About

Nick Bottenus is an Assistant Professor in the Paul M. Rady Mechanical Engineering department at the University of Colorado Boulder. His research focuses on developing system-level solutions to problems in diagnostic ultrasound imaging, aiming to improve image quality in clinical settings such as screening, intervention, and follow-up procedures. His work addresses the complex acoustic environment of the human body that distorts ultrasound signals, leading to operator- and patient-dependent image artifacts that can confound diagnosis. To tackle these challenges, his lab develops complementary transducer sampling, acoustic signal processing, and image interpretation methods to provide more robust and useful information across varied patient populations and applications. His research contributes to societal impact by enhancing the reliability, accessibility, and quality of medical imaging technologies, which are essential for clinical decision making by both expert clinicians and computer algorithms.

Research topics

• Computer Science
• Artificial Intelligence
• Medicine
• Radiology
• Medical physics
• Mathematics
• Pathology
• Computer vision
• Data science

Selected publications

• Optical Tracking for Freehand Swept Synthetic Aperture Imaging

  IEEE Transactions on Ultrasonics Ferroelectrics and Frequency Control · 2025-10-20

  articleOpen accessSenior author

  Achieving higher resolution for deeper tissue structures remains a significant challenge in ultrasound (US) imaging due to the inherent limitations of diffraction. Swept synthetic aperture (SSA) techniques, which utilize the motion of a single transducer to effectively increase the imaging aperture, offer a promising solution. Building on SSA, we propose that freehand SSA provides a flexible approach with real-time adaptability to varying patient anatomies. This article introduces the optically tracked SSA (OT-SSA) platform, an approach that integrates external tracking to ensure accurate transducer positioning during freehand sweeps. Key sources of image degradation, such as spatial calibration error, tracking precision, and out-of-plane motion were directly analyzed and addressed within the system. In in vivo quadriceps imaging, OT-SSA reduced average lateral speckle autocorrelation size from 2.33 to 0.49 mm compared to a stationary aperture, demonstrating substantial resolution gains. The results establish OT-SSA as a robust and adaptable approach for high-resolution imaging.

  PublisherOA PDFDOI

• Improved Spatiotemporal Resolution in Echocardiography Using Mixed Geometry Imaging Sequences

  IEEE Transactions on Ultrasonics Ferroelectrics and Frequency Control · 2024-02-08 · 4 citations

  articleOpen accessSenior author

  Cardiac ultrasound seeks to image the most dynamic environment in the body-the moving heart. Many modern ultrasound imaging techniques address the tradeoff between spatial and temporal resolution using either narrow focused beams or with broad beam, synthetic aperture (SA) sequences that have been shown to suffer from motion artifacts. Retrospective encoding for conventional ultrasound sequences (REFoCUS) unifies the processing of these various geometric sequences, but the motion sensitivity of this approach has yet to be investigated. We hypothesize that a "mixed sequence" enabled by the REFoCUS method incorporating several beam geometries may better resolve cardiac motion over a wide field of view (FOV) and at a high frame rate. First, the motion sensitivity of REFoCUS was evaluated in simulation for several focused and broad transmit profiles. Focused transmissions resolve both lateral and axial motion much more effectively than broad transmissions, with performance similar to conventional beamforming techniques. Second, a mixed sequence was designed that insonifies the full field-of-view with plane wave (PW) transmissions and key moving targets with focused transmissions. This mixed sequence was tested in simulation and in vivo and was used to image the heart as well as the liver, a low-motion control. By combining a sparse PW sequence ( n=60 ) with a small group of targeted focused transmissions ( n = 10), the anterior mitral valve leaflet (AML) at its peak observed velocity was better resolved. We believe that mixed sequences have strong potential to resolve cardiac motion at clinically relevant frame rates.

  PublisherOA PDFDOI

• Improving spatial coherence of multi-line transmit imaging: effects of synthetic focusing

  2024-04-01 · 1 citations

  articleSenior author

  Multi-line transmit (MLT) imaging enables the acquisition of high frame rate (HFR) data in ultrasound imaging, especially in echocardiography where capturing rapid events associated with heart motion can provide valuable information for disease diagnosis. MLT beams are generated by simultaneously transmitting multiple focused beams in different spatial directions within a single pulse-echo event. The main drawback of MLT imaging is the generation of crosstalk artifacts due to the interferences between multiple beams and targets, which will in turn decorrelate the backscattered echoes and will reduce the spatial coherence significantly, leading to poor image quality. In this study, we have investigated the effects of synthetic focusing on the overall coherence of the received signals. We have shown that achieving more accurate focusing due to the implementation of synthetic aperture beamformers could be less susceptible to the artifacts introduced with MLT, and this will in turn improve the coherence of the backscattered signals, resulting in an improved image quality. Simulation, phantom, and in-vivo experiments have been conducted to demonstrate that spatial coherence enhances as a result of synthetic focusing in MLT imaging (especially away from the transmit focus). Furthermore, we have implemented synthetic aperture methods together with coherence-based techniques to investigate their synergistic performance in further suppressing the incoherent backscattered echoes and improving target detectability. The results demonstrate that this provides considerable benefits in rejecting MLT crosstalk artifacts compared to the conventional dynamic receive focusing.

  PublisherDOI

• Encoded Multi-Line Transmissions for the Removal of Crosstalk Artifacts

  2024-09-22

  articleSenior author

  Achieving higher frame rates in ultrasound imaging using traditional transmission methods often involves trade-offs, including reduced resolution and compromised signal-to-noise ratio (SNR). As a promising alternative, multi-line transmit (MLT) imaging has been introduced, where multiple focused beams are generated and insonified simultaneously in various directions, facilitating high frame rate data acquisition. Despite maintaining high SNR and spatial resolution, MLT is known to be susceptible to significant interference between the multiple beams, leading to crosstalk artifacts in the backscattered echoes and consequently degrading the overall image quality. The main objective of this study is to effectively remove these artifacts rather than merely suppressing them by employing spatiotemporal encoding techniques, thereby enhancing the image quality in high-frame rate ultrasound imaging. Specifically, we have presented two encoding methods for separating MLT beams: polarity-encoded MLT and delay-encoded MLT. Both encoding schemes are designed around a Hadamard matrix framework, with the former applying polarity apodization to the simultaneous beams and the latter implementing a zero or half-period time delay. The coding schemes were paired with a linear decoding process to eliminate crosstalk artifacts, and hence improving image quality without compromising the frame rate. We demonstrate that applying encoding schemes in combination with synthetic aperture focusing methods leads to significant improvements in resolution and overall coherence in the point target simulations and in vivo cardiac images, respectively.

  PublisherDOI

• #16. Variable fluid stresses may alter breast cancer expression in a 3D perfusion model of bone metastasis

  Journal of bone oncology · 2024-04-01

  articleOpen access
  PublisherDOI

• Optimization of array encoding for ultrasound imaging

  Physics in Medicine and Biology · 2024-05-30 · 2 citations

  preprintOpen accessSenior author

  Abstract Objective . The transmit encoding model for synthetic aperture imaging is a robust and flexible framework for understanding the effects of acoustic transmission on ultrasound image reconstruction. Our objective is to use machine learning (ML) to construct scanning sequences, parameterized by time delays and apodization weights, that produce high-quality B-mode images. Approach . We use a custom ML model in PyTorch with simulated RF data from Field II to probe the space of possible encoding sequences for those that minimize a loss function that describes image quality. This approach is made computationally feasible by a novel formulation of the derivative for delay-and-sum beamforming. Main results . When trained for a specified experimental setting (imaging domain, hardware restrictions, etc), our ML model produces optimized encoding sequences that, when deployed in the REFoCUS imaging framework, improve a number of standard quality metrics over conventional sequences including resolution, field of view, and contrast. We demonstrate these results experimentally on both wire targets and a tissue-mimicking phantom. Significance . This work demonstrates that the set of commonly used encoding schemes represent only a narrow subset of those available. Additionally, it demonstrates the value for ML tasks in synthetic transmit aperture imaging to consider the beamformer within the model, instead of purely as a post-processing step.

  PublisherDOI

• An Optically Tracked Platform for Swept Synthetic Aperture Ultrasound Imaging

  2024-05-20 · 3 citations

  articleSenior author

  Ultrasound imaging, crucial for clinical diagnostics, is limited by diffraction, affecting resolution at depth. Swept Synthetic Aperture (SSA), counters this issue by simulating a larger aperture through lateral transducer sweeping. Incorporating an innovative calibration optimization, this study presents Optically-Tracked SSA (OT-SSA), as an unconstrained approach shown to significantly improve lateral resolution and target detectability. The paper outlines the OT-SSA frame-work, showcases image quality improvements, and discusses its role as a benchmark for future SSA technologies, including untracked methods. Specifically, we introduce a 3D printed portable motorized translation stage that facilitates data-based motion estimation using optical tracking for accuracy assessment. It signifies a step towards adaptable, clinically integrated SSA ultrasound technology.

  PublisherDOI

• Spatial Calibration for Swept Synthetic Aperture Imaging Using Differentiable Beamforming

  2024-09-22 · 1 citations

  articleSenior author

  Ultrasound imaging is valued for its affordability, non-invasiveness, and ease of use but is fundamentally limited in lateral resolution by diffraction, especially at depth. Previously, we addressed this limitation using freehand swept synthetic aperture (SSA) imaging with optical tracking (OT-SSA), which relies on a calibration matrix to transform optical tracking data into the transducer’s coordinate system for accurate beamforming. Here, we focus on optimizing the calibration matrix to enhance image quality. We propose a differentiable beamforming approach utilizing PyTorch’s automatic differentiation to refine the calibration matrix parameters. Our optimization process improves the definition of targets throughout the field of view and demonstrates repeatability for relevant degrees of freedom.

  PublisherDOI

• Toward widespread use of virtual trials in medical imaging innovation and regulatory science

  Medical Physics · 2024-10-06 · 14 citations

  reviewOpen access

  The rapid advancement in the field of medical imaging presents a challenge in keeping up to date with the necessary objective evaluations and optimizations for safe and effective use in clinical settings. These evaluations are traditionally done using clinical imaging trials, which while effective, pose several limitations including high costs, ethical considerations for repetitive experiments, time constraints, and lack of ground truth. To tackle these issues, virtual trials (aka in silico trials) have emerged as a promising alternative, using computational models of human subjects and imaging devices, and observer models/analysis to carry out experiments. To facilitate the widespread use of virtual trials within the medical imaging research community, a major need is to establish a common consensus framework that all can use. Based on the ongoing efforts of an AAPM Task Group (TG387), this article provides a comprehensive overview of the requirements for establishing virtual imaging trial frameworks, paving the way toward their widespread use within the medical imaging research community. These requirements include credibility, reproducibility, and accessibility. Credibility assessment involves verification, validation, uncertainty quantification, and sensitivity analysis, ensuring the accuracy and realism of computational models. A proper credibility assessment requires a clear context of use and the questions that the study is intended to objectively answer. For reproducibility and accessibility, this article highlights the need for detailed documentation, user-friendly software packages, and standard input/output formats. Challenges in data and software sharing, including proprietary data and inconsistent file formats, are discussed. Recommended solutions to enhance accessibility include containerized environments and data-sharing hubs, along with following standards such as CDISC (Clinical Data Interchange Standards Consortium). By addressing challenges associated with credibility, reproducibility, and accessibility, virtual imaging trials can be positioned as a powerful and inclusive resource, advancing medical imaging innovation and regulatory science.

  PublisherOA PDFDOI

• Implementation of Constrained Swept Synthetic Aperture Using a Mechanical Fixture

  Applied Sciences · 2023-04-11 · 6 citations

  articleOpen access1st authorCorresponding

  Resolution and target detectability in ultrasound imaging are directly tied to the size of the imaging array. This is particularly important for imaging at depth, such as in the detection and diagnosis of hepatocellular carcinoma and other lesions in the liver. Swept synthetic aperture (SSA) imaging has shown promise for building large effective apertures from small physical arrays using motion but has required bulky fixtures and external motion tracking for precise positioning. This study presents an approach that constrains the transducer motion with a simple linear sliding fixture and estimates motion from the ultrasound data itself using either speckle tracking or channel correlation. This work demonstrates, through simulation and phantom experiments, the ability of both techniques to accurately estimate lateral transducer motion and form SSA images with improved resolution and target detectability. In simulation, errors were observed under 83 μm across a 50 mm sweep, and improvements were found of up to 61% in resolution and up to 33% in lesion detectability experimentally even imaging through ex vivo tissue layers. This approach will increase the accessibility of SSA imaging and allow researchers to test its use in clinical settings.

  PublisherOA PDFDOI

Recent grants

• Optically tracked freehand swept synthetic aperture ultrasound

  NIH · $144k · 2021–2024

Frequent coauthors

• Gregg E. Trahey

  Duke University

  65 shared

• Will Long

  Duke University

  21 shared

• James Long

  Duke University

  13 shared

• Jeremy Dahl

  12 shared

• Jacob Spainhour

  University of Colorado Boulder

  8 shared

• David Bradway

  Duke University

  7 shared

• Matthew T. Huber

  Syracuse University

  6 shared

• Katelyn Flint

  Duke University

  6 shared

Education

• Doctor of Philosophy, Biomedical Engineering

  Duke University

  2017

• Bachelor of Science in Engineering, Biomedical Engineering/Electrical Engineering

  Duke University

  2011

Awards & honors

• 2017 Duke BME Award for Outstanding Doctoral Dissertation
• 2015 SPIE Medical Imaging Robert F. Wagner Best Student Pape…
• 2015 SPIE Medical Imaging Cum Laude Poster Award
• 2013 NSF Graduate Research Fellowship Program - Honorable Me…