Brain maps are essential for integrating information and interpreting the structure-function relationship of circuits and behavior. We aimed to generate a systematic classification of the adult mouse brain based purely on the unbiased identification of spatially defining features by employing whole-brain spatial transcriptomics. We found that the molecular information was sufficient to deduce the complex and detailed neuroanatomical organization of the brain. The unsupervised (non-expert, data-driven) classification revealed new area- and layer-specific subregions, for example in isocortex and hippocampus, and new subdivisions of striatum. The molecular atlas further supports the characterization of the spatial identity of neurons from their single-cell RNA profile, and provides a resource for annotating the brain using a minimal gene set—a brain palette. In summary, we have established a molecular atlas to formally define the spatial organization of brain regions, including the molecular code for mapping and targeting of discrete neuroanatomical domains.

脑图对于整合信息和解释电路和行为的结构-功能关系至关重要。我们的目标是通过采用全脑空间转录组学，纯粹基于对空间定义特征的无偏见识别，对成年小鼠大脑进行系统分类。我们发现分子信息足以推断出大脑复杂而详细的神经解剖结构。无监督（非专家，数据驱动）分类揭示了新的区域和层特异性亚区域，例如等皮质和海马，以及纹状体的新细分。分子图谱进一步支持从单细胞 RNA 谱中表征神经元的空间特性，并提供使用最小基因集（大脑调色板）注释大脑的资源。总之，我们已经建立了一个分子图谱来正式定义大脑区域的空间组织，包括用于映射和定位离散神经解剖域的分子代码。