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bioRxiv · 10.64898/2026.05.27.727615

SpatialDataAgent: Autonomous Spatial Omics Data Curation at Decade Scale

Ji, J.-H.·Zou, Q.·Cheng, J.·She, Z.·Hao, Y.·Liu, W.·Zhang, D.·Wang, Z.·Yu, J.-T.·Yuan, Z.
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Abstract

Fragmented metadata in spatial omics archives has rendered large volumes of multimodal molecular-histological data inaccessible as dark data. Here, we introduce SpatialDataAgent, an agentic workflow for autonomous spatial omics data curation, combining schema-constrained evidence evaluation with a self-refining standardization agent. Applied to a decade of GEO records, SpatialDataAgent identified 769 paired H&E-spatial transcriptomics (ST) datasets, representing a 6.4-fold scale expansion over existing manually curated baselines. Within the benchmarking window, the framework achieved a 141% increase in high-confidence Class A paired datasets. We further assembled a recent high-confidence subset into HESRT, a standardized datalake containing 29.2 million spots/cells, establishing a blueprint for evidence-grounded autonomous curation of multimodal biomedical archives.

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Ji, J.-H., Zou, Q., Cheng, J., She, Z., Hao, Y., Liu, W., Zhang, D., Wang, Z., Yu, J.-T., Yuan, Z.. 2026-05-30. SpatialDataAgent: Autonomous Spatial Omics Data Curation at Decade Scale. https://doi.org/10.64898/2026.05.27.727615

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