AUTHOR=Goharbavang Helya , Ashitkov Artem T. , Pillai Athira , Wythe Joshua D. , Chen Guoning , Mayerich David 

TITLE=Segmentation and modeling of large-scale microvascular networks: a survey

JOURNAL=Frontiers in Bioinformatics

VOLUME=Volume 5 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1645520

DOI=10.3389/fbinf.2025.1645520

ISSN=2673-7647

ABSTRACT=Recent advances in three-dimensional microscopy enable imaging of whole-organ microvascular networks in small animals. Since microvasculature plays a crucial role in tissue development and function, its structure may provide diagnostic biomarkers and insight into disease progression. However, the microscopy community currently lacks benchmarks for scalable algorithms to measure these potential biomarkers. While many algorithms exist for segmenting vessel-like structures and extracting their surface features and connectivity, they have not been thoroughly evaluated on modern gigavoxel-scale images. In this paper, we propose a comprehensive yet compact survey of available algorithms. We focus on essential features for microvascular analysis, including extracting vessel surfaces and the network’s associated connectivity. We select a series of algorithms based on popularity and availability and provide a thorough quantitative analysis of their performance on datasets acquired using light sheet fluorescence microscopy (LSFM), knife-edge scanning microscopy (KESM), and X-ray microtomography (µ-CT).