Thor: a platform for cell-level investigation of spatial transcriptomics and histology

Pengzhi Zhang, Weiqing Chen, Tu N. Tran, Minghao Zhou, Kaylee N. Carter, Ibrahem Kandel, Shengyu Li, Xen Ping Hoi, Yuxing Sun, Li Lai, Keith Youker, Qianqian Song, Yu Yang, Fotis Nikolos, Zejuan Li, Keith Syson Chan, John P. Cooke and Guangyu Wang ()
Additional contact information
Pengzhi Zhang: Houston Methodist Research Institute
Weiqing Chen: Houston Methodist Research Institute
Tu N. Tran: Houston Methodist Research Institute
Minghao Zhou: University of Florida
Kaylee N. Carter: Houston Methodist Research Institute
Ibrahem Kandel: Houston Methodist Research Institute
Shengyu Li: Houston Methodist Research Institute
Xen Ping Hoi: Houston Methodist Research Institute
Yuxing Sun: Georgia Institute of Technology
Li Lai: Houston Methodist Research Institute
Keith Youker: Houston Methodist Research Institute
Qianqian Song: University of Florida
Yu Yang: University of Florida
Fotis Nikolos: Houston Methodist Research Institute
Zejuan Li: Houston Methodist Research Institute
Keith Syson Chan: Houston Methodist Research Institute
John P. Cooke: Houston Methodist Research Institute
Guangyu Wang: Houston Methodist Research Institute

Nature Communications, 2025, vol. 16, issue 1, 1-22

Abstract: Abstract 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.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-62593-1 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62593-1

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-62593-1

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().