3D Quantification of the Zebrafish Brain Vasculature 

Vascular diseases are the leading cause of death world-wide. Understanding vascular development and disease is crucial in identifying future options for prevention and treatment.

Detailed insights into vascular development in vivo and 3D can be achieved using zebrafish transgenic lines and light sheet fluorescence microscopy.

However, robust quantification of the zebrafish cerebral vasculature in 3D remains a major challenge due to the lack of tailored analysis tools. 

For her PhD at the University of Sheffield, Elisabeth developed image analysis approaches to understand, quantify, and describe the 3D zebrafish brain vascular architecture.

The developed analysis pipeline included

  • image understanding and characterisation: Contrast-to-Noise ratio, motion artefacts/correction, data scales. 

  • enhancement and segmentation: pre-processing filters (general filters, Sato, Frangi), segmentation (thresholding, advanced methods such as level set), segmentation validation.

  • registration: landmark-based and automatic.

  • quantification: volume, surface, density, length, branching points, diameter, complexity; global scale and sub-regions.

Together, her work allows for more a comprehensive descriptions of vascular development and the identification of the role of genetic or chemical components.


3D quantification of zebrafish cerebrovascular architecture by automated image analysis of light sheet fluorescence microscopy datasets

The effect of absent blood flow on the zebrafish cerebral and trunk vasculature

Segmentation of the Zebrafish Brain Vasculature from Light Sheet Fluorescence Microscopy Datasets