Neighbor transcripts leak into spatial cells: DisCell splits spillover from niche response and gives each finding a breakdown point
Single-cell spatial transcriptomics counts neighboring cells' transcripts inside a cell, and this spillover and a cell's real response to its niche both tie expression to surroundings, so counts alone cannot separate them. DisCell models intrinsic state, niche response and spillover jointly, refits over a range of spillover fractions, and assigns each finding a breakdown point. On ovarian and lung sections its intrinsic state keeps more cell-cycle information than any competing method holding as little neighborhood information, and a published esophageal EMT finding survives the modeled spillover range.