BackgroundThe brain integrates multiple scales of description, from the level of cells and molecules to large-scale networks and behaviour. Understanding relationships across these scales may be fundamental to advancing understanding of brain function in health and disease. Recent neuroimaging research has shown that functional brain alterations that are associated with schizophrenia spectrum disorders (SSD) are already present in young adults at clinical high-risk for psychosis (CHR-P), yet the cellular and molecular determinants of these alterations remain unclear.MethodsHere, we used regional cerebral blood flow (rCBF) data from 425 individuals (122 SSD compared to 116 HCs, and 129 CHR-P compared to 58 HCs) and applied a novel pipeline to integrate brain-wide rCBF case-control maps with publicly available transcriptomic data (17,205 gene maps) and neurotransmitter atlases (19 maps) from 1074 healthy volunteers.ResultsWe identified significant correlations between astrocyte, oligodendrocyte precursor cell, and vascular leptomeningeal cell gene modules for both SSD and CHR-P rCBF phenotypes, and additionally microglia and oligodendrocytes in CHR-P. Receptor distribution significantly predicted case-control rCBF differences, with dominance analysis highlighting dopamine (D1, D2, DAT), acetylcholine (VAChT, M1), GABAA, and NMDA receptors as key predictors for SSD (R2adj=.58, PFDR<.05) and CHR-P (R2adj=.6, PFDR<.05) rCBF phenotypes. These associations were primarily localised in subcortical regions and implicate cell-types involved in stress response and inflammation, alongside specific neuroreceptor systems, in shared and distinct rCBF phenotypes in psychosis.ConclusionsOur findings underscore the value of integrating multi-scale data as a promising hypothesis-generating approach towards decoding biological pathways involved in neuroimaging-based psychosis phenotypes, potentially guiding novel interventions.