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J. Imaging 2019, 5(1), 14; https://doi.org/10.3390/jimaging5010014

Enhancement and Segmentation Workflow for the Developing Zebrafish Vasculature

1
Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, University of Sheffield, Sheffield S10 2JF, UK
2
The Bateson Centre, Firth Court, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
This paper is an extended version of our paper published in Annual Conference on Medical Image Understanding and Analysis, Southampton, UK, 9–11 July, 2018.
*
Author to whom correspondence should be addressed.
Received: 28 November 2018 / Revised: 3 January 2019 / Accepted: 8 January 2019 / Published: 11 January 2019
(This article belongs to the Special Issue Medical Image Understanding and Analysis 2018)
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Abstract

Zebrafish have become an established in vivo vertebrate model to study cardiovascular development and disease. However, most published studies of the zebrafish vascular architecture rely on subjective visual assessment, rather than objective quantification. In this paper, we used state-of-the-art light sheet fluorescence microscopy to visualize the vasculature in transgenic fluorescent reporter zebrafish. Analysis of image quality, vascular enhancement methods, and segmentation approaches were performed in the framework of the open-source software Fiji to allow dissemination and reproducibility. Here, we build on a previously developed image processing pipeline; evaluate its applicability to a wider range of data; apply and evaluate an alternative vascular enhancement method; and, finally, suggest a work-flow for successful segmentation of the embryonic zebrafish vasculature. View Full-Text
Keywords: 3D; analysis; development; in vivo; light sheet fluorescence microscopy (LSFM); segmentation; vasculature; zebrafish 3D; analysis; development; in vivo; light sheet fluorescence microscopy (LSFM); segmentation; vasculature; zebrafish
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Kugler, E.; Plant, K.; Chico, T.; Armitage, P. Enhancement and Segmentation Workflow for the Developing Zebrafish Vasculature. J. Imaging 2019, 5, 14.

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