform for their specific research objectives. In this paper, we will analyze and compare seven major commercially available spatial platforms to guide researchers in choosing the most suitable option for their needs.

Keywords: 10X Visium; 10X visium HD; CosMx SMI; GeoMx DSP; Merscope; RNA sequencing; Spatial transcriptomics; Stereoseq; Xenium.

Publication types

  • Review

MeSH terms

  • Gene Expression Profiling* / methods
  • Humans
  • Transcriptome