{"doi":"10.64898/2025.12.02.691876","title":"Multiscale Spatial Transcriptomic Atlas of Human Basal Ganglia Cell-Type and Cellular Community Organization","abstract":"SUMMARY We generated a multi-region, subcellular-resolution spatial transcriptomic atlas of the human basal ganglia by integrating MERFISH+ and Stereo-seq across four neurotypical donors. These datasets profiled ∼7 million cells spanning the caudate, putamen, nucleus accumbens, and globus pallidus, resolving 60 transcriptionally distinct cell types. We show region-selective, molecular and spatial diversification of medium-spiny-neuron cell types and multiple non-neuronal populations with distinct molecular identities and spatial localizations. Subcellular RNA localization captures somatic size and projection-inferred signatures that reflect direct and indirect pathway topology. Cellular community analyses reveal the enrichment of sub-clusters of astrocytes and oligodendrocytes at striosome–matrix borders, while primate-expanded interneurons are confined to matrix territories. Cross-species mapping uncovers orthologous striosome–matrix organization and conserved dorsolateral-ventromedial gene expression gradients. This atlas provides a foundational molecular and spatial framework for studying human basal ganglia architecture, offering a multi-centimeter scale resource that links cell types, spatial architecture, and subcellular transcript topography across multiple nuclei. Highlights Our multi-centimeter scale spatial taxonomy identifies the precise locations of 60 neuronal and glial cell types of human basal ganglia. MERFISH+ and Stereo-seq platforms map consistent spatial modules that align with classical neuroanatomical nuclei. D1D2 hybrid MSNs and primate-expanded interneurons show regional and domain specific organization Subcellular RNA localization reports soma morphology and projection-inferred signatures.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":556926,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":29.8,"corpus_rank":8723,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9065,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":777168,"name":"Zhiqun Tan","orcid":"0000-0002-2235-4577","position":1,"is_corresponding":false},{"id":1192506,"name":"Ginny Wu","orcid":"0009-0004-3544-3992","position":2,"is_corresponding":false},{"id":1180167,"name":"Sujan C. 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Margarita Behrens","orcid":"0000-0002-7168-8186","position":16,"is_corresponding":false},{"id":136223,"name":"Bing Ren","orcid":"0000-0002-5435-1127","position":17,"is_corresponding":false},{"id":3799,"name":"Joseph R. 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