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PyPlaque is an open-source python package for phenotypic analysis of virus plaque assays

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Veröffentlicht in:Scientific Reports (Nature Publisher Group) vol. 15, no. 1 (2025), p. 36187-36205
1. Verfasser: De, Trina
Weitere Verfasser: Andriasyan, Vardan, Yakimovich, Artur
Veröffentlicht:
Nature Publishing Group
Schlagworte:
Object oriented programming
Infections
Plaque assay
Pathogens
Experimental design
Open source software
Experiments
Phenotypes
Microscopy
Flexibility
Data analysis
Viruses
Data science
Python
Environmental
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Abstract:Virological plaque assays are the primary method for quantifying infectious particles in a suspension, achieved by incubating a serial dilution of the virus with a monolayer of indicator cells. Existing software tools for quantification of plaque assay images lack modularity, show measurements disagreement or are closed-source - a common hurdle in bioimage analysis. We introduce PyPlaque, an open-source Python package focusing on flexibility and modularity rather than a bulky graphic user interface. Unlike previous methods, an abstracted architecture using object-oriented programming allows accommodation of various experimental containers and specimen carriers as data structures while focusing on phenotype-specific information. Aligned with the logical flow of experimental design and desired quantifications, it delivers insights at multiple granularity levels, facilitating detailed analysis. We demonstrate how this approach allows to focus on alleviating the disagreement in measurements. Furthermore, similar design is generalisable to diverse datasets in various biological contexts that fit our structural paradigm.
ISSN:2045-2322
DOI:10.1038/s41598-025-20075-w
Quelle:Science Database