{
  "abstract": "The analysis of spot-like structures is a widespread task in microscopy-based cell biology. Existing solutions are typically specific to single applications and do not use multi-dimensional information from 5D datasets. Therefore, experimental scientists often resort to subjective manual annotation. Here, we present SpotMAX, a generalist AI-driven framework for automated spot detection and quantification. SpotMAX leverages the full scope of multi-dimensional datasets with an easy-to-use interface and an embedded framework for cell segmentation and tracking. SpotMAX outperforms state-of-the-art tools, and in some cases, even expert human annotators. We applied SpotMAX across diverse experimental questions, ranging from meiotic crossover events in C. elegans to mitochondrial DNA dynamics in S. cerevisiae and telomere length in mouse stem cells, leading to new biological insights. With its flexibility in integrating AI workflows, we anticipate that SpotMAX will become the standard for spot analysis in microscopy data. Source code: https://github.com/SchmollerLab/SpotMAX",
  "abstract_shown": true,
  "affiliations": [
    "Institute of Functional Epigenetics, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany",
    "Helmholtz Zentrum Muenchen",
    "Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg, Germany",
    "Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg University, Heidelberg, Baden-Württemberg, Germany",
    "European Molecular Biology Laboratory",
    "Faculty of Medicine, Ludwig-Maximilians Universität München, Munich, Germany",
    "Massachusetts Institute of Technology",
    "University of Helsinki",
    "David H. Koch Institute for Integrative Cancer Research, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA",
    "Centre for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden",
    "Helsinki Institute of Life Science, Institute of Biotechnology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Francesco Padovani",
      "orcid": "0000-0003-2540-8240"
    },
    {
      "affs": [
        2,
        3,
        4
      ],
      "name": "Ivana Čavka",
      "orcid": "0000-0002-2640-8587"
    },
    {
      "affs": [
        2,
        3,
        4
      ],
      "name": "Ana Rita Rodrigues Neves",
      "orcid": "0000-0003-3591-4948"
    },
    {
      "affs": [
        2,
        4
      ],
      "name": "Cristina Piñeiro López",
      "orcid": "0000-0002-0293-4400"
    },
    {
      "affs": [
        5,
        0,
        1
      ],
      "name": "Nada Al-Refaie"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Leonardo Bolcato"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Dimitra Chatzitheodoridou"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Yagya Chadha",
      "orcid": "0000-0002-4824-9935"
    },
    {
      "affs": [
        2,
        3,
        6
      ],
      "name": "Pablo Lagos",
      "orcid": "0000-0003-0762-7802"
    },
    {
      "affs": [
        0,
        7
      ],
      "name": "Timon Stegmaier",
      "orcid": "0009-0003-6354-2667"
    },
    {
      "affs": [
        8,
        1
      ],
      "name": "Xiaofeng A. Su",
      "orcid": "0000-0003-4960-6372"
    },
    {
      "affs": [
        9,
        10,
        4
      ],
      "name": "Jette Lengefeld",
      "orcid": "0000-0001-6021-7613"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Daphne S. Cabianca",
      "orcid": "0000-0002-1834-7868"
    },
    {
      "affs": [
        2
      ],
      "name": "Simone Köhler",
      "orcid": "0000-0002-1119-8855"
    },
    {
      "affs": [
        0
      ],
      "name": "Kurt M. Schmoller",
      "orcid": "0000-0001-5790-5204"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/28w2rs67y90ga.bib",
  "cited_by": 12,
  "doi": "10.1126/sciadv.adw3811",
  "fulltext_url": null,
  "id": "28w2rs67y90ga",
  "issns": [
    "2375-2548"
  ],
  "landing_url": "https://doi.org/10.1126/sciadv.adw3811",
  "language": "en",
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1304|Cell Image Analysis Techniques"
    ]
  ],
  "openalex": "W4403691948",
  "pdf_url": null,
  "pmcid": "PMC13524050",
  "pmid": "42664352",
  "published": "2026-07-08",
  "publisher": "American Association for the Advancement of Science",
  "ris": "https://research.draconitic.com/paper/28w2rs67y90ga.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T13:26:46Z",
      "native_id": "W4403691948",
      "source": "openalex",
      "url": "https://doi.org/10.1126/sciadv.adw3811"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1304|Cell Image Analysis Techniques",
      "subfield": "biophysics"
    }
  ],
  "title": "SpotMAX: A generalist framework for multidimensional automatic spot detection and quantification",
  "title_text": "SpotMAX: A generalist framework for multidimensional automatic spot detection and quantification",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T13:20:43Z",
  "url": "https://research.draconitic.com/paper/28w2rs67y90ga",
  "venue": "Science Advances",
  "versions": []
}