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24th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2020

作者： Lomeli, Gabriela Bosse, Marc Bendall, Sean C. Angelo, Michael Herr, Amy E. UC Berkeley UCSF Joint Graduate Program in Bioengineering CA United States Department of Bioengineering University of California Berkeley United States Department of Pathology Stanford University StanfordCA United States

ISBN: (纸本)9781733419017

Single-cell electrophoretic assays offer proteoform detection specificity, but target multiplexing can be further enhanced by transitioning from fluorescence to mass spectrometry imaging for readout. We report for the first time multiplexed ion beam imaging (MIBI) of isoelectrically separated proteoforms from single cells (scIEF). MIBI of scIEF enables the detection of proteoforms differing by a single charge unit. Additionally, we demonstrate that MIBI's ability to do multiple depth image acquisition-comparable to z-stack confocal imaging-enables us to disregard surface artefacts that would normally confound quantitation. © 2020 CBMS-0001

关键词： Depth profiling

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Miniscope3D:optimized single-shot miniature 3D fluorescence microscopy

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Light(Science & Applications) 2020年第1期9卷 367-379页

作者： Kyrollos Yanny Nick Antipa William Liberti Sam Dehaeck Kristina Monakhova Fanglin Linda Liu Konlin Shen Ren Ng Laura Waller UCB/UCSF Joint Graduate Program in Bioengineering University of CaliforniaBerkeleyCA 94720USA Department of Electrical Engineering&Computer Sciences University of CaliforniaBerkeleyCA 94720USA TIPs Department Universite libre de Bruxelles(ULB)1050 BrusselsBelgium

Miniature fluorescence microscopes are a standard tool in systems ***,widefield miniature microscopes capture only 2D information,and modifications that enable 3D capabilities increase the size and weight and have poor resolution outside a narrow depth ***,we achieve the 3D capability by replacing the tube lens of a conventional 2D Miniscope with an optimized multifocal phase mask at the objective’s aperture *** the phase mask at the aperture stop significantly reduces the size of the device,and varying the focal lengths enables a uniform resolution across a wide depth *** phase mask encodes the 3D fluorescence intensity into a single 2D measurement,and the 3D volume is recovered by solving a sparsity-constrained inverse *** provide methods for designing and fabricating the phase mask and an efficient forward model that accounts for the fieldvarying aberrations in miniature *** demonstrate a prototype that is 17mm tall and weighs 2.5 grams,achieving 2.76μm lateral,and 15μm axial resolution across most of the 900×700×390μm^(3) volume at 40 volumes per *** performance is validated experimentally on resolution targets,dynamic biological samples,and mouse brain *** with existing miniature single-shot volume-capture implementations,our system is smaller and lighter and achieves a more than 2×better lateral and axial resolution throughout a 10×larger usable depth *** microscope design provides single-shot 3D imaging for applications where a compact platform matters,such as volumetric neural imaging in freely moving animals and 3D motion studies of dynamic samples in incubators and lab-on-a-chip devices.

关键词： enable resolution narrow

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Connectivity of single neurons classifies cell subtypes in mouse brains

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Nature Methods 2025年第4期22卷 861-873页

作者： Liu, Lijuan Yun, Zhixi Manubens-Gil, Linus Chen, Hanbo Xiong, Feng Dong, Hongwei Zeng, Hongkui Hawrylycz, Michael Ascoli, Giorgio A. Peng, Hanchuan New Cornerstone Science Laboratory SEU-ALLEN Joint Center Institute for Brain and Intelligence Southeast University Nanjing China School of Biological Science & Medical Engineering Southeast University Nanjing China Tencent AI Lab Bellevue WA United States UCLA Brain Research and Artificial Intelligence Nexus Department of Neurobiology David Geffen School of Medicine University of California Los Angeles Los Angeles CA United States Allen Institute for Brain Science Seattle WA United States Center for Neural Informatics Bioengineering Department and Neuroscience Program Krasnow Institute for Advanced Study George Mason University Fairfax VA United States Shanghai Academy of Natural Sciences Fudan University Shanghai China

Classification of single neurons at a brain-wide scale is a way to characterize the structural and functional organization of brains. Here we acquired and standardized a large morphology database of 20,158 mouse neurons and generated a potential connectivity map of single neurons based on their dendritic and axonal arbors. With such an anatomy–morphology–connectivity mapping, we defined neuron connectivity subtypes for neurons in 31 brain regions. We found that cell types defined by connectivity show distinct separation from each other. Within this context, we were able to characterize the diversity in secondary motor cortical neurons, and subtype connectivity patterns in thalamocortical pathways. Our findings underscore the importance of connectivity in characterizing the modularity of brain anatomy at the single-cell level. These results highlight that connectivity subtypes supplement conventionally recognized transcriptomic cell types, electrophysiological cell types and morphological cell types as factors to classify cell classes and their identities. © The Author(s) 2025.

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Dish-Trend: Intervention Modeling Simulator That Accounts for Trend Influences

Dish-Trend: Intervention Modeling Simulator That Accounts fo...

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2021 Winter Simulation Conference, WSC 2021

作者： Andjelkovic, Stefan Miskov-Zivanov, Natasa Computational and Systems Biology Joint Carnegie Mellon University University of Pittsburgh Computational Biology PhD Program University of Pittsburgh PittsburghPA15213 United States Electrical and Computer Engineering Bioengineering Computational and Systems Biology University of Pittsburgh PittsburghPA15213 United States

ISBN: (纸本)9781665433112

Simulation on directed graphs is an important method for understanding the dynamics in the systems where connectivity graphs contain cycles. Discrete Stochastic Heterogeneous Simulator (DiSH) is one of the simulation tools with wide application, which uses regulator values to calculate state updates of regulated elements. Here we present a new simulation approach DiSH-trend which also takes into account the trends in regulating elements. We demonstrate the features of trend-based regulation, as well as hybrid regulation, which is a combination of the trend-and level-based approaches. The modeling capabilities are demonstrated on a small toy model, showcasing different functionalities. Real-world capabilities are demonstrated on a larger network model of food insecurity in the Ethiopian region Oromia. Adding trend-based regulation to models results in increased modeling flexibility, and hybrid regulation improves qualitative dynamic behavior prediction. With appropriate data, DiSH-trend becomes a powerful tool for exploring intervention strategies. © 2021 IEEE.

关键词： Directed graphs

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Scan-specific Self-supervised Bayesian Deep Non-linear Inversion for Undersampled MRI Reconstruction

arXiv

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arXiv 2022年

作者： Leynes, Andrew P. Deveshwar, Nikhil Nagarajan, Srikantan S. Larson, Peder E.Z. The Department of Radiology and Biomedical Imaging University of California San Francisco San FranciscoCA94158 United States The UC Berkeley UC San Francisco Joint Graduate Program in Bioengineering Berkeley San FranciscoCA United States

Magnetic resonance imaging is subject to slow acquisition times due to the inherent limitations in data sampling. Recently, supervised deep learning has emerged as a promising technique for reconstructing sub-sampled MRI. However, supervised deep learning requires a large dataset of fully-sampled data. Although unsupervised or self-supervised deep learning methods have emerged to address the limitations of supervised deep learning approaches, they still require a database of images. In contrast, scan-specific deep learning methods learn and reconstruct using only the sub-sampled data from a single scan. Here, we introduce Scan-Specific Self-Supervised Bayesian Deep Non-Linear Inversion (DNLINV) that does not require an auto calibration scan region. DNLINV utilizes a Deep Image Prior-type generative modeling approach and relies on approximate Bayesian inference to regularize the deep convolutional neural network. We demonstrate our approach on several anatomies, contrasts, and sampling patterns and show improved performance over existing approaches in scan-specific calibrationless parallel imaging and compressed sensing. © 2022, CC BY.

关键词： Magnetic resonance imaging

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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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Physics-based learned design for Fourier DiffuserScope

Physics-based learned design for Fourier DiffuserScope

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Computational Optical Sensing and Imaging, COSI 2021 - Part of OSA Imaging and Applied Optics Congress 2021

作者： Markley, Eric Liu, Fanglin Linda Kellman, Michael Antipa, Nick 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 Department of Pharmaceutical Chemistry University of California San Francisco United States Department of Electrical and Computer Engineering University of California San Diego United States

We couple a differentiable forward model of diffuser-based single-shot 3D microscopy (Fourier DiffuserScope) with an invertible and differentiable reconstruction algorithm to jointly optimize the imaging system and th... 详细信息

ISBN: (纸本)9781557528209

关键词： Imaging systems

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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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Acromion and Scapular Spine Fractures in Reverse Total Shoulder Arthroplasty An XFEM Study

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Journal of shoulder and elbow surgery 2025年

作者： Shuchun Sun Jian Chen Farhad Ahmadi Jichao Zhao Josef K Eichinger Brandon L Rogalski Hai Yao Richard J Friedman Clemson-MUSC Joint Bioengineering Program Clemson University Clemson SC USA. Department of Orthopedics and Physical Medicine Medical University of South CarolinaCharlestonSCUSA. Clemson-MUSC Joint Bioengineering Program Clemson University Clemson SC USA Department of Orthopedics and Physical Medicine Medical University of South CarolinaCharlestonSCUSA. Electronic address: friedman@musc.edu.

BACKGROUND:Reverse total shoulder arthroplasty (rTSA) is widely used to restore shoulder function and alleviate pain. In approximately 1-4% of patients, acromion and scapular spine fractures (ASF) occur and present a clinical challenge for orthopedic surgeons. While impact trauma, impingement, and excessive muscle forces are proposed causes, the relationship between these loading conditions and ASF types remains unclear, hindering targeted prevention strategies. The objective of this study is to identify the biomechanical relationship between loading conditions and ASF types, with the goal of informing targeted preventive strategies to reduce fracture incidence. METHODS:An extended finite element model (XFEM) was developed using computed tomography (CT)-derived shoulder geometry from virtual surgeries to simulate ASF. Bone material properties were based on CT Hounsfield units (HU). Loading scenarios, including impact trauma, impingement, and excessive deltoid force, were informed by existing literature. Simulations were performed in Abaqus, with mesh independence testing ensuring result accuracy. Fracture locations were analyzed according to the modified Levy ASF classification. RESULTS:For impact traumas, the analysis identified that fractures occurred primarily at the initial contact point of the acromion, predominantly in the lateral region. Specifically, forward and sideway impact traumas typically resulted in modified Levy Type I ASF, while backward impact traumas could produce modified Levy Type IIA ASF. Lateral impingement typically led to lateral fractures, specifically modified Levy Type I ASF. The effects of deltoid force varied with the type of shoulder activity; excessive movements during shoulder abduction and forward flexion could cause modified Levy Type IIA ASF. In contrast, hyperextension of the shoulder could shift the fracture location to the medial region, leading to modified Levy Type III ASF. CONCLUSION:Impact trauma, impingement, and excessive

关键词： Acromion and Spine Fractures Biomechanics Extended Finite Element Analysis Reverse Total Shoulder Arthroplasty

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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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