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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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MICROFLUIDIC PLATFORM FOR MULTI-FREQUENCY VISCOELASTIC PHENOTYPING OF SINGLE CELLS 25

MICROFLUIDIC PLATFORM FOR MULTI-FREQUENCY VISCOELASTIC PHENO...

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25th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2021

作者： Lai, Andre Dong, Alan Lustig, Michael Sohn, Lydia L. UC Berkeley-UC San Francisco Graduate Program in Bioengineering University of California BerkeleyCA United States Electrical Engineering and Computer Sciences University of California BerkeleyCA United States Department of Mechanical Engineering University of California BerkeleyCA United States

ISBN: (纸本)9781733419031

Biomechanics plays an integral role in cancer development and progression. Accurately quantifying the mechanical properties of cells would enable a more comprehensive understanding of cancer, complementing conventional biochemical and genetic analyses. Here, we introduce a microfluidic platform for measuring single cell viscoelasticity at multiple frequencies in a high-throughput and label-free manner. Using the Coulter principal and a unique microfluidic channel geometry, our device records resistance pulses in order to estimate a cell's viscoelastic phenotype. We demonstrate our platform's capabilities by measuring three breast epithelial cell lines. © 2021 MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.

关键词： Biomechanics

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Synthetic CT Generation Using MRI with Deep Learning: How Does the Selection of Input Images Affect the Resulting Synthetic CT?

Synthetic CT Generation Using MRI with Deep Learning: How Do...

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IEEE International Conference on Acoustics, Speech and Signal Processing

作者： Andrew P. Leynes Peder E. Z. Larson UC Berkeley - UC San Francisco Joint Graduate Program in Bioengineering

ISBN: (纸本)9781538646595

Synthetic x-ray computed tomography (CT) images derived from magnetic resonance imaging (MRI) is a recent area of focus for medical imaging researchers for applications in attenuation correction in simultaneous PET/MRI systems and MRI-guided radiotherapy planning. Several research groups have demonstrated the potential of deep learning to generate the synthetic CT images, however, there are several major open questions that remain with this approach. We investigated how the selection of MRI inputs affect the resulting output using a fixed network. We found that Dixon MRI may be sufficient for quantitatively accurate synthetic CT images and ZTE MRI may provide additional information to capture bowel air distributions.

关键词： synthetic ct deep learning mri Dixon mri zero echo-time mri

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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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Microfluidic Strategies for Understanding the Mechanics of Cells and Cell-Mimetic Systems

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Chemical and Biomolecular Engineering 1000年第1期6卷 293-317页

作者： Joanna B. Dahl Jung-Ming G. Lin Susan J. Muller Sanjay Kumar 1Department of Chemical and Biomolecular Engineering 3UC Berkeley/UCSF Graduate Program in Bioengineering University of California Berkeley California 94720 email: skumar@berkeley.edu 2Department of Bioengineering

Microfluidic systems are attracting increasing interest for the high-throughput measurement of cellular biophysical properties and for the creation of engineered cellular microenvironments. Here we review recent applications of microfluidic technologies to the mechanics of living cells and synthetic cell-mimetic systems. We begin by discussing the use of microfluidic devices to dissect the mechanics of cellular mimics, such as capsules and vesicles. We then explore applications to circulating cells, including erythrocytes and other normal blood cells, and rare populations with potential disease diagnostic value, such as circulating tumor cells. We conclude by discussing how microfluidic devices have been used to investigate the mechanics, chemotaxis, and invasive migration of adherent cells. In these ways, microfluidic technologies represent an increasingly important toolbox for investigating cellular mechanics and motility at high throughput and in a format that lends itself to clinical translation.

关键词： particles droplets capsules vesicles migration chemotaxis

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Microfabricated bioprocessor for nanoliter-scale Sanger DNA sequencing

Microfabricated bioprocessor for nanoliter-scale Sanger DNA ...

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10th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2006

作者： Blazej, Robert G. Kumaresan, Palani Mathies, Richard A. UCSF/UC Berkeley Joint Bioengineering Graduate Group University of California Berkeley CA 94720 United States Department of Mechanical Engineering University of California Berkeley CA 94720 United States Department of Chemistry University of California Berkeley CA 94720 United States

Utilizing hybrid glass-PDMS construction, we have developed an efficient, nanoliterscale microfabricated bioprocessor that integrates all three key Sanger sequencing steps-thermal cycling, sample purification and capillary electrophoresis (CE)-into a microdevice capable of read-lengths equivalent to those used in the sequencing of the human genome. The bioprocessor incorporates a range of advanced technologies including miniaturized temperature sensing, nanoliter-scale Sanger extension reactions, microvalves/pumps, DNA affinity-capture and high-performance capillary electrophoresis. Lab-on-a-chip level integration enables sequencing of 556 continuous bases with 99% accuracy from only 1 femtomole of DNA template in a 250-nL reactor. The performance of this miniaturized DNA sequencer provides a benchmark for evaluating the ultimate cost and efficiency limits of Sanger sequencing. © 2006 Society for Chemistry and Micro-Nano Systems.

关键词： DNA sequences

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Multichannel reverse transcription-PCR microdevice for rapid multiplex gene expression analysis

Multichannel reverse transcription-PCR microdevice for rapid...

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10th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2006

作者： Toriello, Nicholas M. Liu, Chung N. Mathies, Richard A. UCSF/UC Berkeley Joint Graduate Group in Bioengineering University of California Berkeley CA 94720 United States Department of Chemical Engineering University of California Berkeley CA 94720 United States Department of Chemistry University of California Berkeley CA 94720 United States

A microdevice is developed for rapid RNA analysis that integrates 1-step reverse transcription and 30 cycles of PCR (RT-PCR) amplification with capillary electrophoresis (CE) separation and fluorescence detection of the amplicons. The 4- layer glass-PDMS-glass-glass hybrid microdevice integrates microvalves, on-chip heaters and temperature sensors, nanoliter reaction chambers (380 nL) and 5-cm long CE separation channels. The direct integration of these processes results in attomolar detection sensitivity (

关键词： Glass

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Integrated affinity capture, purification and capillary electrophoresis microdevice for quantitative double-stranded DNA analysis 11

Integrated affinity capture, purification and capillary elec...

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11th International Conference on Miniaturized Systems for Chemistry and Life Sciences, uTAS 2007

作者： Toriello, Nicholas M. Liu, Chung N. Thaitrong, Numrin Mathies, Richard A. UCSF/UC Berkeley Joint Graduate Group in Bioengineering University of California BerkeleyCA94720 United States Department of Chemical Engineering University of California BerkeleyCA94720 United States Department of Chemistry University of California BerkeleyCA94720 United States

A novel injection method is developed that utilizes a thermally switchable oligonucleotide affinity capture gel to mediate the concentration, purification and injection of double-stranded DNA for quantitative microchi... 详细信息

ISBN: (纸本)9780979806407

关键词： Purification

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A comparison of coil combination strategies in 3D multi-channel MRSI reconstruction for patients with brain tumors (vol 31, e3929, 2018)

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NMR IN BIOMEDICINE 2018年第12期31卷 e3929-e3929页

作者： Vareth, M. Lupo, J. M. Larson, P. E. Z. Nelson, S. J. UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA UC Berkeley-UCSF Graduate Program in Bioengineering University of California Berkeley and University of California San Francisco California USA Surbeck Laboratory of Advanced Imaging Department of Radiology and Biomedical Imaging University of California San Francisco California USA

The goal of this study was to find the most robust algorithm for a phase‐sensitive coil combination of 3D single‐cycle and lactate‐edited, multi‐channel H‐1 point‐resolved spectroscopy (PRESS) localized echo planar spectroscopic imaging (EPSI) data for clinical applications in the brain. Data were acquired over 5-10 minutes at 3T using 8‐ or 32‐channel array coils. Peak referencing with residual water and N‐acetyl‐aspartate, first‐point phasing, generalized least squared (GLS) and whitened singular‐value decomposition (WSVD) combination algorithms were evaluated relative to unsuppressed water with data from a phantom, six volunteers and 55 patients with brain tumors. Comparison metrics were signal‐to‐noise ratio, coefficient of variance and percent signal increase. Where residual water was present, using it as a reference peak for phasing and weighting factors from an imaging calibration scan gave the best overall performance. Greater improvement was seen for large selected volumes (>720 cm³) and for the 32‐channel array (25%) compared with the 8‐channel array (19%). Applying voxel‐by‐voxel phase corrections produced a larger increase in performance for the 32‐ versus 8‐channel coil. We conclude that, for clinically relevant 3D H‐1 PRESS localized EPSI studies, the most robust technique employed individual phase maps generated from high residual water and individual amplitude maps generated from calibration scans.

关键词： coil combination techniques first‐point phasing GLS lactate editing multichannel EPSI peak referencing PRESS localization WSVD

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Biomimetic in silico devices

Biomimetic in silico devices

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International Conference on Computational Methods in Systems Biology, CMSB 2004

作者： Hunt, C. Anthony Ropella, Glen E. P. Roberts, Michael S. Yan, Li Dept. of Biopharmaceutical Sciences Biosystems Group University of California San Francisco CA 94143-0446 United States Department of Medicine University of Queensland Princess Alexandra Hospital Woolloongabba Q 4102 Australia Joint UCSF UC Berkeley Bioengineering Graduate Program

ISBN: (纸本)3540253750

We introduce biomimetic in silico devices, and means for validation along with methods for testing and refining them. The devices are constructed from adaptable software components designed to map logically to biological components at multiple levels of resolution. In this report we focus on the liver;the goal is to validate components that mimic features of the lobule (the hepatic primary functional unit) and dynamic aspects of liver behavior, structure, and function. An assembly of lobule-mimetic devices represents an in silico liver. We validate against outflow profiles for sucrose administered as a bolus to isolated, perfused rat livers. Acceptable in silico profiles are experimentally indistinguishable from those of the in situ referent. This new technology is intended to provide powerful new tools for challenging our understanding of how biological functional units function in vivo. © Springer-Verlag Berlin Heidelberg 2005.

关键词： Biomimetic materials

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