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Every current method fixes in advance where to borrow \u2014 a smoothing scale, a cell outline or a factor model \u2014 and the fixed choice shapes what is visible. Kintsugi removes the fixed choice and lets held-out molecules decide, gene by gene, how much to borrow from spatial neighbours and from other genes at the same location. On a lung section measured by both Xenium and Visium HD, the data-chosen allocation placed an epithelial programme where the Xenium molecules were, ahead of smoothing, cell segmentation and a factor model; the result replicated across tissues and against protein. Across a 45-core pulmonary fibrosis cohort, separating composition from captured amount shows that a fibroblastic focus is not a place with more RNA but a place with different RNA: 2.8-fold higher in activated-fibroblast composition while segmented nuclear density is at most 1.08-fold higher.<\/jats:p>","DOI":"10.64898\/2026.08.30.748061","type":"posted-content","created":{"date-parts":[[2026,9,4]],"date-time":"2026-09-04T02:30:12Z","timestamp":1788489012000},"source":"Crossref","is-referenced-by-count":0,"title":["Kintsugi decides, gene by gene, where spatial transcriptomics borrows information"],"prefix":"10.64898","author":[{"given":"Chen","family":"Yang","sequence":"first","affiliation":[{"name":"Department of Statistics, Texas A&M University, College Station, Texas, 77843, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianyang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Statistics, Texas A&M University, College Station, Texas, 77843, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Chen","sequence":"additional","affiliation":[{"name":"Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, 55905, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026091521301227000_2026.08.30.748061v2.1","doi-asserted-by":"crossref","first-page":"1512","DOI":"10.1038\/s41588-025-02193-3","article-title":"High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer","volume":"57","year":"2025","journal-title":"Nature Genetics"},{"key":"2026091521301227000_2026.08.30.748061v2.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.04.003"},{"key":"2026091521301227000_2026.08.30.748061v2.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2012.02.036"},{"key":"2026091521301227000_2026.08.30.748061v2.4","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2113929118"},{"key":"2026091521301227000_2026.08.30.748061v2.5","unstructured":"Openshaw, S. 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