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Thor: a platform for cell-level investigation of spatial transcriptomics and histology
Pengzhi Zhang1,2,3,4, Weiqing Chen5, Tu Nhi Tran1,2,3,4
1Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute, Houston, TX, 77030, USA.
Research Square
|March 31, 2025
Summary
Thor is a new computational platform that integrates spatial transcriptomics and histology images for deeper biological insights. It enables joint genomic-histology analysis, revealing cellular organization and molecular functions with high accuracy.
Area of Science:
- Spatial biology
- Computational biology
- Genomics
Background:
- Spatial transcriptomics offers insights into cellular organization and molecular functions by integrating transcriptomics with histology.
- Current platforms primarily focus on genomic analysis, lacking seamless integration of genomic and image data.
Purpose of the Study:
- Introduce Thor, a comprehensive computational platform for multi-modal analysis of spatial transcriptomics and histological images.
- Address the gap in seamless integration of genomic and image analysis in spatial biology.
Main Methods:
- Thor employs an anti-shrinking Markov diffusion method to infer single-cell spatial transcriptomes from spot-level data.
- The platform includes 10 modules for cell-level genomic and image analysis.
- Mjolnir, a web-based tool, provides interactive tissue analysis with histology, gene expression, and pathway enrichment data.
Main Results:
- Thor accurately integrates cell morphology with spatial transcriptomics, validated across multiple datasets (ISH, MERFISH, Xenium, Stereo-seq).
- Applications include identifying regenerative signatures in heart failure, analyzing olfactory bulb structure, screening breast cancer hallmarks, and elucidating immune response heterogeneity.
- Thor imputed high-resolution spatial transcriptomics data, revealing stronger spatial patterns aligned with histology in bladder cancer.
Conclusions:
- Thor bridges the gap between genomic and image analysis in spatial biology.
- The platform provides a powerful tool for comprehensive cellular and molecular analysis.
- Thor facilitates deeper understanding of tissue architecture and cellular functions through integrated multi-modal analysis.
