A Practical Guide to the Automated Analysis of Vascular Growth, Maturation and Injury in the Brain

Abstract

The distinct organization of the brain's vasculature ensures the adequate delivery of oxygen and nutrients during development and adulthood. Acute and chronic pathological changes of the vascular system have been implicated in many neurological disorders including stroke and dementia. Here, we describe a fast, automated method that allows the highly reproducible, quantitative assessment of distinct vascular parameters and their changes based on the open source software Fiji (ImageJ). In particular, we developed a practical guide to reliably measure aspects of growth, repair and maturation of the brain's vasculature during development and neurovascular disease in mice and humans. The script can be used to assess the effects of different external factors including pharmacological treatments or disease states. Moreover, the procedure is expandable to blood vessels of other organs and vascular in vitro models.

Distinct changes in all major components of the neurovascular unit across different neuropathological stages of Alzheimer's disease

“…Vessel area fraction, length, branching and nearest distance were quantified using lectin labeling with an automated ImageJ script as previously described for brain and retinal vasculature (44)(45)(46)(47). Briefly, for area fraction, the area covered by lectin labeling was quantified using ImageJ after applying a constant threshold.…”

Characterization of the Blood Brain Barrier Disruption in the Photothrombotic Stroke Model

“…Evans blue signal area in ischemic brain sections was quantified by thresholding at fivefold background signal intensity of the intact sensorimotor cortex (perfused with EB). Pericyte and tight junction coverage of blood vessels was calculated as previously described with an automated Fiji (ImageJ) script (Rust et al, 2019a(Rust et al, , 2020 and normalized to the intact cortex. Briefly, 4-6 random ROIs were selected.…”

Generation of Tubular and Membranous Shape Textures with Curvature Functionals

“…It could also be combined with 3D reconstruction from 2D slices methods [13,53,64]. -Build a synthetic database of textures: the generation algorithm could provide, at a low cost, a complete panel of synthetic textures on which to test and train vascular shape analysis methods [50,84,89], including topological analysis methods [15,47,79], segmentation algorithms, microvascular blood flow simulations [5,86], but also simulations in porous materials [65,95,109]. It could also provide a database to research in shape and texture perception [108]; the way we perceive shapes is intimately linked to the way we want to quantify them.…”