From Cross-Section to Cross-Omics: Conditional Cell Nucleus Image Editing in Spatial Transcriptomics

arXiv cs.AINovember 3, 2026en

arXiv:2611.00226v1 Announce Type: new Abstract: Spatial transcriptomics (ST) platforms simultaneously measure gene expression and capture cell nucleus images at single-cell resolution. A fundamental property of tissue preparation introduces a confounding relationship between the two measurement modalities: sectioning a three-dimensional tissue into a thin slice produces a two-dimensional cross-section whose area depends on the cutting angle. Larger cross-sections expose more cytoplasm, yielding higher mRNA counts, while pathomics features such as nuclear area are measured directly from the same 2D boundary. This sectioning geometry creates an apparent correlation between gene expression and

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