Optimizing synchrotron micro-CT for high-throughput phenotyping of zebrafish

Patrick J. La Rivière, Darin Clark, Alexandra Rojek, Phillip Vargas, Xianghui Xiao, Francesco DeCarlo, Gordon Kindlmann, Keith Cheng

Research output: Chapter in Book/Report/Conference proceedingConference contribution

7 Scopus citations


We are creating a state-of-the-art 2D and 3D imaging atlas of zebrafish development. The atlas employs both 2D histology slides and 3D benchtop and synchrotron micro CT results. Through this atlas, we expect to document normal and abnormal organogenesis, to reveal new levels of structural detail, and to advance image informatics as a form of systems biology. The zebrafish has become a widely used model organism in biological and biomedical research for studies of vertebrate development and gene function. In this work, we will report on efforts to optimize synchrotron microCT imaging parameters for zebrafish at crucial developmental stages. The aim of these studies is to establish protocols for high-throughput phenotyping of normal, mutant and diseased zebrafish. We have developed staining and embedding protocols using different heavy metal stains (osmium tetroxide and uranyl acetate) and different embedding media (Embed 812 and glycol methacrylate). We have explored the use of edge subtraction and multi-energy techniques for contrast enhancement and we have examined the use of different sample-detector distances with unstained samples to explore and optimize phase-contrast enhancement effects. We will report principally on our efforts to optimize energy choice for single- and multi-energy studies as well as our efforts to optimize the degree of phase contrast enhancement.

Original languageEnglish (US)
Title of host publicationDevelopments in X-Ray Tomography VII
StatePublished - 2010
EventDevelopments in X-Ray Tomography VII - San Diego, CA, United States
Duration: Aug 2 2010Aug 5 2010

Publication series

NameProceedings of SPIE - The International Society for Optical Engineering
ISSN (Print)0277-786X


OtherDevelopments in X-Ray Tomography VII
Country/TerritoryUnited States
CitySan Diego, CA

All Science Journal Classification (ASJC) codes

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics
  • Computer Science Applications
  • Applied Mathematics
  • Electrical and Electronic Engineering


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