PyPlaque: An Open-source Python Library for Phenotypic Analysis of Virus Plaque Assays

Virological plaque assay is the primary way for the quantification of infectious virus particles in a virus suspension. It is performed by incubating a serial dilution of the virus inoculum with a monolayer of indicator cells. While some tools for automated quantification have been proposed in the past, they lack modularity and are often closed-source. PyPlaque is open-source software written in Python programming language for the analysis and quantification of plaque phenotypes that are observed in plaque assays by virologists. It is based on an abstract software architecture allowing to take into account glassware and specimen carriers and focus on phenotype-specific information. This, in turn, allows biologist to construct modular and simple program code that follows the logical flow of the experimental design and desired quantification outcomes. Furthermore, we demonstrate the comparability of PyPlaque to existing software and show how phenotype-based abstraction allows for seamless coding using Pythonic conventions.