Volumetric ultrasound localization microscopy of the whole brain microvasculature

Abstract

Technologies to visualize whole organs across scales in vivo are essential for our understanding of biology in health and disease. To date, only post-mortem techniques such as perfused computed tomography scanning or optical microscopy of cleared tissues achieve cellular resolution across entire organs and imaging methods with equal performance in living mammalian organs have yet to be developed. Recently, 2D ultrasound localization microscopy has successfully mapped the fine-scale vasculature of various organs down to a 10 μm precision. However, reprojection issues and out-of-plane motion prevent complex blood flow quantification and fast volumetric imaging of whole organs. Here, we demonstrate for the first time in vivo volumetric ultrasound localization microscopy mapping of the rodent brain vasculature. We developed a complete methodological pipeline that includes specific surgery, a dedicated 3D ultrasound acquisition sequence, localization and tracking algorithms, motion correction and realignment, as well as the post-processing quantification of cerebral blood flow. We illustrate the power of this approach, by mapping the whole rat brain vasculature at a resolution of 12 μm, revealing mesoscopic to macroscopic vascular architectures and cerebral blood flows ranging from 1 to 100 mm/s. Our results pave the way to the investigation of in vivo vascular processes across the mammalian brain in health and disease, in a wide range of contexts and models.

3D Transcranial Ultrasound Localization Microscopy in the Rat Brain With a Multiplexed Matrix Probe

“…In this study, we reached an SNR of 9 dB for microbubbles under the intact skull with only 5 compounded plane waves. As a comparison, [44] used 12 plane waves with the 4-Aixplorer system in the rat brain with craniectomy and 9 plane waves in [33] with the 2-ULA-OP system for flow canal imaging. This new generation of ultrasound scanners increases the ability of volumetric imaging with fewer plane waves, reducing the data generation and increasing the maximal compounded volume rate.…”

“…A custom 3D radial symmetry-based localization kernel [44], [49] was implemented to localize the sub-wavelength position of the microbubble, adapted from a 2D scheme [50], [51], avoiding time and space-consuming interpolation schemes. Positions were paired into trajectories with a tracking algorithm based on the Kuhn-Munkres algorithm (Fig.…”

“…ULM has already been implemented in 3D with encouraging results in vitro [40], [41], with sparse matrix array [33], with RCA matrix probes [42], particularly with synchronized ultrasounds scanners [43]. This last system was used in vivo to image the rat brain with craniectomy [44].…”

An Anatomically Realistic Simulation Framework for 3D Ultrasound Localization Microscopy

“…In terms of imaging parameters, common planewave transmit sequences include planewave compounding of 5-12 tilted planewaves and a pulse length of 1-10 cycles [39], [55], [56]. A single planewave was simulated in this work to reduce computation time, and a pulse length of 4 cycles was selected to send more energy in the medium to increase contrast.…”

Depth‐Resolved Localization Microangiography in the NIR‐II Window

“…[ 21 ] High‐resolution imaging at depths of several millimeters to centimeters is achieved with these methods by capitalizing on the insignificant scattering of US waves as compared to photons in soft biological tissues. US localization microscopy [ 22 , 23 ] has further enabled a striking resolution enhancement (≈tenfold) and simultaneous in‐plane velocity measurements via tracking of intravenously injected microbubbles. A similar approach can be implemented to mitigate resolution degradation due to scattering in wide‐field fluorescence imaging, [ 24 , 25 ] albeit only limited to planar (2D) representations.…”