Gene expression cartography of a developing neuronal structure

Brains are complex structures comprising thousands to billions of neurons that belong to thousands of different neuronal types. These neurons often come from different progenitor domains and have very diverse developmental histories, yet they need to find their precise locations in the brain and integrate into appropriate circuits. While a large number of brain single-cell mRNA sequencing atlases have described the neuronal part list of the brain, spatial transcriptomic studies have lagged behind in offering the spatial information that is essential to understand brain structures. Here, we use a gene expression cartography algorithm called Novosparc to reconstruct the spatial distribution of gene expression and cell type localization in a complex, yet tractable, developing brain structure, the Drosophila optic lobe. We generate a three-dimensional atlas of this structure (https://larva3dnovosparc.ijm.fr); this atlas allowed us to identify spatially patterned transcription factors that define neuronal types. Importantly, we identify caveats in the algorithm and we discuss limitations of the current implementation that should guide future algorithmic improvements. Altogether, this work provides an invaluable tool to test gene expression patterns and paves the way for the generation of three-dimensional atlases of more complex brain structures, which will enhance our understanding of how neurons with diverse developmental lineages can integrate to form a functional brain.