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Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3 — Ex vivo imaging: data processing, comparisons with microscopy, and tractography

arXiv

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arXiv 2024年

作者： Schilling, Kurt G. Howard, Amy F.D. Grussu, Francesco Ianus, Andrada Hansen, Brian Barrett, Rachel L.C. Aggarwal, Manisha Michielse, Stijn Nasrallah, Fatima Syeda, Warda Wang, Nian Veraart, Jelle Roebroeck, Alard Bagdasarian, Andrew F. Eichner, Cornelius Sepehrband, Farshid Zimmermann, Jan Soustelle, Lucas Bowman, Christien Tendler, Benjamin C. Hertanu, Andreea Jeurissen, Ben Verhoye, Marleen Frydman, Lucio van de Looij, Yohan Hike, David Dunn, Jeff F. Miller, Karla Landman, Bennett A. Shemesh, Noam Anderson, Adam McKinnon, Emilie Farquharson, Shawna Dell' Acqua, Flavio Pierpaoli, Carlo Drobnjak, Ivana Leemans, Alexander Harkins, Kevin D. Descoteaux, Maxime Xu, Duan Huang, Hao Santin, Mathieu D. Grant, Samuel C. Obenaus, Andre Kim, Gene S. Wu, Dan Le Bihan, Denis Blackband, Stephen J. Ciobanu, Luisa Fieremans, Els Bai, Ruiliang Leergaard, Trygve B. Zhang, Jiangyang Dyrby, Tim B. Johnson, G. Allan Cohen-Adad, Julien Budde, Matthew D. Jelescu, Ileana O. Radiology and Radiological Sciences Vanderbilt University Medical Center NashvilleTN United States Vanderbilt University Institute of Imaging Science Vanderbilt University NashvilleTN United States Department of Bioengineering Imperial College London London United Kingdom FMRIB Centre Wellcome Centre for Integrative Neuroimaging Nuffield Department of Clinical Neurosciences University of Oxford Oxford United Kingdom Radiomics Group Vall d’Hebron Institute of Oncology Vall d’Hebron Barcelona Hospital Campus Barcelona Spain Queen Square MS Centre Queen Square Institute of Neurology Faculty of Brain Sciences University College London London United Kingdom Champalimaud Research Champalimaud Foundation Lisbon Portugal Center of Functionally Integrative Neuroscience Aarhus University Aarhus Denmark Department of Neuroimaging Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom NatBrainLab Department of Forensics and Neurodevelopmental Sciences Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom Russell H. Morgan Department of Radiology and Radiological Science Johns Hopkins University School of Medicine BaltimoreMD United States Maastricht University Medical Center Maastricht Netherlands The Queensland Brain Institute The University of Queensland Queensland Australia Melbourne Neuropsychiatry Centre The University of Melbourne ParkvilleVIC Australia Department of Radiology and Imaging Sciences Indiana University IN United States Stark Neurosciences Research Institute Indiana University School of Medicine IN United States Center for Biomedical Imaging NYU Grossman School of Medicine New YorkNY United States Faculty of psychology and Neuroscience Maastricht University Maastricht Netherlands Department of Chemical & Biomedical Engineering FAMU-FSU College of Engineering Florida State University TallahasseeFL United States Center for Interdisciplinary Magnetic Res

Preclinical diffusion MRI (dMRI) has proven value in methods development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages that facilitate high spatial resolution and high signal-to-noise ratio (SNR) images, cutting-edge diffusion contrasts, and direct comparison with histological data as a methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work concludes a 3-part series of recommendations and considerations for preclinical dMRI. Herein, we describe best practices for dMRI of ex vivo tissue, with a focus on image pre-processing, data processing and model fitting, and tractography. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. We end by providing guidelines on code sharing and data sharing, and point towards open-source software and databases specific to small animal and ex vivo imaging. © 2024, CC BY.

关键词： Data Sharing

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Multiline orthogonal scanning temporal focusing (mosTF) microscopy for scattering reduction in high-speed in vivo brain imaging

arXiv

引用

arXiv 2019年

作者： Xue, Yi Boivin, Josiah R. Wadduwage, Dushan N. Park, Jong Kang Nedivi, Elly So, Peter T.C. Dept. of Mechanical Engineering Massachusetts Institute of Technology 77 Massachusetts Ave. CambridgeMA02139 Singapore Laser Biomedical Research Center Massachusetts Institute of Technology 77 Massachusetts Ave. CambridgeMA02139 Singapore Picower Institute Massachusetts Institute of Technology 77 Massachusetts Ave. CambridgeMA02139 United States Dept. of Biological Engineering Massachusetts Institute of Technology 77 Massachusetts Ave. CambridgeMA02139 Singapore Dept. of Biology Massachusetts Institute of Technology 77 Massachusetts Ave. CambridgeMA02139 Singapore Dept. of Brain and Cognitive Sciences Massachusetts Institute of Technology 77 Massachusetts Ave. CambridgeMA02139 United States Center for Advanced Imaging Faculty of Arts and Sciences Harvard University CambridgeMA02138 Dept. of Electrical Engineering and Computer Sciences University of California BerkeleyCA94720 United States

Temporal focusing two-photon microscopy enables high resolution imaging of fine structures in vivo over a large volume. A limitation of temporal focusing is that signal-to-background ratio and resolution degrade rapidly with increasing imaging dept.. This degradation originates from the scattered emission photons are widely distributed resulting in a strong background. We have developed Multiline Orthogonal Scanning Temporal Focusing (mosTF) microscopy that overcomes this problem. mosTF captures a sequence of images at each scan location of the excitation line, followed by a reconstruction algorithm reassigns scattered photons back to the correct scan position. We demonstrate mosTF by acquiring mice neuronal images in vivo. Our results show remarkably improvements with mosTF for in vivo brain imaging while maintaining its speed advantage. Copyright © 2019, The Authors. All rights reserved.

关键词： Photons

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A de-centralized framework for data sharing, ontology matching and distributed analytics 1

A de-centralized framework for data sharing, ontology matchi...

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1st International Workshop on Semantic Web Technologies for Health Data Management, SWH 2018

作者： Pezoulas, Vasileios C. Kourou, Konstantina D. Exarchos, Themis P. An-dronikou, Vassiliki Varvarigou, Theodora Tzioufas, Athanasios G. De Vita, Salvatore Fotiadis, Dimitrios I. Unit of Medical Technology and Intelligent Information Systems Dept. of Materials Science and Engineering University of Ioannina IoanninaGR 45110 Greece Dept. of Informatics Ionian University CorfuGR 49100 Greece Division of Communication Electronic and Information Engineering School of Electrical and Computer Engineering National Technical University of Athens AthensGR 15780 Greece Dept. of Pathophysiology Faculty of Medicine National and Kapodistrian University of Athens AthensGR 15772 Greece Clinic of Rheumatology Dept. of Medical and Biological Sciences Udine University UdineIT 33100 Italy

In this paper we present the fundamental concept, as well as, the objectives and the architecture of HarmonicSS EU project. The proposed architecture envisages to address (i) the lack of patient stratification in large patient cohorts, (ii) the dataset heterogeneity across these cohorts, and (iii) the incomplete understanding of disease pathogenesis. In order to do so, ontology matching mechanisms are recruited for harmonizing the clinical data, distributed data analytics services have been designed for the de-centralized analysis of patient data, and different health policies can be assessed, all of them with respect to the data protection guidelines posed by the upcoming General Data Protection Regulation (GDPR). The HarmonicSS architecture has been employed towards the development of a data sharing, harmonization and distributed analytics framework for the recruitment and analysis of heterogeneous regional, national and international longitudinal cohorts of patients with primary Sjögren’s syndrome (pSS). The outcomes can be used by researchers, clinicians, patients, and health policy makers. © 2018 CEUR-WS. All rights reserved.

关键词： Large dataset

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Revealing the Dynamic Magneto-ionic Environments of Repeating Fast Radio Burst Sources through Multi-year Polarimetric Monitoring with CHIME/FRB

arXiv

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arXiv 2023年

作者： McKinven, R. Gaensler, B.M. Michilli, D. Masui, K. Kaspi, V.M. Su, J. Bhardwaj, M. Cassanelli, T. Chawla, P. Dong, F. Fonseca, E. Leung, C. Li, D.Z. Ng, C. Patel, C. Pearlman, A.B. Petroff, E. Pleunis, Z. Rafiei-Ravandi, M. Rahman, M. Sand, K.R. Shin, K. Stairs, I.H. Tendulkar, S. Department of Physics McGill University 3600 rue University MontréalQCH3A 2T8 Canada McGill Space Institute McGill University 3550 rue University MontréalQCH3A 2A7 Canada Dunlap Institute for Astronomy & Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada David A. Dunlap Department of Astronomy & Astrophysics University of Toronto 50 St. George Street TorontoONM5S 3H4 Canada Department of Physics Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States MIT Kavli Institute for Astrophysics and Space Research Massachusetts Institute of Technology 77 Massachusetts Ave CambridgeMA02139 United States Anton Pannekoek Institute for Astronomy University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Dept. of Physics and Astronomy 6224 Agricultural Road VancouverBCV6T 1Z1 Canada Lane Department of Computer Science and Electrical Engineering 1220 Evansdale Drive PO Box 6109 MorgantownWV26506 United States Center for Gravitational Waves and Cosmology West Virginia University Chestnut Ridge Research Building MorgantownWV26505 United States Department of Physics and Astronomy West Virginia University P.O. Box 6315 MorgantownWV26506 United States Cahill Center for Astronomy and Astrophysics California Institute of Technology 1216 E California Boulevard PasadenaCA91125 United States Sidrat Research PO Box 73527 RPO Wychwood TorontoONM6C 4A7 Canada Department of Astronomy and Astrophysics Tata Institute of Fundamental Research Mumbai400005 India National Centre for Radio Astrophysics Post Bag 3 Ganeshkhind Pune411007 India

Fast radio bursts (FRBs) display a confounding variety of burst properties and host galaxy associations. Repeating FRBs offer insight into the FRB population by enabling spectral, temporal and polarimetric properties to be tracked over time. Here, we report on the polarized observations of 12 repeating sources using multi-year monitoring with the Canadian Hydrogen Intensity Mapping Experiment (CHIME) over 400-800 MHz. We observe significant RM variations from many sources in our sample, including RM changes of several hundred rad m−2 over month timescales from FRBs 20181119A, 20190303A and 20190417A, and more modest RM variability (∆RM . few tens rad m−2) from FRBs 20181030A, 20190208A, 20190213B and 20190117A over equivalent timescales. Several repeaters display a frequency dependent degree of linear polarization that is consistent with depolarization via scattering. Combining our measurements of RM variations with equivalent constraints on DM variability, we estimate the average line-of-sight magnetic field strength in the local environment of each repeater. In general, repeating FRBs display RM variations that are more prevalent/extreme than those seen from radio pulsars in the Milky Way and the Magellanic Clouds, suggesting repeating FRBs and pulsars occupy distinct magneto-ionic environments. © 2023, CC BY.

关键词： Polarimeters

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Photonic microwave and radio frequency channelizers based on optical Kerr micro-combs

TechRxiv

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TechRxiv 2020年

作者： Tan, Mengxi Xu, Xingyuan Wu, Jiayang Nguyen, Thach G. Chu, Sai T. Little, Brent E. Morandotti, Roberto Mitchell, Arnan Moss, David J. Optical Sciences Centre Swinburne University of Technology HawthornVIC3122 Australia Electro-Photonics Laboratory Dept. of Electrical and Computer Systems Engineering Monash University VIC3800 Australia School of Engineering RMIT University MelbourneVIC3001 Australia Department of Physics City University of Hong Kong Tat Chee Avenue Hong Kong State Key Laboratory of Transient Optics and Photonics Xi'an Institute of Optics and Precision Mechanics Chinese Academy of Science Xi'an China INRS -Énergie Matériaux et Télécommunications 1650 Boulevard Lionel-Boulet VarennesQCJ3X 1S2 Canada Frontier Sciences University of Electronic Science and Technology of China Chengdu610054 China

We review recent work on broadband RF channelizers based on integrated optical frequency Kerr micro-combs combined with passive micro-ring resonator filters, with microcombs having channel spacings of 200GHz and 49GHz. This approach to realizing RF channelizers offers reduced complexity, size, and potential cost for a wide range of applications to microwave signal detection. © 2020, CC BY.

关键词： Natural frequencies

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Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning

arXiv

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arXiv 2021年

作者： Hering, Alessa Hansen, Lasse Mok, Tony C.W. Chung, Albert C.S. Siebert, Hanna Häger, Stephanie Lange, Annkristin Kuckertz, Sven Heldmann, Stefan Shao, Wei Vesal, Sulaiman Rusu, Mirabela Sonn, Geoffrey Estienne, Théo Vakalopoulou, Maria Han, Luyi Huang, Yunzhi Yap, Pew-Thian Brudfors, Mikael Balbastre, Yaël Joutard, Samuel Modat, Marc Lifshitz, Gal Raviv, Dan Lv, Jinxin Li, Qiang Jaouen, Vincent Visvikis, Dimitris Fourcade, Constance Rubeaux, Mathieu Pan, Wentao Xu, Zhe Jian, Bailiang De Benetti, Francesca Wodzinski, Marek Gunnarsson, Niklas Sjölund, Jens Grzech, Daniel Qiu, Huaqi Li, Zeju Thorley, Alexander Duan, Jinming Großbröhmer, Christoph Hoopes, Andrew Reinertsen, Ingerid Xiao, Yiming Landman, Bennett Huo, Yuankai Murphy, Keelin Lessmann, Nikolas van Ginneken, Bram Dalca, Adrian V. Heinrich, Mattias P. Institute of Medical Informatics Universität zu Lübeck Ratzeburger Allee 160 Lübeck23562 Germany Fraunhofer MEVIS Institute for Digital Medicine Lübeck23562 Germany Department of Radiology and Nuclear Medicine Radboud University Medical Center GA Nijmegen6525 Netherlands The Institute of Medical Informatics Universität zu Lübeck Lübeck23562 Germany The Department of Computer Science and Engineering The Hong Kong University of Science and Technology Hong Kong The Fraunhofer MEVIS Institute for Digital Medicine Lübeck23562 Germany The Department of Radiology Stanford University StanfordCA94305 United States The Department of Urology Stanford University StanfordCA94305 United States The Université Paris-Saclay CentraleSupélec Mathématiques et Informatique pour la Complexité et les Systèmes Inria Saclay Gif-sur-Yvette 91190 France Université Paris-Saclay Institut Gustave Roussy Inserm Radiothérapie Moléculaire et Innovation Thérapeutique Villejuif94800 France The Université Paris-Saclay CentraleSupélec Mathématiques et Informatique pour la Complexité et les Systèmes Inria Saclay Gif-sur-Yvette91190 France The Department of Radiology and Nuclear Medicine Radboud University Medical Center Nijmegen6525 GA Netherlands The School of Automation Nanjing University of Information Science and Technology Nanjing210044 China The School of Biomedical Engineering and Imaging Sciences King’s College London London United Kingdom The Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital United States Harvard Medical School Boston United States The King’s College London United Kingdom The Tel Aviv University The Britton Chance Center for Biomedical Photonics Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology Hubei Wuhan430074 China MoE Key Laboratory for Biomedical Photonics Collaborative Innovation Center for Biomedical Engineering School of Engineering Sciences Huazhong University of Sci

Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration data set for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https://***. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, as well as results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias. While no single approach worked best across all tasks, many methodological aspects could be identified that push the performance of medical image registration to new state-of-the-art performance. Furthermore, we demystified the common belief that conventional registration methods have to be much slower than deep-learning-based methods. © 2021, CC BY.

关键词： Image registration

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Orthogonally polarized RF single sideband generation with Kerr microcombs

TechRxiv

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TechRxiv 2020年

作者： Moss, David J. Tan, Mengxi Xu, Xingyuan Wu, Jiayang Nguyen, Thach G. Chu, Sai T. Little, Brent E. Mitchell, Arnan Morandotti, Roberto Optical Sciences Centre Swinburne University of Technology HawthornVIC3122 Australia Electro-Photonics Laboratory Dept. of Electrical and Computer Systems Engineering Monash University VIC3800 Australia School of Engineering RMIT University MelbourneVIC3001 Australia Department of Physics City University of Hong Kong Tat Chee Avenue Hong Kong State Key Laboratory of Transient Optics and Photonics Xi'an Institute of Optics and Precision Mechanics Chinese Academy of Science Xi'an China INRS -Énergie Matériaux et Télécommunications 1650 Boulevard Lionel-Boulet VarennesQCJ3X 1S2 Canada University of Electronic Science and Technology of China Chengdu610054 China

We review recent work on narrowband orthogonally polarized optical RF single sideband generators as well as dual-channel equalization, both based on high-Q integrated ring resonators. The devices operate in the optical telecommunications C-band and enable RF operation over a range of either fixed or thermally tuneable frequencies. They operate via TE/TM mode birefringence in the resonator. We achieve a very large dynamic tuning range of over 55 dB for both the optical carrier-to-sideband ratio and the dual-channel RF equalization for both the fixed and tunable devices. © 2020, CC BY.

关键词： Microwave photonics

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Additively manufactured WR-10 copper waveguide 19

Additively manufactured WR-10 copper waveguide

引用

19th IEEE International Vacuum Electronics Conference, IVEC 2018

作者： Horn, Timothy Karakurt, Ilbey Ledford, Christopher Gonzalez, Michelle Gamzina, Diana Luhmann, Neville C. Lin, Liwei Center for Additive Manufacturing and Logistics North Carolina State University RaleighNC27607 United States Dept. of Mechanical Engineering UC Berkeley BerkeleyCA94720 United States Dept. of Electrical and Computer Engineering UC Davis DavisCA95616 United States Technology Innovation Direct. SLAC National Accelerator Laboratory Menlo ParkCA94025 United States

ISBN: (纸本)9781538604540

Direct additive manufacturing method utilizing electron beam melting techniques was employed to produce fully dense oxygen free copper W-band waveguides. By employing smaller copper powder, finer deposition layer, and spot-melting methodology surface roughness average has been reduced from 44 μm to 28 μm. A magnetically driven abrasive process was then employed to demonstrate further surface roughness average improvement of 5 μm. Initial RF test results on as-printed WR-10 waveguide confirm that surface post-processing will be essential to implementation of additive manufacturing techniques in vacuum electronics. © 2018 IEEE.

关键词： Surface roughness

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Model Predictive Control for Unmanned Tracked Vehicle Path Following

Model Predictive Control for Unmanned Tracked Vehicle Path F...

引用

International Conference on Sensing, Diagnostics, Prognostics, and Control (SDPC)

作者： Hao Yan Fuwei Yang Zhixiang Wang Dept. of Electrical and Computer Engineering The Ohio State University Columbus USA Technology Center SAIC Motor Corporation Ltd Shanghai China

ISBN: (纸本)9781538660584;9781538660577

Traditional path following algorithms seldom analyze vehicle dynamics so that unintended error would occur when the vehicle steers in high speed. To solve these problems, this paper established a linear path following model, which includes a 3 degree of freedom (DOF) dynamic model based on model predictive control (MPC). In this model, speed of left and right track are used as control variables, and the MPC algorithm is designed to control an electric tracked vehicle follow a desired trajectory and fulfilling its physical constraints. Quadratic programming is used to solve the linear MPC by linearization of the error model. The control system is testified in MATLAB/Simulink and the performance is satisfied in different situations.

关键词： Mathematical model Stress Vehicle dynamics Kinematics Force Predictive models Tracking

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Collective near-field coupling in infrared-phononic metasurfaces for nano-light canalization

arXiv

引用

arXiv 2020年

作者： Li, Peining Hu, Guangwei Dolado, Irene Tymchenko, Mykhailo Qiu, Cheng-Wei Alfaro-Mozaz, Francisco Javier Casanova, Felix Hueso, Luis E. Liu, Song Edgar, James H. Vélez, Saül Alu, Andrea Hillenbrand, Rainer Wuhan National Laboratory for Optoelectronics School of Optical and Electronic Information Huazhong University of Science and Technology Wuhan430074 China CIC nanoGUNE BRTA Donostia-San Sebastián20018 Spain Department of Electrical and Computer Engineering National University of Singapore 4 Engineering Drive 3 Singapore117583 Singapore Advanced Science Research Center City University of New York New York10031 United States IKERBASQUE Basque Foundation for Science Bilbao48013 Spain Tim Taylor Dept. of Chemical Engineering Kansas State University ManhattanKS66506 United States Department of Materials ETH Zürich Zürich8093 Switzerland CIC NanoGUNE BRTA UPV EHU Donostia-San Sebastián20018 Spain

Polaritons - coupled excitations of photons and dipolar matter excitations - can propagate along anisotropic metasurfaces with either hyperbolic or elliptical dispersion. At the transition from hyperbolic to elliptical dispersion (corresponding to a topological transition), various intriguing phenomena are found, such as an enhancement of the photonic density of states, polariton canalization and hyperlensing. Here we investigate theoretically and experimentally the topological transition and the polaritonic coupling of deeply subwavelength elements (structure sizes ∼ λ/100, λ being the free-space wavelength) in a uniaxial infrared-phononic metasurface, a grating of hexagonal boron nitride (hBN) nanoribbons. By hyperspectral infrared nanoimaging, we observe, for the first time, a synthetic transverse optical phonon resonance (that is, the strong collective near-field coupling of the nanoribbons) in the middle of the hBN Reststrahlen band, yielding a topological transition from hyperbolic to elliptical dispersion. We further visualize and characterize the spatial evolution of a deeply subwavelength canalization mode (a spatial confinement of about 300 nm, ∼ λ/22) near the transition frequency, which is a collimated polariton that is the basis for hyperlensing and diffraction-less propagation. Our results provide fundamental insights into the role of polaritonic near-field coupling in metasurfaces for creating topological transitions and polariton canalization. Copyright © 2020, The Authors. All rights reserved.

关键词： Photons

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