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Proceedings Paper

Optimizing synchrotron microCT for high-throughput phenotyping of zebrafish
Author(s): Patrick J. La Rivière; Darin Clark; Alexandra Rojek; Phillip Vargas; Xianghui Xiao; Francesco DeCarlo; Gordon Kindlmann; Keith Cheng
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Paper Abstract

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.

Paper Details

Date Published: 20 September 2010
PDF: 8 pages
Proc. SPIE 7804, Developments in X-Ray Tomography VII, 78040M (20 September 2010); doi: 10.1117/12.860783
Show Author Affiliations
Patrick J. La Rivière, The Univ. of Chicago (United States)
Darin Clark, Penn State College of Medicine (United States)
Alexandra Rojek, The Univ. of Chicago (United States)
Phillip Vargas, The Univ. of Chicago (United States)
Xianghui Xiao, Argonne National Lab. (United States)
Francesco DeCarlo, Argonne National Lab. (United States)
Gordon Kindlmann, The Univ. of Chicago (United States)
Keith Cheng, Penn State College of Medicine (United States)


Published in SPIE Proceedings Vol. 7804:
Developments in X-Ray Tomography VII
Stuart R. Stock, Editor(s)

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