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Sci Rep. 2018 Nov 8;8(1):16531. doi: 10.1038/s41598-018-34848-z.

Quantitative morphometric analysis of adult teleost fish by X-ray computed tomography.

Author information

1
Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, Germany. venera.weinhardt@kit.edu.
2
Centre for Organismal Studies, COS, Heidelberg University, Im Neunheimer Feld 230, Heidelberg, Germany. venera.weinhardt@kit.edu.
3
Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Karlsruhe, Germany. venera.weinhardt@kit.edu.
4
Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Karlsruhe, Germany.
5
Institute for Applied Computer Science, Karlsruhe Institute of Technology, Karlsruhe, Germany.
6
Centre for Organismal Studies, COS, Heidelberg University, Im Neunheimer Feld 230, Heidelberg, Germany.
7
Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany.
8
Center for Biological Systems Analysis, Freiburg, Germany.
9
Centre for Organismal Studies, COS, Heidelberg University, Im Neunheimer Feld 230, Heidelberg, Germany. jochen.wittbrodt@cos.uni-heidelberg.de.
10
Institute for Photon Science and Synchrotron Radiation, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, Germany.
11
Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany. felix.loosli@kit.edu.

Abstract

Vertebrate models provide indispensable paradigms to study development and disease. Their analysis requires a quantitative morphometric study of the body, organs and tissues. This is often impeded by pigmentation and sample size. X-ray micro-computed tomography (micro-CT) allows high-resolution volumetric tissue analysis, largely independent of sample size and transparency to visual light. Importantly, micro-CT data are inherently quantitative. We report a complete pipeline of high-throughput 3D data acquisition and image analysis, including tissue preparation and contrast enhancement for micro-CT imaging down to cellular resolution, automated data processing and organ or tissue segmentation that is applicable to comparative 3D morphometrics of small vertebrates. Applied to medaka fish, we first create an annotated anatomical atlas of the entire body, including inner organs as a quantitative morphological description of an adult individual. This atlas serves as a reference model for comparative studies. Using isogenic medaka strains we show that comparative 3D morphometrics of individuals permits identification of quantitative strain-specific traits. Thus, our pipeline enables high resolution morphological analysis as a basis for genotype-phenotype association studies of complex genetic traits in vertebrates.

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