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Mammalian brain development is a complex process that starts from the neurulation of the early embryo to maturation and functionalization in postnatal brain development (Stiles and Jernigan, 2010). Major biological events that occur during brain development include cell proliferation, neurogenesis, cell migration, gliogenesis, and myelination, during which numerous cells are generated and migrate to specific regions to obtain corresponding functions (Jiang and Nardelli, 2016). These processes adhere to tight spatiotemporal regulation by extrinsic and intrinsic cues across different anatomical regions or layers (Martinez, 2001; Echevarria et al., 2003; Hodge and Hevner, 2011; Manuel et al., 2015). The disruption of gene expression or regulatory factors can lead to developmental dysfunction or neuropsychiatric diseases (Li et al., 2018; Parenti et al., 2020). Previous studies have mainly focused on the molecular features of specific regions; however, a complete understanding of brain development requires comprehensive characterization of cell types, molecular features, and spatial localization of each cell or gene at the whole-brain scale (Tiklova et al., 2019; Tan et al., 2021).

Mouse brain development can be broadly divided into two stages, embryonic and postnatal. During the embryonic stage, starting from embryonic day 10 (E10), a large number of neurons are generated by cell proliferation and neurogenesis. Within the first week after birth, numerous glial cells are generated, which are critical for neuronal synaptogenesis. By postnatal day 7 (P7), many neurons start forming synaptic connections to build the initial neural circuits of the brain …