wrmXpress: A modular package for high-throughput image analysis of parasitic and free-living worms
Advances in high-throughput and high-content imaging technologies require concomitant development of analytical software capable of handling large datasets and generating relevant phenotypic measurements. Several tools have been developed to analyze drug response phenotypes in parasitic and free-liv...
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| Veröffentlicht in: | PLoS neglected tropical diseases 2022-11, Vol.16 (11), p.e0010937 |
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| creator | Wheeler, Nicolas J Gallo, Kendra J Rehborg, Elena J G Ryan, Kaetlyn T Chan, John D Zamanian, Mostafa |
| description | Advances in high-throughput and high-content imaging technologies require concomitant development of analytical software capable of handling large datasets and generating relevant phenotypic measurements. Several tools have been developed to analyze drug response phenotypes in parasitic and free-living worms, but these are siloed and often limited to specific instrumentation, worm species, and single phenotypes. No unified tool exists to analyze diverse high-content phenotypic imaging data of worms and provide a platform for future extensibility. We have developed wrmXpress, a unified framework for analyzing a variety of phenotypes matched to high-content experimental assays of free-living and parasitic nematodes and flatworms. We demonstrate its utility for analyzing a suite of phenotypes, including motility, development/size, fecundity, and feeding, and establish the package as a platform upon which to build future custom phenotypic modules. We show that wrmXpress can serve as an analytical workhorse for anthelmintic screening efforts across schistosomes, filarial nematodes, and free-living model nematodes and holds promise for enabling collaboration among investigators with diverse interests. |
| doi_str_mv | 10.1371/journal.pntd.0010937 |
| format | Article |
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Several tools have been developed to analyze drug response phenotypes in parasitic and free-living worms, but these are siloed and often limited to specific instrumentation, worm species, and single phenotypes. No unified tool exists to analyze diverse high-content phenotypic imaging data of worms and provide a platform for future extensibility. We have developed wrmXpress, a unified framework for analyzing a variety of phenotypes matched to high-content experimental assays of free-living and parasitic nematodes and flatworms. We demonstrate its utility for analyzing a suite of phenotypes, including motility, development/size, fecundity, and feeding, and establish the package as a platform upon which to build future custom phenotypic modules. We show that wrmXpress can serve as an analytical workhorse for anthelmintic screening efforts across schistosomes, filarial nematodes, and free-living model nematodes and holds promise for enabling collaboration among investigators with diverse interests.</description><identifier>ISSN: 1935-2735</identifier><identifier>ISSN: 1935-2727</identifier><identifier>EISSN: 1935-2735</identifier><identifier>DOI: 10.1371/journal.pntd.0010937</identifier><identifier>PMID: 36399491</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Antiparasitic agents ; Aquatic invertebrates ; Biological Assay ; Biology and Life Sciences ; Collaboration ; Computer and Information Sciences ; Culture ; Deep learning ; Engineering and Technology ; Evaluation ; Experiments ; Fecundity ; Fertility ; Flatworms ; Humans ; Image analysis ; Image processing ; Imaging techniques ; Instrumentation ; Morphology ; Motility ; Nematoda ; Nematodes ; Parasites ; Phenotype ; Phenotypes ; Research and Analysis Methods ; Research Personnel ; Science Policy ; Software ; Tropical diseases ; Worms</subject><ispartof>PLoS neglected tropical diseases, 2022-11, Vol.16 (11), p.e0010937</ispartof><rights>Copyright: © 2022 Wheeler et al. This 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.</rights><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Wheeler et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 Wheeler et al 2022 Wheeler et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c624t-8cd4f52a29a1a8a5578dad877452e3d06b0b4175b2fce3480f9de2ba853a78f43</citedby><cites>FETCH-LOGICAL-c624t-8cd4f52a29a1a8a5578dad877452e3d06b0b4175b2fce3480f9de2ba853a78f43</cites><orcidid>0000-0003-4986-972X ; 0000-0002-5909-4190 ; 0000-0001-9233-1760</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9718391/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9718391/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,2096,2915,23847,27905,27906,53772,53774,79349,79350</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36399491$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Cotton, James</contributor><creatorcontrib>Wheeler, Nicolas J</creatorcontrib><creatorcontrib>Gallo, Kendra J</creatorcontrib><creatorcontrib>Rehborg, Elena J G</creatorcontrib><creatorcontrib>Ryan, Kaetlyn T</creatorcontrib><creatorcontrib>Chan, John D</creatorcontrib><creatorcontrib>Zamanian, Mostafa</creatorcontrib><title>wrmXpress: A modular package for high-throughput image analysis of parasitic and free-living worms</title><title>PLoS neglected tropical diseases</title><addtitle>PLoS Negl Trop Dis</addtitle><description>Advances in high-throughput and high-content imaging technologies require concomitant development of analytical software capable of handling large datasets and generating relevant phenotypic measurements. Several tools have been developed to analyze drug response phenotypes in parasitic and free-living worms, but these are siloed and often limited to specific instrumentation, worm species, and single phenotypes. No unified tool exists to analyze diverse high-content phenotypic imaging data of worms and provide a platform for future extensibility. We have developed wrmXpress, a unified framework for analyzing a variety of phenotypes matched to high-content experimental assays of free-living and parasitic nematodes and flatworms. We demonstrate its utility for analyzing a suite of phenotypes, including motility, development/size, fecundity, and feeding, and establish the package as a platform upon which to build future custom phenotypic modules. 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Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wheeler, Nicolas J</au><au>Gallo, Kendra J</au><au>Rehborg, Elena J G</au><au>Ryan, Kaetlyn T</au><au>Chan, John D</au><au>Zamanian, Mostafa</au><au>Cotton, James</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>wrmXpress: A modular package for high-throughput image analysis of parasitic and free-living worms</atitle><jtitle>PLoS neglected tropical diseases</jtitle><addtitle>PLoS Negl Trop Dis</addtitle><date>2022-11-01</date><risdate>2022</risdate><volume>16</volume><issue>11</issue><spage>e0010937</spage><pages>e0010937-</pages><issn>1935-2735</issn><issn>1935-2727</issn><eissn>1935-2735</eissn><abstract>Advances in high-throughput and high-content imaging technologies require concomitant development of analytical software capable of handling large datasets and generating relevant phenotypic measurements. Several tools have been developed to analyze drug response phenotypes in parasitic and free-living worms, but these are siloed and often limited to specific instrumentation, worm species, and single phenotypes. No unified tool exists to analyze diverse high-content phenotypic imaging data of worms and provide a platform for future extensibility. We have developed wrmXpress, a unified framework for analyzing a variety of phenotypes matched to high-content experimental assays of free-living and parasitic nematodes and flatworms. We demonstrate its utility for analyzing a suite of phenotypes, including motility, development/size, fecundity, and feeding, and establish the package as a platform upon which to build future custom phenotypic modules. 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| subjects | Analysis Antiparasitic agents Aquatic invertebrates Biological Assay Biology and Life Sciences Collaboration Computer and Information Sciences Culture Deep learning Engineering and Technology Evaluation Experiments Fecundity Fertility Flatworms Humans Image analysis Image processing Imaging techniques Instrumentation Morphology Motility Nematoda Nematodes Parasites Phenotype Phenotypes Research and Analysis Methods Research Personnel Science Policy Software Tropical diseases Worms |
| title | wrmXpress: A modular package for high-throughput image analysis of parasitic and free-living worms |
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