Cytosplore Gradient Surfer: Comparative Visual Analysis of Spatial Gene Expression Gradients Across Datasets

Soumyadeep Basu, Chang Li, Thomas Kroes, Boudewijn P. F. Lelieveldt, Brian Long, and Thomas Höllt

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Spatial transcriptomics makes gene expression visible within tissue. This helps reveal tissue structure, cell development, or how genes are regulated. While methods exist to identify spatially patterned genes or align tissue structures, comparative analysis of such patterns across datasets or between different modalities remains a challenging task. We present Cytosplore Gradient Surfer, an interactive system for identifying and analyzing spatial gene expression gradients across spatial transcriptomics datasets. The system allows users to interactively probe spatial directions of interest and identify genes exhibiting aligned expression patterns across dataset pairs, even when only a subset of genes is shared between them.

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@journal{bib:basu:2025,
    author       = { Basu, Soumyadeep and Li, Chang and Kroes, Thomas and Lelieveldt, Boudewijn P. F. and Long, Brian and Höllt, Thomas },    
    title        = { Cytosplore Gradient Surfer: Comparative Visual Analysis of Spatial Gene Expression Gradients Across Datasets },
    year         = { 2025 },
    url          = { https://publications.graphics.tudelft.nl/papers/826 },
}