DOI: 10.5061/dryad.w0vt4b8z8
title: Four-dimensional computational ultrasound imaging of brain hemodynamics

description: Four-dimensional ultrasound imaging of complex biological systems such as
 the brain is technically challenging because of the spatiotemporal
 sampling requirements. We present computational ultrasound imaging (cUSi),
 an imaging method that uses complex ultrasound fields that can be
 generated with simple hardware and a physical wave prediction model to
 alleviate the sampling constraints. cUSi allows for high-resolution
 four-dimensional imaging of brain haemodynamics in awake and anesthetized
 mice.
description: In this study, we assessed cUSi via in-vivo imaging experiments
 in both anesthetized (n=1) and awake (n=1) adult C57BL6/J mice (8–10 weeks
 old). The national authority (Centrale Commissie Dierproeven, The Hague,
 The Netherlands; license: AVD1010020197846) granted ethical approval prior
 to the experiments, which were performed according to the institutional,
 national, and European Union guidelines. Data from both mice was collected
 using a custom-built 64-element matrix probe with an output modified by a
 plastic encoding mask. The probe was driven using a Hadamard encoded
 synthetic aperture transmission scheme transmitting continuously for 60
 seconds at a rate of 32 kHz to acquire two data ensembles.  
 This upload contains the reconstructed Power and Colour Doppler
 Volumes from the data ensembles of both the awake and anesthetized mice.
 These were formed by spatio-temporally filtering using a singular value
 decomposition the 60-second acquisitions to remove signal components
 originating from soft-tissue. Next individual B-mode volumes were
 reconstructed by coherently compounding sets of 64 sequential
 transmissions from the filtered dataset with an 8 transmission lag. The
 reconstruction was performed with a model-based approach using a
 calibrated acoustic model of the transmitted matrix field. Finally, the
 Colour and Power Doppler volumes were generated by evaluating the lag-1
 autocorrelation or the average power respectively for each
 voxel. 
description: # Four-Dimensional Computational Ultrasound Imaging of Brain Hemodynamics
 The submission is
 comprised of 4 Nifti volumes: Awake_Color_Doppler, Awake_Power_Doppler,
 Anesthetized_Color_Doppler, and Anesthetized_Power_Doppler. The Nifti
 volumes can be visualised using a range of open source software (e.g.,
 Slicer: ). These four datasets respectively
 contain 3D information on the blood flow direction and power in the awake
 and anesthetized mouse brain and were used to generate the renderings and
 projections shown in Fig. 2 and Fig. S3 of the coupled manuscript. The
 specific details for each data-set are as follows: 1\)
 Awake_Color_Doppler.nii - the color doppler volume formed from the awake
 mouse experiment containing the flow direction. The volume size is
 176x156x180 with an isotropic voxel size of 40 microns the units indicate
 flow speed in m/s. 2\) Awake_Power_Doppler.nii - the power doppler volume
 formed from the awake mouse experiment containing the power in each voxel.
 The volume size is 176x156x180 with an isotropic voxel size of 40 microns
 and the units are in decibels. 3\) Anesthetized_Color_Doppler.nii - the
 color doppler volume formed from the anesthetized mouse experiment
 containing the flow direction. The volume size is 192x240x200 with an
 isotropic voxel size of 40 microns the units indicate flow speed in m/s.
 4\) Anesthetized_Power_Doppler.nii - the power doppler volume formed from
 the awake mouse experiment containing the power in each voxel. The volume
 size is 192x240x200 with an isotropic voxel size of 40 microns and the
 units are in decibels.