Wang, YuhanEddison, MarkFleishman, GregWeigert, MartinXu, ShengjinWang, TimRokicki, KonradGoina, CristianHenry, Fredrick E.Lemire, Andrew L.Schmidt, UweYang, HuiSvoboda, KarelMyers, Eugene W.Saalfeld, StephanKorff, WyattSternson, Scott M.Tillberg, Paul W.2022-01-152022-01-152022-01-152021-12-2210.1016/j.cell.2021.11.024https://infoscience.epfl.ch/handle/20.500.14299/184584WOS:000735385600003Determining the spatial organization and morphological characteristics of molecularly defined cell types is a major bottleneck for characterizing the architecture underpinning brain function. We developed Expansion Assisted Iterative Fluorescence In Situ Hybridization (EASI-FISH) to survey gene expression in brain tissue, as well as a turnkey computational pipeline to rapidly process large EASI-FISH image datasets. EASI-FISH was optimized for thick brain sections (300 mm) to facilitate reconstruction of spatio-molecular domains that generalize across brains. Using the EASI-FISH pipeline, we investigated the spatial distribution of dozens of molecularly defined cell types in the lateral hypothalamic area (LHA), a brain region with poorly defined anatomical organization. Mapping cell types in the LHA revealed nine spatially and molecularly defined subregions. EASI-FISH also facilitates iterative reanalysis of scRNA-seq datasets to determine marker-genes that further dissociated spatial and morphological heterogeneity. The EASI-FISH pipeline democratizes mapping molecularly defined cell types, enabling discoveries about brain organization.Biochemistry & Molecular BiologyCell Biologysingle cellsmouseneuronsarearnaexpressionparallelratpopulationsprojectionstext::journal::journal article::research article