Deep and complex vascular anatomy in the rat brain described with Ultrasound Localization Microscopy in 3D

Abstract: Ultrasound Localization Microscopy (ULM) enables imaging microvessels in the brain with a resolution of a few tens of micrometers in vivo. The planar architecture of arterioles and venules was revealed with a 2D ultrasound scanner in the cortex of the rat brain. However, deeper in the brain, where the vascularization becomes tri-dimensional, 2D imaging remains limited by the elevation projection. In this study, volumetric ultrasound imaging was performed in the craniotomized rat brain to yield 3D ULM in vivo within 7.5 min of acquisition with a commercial system. For instance, it highlighted the thalamus or the circle of Willis with small vessels down to 21 µm. Microbubbles tracking also gave access to the 3D velocity vector of blood flow allowing to distinguish flow directions. Volumetric ULM resolved deep complex tri-dimensional vascular structures and was compared to 2D ULM. It is a safe, simple and repeatable system to image wide field of view in the brain. Data Description: Microbubbles have been detected, localized, and tracking with 3D ultrasound imaging in vivo in a rat brain with skull removal. Individual microbubble trajectories are described in 4 columns vectores: [z, x, y, time] for each position of the path. Space positions are given in [mm], and times are given in [ms]. Trajectories data are stored in .mat files (tracks_0xx.mat and zipped inside tracks.zip) as cell arrays. Tracks can be binned inside a volumetric grid with the sample code (ULM_rendering.m). Reference to be cited: Chavignon, Heiles, Hingot, Orset, Vivien and Couture. Deep and complex vascular anatomy in the rat brain described with Ultrasound Localization Microscopy in 3D.