Mapping bioimage-analysis software adoption in microscopy
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.
Authors
- Inês Cunha (ORCID: https://orcid.org/0000-0002-1327-9018)
- Guillaume Jacquemet (ORCID: https://orcid.org/0000-0002-9286-920X)
- Caron Jacobs (ORCID: https://orcid.org/0000-0002-8072-4433)
- Tayla Shakespeare (ORCID: https://orcid.org/0000-0002-4159-0460)
- Bruno M. Saraiva (ORCID: https://orcid.org/0000-0002-9151-5477)
- Ricardo Henriques (ORCID: https://orcid.org/0000-0002-2043-5234)
Institutions
- Åbo Akademi University (FI)
- University of Turku (FI)
- University of Cape Town (ZA)
- Stockholm University (SE)
- Turku Centre for Computer Science (FI)
- Science for Life Laboratory (SE)
- Wellcome Centre for Infectious Diseases Research in Africa (ZA)
- Instituto de Biologia Experimental e Tecnológica (PT)
- Gulbenkian Institute for Molecular Medicine (PT)
- Institute of Infectious Disease and Molecular Medicine (ZA)
- Finnish Cancer Institute (FI)
- Instituto de Tecnologia Química e Biológica António Xavier (PT)
- Instituto Gulbenkian de Ciência (PT)
- Universidade Nova de Lisboa (PT)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-10-26
- DOI
- https://doi.org/10.64898/2026.10.21.760457
- Primary Topic
- Cell Image Analysis Techniques
- Type
- preprint
Funders
- Silicon Valley Community Foundation
- Finnish Cancer Institute
- European Commission
- Knut och Alice Wallenbergs Stiftelse
- Syöpäjärjestöt
- Åbo Akademi
- HORIZON EUROPE Framework Programme
- Fundação para a Ciência e a Tecnologia
- National Supercomputer Centre, Linköpings Universitet