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Whole‐body 3D imaging at cell resolutions to define the phenomic landscape for genes, chemicals, and diseases
Author(s) -
Cheng Keith,
La Riviere Patrick,
De Carlo Francesco,
Xiao Xianghui,
Clark Darin,
Xin Xuying,
Kindlmann Gordon
Publication year - 2011
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.25.1_supplement.793.17
Subject(s) - zebrafish , throughput , computer science , computational biology , biology , gene , genetics , telecommunications , wireless
Phenotypic patterns caused by gene deficiency or chemical exposure cross organ systems and make up genetic and chemical phenomes , respectively. Defining phenomes requires 1) high throughput to test large numbers of genes and chemicals, 2) whole organism imaging for more complete phenotyping, and 3) cell resolutions to define cellular mechanism. The zebrafish's small size makes it an ideal vertebrate model for pursuing high‐throughput, whole animal imaging at cell resolutions. Quantitative analysis of 3D images of whole animals is needed to achieve high throughput, consistency and accuracy of phenotyping. We utilized the high‐energy, monochromatic, parallel‐beam, X‐rays of the synchrotron at Argonne National Labs for micron‐scale tomographic imaging. Whole animal 3D images of fixed and stained larval and juvenile zebrafish at voxel sizes of 0.743 and 1.43 microns (fields of view of 2.93 and 1.52 mm, respectively) allow visualization of nearly every cell type in whole‐body images. Individual retinal cells were modeled from higher resolution images. We are working towards high throughput of imaging, image processing, feature extraction and measurement of abnormality. This work will advance understanding of gene function, toxicity, and disease, and also accelerate drug development and safety testing for human and environmental exposures. Supported by NIH R24 RR01744, DOD and Penn State.