Track-a-worm, an open-source system for quantitative assessment of C. elegans locomotory and bending behavior
A major challenge of neuroscience is to understand the circuit and gene bases of behavior. C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The inves...
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description | A major challenge of neuroscience is to understand the circuit and gene bases of behavior. C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The investigation generally requires quantitative behavioral analyses using an automated single-worm tracker, which constantly records and analyzes the position and body shape of a freely moving worm at a high magnification. Many single-worm trackers have been developed to meet lab-specific needs, but none has been widely implemented for various reasons, such as hardware difficult to assemble, and software lacking sufficient functionality, having closed source code, or using a programming language that is not broadly accessible. The lack of a versatile system convenient for wide implementation makes data comparisons difficult and compels other labs to develop new worm trackers. Here we describe Track-A-Worm, a system rich in functionality, open in source code, and easy to use. The system includes plug-and-play hardware (a stereomicroscope, a digital camera and a motorized stage), custom software written to run with Matlab in Windows 7, and a detailed user manual. Grayscale images are automatically converted to binary images followed by head identification and placement of 13 markers along a deduced spline. The software can extract and quantify a variety of parameters, including distance traveled, average speed, distance/time/speed of forward and backward locomotion, frequency and amplitude of dominant bends, overall bending activities measured as root mean square, and sum of all bends. It also plots worm travel path, bend trace, and bend frequency spectrum. All functionality is performed through graphical user interfaces and data is exported to clearly-annotated and documented Excel files. These features make Track-A-Worm a good candidate for implementation in other labs. |
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C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The investigation generally requires quantitative behavioral analyses using an automated single-worm tracker, which constantly records and analyzes the position and body shape of a freely moving worm at a high magnification. Many single-worm trackers have been developed to meet lab-specific needs, but none has been widely implemented for various reasons, such as hardware difficult to assemble, and software lacking sufficient functionality, having closed source code, or using a programming language that is not broadly accessible. The lack of a versatile system convenient for wide implementation makes data comparisons difficult and compels other labs to develop new worm trackers. Here we describe Track-A-Worm, a system rich in functionality, open in source code, and easy to use. The system includes plug-and-play hardware (a stereomicroscope, a digital camera and a motorized stage), custom software written to run with Matlab in Windows 7, and a detailed user manual. Grayscale images are automatically converted to binary images followed by head identification and placement of 13 markers along a deduced spline. The software can extract and quantify a variety of parameters, including distance traveled, average speed, distance/time/speed of forward and backward locomotion, frequency and amplitude of dominant bends, overall bending activities measured as root mean square, and sum of all bends. It also plots worm travel path, bend trace, and bend frequency spectrum. All functionality is performed through graphical user interfaces and data is exported to clearly-annotated and documented Excel files. These features make Track-A-Worm a good candidate for implementation in other labs.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0069653</identifier><identifier>PMID: 23922769</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Automation ; Behavior, Animal - physiology ; Bends ; Biology ; Caenorhabditis elegans ; Caenorhabditis elegans - physiology ; Calibration ; Computer programs ; Computer Science ; Digital cameras ; Engineering ; Frequency spectrum ; Graphical user interface ; Hardware ; Imaging, Three-Dimensional ; Interfaces ; Localization ; Locomotion ; Locomotion - physiology ; Nematodes ; Nervous system ; Neurons ; Operating systems ; Programming languages ; Software ; Source code ; User interfaces ; Worms</subject><ispartof>PloS one, 2013-07, Vol.8 (7), p.e69653-e69653</ispartof><rights>2013 Wang, Wang. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://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>2013 Wang, Wang 2013 Wang, Wang</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-90df4e831630844dfbd9a7588e97ce66df0b307b981109491d738e0533962ff13</citedby><cites>FETCH-LOGICAL-c526t-90df4e831630844dfbd9a7588e97ce66df0b307b981109491d738e0533962ff13</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724933/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3724933/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,725,778,782,862,883,2098,2917,23849,27907,27908,53774,53776,79351,79352</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23922769$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Gilestro, Giorgio F.</contributor><creatorcontrib>Wang, Sijie Jason</creatorcontrib><creatorcontrib>Wang, Zhao-Wen</creatorcontrib><title>Track-a-worm, an open-source system for quantitative assessment of C. elegans locomotory and bending behavior</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>A major challenge of neuroscience is to understand the circuit and gene bases of behavior. C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The investigation generally requires quantitative behavioral analyses using an automated single-worm tracker, which constantly records and analyzes the position and body shape of a freely moving worm at a high magnification. Many single-worm trackers have been developed to meet lab-specific needs, but none has been widely implemented for various reasons, such as hardware difficult to assemble, and software lacking sufficient functionality, having closed source code, or using a programming language that is not broadly accessible. The lack of a versatile system convenient for wide implementation makes data comparisons difficult and compels other labs to develop new worm trackers. Here we describe Track-A-Worm, a system rich in functionality, open in source code, and easy to use. The system includes plug-and-play hardware (a stereomicroscope, a digital camera and a motorized stage), custom software written to run with Matlab in Windows 7, and a detailed user manual. Grayscale images are automatically converted to binary images followed by head identification and placement of 13 markers along a deduced spline. The software can extract and quantify a variety of parameters, including distance traveled, average speed, distance/time/speed of forward and backward locomotion, frequency and amplitude of dominant bends, overall bending activities measured as root mean square, and sum of all bends. It also plots worm travel path, bend trace, and bend frequency spectrum. All functionality is performed through graphical user interfaces and data is exported to clearly-annotated and documented Excel files. These features make Track-A-Worm a good candidate for implementation in other labs.</description><subject>Animals</subject><subject>Automation</subject><subject>Behavior, Animal - physiology</subject><subject>Bends</subject><subject>Biology</subject><subject>Caenorhabditis elegans</subject><subject>Caenorhabditis elegans - physiology</subject><subject>Calibration</subject><subject>Computer programs</subject><subject>Computer Science</subject><subject>Digital cameras</subject><subject>Engineering</subject><subject>Frequency spectrum</subject><subject>Graphical user interface</subject><subject>Hardware</subject><subject>Imaging, Three-Dimensional</subject><subject>Interfaces</subject><subject>Localization</subject><subject>Locomotion</subject><subject>Locomotion - physiology</subject><subject>Nematodes</subject><subject>Nervous system</subject><subject>Neurons</subject><subject>Operating systems</subject><subject>Programming languages</subject><subject>Software</subject><subject>Source code</subject><subject>User interfaces</subject><subject>Worms</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNptkktv1DAUhSMEoqXwDxBYYsOCDH7FsTdIaMSjUiU2ZW05zvU0g2NP7WTQ_Hs8TFq1iNW17HM_n3t1quo1wSvCWvJxG-cUjF_tYoAVxkKJhj2pzolitBYUs6cPzmfVi5y3GDdMCvG8OqNMUdoKdV6N18nYX7Wpf8c0fkAmoLiDUOcCt4DyIU8wIhcTup1NmIbJTMMekMkZch4hTCg6tF4h8LAxISMfbRzjFNOhoHrUQeiHsCn1xuyHmF5Wz5zxGV4t9aL6-fXL9fp7ffXj2-X681VtGyqmWuHecZCMCIYl573remXaRkpQrQUheoc7httOSUKw4or0LZNQpmNKUOcIu6jenrg7H7NeNpU14VQSzgQWRXF5UvTRbPUuDaNJBx3NoP9exLTRJk2D9aCJ4M42kpOOcC6gkcWkNawhopWcOlpYn5bf5m6E3pa1JOMfQR-_hOFGb-Jes5ZyxVgBvF8AKd7OkCc9DtmC9yZAnI--iRRcKN4U6bt_pP-fjp9UNsWcE7h7MwTrY3ruuvQxPXpJT2l783CQ-6a7uLA_ZHXCsw</recordid><startdate>20130726</startdate><enddate>20130726</enddate><creator>Wang, Sijie Jason</creator><creator>Wang, Zhao-Wen</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130726</creationdate><title>Track-a-worm, an open-source system for quantitative assessment of C. elegans locomotory and bending behavior</title><author>Wang, Sijie Jason ; Wang, Zhao-Wen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-90df4e831630844dfbd9a7588e97ce66df0b307b981109491d738e0533962ff13</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Animals</topic><topic>Automation</topic><topic>Behavior, Animal - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Sijie Jason</au><au>Wang, Zhao-Wen</au><au>Gilestro, Giorgio F.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Track-a-worm, an open-source system for quantitative assessment of C. elegans locomotory and bending behavior</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-07-26</date><risdate>2013</risdate><volume>8</volume><issue>7</issue><spage>e69653</spage><epage>e69653</epage><pages>e69653-e69653</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>A major challenge of neuroscience is to understand the circuit and gene bases of behavior. C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The investigation generally requires quantitative behavioral analyses using an automated single-worm tracker, which constantly records and analyzes the position and body shape of a freely moving worm at a high magnification. Many single-worm trackers have been developed to meet lab-specific needs, but none has been widely implemented for various reasons, such as hardware difficult to assemble, and software lacking sufficient functionality, having closed source code, or using a programming language that is not broadly accessible. The lack of a versatile system convenient for wide implementation makes data comparisons difficult and compels other labs to develop new worm trackers. Here we describe Track-A-Worm, a system rich in functionality, open in source code, and easy to use. The system includes plug-and-play hardware (a stereomicroscope, a digital camera and a motorized stage), custom software written to run with Matlab in Windows 7, and a detailed user manual. Grayscale images are automatically converted to binary images followed by head identification and placement of 13 markers along a deduced spline. The software can extract and quantify a variety of parameters, including distance traveled, average speed, distance/time/speed of forward and backward locomotion, frequency and amplitude of dominant bends, overall bending activities measured as root mean square, and sum of all bends. It also plots worm travel path, bend trace, and bend frequency spectrum. All functionality is performed through graphical user interfaces and data is exported to clearly-annotated and documented Excel files. These features make Track-A-Worm a good candidate for implementation in other labs.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23922769</pmid><doi>10.1371/journal.pone.0069653</doi><oa>free_for_read</oa></addata></record> |
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subjects | Animals Automation Behavior, Animal - physiology Bends Biology Caenorhabditis elegans Caenorhabditis elegans - physiology Calibration Computer programs Computer Science Digital cameras Engineering Frequency spectrum Graphical user interface Hardware Imaging, Three-Dimensional Interfaces Localization Locomotion Locomotion - physiology Nematodes Nervous system Neurons Operating systems Programming languages Software Source code User interfaces Worms |
title | Track-a-worm, an open-source system for quantitative assessment of C. elegans locomotory and bending behavior |
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