{
  "abstract": "Most quantitative microscopy measurements pass through image-analysis software, and different programs can return different measurements from the same images. Which programs researchers rely on therefore matters for reproducibility; however, this information lies scattered across the methods sections of the microscopy literature. In this analysis, we show how mentions of 30 software packages changed across 1.7 million full-text microscopy papers published between 2010 and 2025. In 2010, 12% of these papers mentioned at least one of the 22 analysis packages we tracked; by 2025, 30% did. Mentions stayed concentrated on a few general-purpose platforms, led by ImageJ/Fiji. Newer packages are mentioned more often in particular fields, such as QuPath in pathology and napari in electron microscopy. Deep-learning methods are usually mentioned alongside an established platform; papers often run StarDist inside Fiji and Cellpose on its own. Many papers mention a package without citing it, so citation counts understate how often packages appear in published work; authors should make that use visible by citing each package and reporting how they ran it.",
  "abstract_shown": true,
  "affiliations": [
    "Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal; Gulbenkian Institute for Molecular Medicine, Oeiras,"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "T. Shakespeare"
    },
    {
      "name": "B. M. Saraiva"
    },
    {
      "name": "I. Cunha"
    },
    {
      "name": "C. Jacobs"
    },
    {
      "name": "G. Jacquemet"
    },
    {
      "affs": [
        0
      ],
      "name": "R. Henriques"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/8q2x10hp5ry20.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.21.760457",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760457v1.full",
  "id": "8q2x10hp5ry20",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760457v1",
  "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",
      "1304|Cell Image Analysis Techniques"
    ]
  ],
  "openalex": "W7223707034",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760457v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-21",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/8q2x10hp5ry20.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:29:43Z",
      "native_id": "10.64898/2026.10.21.760457",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.21.760457v3"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "Mapping bioimage-analysis software adoption in microscopy",
  "title_text": "Mapping bioimage-analysis software adoption in microscopy",
  "type": "preprint",
  "updated_at": "2026-11-07T00:21:06Z",
  "url": "https://research.draconitic.com/paper/8q2x10hp5ry20",
  "venue": "bioRxiv",
  "versions": []
}