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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 Department of Biomedical Engineering University of Texas at San Antonio San Antonio Texas United States of America Department of Computer Science University of Texas at San Antonio San Antonio Texas United States of America Systems Synthetic and Physical Biology Program Rice University Houston 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 Department of Biosciences Rice University Houston Texas United States of America UTSA–UT Health Joint Graduate Group in Biomedical Engineering San Antonio Texas United States of America Programs in Integrated Biomedical Sciences Translational Sciences Radiological Sciences University of Texas Health Science Center at San Antonio San Antonio Texas United States of America UTSA AI MATRIX Consortium San Antonio 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

Loss tangent fluctuations due to two-level systems in superconducting microwave resonators

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arXiv 2024年

作者： Vallières, André Russell, Megan E. You, Xinyuan Garcia-Wetten, David A. Goronzy, Dominic P. Walker, Mitchell J. Bedzyk, Michael J. Hersam, Mark C. Romanenko, Alexander Lu, Yao Grassellino, Anna Koch, Jens McRae, Corey Rae H. Graduate Program in Applied Physics Northwestern University EvanstonIL60208 United States Fermi National Accelerator Laboratory BataviaIL60510 United States Department of Physics and Astronomy Northwestern University EvanstonIL60208 United States Department of Materials Science and Engineering Northwestern University EvanstonIL60208 United States Department of Chemistry Northwestern University EvanstonIL60208 United States Department of Electrical and Computer Engineering Northwestern University EvanstonIL60208 United States Center for Applied Physics and Superconducting Technologies Northwestern University EvanstonIL60208 United States Electrical Computing and Energy Engineering Department University of Colorado BoulderCO80309 United States Department of Physics University of Colorado BoulderCO80309 United States National Institute of Standards and Technology BoulderCO80305 United States

Superconducting microwave resonators are critical to quantum computing and sensing technologies. Additionally, they are common proxies for superconducting qubits when determining the effects of performance-limiting loss mechanisms such as from two-level systems (TLS). The extraction of these loss mechanisms is often performed by measuring the internal quality factor Qi as a function of power or temperature. In this work, we investigate large temporal fluctuations of Qi at low powers over periods of 12 to 16 hours (relative standard deviation σQi/Qi = 13%). These fluctuations are ubiquitous across multiple resonators, chips and cooldowns. We are able to attribute these fluctuations to variations in the TLS loss tangent due to two main indicators. First, measured fluctuations decrease as power and temperature increase. Second, for interleaved measurements, we observe correlations between low- and medium-power Qi fluctuations and an absence of correlations with high-power fluctuations. Agreement with the TLS loss tangent mean is obtained by performing measurements over a time span of a few hours. We hypothesize that, in addition to decoherence due to coupling to individual near-resonant TLS, superconducting qubits are affected by these observed TLS loss tangent fluctuations. © 2024, CC BY.

关键词： Qubits

Landau Polaritons in the Ultrastrong and Superstrong Coupling Regime in a Multimode Terahertz Photonic-Crystal Cavity

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Landau Polaritons in the Ultrastrong and Superstrong Couplin...

International Conference on Infrared and Millimeter Waves

作者： Fuyang Tay Ali Mojibpour Stephen Sanders Shuang Liang Hongjing Xu Geoff C. Gardner Andrey Baydin Michael J. Manfra Alessandro Alabastri David Hagenmüller Junichiro Kono Department of Electrical and Computer Engineering Rice University Houston TX USA Applied Physics Graduate Program Smalley–Curl Institute Rice University Houston TX USA Department of Physics and Astronomy Purdue University West Lafayette IN USA Birck Nanotechnology Center Purdue University West Lafayette IN USA Department of Physics and Astronomy Rice University Houston TX USA Smalley–Curl Institute Rice University Houston TX USA School of Electrical and Computer Engineering Purdue University West Lafayette IN USA School of Materials Engineering Purdue University West Lafayette IN USA ISIS (UMR 7006) Université de Strasbourg and CNRS Strasbourg France Department of Materials Science and NanoEngineering Rice University Houston TX USA

We have demonstrated ultrastrong and superstrong coupling of a Landau-quantized two-dimensional electron gas in GaAs with a multiple-mode three-dimensional terahertz photonic-crystal cavity. The cavity had an asymmetric design such that the real-space profiles of photonic modes depended on the electric field polarization. Terahertz magnetospectroscopy experiments with polarized radiation clearly showed that the degree of hybridization of multiple cavity modes is a function of the spatial overlap of the photonic modes. These findings can be utilized for the dynamical tuning of multimode light–matter interactions, which can lead to the development of novel terahertz devices.

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Learning Vector Quantized Shape Code for Amodal Blastomere Instance Segmentation

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Learning Vector Quantized Shape Code for Amodal Blastomere I...

IEEE International Symposium on Biomedical Imaging

作者： Won-Dong Jang Donglai Wei Xingxuan Zhang Brian Leahy Helen Yang James Tompkin Dalit Ben-Yosef Daniel Needleman Hanspeter Pfister School of Engineering and Applied Sciences Harvard University MA USA Boston College MA USA Department of Molecular and Cellular Biology Harvard University MA USA Harvard Graduate Program in Biophysics Harvard University MA USA Department of Computer Science Brown University RI USA Tel Aviv Sourasky Medical Center Fertility & IVF Institute Israel Dept. of Cell and Developmental Biology Sagol School of Neuroscience Tel Aviv University Israel

Blastomere instance segmentation is important for analyzing embryos’ abnormality. To measure the accurate shapes and sizes of blastomeres, their amodal segmentation is necessary. Amodal instance segmentation aims to recover an object’s complete silhouette even when the object is not fully visible. For each detected object, previous methods directly regress the target mask from input features. However, images of an object under different amounts of occlusion should have the same amodal mask output, making it harder to train the regression model. To alleviate the problem, we propose to classify input features into intermediate shape codes and recover complete object shapes. First, we pre-train the Vector Quantized Variational Autoencoder (VQ-VAE) model to learn these discrete shape codes from ground truth amodal masks. Then, we incorporate the VQ-VAE model into the amodal instance segmentation pipeline with an additional refinement module. We also detect an occlusion map to integrate occlusion information with a backbone feature. As such, our network faithfully detects bounding boxes of amodal objects. On an internal embryo cell image benchmark, the proposed method outperforms previous state-of-the-art methods. To show generalizability, we show segmentation results on the public KINS natural image benchmark. Our method would enable accurate measurement of blastomeres in In Vitro Fertilization (IVF) clinics, potentially increasing the IVF success rate.

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Automatic rigging of 3D models with stacked hourglass networks and descriptors

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AIP Conference Proceedings 2024年第1期2919卷

作者： Ritika Verma Sarthak Mittal Siddharth Pawar Moolchand Sharma Shalini Goel Victor Hugo C. de Albuquerque Department of Computer Science & Engineering MAIT GGSIPU New Delhi India HMR Institute of Technology and Management New Delhi India Graduate Program in Telecommunication Engineering Federal Institute of Education Science and Technology of Ceará Fortaleza/CE Brazil Department of Teleinformatics Engineering Federal University of Ceará Fortaleza/CE Brazil

We put forward an approach for automated skeleton rigging of 3D point cloud models of segmented characters. Unlike earlier systems that fit predetermined skeleton templates or forecast predetermined sets of joints, our approach generates an animation skeleton that is tuned to the structure and geometry of the input 3D model. Our architecture is built on a stack of hourglass models trained using a large dataset of 3D-rigged characters mined from the web. It works with a volumetric representation of the input 3D shapes enhanced with geometric shape elements that provide different indications for joint and bone positions. The proposed method also allows straightforward user customization of the output skeleton’s level of detail. Our study shows that, compared to many alternatives and baselines, our approach predicts animation skeletons that are significantly more comparable to those made by people.

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Outcoupling Hyperbolic Modes from Aligned Carbon Nanotube Films

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Outcoupling Hyperbolic Modes from Aligned Carbon Nanotube Fi...

Conference on Lasers and Electro-Optics (CLEO)

作者： Bryant Jerome Ciril S. Prasad Jacques Doumani Oliver S. Dewey Andrey Baydin Matteo Pasquali Junichiro Kono Weilu Gao Alessandro Alabastri Gururaj V. Naik Department of Electrical and Computer Engineering Rice University Houston TX USA Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston TX USA Department of Chemical and Biomolecular Engineering Rice University Houston TX USA Smalley-Curl Institute Rice University Houston TX USA Department of Chemistry Rice University Houston TX USA Department of Materials Science and NanoEngineering Rice University Houston TX USA Department of Physics and Astronomy Rice University Houston TX USA Department of Electrical and Computer Engineering University of Utah Salt Lake City UT USA

Aligned carbon nanotube films make an excellent hyperbolic material plat-form in the infrared. Here, we experimentally demonstrate the presence of high-k modes in aligned carbon nanotube films and outcouple them to fr... 详细信息

ISBN: (数字)9781957171050

ISBN: (纸本)9781665466660

关键词： Films Carbon nanotubes Lasers and electrooptics Laser modes High-k dielectric materials Gratings Laser applications

Magneto-optical Spectroscopy with RAMBO: A Table-Top 30 T Magnet

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arXiv 2022年

作者： Tay, Fuyang Baydin, Andrey Katsutani, Fumiya Kono, Junichiro Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Department of Physics and Astronomy Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States

Optically probing materials in high magnetic fields can provide enlightening insight into field-modified electronic states and phases, while optically driving materials in high magnetic fields can induce novel nonequilibrium many-body dynamics of spin and charge carriers. While there are high-field magnets compatible with standard optical spectroscopy methods, they are generally bulky and have limited optical access, which prohibit performing state-of-the-art ultrafast and/or nonlinear optical experiments. The Rice Advanced Magnet with Broadband Optics (RAMBO), a unique 30-T pulsed mini-coil magnet system with direct optical access, has enabled previously challenging experiments using femtosecond optical pulses, including time-domain terahertz spectroscopy, in cutting-edge materials placed in strong magnetic fields. Here, we review recent experimental advances made possible by the first-generation RAMBO setup. After summarizing technological aspects of combining optical spectroscopic techniques with the mini-coil magnet, we describe results of magneto-optical studies of a wide variety of materials, providing new insight into the states and dynamics of four types of quasiparticles in solids – excitons, plasmons, magnons, and phonons – in high magnetic fields. Copyright © 2022, The Authors. All rights reserved.

关键词： Magnets

Reducing system dimensionality with long-range collective dipole-dipole interactions

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arXiv 2023年

作者： Boddeti, Ashwin K. Wang, Yi Juarez, Xitlali G. Boltasseva, Alexandra Odom, Teri W. Shalaev, Vladimir Alaeian, Hadiseh Jacob, Zubin Elmore Family School of Electrical and Computer Engineering Purdue University West LafayetteIN47907 United States Birck Nanotechnology Center Purdue University West LafayetteIN47907 United States Graduate Program in Applied Physics Northwestern University EvanstonIL60208 United States Department of Materials Science and Engineering Northwestern University EvanstonIL60208 United States Department of Chemistry Northwestern University EvanstonIL60208 United States School of Physics and Astronomy Purdue University West LafayetteIN47907 United States

Dimensionality plays a crucial role in long-range dipole-dipole interactions (DDIs). We demonstrate that a resonant nanophotonic structure modifies the apparent dimensionality in an interacting ensemble of emitters, as revealed by population decay dynamics. Our measurements on a dense ensemble of interacting quantum emitters in a resonant nanophotonic structure with long-range DDIs reveal an effective dimensionality reduction to d¯ = 2.20(12), despite the emitters being distributed in 3D. This contrasts the homogeneous environment, where the apparent dimension is d¯ = 3.00. Our work presents a promising avenue to manipulate dimensionality in an ensemble of interacting emitters. © 2023, CC0.

关键词： Dipole moment

Topological Surface State Evolution in Bi2Se3 via Surface Etching

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arXiv 2024年

作者： Yue, Ziqin Huang, Jianwei Wang, Ruohan Li, Jia-Wan Rong, Hongtao Guo, Yucheng Wu, Han Zhang, Yichen Kono, Junichiro Zhou, Xingjiang Hou, Yusheng Wu, Ruqian Yi, Ming Department of Physics and Astronomy Rice University HoustonTX77005 United States Applied Physics Graduate Program Smalley-Curl Institute Rice University HoustonTX77005 United States Guangdong Provincial Key Laboratory of Magnetoelectric Physics and Devices Center for Neutron Science and Technology School of Physics Sun Yat-Sen University Guangzhou510275 China Institute of Physics Chinese Academy of Sciences Beijing100190 China Department of Electrical and Computer Engineering Rice University HoustonTX77005 United States Department of Materials Science and NanoEngineering Rice University HoustonTX77005 United States Department of Physics and Astronomy University of California Irvine IrvineCA92697 United States

Topological insulators are materials with an insulating bulk interior while maintaining gapless boundary states against back scattering. Bi2Se3 is a prototypical topological insulator with a Dirac-cone surface state around Γ. Here, we present a controlled methodology to gradually remove Se atoms from the surface Se-Bi-Se-Bi-Se quintuple layers, eventually forming bilayer-Bi on top of the quintuple bulk. Our method allows us to track the topological surface state and confirm its robustness throughout the surface modification. Importantly, we report a relocation of the topological Dirac cone in both real space and momentum space, as the top surface layer transitions from quintuple Se-Bi-Se-Bi-Se to bilayer-Bi. Additionally, charge transfer among different surface layers is identified. Our study provides a precise method to manipulate surface configurations, allowing for the fine-tuning of the topological surface states in Bi2Se3, which represents a significant advancement towards nano-engineering of topological states. Copyright © 2024, The Authors. All rights reserved.

关键词： Topological insulators