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

## TL;DR

PyPlaque is an open-source Python package that improves virus plaque assay analysis by offering a flexible and modular approach.

## Contribution

PyPlaque introduces a modular and open-source framework for virus plaque analysis using object-oriented programming.

## Key findings

- PyPlaque's architecture allows compatibility with various experimental containers and specimen carriers.
- The package reduces measurement disagreement in plaque assays through its abstracted design.
- The approach is generalizable to other biological datasets fitting its structural model.

## 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.