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bioRxiv · 10.64898/2026.08.13.744704

Bridging Biomedical Atlas Ecosystem: Cross-Atlas Alignment And Scalable Tissue Specimen Registration

Jain, Y.·Desai, B.·Qaurooni, D.·Bhavsar, A.·Kienle, P.·Pouch, A. M.·ONeill, K.·Apte, S.·Herr, B. W.·Fisher, S. A.·Börner, K.
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Abstract

Over the last five years, over 13,000 tissue datasets with 200+ million cells from 20 consortia have been spatially registered into the Human Reference Atlas (HRA) common coordinate framework (CCF). The shared 3D spatial and semantic reference system enables exploration of datasets in the context of all other data across organs, assay types, and spatial scales. However, manual registration of individual samples remains resource intensive, posing feasibility challenges exacerbated by the proliferation of samples, assays, and atlasing efforts. This paper presents two approaches to scale up HRA construction: (1) projecting data across biomedical reference atlas systems and (2) using millitomes to bulk register tissue blocks into a reference organ. Both methods use the AutoMated Alignment and Projection (AMAP) pipeline to align 3D mesh models using point cloud registration. We demonstrate the evolving HRA-aligned atlas ecosystem for 6 models from the SPARC Program (heart), Gut Cell Atlas (large intestine), 500-subject consensus kidneys, and the Julich Brain Atlas. Additionally, we used AMAP to project 7 millitome models across 5 organs onto the HRA ecosystem, integrating 300+ tissue extraction sites. AMAP enables scalable tissue registration of data across atlas ecosystems enabling the construction of detailed reference maps of the human body.

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Jain, Y., Desai, B., Qaurooni, D., Bhavsar, A., Kienle, P., Pouch, A. M., ONeill, K., Apte, S., Herr, B. W., Fisher, S. A., Börner, K.. 2026-08-22. Bridging Biomedical Atlas Ecosystem: Cross-Atlas Alignment And Scalable Tissue Specimen Registration. https://doi.org/10.64898/2026.08.13.744704

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