AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis

BMC Bioinformatics. 2006 Jun 1;7:275. doi: 10.1186/1471-2105-7-275.

Abstract

Background: The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point.

Results: We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data.

Conclusion: By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Caenorhabditis elegans / embryology*
  • Cell Lineage
  • Computational Biology / methods*
  • Embryo, Nonmammalian / pathology*
  • Green Fluorescent Proteins / chemistry
  • Histones / chemistry
  • Mutation
  • Phenotype
  • Phylogeny
  • Programming Languages
  • Software
  • User-Computer Interface

Substances

  • Histones
  • Green Fluorescent Proteins