Spatial and Functional Analysis of the Mammalian Brain

The mammalian brain is composed of an extraordinarily diverse cell types, yet how these cells are spatially organized in the human brain—and how this organization differs across species or in disease—remains poorly understood. In this talk, I will present two innovations in spatial transcriptomics aimed at addressing this gap. In the first part, I will introduce genome-scale MERFISH, a transcriptome imaging method capable of profiling over 4,000 genes in situ at single-cell resolution. Applying this approach to the human cerebral cortex, we identified more than 100 transcriptionally distinct cell populations and constructed a spatially resolved, molecularly defined cell atlas. Comparative analysis with mouse cortex revealed conserved laminar organization, but also species-specific differences—particularly in somatic interactions between neurons and non-neuronal cells—highlighting unique aspects of human brain organization. While MERFISH has primarily been applied to thin tissue sections (~10 µm), many biological questions require volumetric analysis of thicker tissue samples. In the second part of the talk, I will present 3D MERFISH, a method that combines MERFISH with confocal microscopy for optical sectioning and deep learning for enhanced image reconstruction. We applied this technique to mouse brain tissue up to 200 µm thick, achieving high detection sensitivity and spatial fidelity. Together, these genome-scale and volumetric transcriptome imaging methods expand the capabilities of spatial genomics, enabling unprecedented insight into brain organization, species evolution, and disease mechanisms.