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Three-Dimensional Histology of Whole Zebrafish by Sub-Micron Synchrotron X-ray Micro-Tomography

View ORCID ProfileYifu Ding, View ORCID ProfileDaniel J. Vanselow, View ORCID ProfileMaksim A. Yakovlev, View ORCID ProfileSpencer R. Katz, Alex Y. Lin, Darin P. Clark, Phillip Vargas, Xuying Xin, Jean E. Copper, Victor A. Canfield, Khai C. Ang, Yuxin Wang, Xianghui Xiao, Francesco De Carlo, View ORCID ProfileDamian B. van Rossum, Patrick La Rivière, View ORCID ProfileKeith C. Cheng
doi: https://doi.org/10.1101/392381
Yifu Ding
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
3Medical Scientist Training Program, Penn State College of Medicine, Hershey, PA 17033, USA.
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Daniel J. Vanselow
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
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Maksim A. Yakovlev
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
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Spencer R. Katz
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
3Medical Scientist Training Program, Penn State College of Medicine, Hershey, PA 17033, USA.
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Alex Y. Lin
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
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Darin P. Clark
4Center for In Vivo Microscopy, Box 3302, Duke University Medical Center Durham, NC 27710, USA.
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Phillip Vargas
5Department of Radiology, The University of Chicago, Chicago, IL 60637, USA.
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Xuying Xin
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
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Jean E. Copper
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
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Victor A. Canfield
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
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Khai C. Ang
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
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Yuxin Wang
6Motorola Mobility, Chicago, IL 60654, USA.
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Xianghui Xiao
7Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA.
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Francesco De Carlo
7Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA.
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Damian B. van Rossum
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
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Patrick La Rivière
5Department of Radiology, The University of Chicago, Chicago, IL 60637, USA.
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Keith C. Cheng
1The Jake Gittlen Laboratories for Cancer Research, Penn State College of Medicine, Hershey, PA, 17033, USA.
2Division of Experimental Pathology, Department of Pathology, Penn State College of Medicine, Hershey, PA 17033, USA.
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  • For correspondence: kcheng76@gmail.com
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Abstract

Histological studies providing cellular insights into tissue architecture have been central to biological discovery and remain clinically invaluable today. Extending histology to three dimensions would be transformational for research and diagnostics. However, three-dimensional histology is impractical using current techniques. We have customized sample preparation, synchrotron X-ray tomographic parameters, and three-dimensional image analysis to allow for complete histological phenotyping using whole larval and juvenile zebrafish. The resulting digital zebrafish can be virtually sectioned and visualized in any plane. Whole-animal reconstructions at subcellular resolution also enable computational characterization of the zebrafish nervous system by region-specific detection of cell nuclei and quantitative assessment of individual phenotypic variation. Three-dimensional histological phenotyping has potential use in genetic and chemical screens, and in clinical and toxicological tissue diagnostics.

One Sentence Summary Synchrotron X-ray micro-tomography can be used to rapidly create 3-dimensional images of fixed and stained specimens without sectioning, enabling computational histological phenotyping at cellular resolution.

Abbreviations
3D
three-dimensional
H&E
hematoxylin & eosin
2D
two-dimensional
micro-CT
X-ray micro-tomography
dpf
days post-fertilization
PTA
phosphotungstic acid
RBC
red blood cell
Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted August 25, 2018.
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Three-Dimensional Histology of Whole Zebrafish by Sub-Micron Synchrotron X-ray Micro-Tomography
Yifu Ding, Daniel J. Vanselow, Maksim A. Yakovlev, Spencer R. Katz, Alex Y. Lin, Darin P. Clark, Phillip Vargas, Xuying Xin, Jean E. Copper, Victor A. Canfield, Khai C. Ang, Yuxin Wang, Xianghui Xiao, Francesco De Carlo, Damian B. van Rossum, Patrick La Rivière, Keith C. Cheng
bioRxiv 392381; doi: https://doi.org/10.1101/392381
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Three-Dimensional Histology of Whole Zebrafish by Sub-Micron Synchrotron X-ray Micro-Tomography
Yifu Ding, Daniel J. Vanselow, Maksim A. Yakovlev, Spencer R. Katz, Alex Y. Lin, Darin P. Clark, Phillip Vargas, Xuying Xin, Jean E. Copper, Victor A. Canfield, Khai C. Ang, Yuxin Wang, Xianghui Xiao, Francesco De Carlo, Damian B. van Rossum, Patrick La Rivière, Keith C. Cheng
bioRxiv 392381; doi: https://doi.org/10.1101/392381

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