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.