RNA assignment and segmentation geometry in Visium HD profiles of fibrostenotic Crohn's disease

Image-based segmentation in Visium HD fibrostenotic Crohn’s disease sections yields RNA assignment only up to 74.68% (CD1) and 64.05% (CD2), with substantial unassigned nuclear regions.

• Why it matters: Retrospective spatial transcriptomics reuse often begins from bin-level Seurat objects, but it is unclear whether segmentation alone can reconstruct defensible cell-like expression without rerunning upstream processing.
• What they did: Using two complete H&E sections from GSE302569, the team tested 20 segmentation configurations in preserved image coordinates and assigned RNA with a bin-centre rule, then ran native full-mode RCTD for 38 non-empty configuration-slice combinations against a nine-group scIBD reference.
• The result: RNA recovery increased with expansion but did not remove merged regions or boundary ambiguity; mean slice-level recovery was negatively associated with primary-component dominance (Spearman rho = -0.77), and neither dominant-call agreement nor RCTD support validated boundaries or cell identity.

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