TY - JOUR
T1 - Thor
T2 - a platform for cell-level investigation of spatial transcriptomics and histology
AU - Zhang, Pengzhi
AU - Chen, Weiqing
AU - Tran, Tu N
AU - Zhou, Minghao
AU - Carter, Kaylee N
AU - Kandel, Ibrahem
AU - Li, Shengyu
AU - Hoi, Xen Ping
AU - Sun, Yuxing
AU - Lai, Li
AU - Youker, Keith
AU - Song, Qianqian
AU - Yang, Yu
AU - Nikolos, Fotis
AU - Li, Zejuan
AU - Chan, Keith Syson
AU - Cooke, John P
AU - Wang, Guangyu
N1 - Publisher Copyright:
© The Author(s) 2025.
PY - 2025/8/5
Y1 - 2025/8/5
N2 - Spatial transcriptomics links gene expression with tissue morphology, however, current tools often prioritize genomic analysis, lacking integrated image interpretation. To address this, we present Thor, a comprehensive platform for cell-level analysis of spatial transcriptomics and histological images. Thor employs an anti-shrinking Markov diffusion method to infer single-cell spatial transcriptome from spot-level data, effectively combining gene expression and cell morphology. The platform includes 10 modular tools for genomic and image-based analysis, and is paired with Mjolnir, a web-based interface for interactive exploration of gigapixel images. Thor is validated on simulated data and multiple spatial platforms (ISH, MERFISH, Xenium, Stereo-seq). Thor characterizes regenerative signatures in heart failure, screens breast cancer hallmarks, resolves fine layers in mouse olfactory bulb, and annotates fibrotic heart tissue. In high-resolution Visium HD data, it enhances spatial gene patterns aligned with histology. By bridging transcriptomic and histological analysis, Thor enables holistic tissue interpretation in spatial biology.
AB - Spatial transcriptomics links gene expression with tissue morphology, however, current tools often prioritize genomic analysis, lacking integrated image interpretation. To address this, we present Thor, a comprehensive platform for cell-level analysis of spatial transcriptomics and histological images. Thor employs an anti-shrinking Markov diffusion method to infer single-cell spatial transcriptome from spot-level data, effectively combining gene expression and cell morphology. The platform includes 10 modular tools for genomic and image-based analysis, and is paired with Mjolnir, a web-based interface for interactive exploration of gigapixel images. Thor is validated on simulated data and multiple spatial platforms (ISH, MERFISH, Xenium, Stereo-seq). Thor characterizes regenerative signatures in heart failure, screens breast cancer hallmarks, resolves fine layers in mouse olfactory bulb, and annotates fibrotic heart tissue. In high-resolution Visium HD data, it enhances spatial gene patterns aligned with histology. By bridging transcriptomic and histological analysis, Thor enables holistic tissue interpretation in spatial biology.
KW - Animals
KW - Mice
KW - Transcriptome/genetics
KW - Gene Expression Profiling/methods
KW - Humans
KW - Single-Cell Analysis/methods
KW - Image Processing, Computer-Assisted/methods
KW - Software
KW - Breast Neoplasms/genetics
KW - Female
UR - https://www.scopus.com/pages/publications/105012624993
UR - https://www.scopus.com/inward/citedby.url?scp=105012624993&partnerID=8YFLogxK
U2 - 10.1038/s41467-025-62593-1
DO - 10.1038/s41467-025-62593-1
M3 - Article
C2 - 40764306
SN - 2041-1723
VL - 16
SP - 7178
JO - Nature Communications
JF - Nature Communications
IS - 1
M1 - 7178
ER -