Mapping bioimage-analysis software adoption in microscopy

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.

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• biorxiv v1 2026-10-26 source ↗

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