Software tools for 3D nuclei segmentation and quantitative analysis in multicellular aggregates

Filippo Piccinini, Tamas Balassa, Antonella Carbonaro, Akos Diosdi, Timea Toth, Nikita Moshkov, Ervin A Tasnadi, Peter Horvath

Research output: Contribution to journalReview articlepeer-review


Today, we are fully immersed into the era of 3D biology. It has been extensively demonstrated that 3D models: (a) better mimic the physiology of human tissues; (b) can effectively replace animal models; (c) often provide more reliable results than 2D ones. Accordingly, anti-cancer drug screenings and toxicology studies based on multicellular 3D biological models, the so-called "-oids" (e.g. spheroids, tumoroids, organoids), are blooming in the literature. However, the complex nature of these systems limit the manual quantitative analyses of single cells' behaviour in the culture. Accordingly, the demand for advanced software tools that are able to perform phenotypic analysis is fundamental. In this work, we describe the freely accessible tools that are currently available for biologists and researchers interested in analysing the effects of drugs/treatments on 3D multicellular -oids at a single-cell resolution level. In addition, using publicly available nuclear stained datasets we quantitatively compare the segmentation performance of 9 specific tools.

Original languageEnglish
Pages (from-to)1287-1300
Number of pages14
JournalComputational and Structural Biotechnology Journal
Publication statusPublished - 2020


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