{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T22:48:29Z","timestamp":1780699709962,"version":"3.54.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3240,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: \u00a0Caenorhabditis elegans, a roundworm found in soil, is a widely studied model organism with about 1000 cells in the adult. Producing high-resolution fluorescence images of C.elegans to reveal biological insights is becoming routine, motivating the development of advanced computational tools for analyzing the resulting image stacks. For example, worm bodies usually curve significantly in images. Thus one must \u2018straighten\u2019 the worms if they are to be compared under a canonical coordinate system.<\/jats:p>\n               <jats:p>Results: We develop a worm straightening algorithm (WSA) that restacks cutting planes orthogonal to a \u2018backbone\u2019 that models the anterior\u2013posterior axis of the worm. We formulate the backbone as a parametric cubic spline defined by a series of control points. We develop two methods for automatically determining the locations of the control points. Our experimental methods show that our approaches effectively straighten both 2D and 3D worm images.<\/jats:p>\n               <jats:p>Contact: \u00a0pengh@janelia.hhmi.org<\/jats:p>\n               <jats:p>Supplementary information: The example data sets and programs are available upon request.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm569","type":"journal-article","created":{"date-parts":[[2007,11,20]],"date-time":"2007-11-20T01:13:06Z","timestamp":1195521186000},"page":"234-242","source":"Crossref","is-referenced-by-count":54,"title":["Straightening <i>Caenorhabditis elegans<\/i> images"],"prefix":"10.1093","volume":"24","author":[{"given":"Hanchuan","family":"Peng","sequence":"first","affiliation":[{"name":"1 Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 and 2Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuhui","family":"Long","sequence":"additional","affiliation":[{"name":"1 Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 and 2Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Liu","sequence":"additional","affiliation":[{"name":"1 Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 and 2Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stuart K.","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 and 2Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugene W.","family":"Myers","sequence":"additional","affiliation":[{"name":"1 Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147 and 2Department of Developmental Biology, Stanford University Medical Center, Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2007,11,19]]},"reference":[{"key":"2023020209473455600_B1","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1109\/TITB.2002.1006304","article-title":"Rapid automated three-dimensional tracing of neurons from confocalimage stacks","volume":"6","author":"Al-Kofahi","year":"2002","journal-title":"IEEE Trans. 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