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Bioinformatics. 2008 Jan 15;24(2):234-42. Epub 2007 Nov 19.

Straightening Caenorhabditis elegans images.

Author information

1
Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA. pengh@janelia.hhmi.org

Abstract

MOTIVATION:

Caenorhabditis 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.

PMID:
18025002
PMCID:
PMC2940239
DOI:
10.1093/bioinformatics/btm569
[Indexed for MEDLINE]
Free PMC Article
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