Fig. 1: Overview and validation of the IRISeq platform.

a, Schematic illustrating the generation of barcoded hydrogel beads (‘sender beads’ and ‘receiver beads’) through combinatorial indexing. b, Diagram showing the dual interaction between sender and receiver beads for capturing RNA from tissue samples and indexing spatial locations on the array. c, Schematic illustrating the IRISeq experimental pipeline utilizing barcoded gel beads (‘receiver beads’) to capture mRNA expression from nearby cells, along with barcoded oligos from adjacent ‘sender beads’ for spatial localization. d, Pie chart detailing the reagent cost breakdown for profiling a tissue section using a 0.6 cm × 0.6 cm bead array. e, Diagram showing the generation of gene count and bead–bead connection matrices from IRISeq data to identify region-specific gene expression and infer bead spatial locations for image reconstruction. f, Depiction of a small-scale IRISeq experiment using a 0.6 cm × 0.6 cm bead array to profile a mouse brain hemisection. g, Box plots displaying the distribution of unique transcripts and gene counts across 5,028 receiver beads from a single tissue section (n = 5,028 observations from one section). Center line, median; box, interquartile range; whiskers, minimum to maximum. h, UMAP plot showing the spatial distribution of receiver beads based on interactions with sender beads, colored by the number of unique transcripts per bead. i, We integrated the gene expression data of receiver beads with spatial transcriptome data from 10x Visium¹⁶. The UMAP plot shows the integrated gene expression clusters, with each bead colored by annotated brain regions. j, UMAP plot visualizing the spatial distribution of receiver beads, with each bead colored by annotated brain regions. Schematics created in BioRender: a, Cao, J. https://biorender.com/6cr9gte (2026); b,c,e,f, Cao, J. https://biorender.com/i2ew4vq (2026).