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IEEE Symposium on Nuclear Science (NSS/MIC)

作者： Qian Dong Salar Sajedi Ilaria Sacco Peter Fischer Craig S. Levin Departments of Electrical Engineering and Radiology Stanford University Stanford CA USA Departments of Radiology Stanford University Stanford CA USA Department of Computer Science Heidelberg University Baden-Württemberg Germany Department of Radiology Electrical Engineering Bioengineering and Physics Stanford University Molecular Imaging Program at Stanford (MIPS) Stanford CA USA

Developing positron emission tomography (PET) systems with high channel number has driven the need for application-specific integrated circuits (ASICs) owing to their compactness, multi-channel readout capability, and excellent time and energy resolution performance. They can also be quite flexible by employing field-programmable gate arrays (FPGAs) in the readout circuit. In particular, the ASIC+FPGA approach provides a high performance and compact solution for TOF-PET applications. ASICs serve functions of extracting time and energy information from analog SiPM signals, and an FPGA is employed for other application-specific requirements like on-board chip configuration, communication with data acquisition (DAQ) systems, and system monitoring. Based on this foundation, we developed TOF-capable detector modules for our second generation RF-penetrable PET insert. During our previous experiments, we found that different trigger and readout methods lead to different noise pattern and intensity in MR environment, and also have different singles count loss ratio. This paper aims to study and compare different readout configurations for our MR-compatible detectors. We studied four trigger and readout methods: hit-standard, frequent-standard, hit-bypass, and frequent-bypass, and compared their singles count loss ratios with both theoretical models and experimental results. For all four methods, the theoretical results matched the experimental results well. The two methods which used bypass mode performed better than those using the standard mode approach. With the most optimized trigger and readout method (hit-bypass), we achieved 1.2% singles count loss ratio at a 20 kcps count rate per channel.

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Biophysics of amplitude-modulated giga-hertz electromagnetic waves stimulation

Biophysics of amplitude-modulated giga-hertz electromagnetic...

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Asilomar Conference on Signals, Systems & computers

作者： Fatima Ahsan Aravind C. Govindaraju Robert M. Raphael Taiyun Chi Sameer A. Sheth Wayne Goodman Behnaam Aazhang Department of Electrical and Computer Engineering Rice University Houston TX USA Applied Physics Graduate Program Smalley-Curly Institute Rice University Houston TX Department of Bioengineering Rice University Houston TX USA Department of Neurosurgery Baylor College of Medicine Houston TX USA Menninger Department of Psychiatry and Behavioral Sciences Baylor College of Medicine Houston TX USA

This paper presents the biophysical modeling for neuronal stimulation caused by amplitude-modulated giga-hertz (GHz) electromagnetic (EM) waves. We model a 1D cable equation for electrical signal propagation in a vestibular ganglion neuronal fiber and use Hodgkin-Huxley formalism to model voltage-dependent channel conductances. We find out that for a given stimulation signal strength, the GHz waveform amplitude-modulated at a low frequency of Δf causes neuronal firing with the frequency of Δf whereas the continuous wave GHz did not elicit any neuronal firing. Moreover, the voltage-dependent channel gating dynamics of the Δf amplitude-modulated GHz stimulation matches that of a simple low frequency stimulation at Δf. Additionally, we find that the modulation depth controls the firing rate of the neurons. The significance of this property is that the amplitude modulation caused by the interference of two similar high frequency signals could be leveraged to focally excite neurons at depth without stimulating overlying cortical regions. These theoretical predictions based on the Hodgkin-Huxley model can later be tested experimentally.

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Snapshot hyperspectral imaging using a random phase mask and spectral filter array

Snapshot hyperspectral imaging using a random phase mask and...

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Computational Optical Sensing and Imaging, COSI 2020 - Part of Imaging and Applied Optics Congress 2020

作者： Monakhova, Kristina Yanny, Kyrollos Waller, Laura Department of Electrical Engineering and Computer Sciences University of California Berkeley United States UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States

We introduce a snapshot hyperspectral imager that uses a random phase mask, repeated spectral filter array, and compressive recovery to achieve high spatial and spectral resolution in a small form factor. © 2020 ... 详细信息

ISBN: (纸本)9781557528209

关键词： Hyperspectral imaging

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Guiding Brain-to-Vocalization Decoder Design Using Structured Generalization Error

Guiding Brain-to-Vocalization Decoder Design Using Structure...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Jingya Huang Pablo Tostado-Marcos Sowmya Manojna Narasimha Aashish N. Patel Ezequiel. M. Arneodo Timothy Q. Gentner Gal Mishne Vikash Gilja Department of Electrical and Computer Engineering University of California San Diego CA Department of Bioengineering University of California San Diego CA Institute for Neural Computation University of California San Diego CA Neuroscience Graduate Program University of California San Diego CA Department of Physics University of California San Diego CA Department of Psychology University of California San Diego CA Halıcıoğlu Data Science Institute University of California San Diego CA

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

State-of-the-art intracortical neuroprostheses currently enable communication at 60+ words per minute for anarthric individuals by training on over 10K sentences to account for phoneme variability in different word contexts. There is limited understanding about whether this performance can be maintained in decoding naturalistic speech with 40K+ word vocabularies across elicited, spontaneous, and conversational speech contexts. We introduce a vocal-unit-level generalization test to explicitly evaluate neural decoder performance with an expanded and more diverse behavioral repertoire. Tested on neural decoders modeling zebra finch vocalization, an analog to human vocal production, we compare three decoders with different input types: spike trains, neural factors, and firing rates. The factors and rates are latent neural features inferred using trained Latent Factor Analysis via Dynamical Systems (LFADS) models that capture the population neural dynamics during vocal production. While the conventional random holdout generalization error measure is similar for all three decoders, factor- and rate-based decoders outperform spike-based decoders when testing vocal-unit-holdout generalization error. These results suggest the later models better adapt to flexible vocalization inference when trained with partial observation of data variation, motivating further exploration of decoders incorporating latent neural and vocalization dynamics.

关键词： Training Adaptation models Vocabulary Firing Measurement uncertainty Neuroprostheses Production Decoding engineering in medicine and biology Testing

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A DIRECT METHOD OF GENERATING QUADRATIC CURVILINEAR TETRAHEDRAL MESHES USING AN ADVANCING FRONT APPROACH 29

A DIRECT METHOD OF GENERATING QUADRATIC CURVILINEAR TETRAHED...

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29th International Meshing Roundtable, IMR 2021

作者： Mohammadi, Fariba Shontz, Suzanne M. Department of Mechanical Engineering Information and Telecommunication Technology Center The University of Kansas 1520 W. 15th Street LawrenceKS66045 United States Department of Electrical Engineering and Computer Science Bioengineering Program Information and Telecommunication Technology Center University of Kansas 1520 W. 15th Street LawrenceKS66045 United States

ISBN: (纸本)9781733489010

Computational modeling and simulation of real-world problems, e.g., various applications in the automotive, aerospace, and biomedical industries, often involve geometric objects which are bounded by curved surfaces. The geometric modeling of such objects can be performed via high-order meshes. Such a mesh, when paired with a high-order partial differential equation (PDE) solver, can realize more accurate solution results with a decreased number of mesh elements (in comparison to a low-order mesh). There are several types of high-order mesh generation approaches, such as direct methods, a posteriori methods, and isogeometric analysis (IGA)-based spline modeling approaches. In this paper, we propose a direct, high-order, curvilinear tetrahedral mesh generation method using an advancing front technique. After generating the mesh, we apply mesh optimization to improve the quality and to take advantage of the degrees of freedom available in the initially straight-sided quadratic elements. Our method aims to generate high-quality tetrahedral mesh elements from various types of boundary representations including the cases where no computer-aided design files are available. Such a method is essential, for example, for generating meshes for various biomedical models where the boundary representation is obtained from medical images instead of CAD files. We present several numerical examples of second-order tetrahedral meshes generated using our method based on input triangular surface meshes. © 2021 held by the authors of the individual papers.

关键词： Mesh generation

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Compressed sensing 3D fluorescence microscopy using optimized phase mask

Compressed sensing 3D fluorescence microscopy using optimize...

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Computational Optical Sensing and Imaging, COSI 2020 - Part of Imaging and Applied Optics Congress 2020

作者： Yanny, Kyrollos Antipa, Nick Liberti, William Dehaeck, Sam Monakhova, Kristina Liu, Fanglin Linda Shen, Konlin Ng, Ren Waller, Laura UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley United States Department of Electrical Engineering and Computer Sciences University of California Berkeley United States Brussels1050 Belgium

We demonstrate a single-shot miniature 3D computational microscope with an optimized phase encoder. Our method uses sparsity-based reconstruction to achieve a 2.76µm lateral and 15µm axial resolution across ... 详细信息

ISBN: (纸本)9781557528209

关键词： Fluorescence microscopy

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cytoNet: Spatiotemporal network analysis of cell communities (vol 18, e1009846, 2022)

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PLOS COMPUTATIONAL BIOLOGY 2022年第11期18卷 e1009846页

作者： Mahadevan, A. S. Long, B. L. Hu, C. W. Ryan, D. T. Grandel, N. E. Department of Bioengineering University of Pennsylvania Philadelphia Pennsylvania United States of America. Department of Bioengineering Rice University Houston Texas United States of America. Systems Synthetic and Physical Biology Program Rice University Houston Texas United States of America. Department of Biomedical Engineering University of Texas at San Antonio San Antonio Texas United States of America. Biophysics Graduate Program University of California Berkeley California United States of America. Department of Oral & Maxillofacial Surgery University of Texas Health Science Center at San Antonio San Antonio Texas United States of America. Department of Electrical and Computer Engineering Rice University Houston Texas United States of America.

We introduce cytoNet, a cloud-based tool to characterize cell populations from microscopy images. cytoNet quantifies spatial topology and functional relationships in cell communities using principles of network science. Capturing multicellular dynamics through graph features, cytoNet also evaluates the effect of cell-cell interactions on individual cell phenotypes. We demonstrate cytoNet's capabilities in four case studies: 1) characterizing the temporal dynamics of neural progenitor cell communities during neural differentiation, 2) identifying communities of pain-sensing neurons in vivo, 3) capturing the effect of cell community on endothelial cell morphology, and 4) investigating the effect of laminin α4 on perivascular niches in adipose tissue. The analytical framework introduced here can be used to study the dynamics of complex cell communities in a quantitative manner, leading to a deeper understanding of environmental effects on cellular behavior. The versatile, cloud-based format of cytoNet makes the image analysis framework accessible to researchers across domains.

关键词： Calcium imaging Fluorescence imaging Growth factors Centrality Cell cycle and cell division Endothelial cells Network analysis Stem cells

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Phased Array Beamforming Methods for Powering Biomedical Ultrasonic Implants

arXiv

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arXiv 2022年

作者： Benedict, Braeden C. Ghanbari, Mohammad Meraj Muller, Rikky UC Berkeley UC San Francisco Joint Program in Bioengineering BerkeleyCA94720 United States The Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA94720 United States The Chan Zuckerberg Biohub San FranciscoCA94158 United States

Millimeter-scale implants using ultrasound for power and communication have been proposed for a range of deep-tissue applications, including neural recording and stimulation. However, published implementations have shown high sensitivity to misalignment with the external ultrasound transducer. Ultrasonic beamforming using a phased array to these implants can improve tolerance to misalignment, reduce implant volume, and allow multiple implants to be operated simultaneously in different locations. This paper details the design of a custom planar phased array ultrasound system, which is capable of steering and focusing ultrasound power within a 3D volume. Analysis and simulation is performed to determine the choice of array element pitch, with special attention given to maximizing the power available at the implant while meeting FDA limits for diagnostic ultrasound. Time reversal is proposed as a computationally simple approach to beamforming that is robust despite scattering and inhomogeneity of the acoustic medium. This technique is demonstrated both in active drive and pulse-echo modes, and it is experimentally compared with other beamforming techniques by measuring energy transfer efficiency. Simultaneous power delivery to multiple implants is also demonstrated. Copyright © 2022, The Authors. All rights reserved.

关键词： Beamforming

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Neural Constraints on Cognitive Experience and Mental Health

arXiv

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arXiv 2025年

作者： Shariatpanahi, Bita Nozari, Erfan Daftarian, Soroush Arab, Fahimeh Kheirkhah, Mina Bernhard, Felix P. Khodadadi, Shiva Giltay, Erik J. Hebbrecht, Kaat Hofmann, Stefan G. Hahn, Tim Jamalabadi, Hamidreza Department of Psychiatry and Psychotherapy University of Marburg Germany Department of Mechanical Engineering University of California RiversideCA United States Department of Electrical and Computer Engineering University of California Riverside RiversideCA United States Department of Bioengineering University of California Riverside RiversideCA United States Neuroscience Graduate Program University of California Riverside RiversideCA United States Experimental Therapeutics and Pathophysiology Branch National Institute of Mental Health Bethesda MD United States University of Antwerp Belgium Department of Psychiatry Leiden University Medical Center Netherlands Department of Psychology University of Marburg Germany Institute for Translational Psychiatry University of Münster Germany University of Marburg Germany

Understanding how neural dynamics shape cognitive experiences remains a central challenge in neuroscience and psychiatry. Here, we present a novel framework leveraging state-to-output controllability from dynamical systems theory to model the interplay between cognitive perturbations, neural activity, and subjective experience. We demonstrate that large-scale fMRI signals are constrained to low-dimensional manifolds, where affective and cognitive states are naturally organized. Furthermore, we provide a theoretically robust method to estimate the controllability Gramian from steady-state neural responses, offering a direct measure of the energy required to steer cognitive outcomes. In five healthy participants viewing 2,185 emotionally evocative short videos, our analyses reveal a strong alignment between neural activations and affective ratings, with an average correlation of r ≈ 0.7. In a clinical cohort of 255 patients with major depressive disorder, biweekly Hamilton Rating Scale trajectories over 11 weeks significantly mapped onto these manifolds, explaining approximately 20% more variance than chance (p −10, numerically better than chance in 93% reaching statistical significance in one-third of subjects). Our work bridges dynamical systems theory and clinical neuroscience, providing a principled approach to optimize mental health treatments by targeting the most efficient neural pathways for cognitive change. © 2025, CC BY-NC-SA.

关键词： System theory

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High-Order Cardiomyopathy Human Heart Model and Mesh Generation

High-Order Cardiomyopathy Human Heart Model and Mesh Generat...

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2021 Computing in Cardiology, CinC 2021

作者： Mohammadi, Fariba Shontz, Suzanne M Linte, Cristian A Department of Mechanical Engineering University of Kansas LawrenceKS United States Department of Electrical Engineering and Computer Science University of Kansas LawrenceKS United States Bioengineering Program University of Kansas LawrenceKS United States Information and Telecommunication Technology Center University of Kansas LawrenceKS United States Chester F Carlson Center for Imaging Science Rochester Institute of Technology RochesterNY United States Department of Biomedical Engineering Rochester Institute of Technology RochesterNY United States

ISBN: (纸本)9781665479165

Faithful, accurate, and successful cardiac biomechanics and electrophysiological simulations require patient-specific geometric models of the heart. Since the cardiac geometry consists of highly-curved boundaries, the use of high-order meshes with curved elements would ensure that the various curves and features present in the cardiac geometry are well-captured and preserved in the corresponding mesh. Most other existing mesh generation techniques require computer-aided design files to represent the geometric boundary, which are often not available for biomedical applications. Unlike such methods, our technique takes a high-order surface mesh, generated from patient medical images, as input and generates a high-order volume mesh directly from the curved surface mesh. In this paper, we use our direct high-order curvilinear tetrahedral mesh generation method [1] to generate several second-order cardiac meshes. Our meshes include the left ventricle myocardia of a healthy heart and hearts with dilated and hypertrophic cardiomyopathy. We show that our high-order cardiac meshes do not contain inverted elements and are of sufficiently high quality for use in cardiac finite element simulations. © 2021 Creative Commons.

关键词： Heart

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