Computer-based three-dimensional visualization of developmental gene expression

Nat Genet. 2000 Jun;25(2):147-52. doi: 10.1038/75989.


A broad understanding of the relationship between gene activation, pattern formation and morphogenesis will require adequate tools for three-dimensional and, perhaps four-dimensional, representation and analysis of molecular developmental processes. We present a novel, computer-based method for the 3D visualization of embryonic gene expression and morphological structures from serial sections. The information from these automatically aligned 3D reconstructions exceeds that from single-section and whole-mount visualizations of in situ hybridizations. In addition, these 3D models of gene-expression patterns can become a central component of a future developmental database designed for the collection and presentation of digitized, morphological and gene-expression data. This work is accompanied by a web site (

MeSH terms

  • Anatomy, Cross-Sectional / methods
  • Animals
  • Automation
  • Computer Simulation*
  • Databases, Factual
  • Embryo, Mammalian / anatomy & histology*
  • Embryo, Mammalian / metabolism*
  • Embryonic and Fetal Development
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Developmental*
  • Genetic Markers / genetics
  • Image Processing, Computer-Assisted / methods*
  • In Situ Hybridization / methods
  • Internet
  • Mice
  • Morphogenesis / genetics
  • Organ Specificity
  • Pattern Recognition, Automated
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Software
  • Transcriptional Activation / genetics


  • Genetic Markers