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easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler

High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput mi...

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Detalles Bibliográficos
Autores principales: Nyaanga, Joy, Crombie, Timothy A., Widmayer, Samuel J., Andersen, Erik C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8360505/
https://www.ncbi.nlm.nih.gov/pubmed/34383778
http://dx.doi.org/10.1371/journal.pone.0252000
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author Nyaanga, Joy
Crombie, Timothy A.
Widmayer, Samuel J.
Andersen, Erik C.
author_facet Nyaanga, Joy
Crombie, Timothy A.
Widmayer, Samuel J.
Andersen, Erik C.
author_sort Nyaanga, Joy
collection PubMed
description High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfiler’s WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets.
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spelling pubmed-83605052021-08-13 easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler Nyaanga, Joy Crombie, Timothy A. Widmayer, Samuel J. Andersen, Erik C. PLoS One Research Article High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfiler’s WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets. Public Library of Science 2021-08-12 /pmc/articles/PMC8360505/ /pubmed/34383778 http://dx.doi.org/10.1371/journal.pone.0252000 Text en © 2021 Nyaanga et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Nyaanga, Joy
Crombie, Timothy A.
Widmayer, Samuel J.
Andersen, Erik C.
easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler
title easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler
title_full easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler
title_fullStr easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler
title_full_unstemmed easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler
title_short easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler
title_sort easyxpress: an r package to analyze and visualize high-throughput c. elegans microscopy data generated using cellprofiler
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8360505/
https://www.ncbi.nlm.nih.gov/pubmed/34383778
http://dx.doi.org/10.1371/journal.pone.0252000
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