PyPlaque is an open-source python package for phenotypic analysis of virus plaque assays
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| Publicat a: | Scientific Reports (Nature Publisher Group) vol. 15, no. 1 (2025), p. 36187-36205 |
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| Altres autors: | , |
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Nature Publishing Group
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| 022 | |a 2045-2322 | ||
| 024 | 7 | |a 10.1038/s41598-025-20075-w |2 doi | |
| 035 | |a 3261988397 | ||
| 045 | 2 | |b d20250101 |b d20251231 | |
| 084 | |a 274855 |2 nlm | ||
| 100 | 1 | |a De, Trina |u Center for Advanced Systems Understanding (CASUS), Görlitz, Germany (ROR: https://ror.org/042b69396) (GRID: grid.510908.5); Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany (ROR: https://ror.org/01zy2cs03) (GRID: grid.40602.30) (ISNI: 0000 0001 2158 0612) | |
| 245 | 1 | |a PyPlaque is an open-source python package for phenotypic analysis of virus plaque assays | |
| 260 | |b Nature Publishing Group |c 2025 | ||
| 513 | |a Journal Article | ||
| 520 | 3 | |a 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. | |
| 653 | |a Object oriented programming | ||
| 653 | |a Infections | ||
| 653 | |a Plaque assay | ||
| 653 | |a Pathogens | ||
| 653 | |a Experimental design | ||
| 653 | |a Open source software | ||
| 653 | |a Experiments | ||
| 653 | |a Phenotypes | ||
| 653 | |a Microscopy | ||
| 653 | |a Flexibility | ||
| 653 | |a Data analysis | ||
| 653 | |a Viruses | ||
| 653 | |a Data science | ||
| 653 | |a Python | ||
| 653 | |a Environmental | ||
| 700 | 1 | |a Andriasyan, Vardan |u Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland (ROR: https://ror.org/02crff812) (GRID: grid.7400.3) (ISNI: 0000 0004 1937 0650); Institute of Computer Science, University of Wrocław, Wrocław, Poland (ROR: https://ror.org/00yae6e25) (GRID: grid.8505.8) (ISNI: 0000 0001 1010 5103) | |
| 700 | 1 | |a Yakimovich, Artur |u Center for Advanced Systems Understanding (CASUS), Görlitz, Germany (ROR: https://ror.org/042b69396) (GRID: grid.510908.5); Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany (ROR: https://ror.org/01zy2cs03) (GRID: grid.40602.30) (ISNI: 0000 0001 2158 0612); Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland (ROR: https://ror.org/02crff812) (GRID: grid.7400.3) (ISNI: 0000 0004 1937 0650); Institute of Computer Science, University of Wrocław, Wrocław, Poland (ROR: https://ror.org/00yae6e25) (GRID: grid.8505.8) (ISNI: 0000 0001 1010 5103) | |
| 773 | 0 | |t Scientific Reports (Nature Publisher Group) |g vol. 15, no. 1 (2025), p. 36187-36205 | |
| 786 | 0 | |d ProQuest |t Science Database | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/3261988397/abstract/embedded/L8HZQI7Z43R0LA5T?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text |u https://www.proquest.com/docview/3261988397/fulltext/embedded/L8HZQI7Z43R0LA5T?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/3261988397/fulltextPDF/embedded/L8HZQI7Z43R0LA5T?source=fedsrch |