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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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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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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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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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Hybrid dedicated and distributed coding in PMd/M1 provides separation and interaction of bilateral arm signals

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PLoS Computational Biology 2021年第11期17卷 e1009615-e1009615页

作者： Dixon, Tanner C. Merrick, Christina M. Wallis, Joni D. Ivry, Richard B. Carmena, Jose M. UC Berkeley-UCSF Graduate Program in Bioengineering University of California-Berkeley BerkeleyCA United States Department of Psychology University of California-Berkeley BerkeleyCA United States Helen Wills Neuroscience Institute University of California-Berkeley BerkeleyCA United States Department of Electrical Engineering and Computer Sciences University of California-Berkeley BerkeleyCA United States

Pronounced activity is observed in both hemispheres of the motor cortex during preparation and execution of unimanual movements. The organizational principles of bi-hemispheric signals and the functions they serve throughout motor planning remain unclear. Using an instructed-delay reaching task in monkeys, we identified two components in population responses spanning PMd and M1. A "dedicated"component, which segregated activity at the level of individual units, emerged in PMd during preparation. It was most prominent following movement when M1 became strongly engaged, and principally involved the contralateral hemisphere. In contrast to recent reports, these dedicated signals solely accounted for divergence of arm-specific neural subspaces. The other "distributed"component mixed signals for each arm within units, and the subspace containing it did not discriminate between arms at any stage. The statistics of the population response suggest two functional aspects of the cortical network: One that spans both hemispheres for supporting preparatory and ongoing processes, and another that is predominantly housed in the contralateral hemisphere and specifies unilateral output. © 2021 Dixon et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

关键词： Population statistics

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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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Spatially-varying microscope calibration from unstructured sparse inputs

Spatially-varying microscope calibration from unstructured s...

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

作者： Kuo, Grace Monakhova, Kristina Yanny, Kyrollos Ng, Ren Waller, Laura Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA94720 United States UCB/UCSF Joint Graduate Program in Bioengineering University of California Berkeley BerkeleyCA94720 United States

We propose a method based on blind deconvolution to calibrate the spatially-varying point spread functions of a coded-aperture microscope system. From easy-to-acquire measurements of unstructured fluorescent beads, we... 详细信息

ISBN: (纸本)9781557528209

关键词： Optical transfer function

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Node-pore sensing device to detect tumor-derived extracellular vesicles 23

Node-pore sensing device to detect tumor-derived extracellul...

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23rd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2019

作者： Carey, Thomas R. Hall, Jennifer Sohn, Lydia L. UC Berkeley-UCSF Graduate Program in Bioengineering United States UC Berkeley Molecular and Cell Biology United States UC Berkeley Mechanical Engineering United States

ISBN: (纸本)9781733419000

We present the theory, design, and proof-of-concept demonstration of a tumor-derived extracellular vesicle (EV) detection platform. Our platform detects EVs displaying specific surface antigens by electronically measuring the effective size increase of antibody-coated colloids when EVs specifically bind to them. We show that we can distinguish EVs derived from a lung cancer cell line (A549) and a non-malignant bronchial epithelial cell line (BEAS-2B) based on the CA12 surface marker. © 2019 CBMS-0001.

关键词： Tumors

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Imaging neurotransmitter transport in live cells with stimulated Raman scattering microscopy

arXiv

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arXiv 2022年

作者： Manifold, Bryce Dorlhiac, Gabriel F. Landry, Markita P. Streets, Aaron Department of Bioengineering University of California Berkeley BerkeleyCA94720 United States Biophysics Graduate Group University of California Berkeley BerkeleyCA94720 United States Department of Chemical and Biomolecular Engineering University of California Berkeley BerkeleyCA94720 United States Innovative Genomics Institute University of California Berkeley BerkeleyCA94720 United States California Institute for Quantitative Biosciences QB3 University of California Berkeley BerkeleyCA94720 United States Chan-Zuckerberg Biohub San FranciscoCA94158 United States UC Berkeley-UC San Francisco Graduate Program in Bioengineering University of California Berkeley BerkeleyCA94720 United States

Chemical neurotransmission is central to neurotypical brain function but also implicated in a variety of psychiatric and neurodegenerative diseases. The release dynamics of neurotransmitters is correlated with but distinct from neuronal electrical signal propagation. It is therefore necessary to track neurotransmitter modulation separately from neuron electrical activity. Here, we present a new approach for imaging deuterated neurotransmitter molecules in the cell-silent window with stimulated Raman scattering (SRS) microscopy. Using SRS microscopy, we perform direct imaging of deuterated dopamine and GABA in PC12 chromaffin cells, and in primary hippocampal neurons, respectively, based on the carbon-deuterium vibrational frequencies. We demonstrate that SRS imaging of these isotopologues directly visualizes intracellular neurotransmitters without changing the neurotransmitters’ chemical identity, and requiring custom synthesis or genetic encoding protocols. We further show that stimulation of neurotransmitter release results in an overall 20-50% intracellular neurotransmitter signal reduction in agreement with comparable neurotransmission dynamics studies, with the ability to observe inter- and intracellular variation in vesicular neurotransmitter release. Taken together, our data suggest that neurotransmitter isotopologues can serve as a commercially-available, biocompatible, and generalizable method to image neurotransmitters with deuterated molecules that are virtually chemically identical to their native counterparts. © 2022, CC BY.

关键词： Stimulated Raman scattering

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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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