QuantWorm: A Comprehensive Software Package for Caenorhabditis elegans Phenotypic Assays

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dc.citation.firstpagee84830
dc.citation.issueNumber1
dc.citation.journalTitlePLoS ONE
dc.citation.volumeNumber9
dc.contributor.authorJung, Sang-Kyu
dc.contributor.authorAleman-Meza, Boanerges
dc.contributor.authorRiepe, Celeste
dc.contributor.authorZhong, Weiwei
dc.contributor.authorHendricks, Michael
dc.date.accessioned2014-01-21T20:19:37Z
dc.date.available2014-01-21T20:19:37Z
dc.date.issued2014
dc.description.abstractPhenotypic assays are crucial in genetics; however, traditional methods that rely on human observation are unsuitable for quantitative, large-scale experiments. Furthermore, there is an increasing need for comprehensive analyses of multiple phenotypes to provide multidimensional information. Here we developed an automated, high-throughput computer imaging system for quantifying multiple Caenorhabditis elegans phenotypes. Our imaging system is composed of a microscope equipped with a digital camera and a motorized stage connected to a computer running the QuantWorm software package. Currently, the software package contains one data acquisition module and four image analysis programs: WormLifespan, WormLocomotion, WormLength, and WormEgg. The data acquisition module collects images and videos.The WormLifespan software counts the number of moving worms by using two time-lapse images; the WormLocomotion software computes the velocity of moving worms; the WormLength software measures worm body size; and the WormEgg software counts the number of eggs. To evaluate the performance of our software, we compared the results of our software with manual measurements. We then demonstrated the application of the QuantWorm software in a drug assay and a genetic assay. Overall, the QuantWorm software provided accurate measurements at a high speed. Software source code, executable programs, and sample images are available at www.quantworm.org. Our software package has several advantages over current imaging systems for C. elegans. It is an all-in-one package for quantifying multiple phenotypes. The QuantWorm software is written in Java and its source code is freely available, so it does not require use of commercial software or libraries. It can be run on multiple platforms and easily customized to cope with new methods and requirements.
dc.identifier.citationJung, Sang-Kyu, Aleman-Meza, Boanerges, Riepe, Celeste, et al.. "QuantWorm: A Comprehensive Software Package for Caenorhabditis elegans Phenotypic Assays." <i>PLoS ONE,</i> 9, no. 1 (2014) Public Library of Science: e84830. http://dx.doi.org/10.1371/journal.pone.0084830.
dc.identifier.doihttp://dx.doi.org/10.1371/journal.pone.0084830
dc.identifier.urihttps://hdl.handle.net/1911/75344
dc.language.isoeng
dc.publisherPublic Library of Science
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.titleQuantWorm: A Comprehensive Software Package for Caenorhabditis elegans Phenotypic Assays
dc.typeJournal article
dc.type.dcmiTexten_US
dc.type.publicationpublisher version
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