Greg Fleishman

Abstract Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. Here, we introduce cycle Hybridization Chain Reaction (HCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system.

Highlights • EASI-FISH enables robust gene expression profiling in thick brain slices • A turnkey analysis pipeline for facile analysis of large EASI-FISH image datasets • EASI-FISH reveals molecularly defined subregions of the lateral hypothalamus • Cell type subdivisions corresponding to morphology, functional tuning, and location Summary Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the...