Visualization and analysis of pharyngeal arch arteries using whole-mount immunohistochemistry and 3d reconstruction

Annjosette Ramirez, Sophie Astrof

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


Improper formation or remodeling of the pharyngeal arch arteries (PAAs) 3, 4, and 6 contribute to some of the most severe forms of congenital heart disease. To study the formation of PAAs, we developed a protocol using whole-mount immunofluorescence coupled with benzyl alcohol/ benzyl benzoate (BABB) tissue clearing, and confocal microscopy. This allows for the visualization of the pharyngeal arch endothelium at a fine cellular resolution as well as the 3D connectivity of the vasculature. Using software, we have established a protocol to quantify the number of endothelial cells (ECs) in PAAs, as well as the number of ECs within the vascular plexus surrounding the PAAs within pharyngeal arches 3, 4, and 6. When applied to the whole embryo, this methodology provides a comprehensive visualization and quantitative analysis of embryonic vasculature.

Original languageEnglish (US)
Article numbere60797
JournalJournal of Visualized Experiments
Issue number157
StatePublished - Mar 2020

All Science Journal Classification (ASJC) codes

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)


  • 3D reconstruction
  • Confocal microscopy
  • Developmental Biology
  • Endothelial cells
  • Issue 157
  • Pharyngeal arch artery development
  • Tissue clearing
  • Whole-mount immunofluorescence


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