Automated analysis of zebrafish vascular networks using the VISTA-Z pipeline

Abstract

Abstract High-resolution vascular imaging in zebrafish embryos offers unparalleled insight into angiogenesis, yet quantitative analysis remains limited by manual workflows and inconsistent segmentation. To overcome this, we developed VISTA-Z (Vascular Imaging and Segmentation for Topology Analysis in Zebrafish), an automated Python-based pipeline designed to standardise vascular quantification across diverse fluorescent datasets. The workflow combines adaptive contrast enhancement, vessel segmentation using Meijering filtering, artefact removal through segment labelling, and skeleton-based topology analysis with refined branchpoint detection. Metrics are normalised to physical units and imaging depth, enabling reproducible comparisons across experiments. We validated VISTA-Z using multiple endothelial transgenic lines and developmental stages. The pipeline detected subtle and severe phenotypes, including brain vessel loss in foxc1a mutants, brain and trunk vessel loss in kdrl mutants and widespread hyper-angiogenesis in plxnd1 crispants. VISTA-Z is an open-source, scalable platform for reproducible high-throughput quantification of zebrafish vascular architecture, providing a standardised framework for developmental research and preclinical screening