Functional ultrasound (fUS) is an emerging neuroimaging modality that records changes in local blood dynamics. While it is known that the brain can respond variably to the same stimuli presented at different time instants, the extent to which fUS detects this variability based on the measured hemodynamics remains an open question. In this work, we characterize trial variability using fUS by estimating activation coefficients per trial using region-specific hemodynamic response functions. Our visual fUS experiments conducted on a mouse consistently reveal an increase of trial variability from the lateral geniculate nucleus to the visual cortex across different brain slices. These results are in parallel with prior findings in neuronal studies, suggesting a link between fluctuations of the evoked fUS response and true neural variability.

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Analysis of functional neuroimaging data aims to unveil spatial and temporal patterns of interest. Existing analysis methods fall into two categories: fully data-driven approaches and those reliant on prior information, e.g. the stimulus time course. While using the stimulus signal directly can help identify the activated brain areas, it is known that the relationship between stimuli and the brain's response exhibits nonlinear and time-varying characteristics. As such, relying completely on the stimulus signal to describe the brain's temporal response leads to a restricted interpretation of the brain function. In this paper, we present a new technique called Evoked Component Analysis (ECA), which leverages prior information up to a defined extent. This is achieved by including the general linear model (GLM) design matrix as a regulatory term and estimating the factor matrices in both space and time through an alternating minimization approach. We apply ECA to 2D and swept-3D functional ultrasound (fUS) experiments conducted with mice. When decomposing 2D fUS data, we employ GLM regularization at various intensities to emphasize the role of prior information. Furthermore, we show that incorporating multiple hemodynamic response functions within the design matrix can provide valuable insights into region-specific characteristics of evoked activity. Finally, we use ECA to analyze swept-3D fUS data recorded from five mice engaged in two distinct visual tasks. Swept-3D fUS images the 3D brain sequentially using a moving probe, resulting in different slice acquisition time instants. We show that ECA can estimate factor matrices with a fine resolution at each slice acquisition time instant and yield higher t-statistics compared to GLM and correlation analysis for all subjects.

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Computational ultrasound imaging (cUSi) offers high-resolution 3D imaging with simpler hardware by relying on computational power. Central to cUSi is a large model matrix that stores all pulse-echo signals. For 3D imaging this matrix easily surpasses 1 terabyte, hindering in-memory storage and real-time processing. This paper presents a solution for cUSi through an aberrating layer by introducing a virtual array concept, which uses transfer functions to map data from the real to a virtual array, enabling the use of conventional reconstruction techniques like delay-and-sum (DAS). We demonstrate the mathematical similarity of this approach to using a full model matrix and validate it with promising imaging results.@en

In recent decades, increasing ultrasound frame rates has been the main motivation behind many novel ultrasound imaging applications [1]-[3]. With this work, we propose an efficient ultrafast FPGA beamformer that applies coherent compounding, through a delay-reuse optimization.

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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 hemodynamics in awake and anesthetized mice.

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Functional ultrasound (fUS) is a novel neuroimaging technique that measures brain hemodynamics through a time series of Doppler images. The measured spatiotemporal hemodynamic changes reflect changes in neural activity through the neurovascular coupling (NVC). Often, such image time series is used to analyze dynamic functional connectivity (dFC) by directly computing a connectivity metric between the measured hemodynamic signals, ignoring the functional connectomics of underlying neural populations. This work proposes a novel fUS signal model, consisting of a hidden Markov model (HMM) cascaded with a convolutive model, that captures how fUS signals arise from a generative perspective while incorporating high-level biological functioning of neural populations. Consequently, the developed model enables inference of functional connectivity networks, being co-activation patterns (CAPs) of neural populations. Our results show that our methods can identify biologically plausible networks of functional connectivity. Furthermore, this method captures a difference in brain dynamics between wild-type and ${Shank2}^{-/-}$ mouse mutants.

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It has been previously demonstrated that applying an aberrating mask for 2D compressive imaging using a low number of sensors (elements) can significantly improve image resolution, as evaluated via the point spread function. Here we investigate the potential to apply a similar approach for 3D flow monitoring. We conducted a 3D k-Wave simulation using a 5x5 sensor array coupled to a physical coding mask, performing B-mode and power Doppler imaging on a 3D carotid artery flow model. An approximately three times smaller lateral PSF was achieved at the cost of increased background clutter level and slightly increased axial PSF. A better definition of the vessel border and finer flow speckle were observed in power Doppler imaging. Our results suggest that 3D compressive imaging using a very low sensor count of 25 with spatial coding mask has the potential to monitor 3D carotid artery flow.@en

Functional ultrasound (fUS) is an emerging neuroimaging modality that indirectly measures neural activity by detecting fluctuations in local blood dynamics. fUS acquisitions typically rely on the use of a 1D array transducer, which records hemodynamic activity in a single plane. A new technique named swept-3D fUS imaging obtains a full 3D volume of the brain by continuously moving a 1D array back-and-forth over the volume of interest. The standard procedure in fUS imaging involves filtering and averaging a number of ultrasound frames obtained at a single location to compute power-Doppler images, yet, in case of swept-3D fUS, the location of the recorded slice shifts at each time instant due to probe motion. In this work, we aim at discovering task-relevant components from 3D fUS data while taking into account the spatiotemporal differences in adjacent slices. We propose an alternating optimization scheme with general liner model-based regularization, and validate our method on swept-3D fUS data by identifying active regions and time traces within the mouse brain during a visual experiment.

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Volumetric 3-D Doppler ultrasound imaging can be used to investigate large scale blood dynamics outside of the limited view that conventional 2-D power Doppler images (PDIs) provide. To create 3-D PDIs, 2-D-matrix array transducers can be used to insonify a large volume for every transmission; however, these matrices suffer from low sensitivity, high complexity, and high cost. More typically, a 1-D-Array transducer is used to scan a series of stationary 2-D PDIs, after which a 3-D volume is created by concatenating the 2-D PDIs in postprocessing, which results in long scan times due to repeated measurements. Our objective was to achieve volumetric 3-D Doppler ultrasound imaging with a high Doppler sensitivity, similar to that of a typical stationary recording using a 1-D-Array transducer, while being more affordable than using 2-D-matrix arrays. We achieved this by mounting a 1-D-Array transducer to a high-precision motorized linear stage and continuously translating over the mouse brain in a sweeping manner. For Part I of this article, we focused on creating the best vascular images by investigating how to best combine filtered beamformed ultrasound frames, which were not acquired at the same spatial locations, into PDIs. Part II focuses on the implications of sampling transient brain hemodynamics through functional ultrasound (fUS) while continuously translating over the mouse brain. In Part I, we show how the speed at which we sweep our 1-D-Array transducer affects the Doppler spectrum in a flow phantom. In vivo recordings were performed on the mouse brain while varying the sweeping speed, showing how higher sweeping speeds negatively affect the PDI quality. A weighting vector is found to combine frames while continuously moving over the mouse brain, allowing us to create swept PDIs of similar sensitivity when compared with those obtained using a stationary 1-D-Array while allowing a significantly higher 3-D Doppler volume rate and maintaining the benefits of having a low computational and monetary cost. We show that a vascular subvolume of 6 mm can be scanned in 2.5 s, with a PDI reconstructed every $200 \mu \text{m}$ , outperforming classical staged recording methods.

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We consider the scenario of finding the transfer function of an aberrating layer in front of a receiving ultrasound (US) array, assuming a separate non-aberrated transmit source. We propose a method for blindly estimating this transfer function without exact knowledge of the ultrasound sources or acoustic contrast image, and without directly measuring the transfer function using a separate controlled calibration experiment. Instead, the measurement data of many unknown random images is collected, such as from blood flow, and its second-order statistics are exploited. A measurement model is formulated that explicitly defines the layer's transfer function. A covariance domain problem is then defined to eliminate the image variable, and it is solved for the layer's transfer function using manifold-based optimization. The proposed approach and calibration algorithm are evaluated on a range of challenging and realistic simulations using the k-Wave toolbox. Our results show that, given a sufficiently efficient parameterization of the layer's transfer function, and by jointly estimating the transfer function at multiple frequencies, the proposed algorithm is able to obtain an accurate estimate. Subsequent simulated imaging experiments using the obtained transfer function also show increased imaging performance in various aberrating layers, including a skull layer.

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Functional ultrasound (fUS) using a 1-D-array transducer normally is insufficient to capture volumetric functional activity due to being restricted to imaging a single brain slice at a time. Typically, for volumetric fUS, functional recordings are repeated many times as the transducer is moved to a new location after each recording, resulting in a nonunique average mapping of the brain response and long scan times. Our objective was to perform volumetric 3-D fUS in an efficient and cost-effective manner. This was achieved by mounting a 1-D-array transducer to a high-precision motorized linear stage and continuously translating over the mouse brain in a sweeping manner. We show how the speed at which the 1-D-array is translated over the brain affects the sampling of the hemodynamic response (HR) during visual stimulation as well as the quality of the resulting power Doppler image (PDI). Functional activation maps were compared between stationary recordings, where only one functional slice is obtained for every recording, and our swept-3-D method, where volumetric fUS was achieved in a single functional recording. The results show that the activation maps obtained with our method closely resemble those obtained during a stationary recording for that same location, while our method is not restricted to functional imaging of a single slice. Lastly, a mouse brain subvolume of 6 mm is scanned at a volume rate of 1.5 s per volume, with a functional PDI reconstructed every 200\mu \text{m} , highlighting swept-3-D's potential for volumetric fUS. Our method provides an affordable alternative to volumetric fUS using 2-D-matrix transducers, with a high SNR due to using a fully sampled 1-D-array transducer, and without the need to repeat functional measurements for every 2-D slice, as is most often the case when using a 1-D-array. This places our swept-3-D method as a potentially valuable addition to conventional 2-D fUS, especially when investigating whole-brain functional connectivity, or when shorter recording durations are desired.

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Functional Ultrasound (fUS) is a relatively new modality to measure brain activity with a high spatio-temporal resolution. In order to collect full-brain information with this 2D imaging technique, fUS data is typically collected for a fixed position of the ultrasound probe for the duration of the experiment, before the probe is moved to the next position. As a result, a 3D functional volume consists of subsequent, time-disjunct 2D datasets. The gold-standard way to analyze fUS datasets is using correlation images or a general linear model. However, these analyses are performed slice by slice; thus, common information across slices is not exploited. We propose the use of two data-driven models, Independent Component Analysis (ICA) and its multiset extension Independent Vector Analysis (IVA), in order to map the mouse visual information processing pathway in 3D. We demonstrate the successful application of ICA and then of IVA, which leverages the dependence across slices in a unique fashion. Furthermore, we provide guidance as to when which approach might be desirable.@en

Functional ultrasound (fUS) indirectly measures brain activity by detecting changes in cerebral blood volume following neural activation. Conventional approaches model such functional neuroimaging data as the convolution between an impulse response, known as the hemodynamic response function (HRF), and a binarized representation of the input signal based on the stimulus onsets, the so-called experimental paradigm (EP). However, the EP may not characterize the whole complexity of the activity-inducing signals that evoke the hemodynamic changes. Furthermore, the HRF is known to vary across brain areas and stimuli. To achieve an adaptable framework that can capture such dynamics of the brain function, we model the multivariate fUS time-series as convolutive mixtures and apply block-term decomposition on a set of lagged fUS autocorrelation matrices, revealing both the region-specific HRFs and the source signals that induce the hemodynamic responses. We test our approach on two mouse-based fUS experiments. In the first experiment, we present a single type of visual stimulus to the mouse, and deconvolve the fUS signal measured within the mouse brain’s lateral geniculate nucleus, superior colliculus and visual cortex. We show that the proposed method is able to recover back the time instants at which the stimulus was displayed, and we validate the estimated region-specific HRFs based on prior studies. In the second experiment, we alter the location of the visual stimulus displayed to the mouse, and aim at differentiating the various stimulus locations over time by identifying them as separate sources.

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We intend to develop an ultrasound compressive imaging device to perform carotid artery (CA) function and flow monitoring/imaging by using just a few single element transducers equipped with spatial coding masks. The spatially unique impulse responses can be exploited in compressive reconstructions. To explore the potential of different configurations, in this study we emulated such a device using a linear array system. We combined its elements with individual digital delays into a small number of groups. The results suggest our spatial coding mask approach based on reconstructions regularized with a least squares method has potential for CA monitoring with only 10 to 12 sensors.

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The original version of this article was revised to update the Figure 8 (panel B) image. The correct image should have a yellow shape as presented below. (Figure presented.). The original article has been corrected.

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Ultrasound imaging of the vasculature has major significance for the detection of cardiovascular diseases and cancer. However, limited spatial resolution or long acquisition times of existing techniques limit the visualization of the microvascular structures. Enforcing sparsity in the underlying vasculature as well as exploiting statistical independence between voxels have become prominent for fast super-resolution imaging. However, such a statistical independence may not be valid for all voxels and may hence lead to a distorted signal model. Here we present an image reconstruction method that exploits the sparsity of the vasculature data without distorting the original signal model. We employ a multiple measurement vector (MMV) model to enforce the joint sparsity over the images at different time instants. To reduce the computational complexity of obtaining the solution, the ℓ1-SVD method is applied to the MMV model. We demonstrate that our method improves spatial resolution and provides a clear separation between blood vessels. Although our method is slightly slower than existing approaches, it outperforms them in terms of image reconstruction quality.@en

Functional ultrasound (fUS) is an exciting new neuroimaging technique that is able to record brain activity similar to functional magnetic resonance imaging, yet with higher spatiotemporal resolution and at lower cost. We consider the problem of jointly estimating the underlying neural sources and the hemodynamic response function (HRF) from fUS recordings. We propose to model the measured voxel time-series as a convolutive mixture of multiple source signals and solve the blind deconvolution problem via block-term decomposition. This allows us to estimate both the source time courses and a different HRF for each voxel and source combination, which accounts for the variability of HRF across different brain regions and events respectively. The proposed approach is proven to be robust against noise via simulations and further validated on real fUS data by performing a visual experiment on a mouse. The obtained results show that the proposed method is able to recover the timings of the visual paradigm.@en

We study the design of a coding mask for pulse-echo ultrasound imaging. We are interested in the scenario of a single receiving transducer with an aberrating layer, or ‘mask,’ in front of the transducer's receive surface, with a separate co-located transmit transducer. The mask encodes spatial measurements into a single output signal, containing more information about a reflector's position than a transducer without a mask. The amount of information in such measurements is dependent on the mask geometry, which we propose to optimize using an image reconstruction mean square error (MSE) criterion. We approximate the physics involved to define a linear measurement model, which we use to find an expression for the image error covariance matrix. By discretizing the mask surface and defining a discrete number of mask thickness levels per point on its surface, we show how finding the best mask can be posed as a variation of a sensor selection problem. We propose a convex relaxation in combination with randomized rounding, as well as a greedy optimization algorithm to solve this problem. We show empirically that both algorithms come close to the global optimum. Our simulations further show that the optimized masks have better a MSE than nearly all randomly shaped masks. We observe that an optimized mask amplifies echoes coming from within the region of interest (ROI), and strongly reduces the correlation between echoes of pixels within the ROI.@en

We consider a model-based ultrasound imaging scenario using a single transducer with a coding mask, and assume that the pulse-echo model is erroneously estimated, resulting in decreased imaging performance. Although the pulse-echo Green's function to each pixel has to be measured to obtain a good model, typically only forward-field measurements are obtained for better SNR, from which the pulse-echo Green's functions are estimated. However, if the transducer's receive transfer function is different from the transmit transfer function, the forward-field measurements do not incorporate the receive transfer function, resulting in an incorrect pulse-echo model. We propose two calibration techniques that start with this erroneous model, and update it using pulse-echo measurements. In the first technique we assume the calibration phantom is known a priori, whereas in the second technique we use multiple random calibration phantoms of which only the second-order statistics are assumed to be known beforehand. Both methods are able to significantly improve the pulse-echo model, strongly improving imaging performance. Our simulation results show that the first technique works best, since there is no uncertainty about the calibration image, whereas the blind calibration technique requires no exact knowledge of the calibration phantom, making it robust to positioning or manufacturing errors.

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In interventional electrophysiology, catheter-based radiofrequency (RF) ablation procedures restore cardiac heart rhythm by interrupting aberrant conduction paths. Real-time feedback on lesion formation and post-treatment lesion assessment could overcome procedural challenges related to ablation of underlying structures and lesion gaps. This study aims to evaluate real-time visualization of lesion progression and continuity during intra-atrial ablation with photoacoustic (PA) imaging, using clinically deployable technology. A PA-enabled RF ablation catheter was used to ablate and illuminate porcine left atrium, both excised and intact in a passive beating heart ex-vivo, for photoacoustic signal generation. PA signals were received with an intracardiac echography catheter. Using the ratio of PA images acquired with excitation wavelengths of 790 nm and 930 nm, ablation lesions were successfully imaged through circulating saline and/or blood, and lesion gaps were identified in real-time. PA-based assessment of RF-ablation lesions was successful in a realistic preclinical model of atrial intervention.

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