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Bioinformatics Advance Access first published online on November 19, 2007
This version published online on December 4, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm569
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Straightening C. elegans Images

Hanchuan Peng 1,*, Fuhui Long 1, Xiao Liu 2, Stuart K. Kim 2 and Eugene W. Myers 1

1 Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn VA, 20147.
2 Department of Developmental Biology, Stanford University Medical Center, Stanford, CA, 94305

*To whom correspondence should be addressed. Dr. Hanchuan Peng, E-mail: pengh{at}janelia.hhmi.org


  Abstract

Motivation: C. 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 "straighten" the worms if they are to be compared under a canonical coordinate system.

Results: We develop a worm straightening algorithm (WSA) that restacks cutting planes orthogonal to a "backbone" that models the anterior-posterior 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.

Supplementary Information: The example data sets and programs are available upon request.

Contact: pengh{at}janelia.hhmi.org

Associate Editor: Dr. Jonathan Wren

Received on June 13, 2007; revised on October 11, 2007; accepted on November 6, 2007

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