The cell-type-specific spatial organization of the anterior thalamic nuclei of the mouse brain

Understanding the cell-type composition and spatial organization of brain regions is crucial for interpreting brain computation and function. In the thalamus, the anterior thalamic nuclei (ATN) are involved in a wide variety of functions, yet the cell-type composition of the ATN remains unmapped at a single-cell and spatial resolution. Combining single-cell RNA sequencing, spatial transcriptomics, and multiplexed fluorescent in situ hybridization, we identify three discrete excitatory cell-type clusters that correspond to the known nuclei of the ATN and uncover marker genes, molecular pathways, and putative functions of these cell types. We further illustrate graded spatial variation along the dorsomedial-ventrolateral axis for all individual nuclei of the ATN and additionally demonstrate that the anteroventral nucleus exhibits spatially covarying protein products and long-range inputs. Collectively, our study reveals discrete and continuous cell-type organizational principles of the ATN, which will help to guide and interpret experiments on ATN computation and function. [Display omitted] •The cell-type landscape of the ATN is investigated with spatial transcriptomics•Sharp spatial delineations in gene expression are found across nucleus boundaries•Graded transcriptomic heterogeneity is present within all individual nuclei•Graded transcriptomic properties spatially covary with proteins and inputs Kapustina et al. investigate the cell-type composition and spatial organization of the anterior thalamic nuclei (ATN) of the mouse brain. They find that the three nuclei forming the ATN are comprised of distinct excitatory cell types and that additional spatially patterned graded heterogeneity is present within each nucleus.