Imaging-based approaches typically use fluorescent in situ hybridization to visualize transcripts directly within intact tissue, achieving subcellular resolution across selected gene panels. These methods reveal fine spatial patterns of gene expression with exceptional precision.

Sequencing-based approaches capture transcripts from defined tissue regions, preserving spatial information through spatially encoded capture areas. After NGS, reads are mapped back to their original locations to reconstruct spatial gene expression patterns, enabling cell-level resolution across large tissue regions.

These approaches allow researchers to link molecular activity with tissue structure and reveal spatial relationships underlying biological function.

Tissue preparation for spatial transcriptomics
Tissue sections are mounted, fixed, stained, and imaged to provide histological context. These preparatory steps preserve tissue morphology and enable the subsequent generation of spatially resolved gene expression data.