Synchrotron microCT imaging of soft tissue in juvenile zebrafish reveals retinotectal projections

Xuying Xin, Darin Clark, Khai Chung Ang, Damian B. Van Rossum, Jean Copper, Xianghui Xiao, Patrick J. La Riviere, Keith C. Cheng

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


Biomedical research and clinical diagnosis would benefit greatly from full volume determinations of anatomical phenotype. Comprehensive tools for morphological phenotyping are central for the emerging field of phenomics, which requires high-throughput, systematic, accurate, and reproducible data collection from organisms affected by genetic, disease, or environmental variables. Theoretically, complete anatomical phenotyping requires the assessment of every cell type in the whole organism, but this ideal is presently untenable due to the lack of an unbiased 3D imaging method that allows histopathological assessment of any cell type despite optical opacity. Histopathology, the current clinical standard for diagnostic phenotyping, involves the microscopic study of tissue sections to assess qualitative aspects of tissue architecture, disease mechanisms, and physiological state. However, quantitative features of tissue architecture such as cellular composition and cell counting in tissue volumes can only be approximated due to characteristics of tissue sectioning, including incomplete sampling and the constraints of 2D imaging of 5 micron thick tissue slabs. We have used a small, vertebrate organism, the zebrafish, to test the potential of microCT for systematic macroscopic and microscopic morphological phenotyping. While cell resolution is routinely achieved using methods such as light sheet fluorescence microscopy and optical tomography, these methods do not provide the pancellular perspective characteristic of histology, and are constrained by the limited penetration of visible light through pigmented and opaque specimens, as characterizes zebrafish juveniles. Here, we provide an example of neuroanatomy that can be studied by microCT of stained soft tissue at 1.43 micron isotropic voxel resolution. We conclude that synchrotron microCT is a form of 3D imaging that may potentially be adopted towards more reproducible, large-scale, morphological phenotyping of optically opaque tissues. Further development of soft tissue microCT, visualization and quantitative tool development will enhance its utility.

Original languageEnglish (US)
Title of host publicationOptical Biopsy XV
Subtitle of host publicationToward Real-Time Spectroscopic Imaging and Diagnosis
EditorsRobert R. Alfano, Stavros G. Demos
ISBN (Electronic)9781510605619
StatePublished - 2017
EventOptical Biopsy XV: Toward Real-Time Spectroscopic Imaging and Diagnosis - San Francisco, United States
Duration: Jan 31 2017Feb 1 2017

Publication series

NameProgress in Biomedical Optics and Imaging - Proceedings of SPIE
ISSN (Print)1605-7422


OtherOptical Biopsy XV: Toward Real-Time Spectroscopic Imaging and Diagnosis
Country/TerritoryUnited States
CitySan Francisco

All Science Journal Classification (ASJC) codes

  • Electronic, Optical and Magnetic Materials
  • Biomaterials
  • Atomic and Molecular Physics, and Optics
  • Radiology Nuclear Medicine and imaging


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