Steller: a high-resolution platform for spatial clonal tracing of mammalian brain development

Resolving both lineage history and spatial position at single-cell resolution is essential for understanding how tissue assemble, yet simultaneously interrogation of both dimensions remains technically challenging. Here, we present Steller (Spatio-temporal cell lineage tracker), an integrated experimental and computational framework that overcomes the sensitivity bottleneck limiting lineage barcode detection in high-resolution spatial transcriptomics (ST). By co-depositing capture probes alongside conventional poly(T) oligonucleotides on high-density spatial arrays, Steller achieves targeted enrichment of lineage barcodes at spatial single cell resolution. Applied to clonally labeled embryonic day 12.5 (E12.5) mouse forebrain development harvested at postnatal day 4 (P4), Steller increased the proportion of barcode-detectable cells and recovered higher clonal diversity compared with poly(T) chip. Leveraging this enhanced sensitivity, we resolved distinct spatial clonal architectures across three forebrain regions: horizontal or radial-to-horizontal transitions in hippocampal pyramidal neurons, dorsoventrally restricted yet multi-nuclei spread in thalamus, and fate-restricted spiny projection neuron lineages. Steller establishes a generalizable strategy for lineage-enhanced spatial profiling compatible with existing high-resolution spatial transcriptomics platforms and adaptable to diverse biologic process, providing a framewrok for investigating lineage-dependent tissue organization. HighlightsO_LISteller integrates targeted lineage-barcode enrichment with high-resolution spatial transcriptomics C_LIO_LISteller substantially improves clonal detection sensitivity at single-cell resolution C_LIO_LISteller reveals region-specific spatial clonal architectures across the developing mouse forebrain C_LI