Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT

Elife. 2021 Sep 16;10:e68920. doi: 10.7554/eLife.68920.


We previously described X-ray histotomography, a high-resolution, non-destructive form of X-ray microtomography (micro-CT) imaging customized for three-dimensional (3D), digital histology, allowing quantitative, volumetric tissue and organismal phenotyping (Ding et al., 2019). Here, we have combined micro-CT with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and further allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, including subtle phenotypes not previously noticed. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution, with potential applications in other model organisms and melanocytic neoplasms. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables.

Keywords: 3D imaging; cell biology; developmental biology; melanin; micro-CT; pigmentation; silver staining; whole-organism phenomics; zebrafish.

Publication types

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

MeSH terms

  • Animals
  • Imaging, Three-Dimensional / methods*
  • Melanins* / analysis
  • Melanins* / chemistry
  • Silver Staining / methods*
  • X-Ray Microtomography / methods*
  • Zebrafish
  • Zebrafish Proteins* / analysis
  • Zebrafish Proteins* / chemistry


  • Melanins
  • Zebrafish Proteins

Associated data

  • Dryad/10.5061/dryad.wwpzgmsjn