Technical advance: an aniline blue staining procedure for confocal microscopy and 3D imaging of normal and perturbed cellular phenotypes in mature Arabidopsis embryos

Plant J. 2000 Nov;24(4):543-50. doi: 10.1046/j.1365-313x.2000.00892.x.


A new method is described for fluorescent imaging of mature Arabidopsis embryos that enables their cellular architecture to be visualized without the need for histological sectioning. Mature embryos are stained with aniline blue and cleared with chloral hydrate to allow high-resolution confocal imaging of individual cells within the embryo prior to germination. The technique allows the collection of longitudinal optical sections throughout the cotyledon, hypocotyl and root of wild-type Arabidopsis C24 embryos. Every cell within the mature embryo can be visualized with sufficient clarity and resolution to allow three-dimensional analysis of cellular architecture. Optical sectioning of mutant gnom, short-root and scarecrow embryos, and through root meristems disrupted as a consequence of targeted misexpression of diphtheria toxin, demonstrate the potential of this technique for visualizing the cellular organization of mutant and perturbed embryonic phenotypes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aniline Compounds*
  • Arabidopsis / cytology*
  • Arabidopsis / genetics
  • Fluorescent Dyes*
  • Green Fluorescent Proteins
  • Luminescent Proteins / genetics
  • Luminescent Proteins / metabolism
  • Microscopy, Confocal
  • Mutation
  • Phenotype
  • Plants, Genetically Modified
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Seeds / cytology*
  • Seeds / genetics
  • Staining and Labeling / methods*
  • Trans-Activators / genetics
  • Trans-Activators / metabolism


  • Aniline Compounds
  • Fluorescent Dyes
  • Gal-VP16
  • Luminescent Proteins
  • Recombinant Fusion Proteins
  • Trans-Activators
  • Green Fluorescent Proteins
  • aniline blue