ClearSee: a rapid optical clearing reagent for whole-plant fluorescence imaging

Development. 2015 Dec 1;142(23):4168-79. doi: 10.1242/dev.127613. Epub 2015 Oct 22.


Imaging techniques for visualizing and analyzing precise morphology and gene expression patterns are essential for understanding biological processes during development in all organisms. With the aid of chemical screening, we developed a clearing method using chemical solutions, termed ClearSee, for deep imaging of morphology and gene expression in plant tissues. ClearSee rapidly diminishes chlorophyll autofluorescence while maintaining fluorescent protein stability. By adjusting the refractive index mismatch, whole-organ and whole-plant imaging can be performed by both confocal and two-photon excitation microscopy in ClearSee-treated samples. Moreover, ClearSee is applicable to multicolor imaging of fluorescent proteins to allow structural analysis of multiple gene expression. Given that ClearSee is compatible with staining by chemical dyes, the technique is useful for deep imaging in conjunction with genetic markers and for plant species not amenable to transgenic approaches. This method is useful for whole imaging for intact morphology and will help to accelerate the discovery of new phenomena in plant biological research.

Keywords: Arabidopsis thaliana; Clearing; Confocal microscopy; Deep imaging; Physcomitrella patens; Two-photon microscopy; Whole plant.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis
  • Chlorophyll / chemistry
  • Cloning, Molecular
  • Fluorescence
  • Fluorescent Dyes / chemistry*
  • Green Fluorescent Proteins / metabolism
  • Indicators and Reagents / chemistry*
  • Microscopy, Confocal
  • Microscopy, Fluorescence / instrumentation
  • Microscopy, Fluorescence / methods*
  • Phloem
  • Photons
  • Plant Leaves / metabolism
  • Plant Roots / metabolism
  • Plants / metabolism*
  • Plants, Genetically Modified / metabolism
  • Urea / chemistry*
  • Xylitol / chemistry*


  • ClearSee
  • Fluorescent Dyes
  • Indicators and Reagents
  • Chlorophyll
  • Green Fluorescent Proteins
  • Urea
  • Xylitol