{
  "abstract": "Retrospective reuse of spatial transcriptomics often starts from a deposited bin-level Seurat object rather than the inputs needed to revisit upstream molecular processing. We tested whether image segmentation could support a defensible cell-like reconstruction under this constraint in two complete H&E-stained intestinal sections from a Visium HD study of Crohn's disease-associated fibrostenosis (GSE302569). The available data comprised 18,085 genes, 988,942 original 8 {micro}m bins and 179,596,575 UMIs. We evaluated 20 segmentation configurations in the preserved image coordinate system using a common bin-centre assignment rule, without restarting Space Ranger or introducing higher-resolution expression. RNA assignment ranged from 0% to 74.68% in CD1 and 0% to 64.05% in CD2. Expansion increased recovery but did not eliminate merged regions, straight boundaries or within-bin ambiguity; approximately 70-73% of InstanSeg brightfield nuclear regions received no assigned RNA. All 38 non-empty configuration-slice combinations underwent native full-mode RCTD against the same nine-group scIBD reference. Mean slice-level RNA recovery was negatively associated with primary-component dominance across 19 configurations (descriptive Spearman {rho} = -0.77). Neither dominant-call agreement nor concentrated RCTD support validates boundaries or cell identity. The observed limitations in RNA recovery, region geometry, and compositional support did not establish any tested configuration as a reliable single-cell reconstruction from these inputs. The findings identify limitations of retrospective single-cell reconstruction from the available binned inputs, not the impossibility of cell-resolved analysis from suitable original data.",
  "abstract_shown": true,
  "affiliations": [
    "IRCCS Ospedale San Raffaele, Institute of Immunology and Transplantation Disease, Via Olgettina 60, 20132 Milano, Italy"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "L. Massimino"
    },
    {
      "name": "F. Ungaro"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/38repfg6v4dtc.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.27.762235",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.27.762235v1.full",
  "id": "38repfg6v4dtc",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.27.762235v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7225045952",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.27.762235v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-27",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/38repfg6v4dtc.ris",
  "sources": [
    {
      "first_seen": "2026-11-02T12:20:48Z",
      "native_id": "10.64898/2026.10.27.762235",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.27.762235v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "RNA assignment and segmentation geometry in Visium HD profiles of fibrostenotic Crohn's disease",
  "title_text": "RNA assignment and segmentation geometry in Visium HD profiles of fibrostenotic Crohn's disease",
  "type": "preprint",
  "updated_at": "2026-11-03T00:20:25Z",
  "url": "https://research.draconitic.com/paper/38repfg6v4dtc",
  "venue": "bioRxiv",
  "versions": []
}