3D spatial single cell omics by jetlet barcoding

Stanford researchers have developed a powerful new method for 3D spatial single-cell omics with cellular resolution using jetlet molecular barcoding.

Current spatial omics tools are limited to thin, 2D tissue slices and cannot achieve cellular resolution in three-dimensional samples. Imaging-based approaches target only a limited set of genes and are unable to capture full-transcriptome or multiomic data.

This platform overcomes those limitations by injecting unique spatial barcodes into intact cells across multiple tissue layers, enabling mapping of each cell's 3D position alongside its molecular profile. Arrays of high-precision fluidic injectors ("jetlets") deliver barcodes from multiple angles without disrupting cell integrity. The platform integrates seamlessly with single-cell sequencing workflows and supports untargeted transcriptomic, proteomic, or multiomic analyses. When paired with confocal microscopy, it also enhances cell boundary and morphology mapping.

This innovation enables deep 3D exploration of tissue architecture, cell–cell interactions, and disease mechanisms, advancing new applications in biomedical research, organoid modeling, drug discovery, and precision diagnostics.