Unifying physical and molecular coordinate systems across modalities in spatial biology
Year: 2026
Type: preprint
Abstract: Establishing a unified physical and molecular coordinate system from fragmented multi-modal data is a longstanding challenge in biology. Here, we present MAPS, a modality-agnostic platform for spatial biology comprising (1) MAPS-alignment for ultrafast alignment of any modality, (2) MAPS-integration for both anchored and unanchored integration across orthogonal modalities for 3D multi-modal reconstruction, and (3) MAPS-Explorer for large-scale interactive 3D analysis. MAPS outperformed existing methods across extensive benchmarks on 34 datasets spanning 16 technology platforms and 6 modalities, while delineating fine-grained multi-modal tissue architectures across diverse biological systems in mouse and human. At cross-consortium scale, MAPS integrated 434 slices comprising 21 million cells from 18 atlases and 5 modalities to construct the most comprehensive 3D multi-modal mouse brain atlas. At individual laboratory scale, MAPS empowered routine 2D spatial assays to reconstruct continuous 3D multi-modal landscapes of human hepatocellular carcinoma, revealing the limitations of 2D spatial relationships and uncovering depth-dependent immune-state transitions.
Authors: Bingjie Dai, Yunzhi Yan, Zhikang Wang, Yuchao Liang, Sijie Li, Pengwei Hu, Xinwang Yang, Chuyao Wang, Litai Yi, Chenglong Sun, Jinhai Huang, Xingtao Zhou, Hebing Chen, Daoliang Zhang, Qi Zou, Yixuan Du, Zheqi Hu, Yongqiang Xing, Guifang Cao, Zhenxing Feng, Jianfeng Feng, Shuhua Xu, Wei Hu, Yongchun Zuo, Bin-Zhi Qian, Zhiyuan Yuan
Institutions: Inner Mongolia University, Shanghai Medical College of Fudan University, Fudan University, Fudan University Shanghai Cancer Center, Frontiers Center for Brain Science of the Ministry of Education, Harbin Institute of Technology, Jilin University, Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Qilu University of Technology, Shandong Academy of Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Eye & ENT Hospital of Fudan University, State Key Laboratory of Proteomics, Inner Mongolia University of Science and Technology, Inner Mongolia University of Technology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7208823688