Facemap: a framework for modeling neural activity based on orofacial tracking.

Recent studies in mice have shown that orofacial behaviors drive a large fraction of neural activity across the brain. To understand the nature and function of these signals, we need better computational models to characterize the behaviors and relate them to neural activity. Here we developed Facemap, a framework consisting of a keypoint tracker and a deep neural network encoder for predicting neural activity.

Spatial Coherence Adaptive Clutter Filtering in Color Flow Imaging-Part I: Simulation Studies.

The appropriate selection of a clutter filter is critical for ensuring the accuracy of velocity estimates in ultrasound color flow imaging. Given the complex spatio-temporal dynamics of flow signal and clutter, however, the manual selection of filters can be a significant challenge, increasing the risk for bias and variance introduced by the removal of flow signal and/or poor clutter suppression. We propose a novel framework to adaptively select clutter filter settings based on color flow image quality feedback derived from the spatial coherence of ultrasonic backscatter.

Spatial Coherence Adaptive Clutter Filtering in Color Flow Imaging-Part II: Phantom and Experiments.

Conventional color flow processing is associated with a high degree of operator dependence, often requiring the careful tuning of clutter filters and priority encoding to optimize the display and accuracy of color flow images. In a companion paper, we introduced a novel framework to adapt color flow processing based on local measurements of backscatter spatial coherence. Through simulation studies, the adaptive selection of clutter filters using coherence image quality characterization was demonstrated as a means to dynamically suppress weakly-coherent clutter while preserving coherent flow signal in order to reduce velocity estimation bias.

Occult Regions of Suppressed Coherence in Liver B-Mode Images.

Ultrasound is an essential tool for diagnosing and monitoring diseases, but it can be limited by poor image quality. Lag-one coherence (LOC) is an image quality metric that can be related to signal-to-noise ratio and contrast-to-noise ratio. In this study, we examine matched LOC and B-mode images of the liver to discern patterns of low image quality, as indicated by lower LOC values, occurring beneath the abdominal wall, near out-of-plane vessels and adjacent to hyperechoic targets such the liver capsule.

Structure-based charge calculations for predicting isoelectric point, viscosity, clearance, and profiling antibody therapeutics.

The effect of hydrophobicity on antibody aggregation is well understood, and it has been shown that charge calculations can be useful for high-concentration viscosity and pharmacokinetic (PK) clearance predictions. In this work, structure-based charge descriptors are evaluated for their predictive performance on recently published antibody pI, viscosity, and clearance data. From this, we devised four rules for therapeutic antibody profiling which address developability issues arising from hydrophobicity and charged-based solution behavior, PK, and the ability to enrich for those that are approved by the U.

Coherence-based quantification of acoustic clutter sources in medical ultrasound.

The magnitudes by which aberration and incoherent noise sources, such as diffuse reverberation and thermal noise, contribute to degradations in image quality in medical ultrasound are not well understood. Theory predicting degradations in spatial coherence and contrast in response to combinations of incoherent noise and aberration levels is presented, and the theoretical values are compared to those from simulation across a range of magnitudes. A method to separate the contributions of incoherent noise and aberration in the spatial coherence domain is also presented and applied to predictions for losses in contrast.

Incoherent Clutter Suppression Using Lag-One Coherence.

The lag-one coherence (LOC), derived from the correlation between the nearest-neighbor channel signals, provides a reliable measure of clutter which, under certain assumptions, can be directly related to the signal-to-noise ratio of individual channel signals. This offers a direct means to decompose the beamsum output power into contributions from speckle and spatially incoherent noise originating from acoustic clutter and thermal noise. In this study, we applied a novel method called lag-one spatial coherence adaptive normalization (LoSCAN) to locally estimate and compensate for the contribution of spatially incoherent clutter from conventional delay-and-sum (DAS) images.

MimickNet, Mimicking Clinical Image Post- Processing Under Black-Box Constraints.

Image post-processing is used in clinical-grade ultrasound scanners to improve image quality (e.g., reduce speckle noise and enhance contrast).

Lag-One Coherence as a Metric for Ultrasonic Image Quality.

Reliable assessment of image quality is an important but challenging task in complex imaging environments such as those encountered in vivo. To address this challenge, we propose a novel imaging metric, known as the lag-one coherence (LOC), which leverages the spatial coherence between nearest-neighbor array elements to provide a local measure of thermal and acoustic noise. In this paper, we derive the theory that relates LOC and the conventional image quality metrics of contrast and contrast-to-noise ratio (CNR) to channel noise.

Clinical Utility of Fetal Short-Lag Spatial Coherence Imaging.

In this study, we evaluate the clinical utility of fetal short-lag spatial coherence (SLSC) imaging. Previous work has documented significant improvements in image quality with fetal SLSC imaging as quantified by measurements of contrast and contrast-to-noise ratio (CNR). The objective of this study was to examine whether this improved technical efficacy is indicative of the clinical utility of SLSC imaging.

Evaluation of Large-Aperture Imaging Through the ex Vivo Human Abdominal Wall.

Current clinical abdominal imaging arrays are designed to maximize angular field of view rather than the extent of the coherent aperture. We illustrate, in ex vivo experiments, the use of a large effective aperture to perform high-resolution imaging, even in the presence of abdominal wall-induced acoustic clutter and aberration. Point and lesion phantom targets were imaged through a water path and through three excised cadaver abdominal walls to create different clinically relevant clutter effects with matched imaging targets.

Inferring the Joint Demographic History of Multiple Populations: Beyond the Diffusion Approximation.

Understanding variation in allele frequencies across populations is a central goal of population genetics. Classical models for the distribution of allele frequencies, using forward simulation, coalescent theory, or the diffusion approximation, have been applied extensively for demographic inference, medical study design, and evolutionary studies. Here we propose a tractable model of ordinary differential equations for the evolution of allele frequencies that is closely related to the diffusion approximation but avoids many of its limitations and approximations.

Feasibility of Swept Synthetic Aperture Ultrasound Imaging.

Ultrasound image quality is often inherently limited by the physical dimensions of the imaging transducer. We hypothesize that, by collecting synthetic aperture data sets over a range of aperture positions while precisely tracking the position and orientation of the transducer, we can synthesize large effective apertures to produce images with improved resolution and target detectability. We analyze the two largest limiting factors for coherent signal summation: aberration and mechanical uncertainty.