Rapid and fully automated blood vasculature analysis in 3D light-sheet image volumes of different organs

Microvascular Network Remodeling in the Ischemic Mouse Brain Defined by Light Sheet Microscopy

“…Using VesselExpress, an integrated pipeline for the segmentation, skeletonization, and graph analysis of light sheet images, 15 we provide a comprehensive analysis of microvascular network remodeling and angiogenesis in mice exposed to transient MCAO. Through analysis of a broad set of network characteristics, we found that the topology of cerebral microvessels is profoundly and chronically altered post-I/R, which likely has an impact on brain hemodynamics, tissue survival, and stroke recovery.…”

“…Following whole brain clearing, brains were scanned using an Ultramicroscope 2 light sheet microscope (LaVision BioTec, Bielefeld, Germany). 15 The Ultramicroscope 2 microscope is based on an Olympus MVX10 zoom microscope, which, when combined with a 2×0.5 numerical aperture objective, provided a magnification range from 1.26 to 12.6. The Ultramicroscope 2 microscope was equipped with bidirectional light sheet illumination and an Andor Neo sCMOS camera having a 2560×2160 chip of 6.5 µm pixel size.…”

“…Due to a high degree of automation, robustness, and parallelized data processing, VesselExpress allows evaluating a large variety of 3D microvascular characteristics not only in brain but also in various other tissues. 15 VesselExpress is based on a novel dual Frangi filter approach for thin and thick microvessels, which allows for the reliable segmentation of microvessels across a large range of microvessel diameters. 15 Thereby, VesselExpress improves the validity of microvascular diameter assessments, which have been overestimated by previous image-processing approaches.…”

“…15 VesselExpress is based on a novel dual Frangi filter approach for thin and thick microvessels, which allows for the reliable segmentation of microvessels across a large range of microvessel diameters. 15 Thereby, VesselExpress improves the validity of microvascular diameter assessments, which have been overestimated by previous image-processing approaches. Using VesselExpress, we determined a comprehensive set of 8 network characteristics from the graphs, which included (1) microvascular length density (ie, the total vessel length per brain volume), ( 2) branching point density (ie, the total number of branching points per brain volume), (3) microvascular volume density (ie, the total vessel volume per brain volume), (4) mean branch length between 2 branching points, (5) terminal point density (the number of terminal vessels, ie, dead-ends, per brain volume; this variable excluded terminal points on the volume surface reflecting vessels entering or exiting the volume), ( 6) mean vessel diameter, (7) microvessel tortuosity (ie, microvascular branch length divided by the distance between branching points), and (8) total vessel length for the whole striatum.…”

“…We recently established VesselExpress, an integrated pipeline allowing fully automated segmentation, skeletonization, and graph analysis of microvascular networks. 15 With this tool, a comprehensive set of microvascular network characteristics can reliably be studied, which includes microvascular density, branching point density, branch length, and branch diameter, besides others. Changes of network density and architecture strongly influence regional cerebral blood flow by influencing regional blood flow and, upon vascular occlusion, collateral flow.…”