{
  "abstract": "Summary\n\nTissue microarrays (TMAs) enable high-throughput spatial transcriptomic profiling of dozens of tissue cores on a single slide. However, existing dearraying methods operate on histological images and do not support the coordinate-based outputs of spatial transcriptomics platforms. Therefore, task of assigning cells to their respective cores (dearraying) remains a manual bottleneck. We present STiLE, a tool for automated TMA dearraying that operates solely on cell centroid coordinates. By eliminating dependence on image data, STiLE is robust to artefacts such as variable staining quality and uneven illumination. The algorithm combines connectivity-based component detection, density-based clustering (HDBSCAN), component-guided cluster merging, and optional grid-based peak detection. Validation on seven public TMA samples (50-150 cores, three platforms) achieved ARI > 0.99, while systematic benchmarking on 396 synthetic datasets with realistic artefacts demonstrated consistently robust performance (mean ARI = 0.992). STiLE accepts standard formats (AnnData, CSV) and is platform-agnostic, supporting diverse platforms including Vizgen MERSCOPE, 10× Xenium, and NanoString CosMx. An interactive Streamlit interface enables parameter tuning, visual inspection, and region-based processing for large slides.Availability and implementation\n\nhttps://pypi.org/project/stile; source at https://github.com/Huang-AI4Medicine-Lab/stile.",
  "abstract_shown": true,
  "affiliations": [
    "Intelligent Systems Program, University of Pittsburgh, Pittsburgh, PA, United States.",
    "Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, United States.",
    "Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.",
    "Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.",
    "Cancer Therapeutics Program, UPMC Hillman Cancer Center, Pittsburgh, PA, United States.",
    "Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.",
    "Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA, United States."
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Harsh Sinha",
      "orcid": "0000-0002-8498-8559"
    },
    {
      "affs": [
        1,
        2
      ],
      "name": "Arun Das"
    },
    {
      "affs": [
        2,
        3,
        4
      ],
      "name": "Yu-Chiao Chiu",
      "orcid": "0000-0003-1647-8634"
    },
    {
      "affs": [
        1,
        5
      ],
      "name": "Shou-Jiang Gao",
      "orcid": "0000-0001-6194-1742"
    },
    {
      "affs": [
        0,
        1,
        2,
        6
      ],
      "name": "Yufei Huang",
      "orcid": "0000-0001-6268-5357"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/60abpppqj4s75.bib",
  "cited_by": 0,
  "doi": "10.1093/bioinformatics/btag572",
  "fulltext_url": "https://europepmc.org/articles/PMC13652026",
  "id": "60abpppqj4s75",
  "issns": [
    "1367-4803",
    "1367-4811"
  ],
  "landing_url": "https://europepmc.org/article/MED/42836654",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7134810100",
  "pdf_url": "https://europepmc.org/articles/PMC13652026?pdf=render",
  "pmcid": "PMC13652026",
  "pmid": "42836654",
  "published": "2026-10-01",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/60abpppqj4s75.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:10Z",
      "native_id": "MED:42836654",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42836654"
    },
    {
      "first_seen": "2026-10-30T12:19:38Z",
      "native_id": "10.1093/bioinformatics/btag572",
      "source": "crossref",
      "url": "https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btag572/8868947"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Single-cell and spatial transcriptomics",
      "subfield": "molecular-biology"
    }
  ],
  "title": "STiLE: automated tissue microarray dearraying for spatial transcriptomics.",
  "title_text": "STiLE: automated tissue microarray dearraying for spatial transcriptomics.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:38Z",
  "url": "https://research.draconitic.com/paper/60abpppqj4s75",
  "venue": "Bioinformatics (Oxford, England)",
  "versions": []
}