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1. Single-molecule localization microscopy

Author

Markus Sauer, Florian Schueder, Melike Lakadamyali, Gerti Beliu, Melina Theoni Gyparaki, Suliana Manley, Ralf Jungmann, Juliette Griffié, Mickaël Lelek, Christophe Zimmer, Imagerie et Modélisation - Imaging and Modeling, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania, University of Würzburg = Universität Würzburg, Ludwig Maximilian University [Munich] (LMU), Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB), Max-Planck-Gesellschaft, Ecole Polytechnique Fédérale de Lausanne (EPFL), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), C.Z. acknowledges funding by Institut Pasteur, Fondation pour la Recherche Médicale (grant DEQ 20150331762), Région Ile de France, Agence Nationale de la Recherche and Investissement d’Avenir grant ANR-16-CONV-0005. M.La. acknowledges funding from the National Institutes of Health/National Institutes of General Medical Sciences (NIH/NIGMS) under grant RO1 GM133842-01. G.B. and M.S. acknowledge funding by the German Research Foundation (DFG) (SA829/19-1) and the European Regional Development Fund (EFRE project ‘Center for Personalized Molecular Immunotherapy’). F.S. and R.J. acknowledge support by the DFG through SFB1032 (project A11) and the Max Planck Society. J.G. and S.M. acknowledge funding by the European Union’s H2020 programme under the Marie Skłodowska-Curie grant BALTIC (to J.G.) and ERC Piko (to S.M.)., The authors apologize to the authors of numerous papers that could not be cited owing to limited space. M.Le. and C.Z. thank B. Lelandais for excellent comments on the manuscript and M. Singh for acquiring the image shown in Fig. 3b., ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), University of Pennsylvania [Philadelphia], Max Planck Institute of Biochemistry (MPIB), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC)

Subjects
Single molecule localization, light-microscopy, Computer science, business.industry, General Medicine, Article, General Biochemistry, Genetics and Molecular Biology, optical reconstruction microscopy, diffraction-limit, Fluorescent labelling, 3-dimensional superresolution, live-cell, correlative superresolution fluorescence, Microscopy, Time course, Image acquisition, colocalization analysis, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Computer vision, Artificial intelligence, business, living cells, intramolecular spirocyclization, Image resolution, electron-microscopy
Abstract

Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM. This Primer explains the central concepts of single-molecule localization microscopy (SMLM) before discussing experimental considerations regarding fluorophores, optics and data acquisition, processing and analysis. The Primer further describes recent high-impact discoveries made by SMLM techniques and concludes by discussing emerging methodologies.

Published
2021

2. Foreground-Background Ambient Sound Scene Separation

Author

Michel Olvera, Romain Serizel, Emmanuel Vincent, Gilles Gasso, Speech Modeling for Facilitating Oral-Based Communication (MULTISPEECH), Inria Nancy - Grand Est, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Department of Natural Language Processing & Knowledge Discovery (LORIA - NLPKD), Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique, de Traitement de l'Information et des Systèmes (LITIS), Université Le Havre Normandie (ULH), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA), This work was made with the support of the French National Research Agency, in the framework of the project LEAUDS 'Learning to understandaudio scenes' (ANR-18-CE23-0020). Experiments presented in this paper were carried out using the Grid’5000 testbed, supported by a scientificinterest group hosted by Inria and including CNRS, RENATER and several Universities as well as other organizations (see https://www.grid5000.fr)., GRID5000, ANR-18-CE23-0020,LEAUDS,Apprentissage statistique pour la compréhension de scènes audio(2018), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire Lorrain de Recherche en Informatique et ses Applications (LORIA), Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université de Lorraine (UL), Institut national des sciences appliquées Rouen Normandie (INSA Rouen Normandie), Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Normandie Université (NU)-Institut National des Sciences Appliquées (INSA)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Université Le Havre Normandie (ULH), Normandie Université (NU), and ANR-18-CE23-0020,LEAUDS,LEARNING TO UNDERSTAND AUDIO SCENES(2018)

Subjects
Normalization (statistics), Signal Processing (eess.SP), FOS: Computer and information sciences, Sound (cs.SD), Computer Science - Machine Learning, Computer science, Generalization, Ambient noise level, 02 engineering and technology, Computer Science - Sound, Machine Learning (cs.LG), Signal-to-noise ratio, [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-TS]Computer Science [cs]/Signal and Image Processing, Audio and Speech Processing (eess.AS), 0202 electrical engineering, electronic engineering, information engineering, ambient sound scenes, FOS: Electrical engineering, electronic engineering, information engineering, Foreground-background, Computer vision, generalization ability, Electrical Engineering and Systems Science - Signal Processing, Sound (geography), Signal processing, geography, geography.geographical_feature_category, business.industry, Deep learning, deep learning, audio source separation, 020206 networking & telecommunications, Feature (computer vision), [INFO.INFO-SD]Computer Science [cs]/Sound [cs.SD], 020201 artificial intelligence & image processing, Artificial intelligence, business, Electrical Engineering and Systems Science - Audio and Speech Processing
Abstract

International audience; Ambient sound scenes typically comprise multiple short events occurring on top of a somewhat stationary background. We consider the task of separating these events from the background, which we call foreground-background ambient sound scene separation. We propose a deep learning-based separation framework with a suitable feature normaliza-tion scheme and an optional auxiliary network capturing the background statistics, and we investigate its ability to handle the great variety of sound classes encountered in ambient sound scenes, which have often not been seen in training. To do so, we create single-channel foreground-background mixtures using isolated sounds from the DESED and Audioset datasets, and we conduct extensive experiments with mixtures of seen or unseen sound classes at various signal-to-noise ratios. Our experimental findings demonstrate the generalization ability of the proposed approach.

Published
2020

3. Geometry description and mesh construction from medical imaging

Author

Silvia Bertoluzza, Minh Phan, Michela Spagnuolo, Philippe Ricka, Micol Pennacchio, Giuseppe Patanè, Michele Giuliano Carlino, Institut de Mathématiques de Bordeaux (IMB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Modeling Enablers for Multi-PHysics and InteractionS (MEMPHIS), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de Recherche Mathématique Avancée (IRMA), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut de Mathématiques de Toulon - EA 2134 (IMATH), Université de Toulon (UTLN), Istituto di Matematica Applicata e Tecnologie Informatiche (IMATI), Consiglio Nazionale delle Ricerche (CNR), Istituto di Matematica Applicata e Tecnologie Informatiche (IMATI-CNR), Consiglio Nazionale delle Ricerche [Roma] (CNR), his paper has been realized in the framework of ERC Project CHANGE, which has received funding from the EuropeanResearch Council (ERC) under the European Unions Horizon 2020 research and innovation programme (grant agreement No694515., European Project: 8509436(1986), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS)-Inria Bordeaux - Sud-Ouest, Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), and National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR)

Subjects
T57-57.97, Applied mathematics. Quantitative methods, Computer simulation, Computer science, business.industry, Atlas (topology), ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, Image segmentation, Modular design, Reference image, N/A, QA1-939, Medical imaging, [INFO.INFO-IM]Computer Science [cs]/Medical Imaging, A priori and a posteriori, Computer vision, [INFO]Computer Science [cs], Artificial intelligence, business, Mathematics, ComputingMethodologies_COMPUTERGRAPHICS
Abstract

International audience; We present a new method for defining and meshing patient-specific domains from medical images. Our approach is based on an atlas image segmentation technique, and relies on the modular registration algorithm of S. Bertoluzza et al. [25]. The mesh of the patient-specific domain is generated by deforming the corresponding mesh on an a priori segmented and meshed reference image (the atlas). Our method aims at automating the process at the interface of medical imaging and numerical simulation, thus reducing the computational cost in those situations where simulations have to be managed on numerous medical images of similar patients.; Nous présentons une nouvelle méthode de reconnaissance et de maillage d’un domaine d’intérêt d’une image médicale. Notre approche se base sur une méthode de segmentation à partir d’un atlas, et dépend de la boîte à outils modulaire pour la co-registration d’images développée par S. Bertoluzza et al. [25]. Le maillage du domaine spécifique au patient est généré par déformation du maillage correspondant sur une image de référence segmentée a priori (l’atlas). Notre méthode vise à automatiser le processus à l’interface entre l’imagerie médicale et la simulation numérique, avec pour but de réduire le coût de calcul dans les situations dans lesquelles des simulations doivent être faites sur de nombreuses images similaires.

Published
2020

4. Linear Search by a Pair of Distinct-Speed Robots

Author

Tomasz Kociumaka, Jurek Czyzowicz, David Ilcinkas, Leszek Gąsieniec, Ralf Klasing, Dominik Pająk, Evangelos Bampas, School of of Electrical and Computer Engineering [Athens] (School of E.C.E), National Technical University of Athens [Athens] (NTUA), Département d'Informatique et d'Ingénierie (DII), Université du Québec en Outaouais (UQO), Department of Computer Science [Liverpool], University of Liverpool, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), University of Warsaw (UW), Institute of informatics [Wrocław], See paper for details., ANR-11-BS02-0014,DISPLEXITY,Calculabilité et complexité en distribué(2011), ANR-13-JS02-0002,MACARON,Bouger et Calculer: Agents, Robots et Réseaux(2013), ANR-16-CE40-0023,DESCARTES,Abstraction modulaire pour le calcul distribué(2016), ANR-10-IDEX-0003,IDEX BORDEAUX,Initiative d'excellence de l'Université de Bordeaux(2010), Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory, Pajak, Dominik S, Laboratoire d'informatique Fondamentale de Marseille (LIF), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Institute of Informatics [Warsaw], Faculty of Mathematics, Informatics, and Mechanics [Warsaw] (MIMUW), University of Warsaw (UW)-University of Warsaw (UW), and Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)

Subjects
Engineering, General Computer Science, Computer science, different speeds, [INFO.INFO-DS]Computer Science [cs]/Data Structures and Algorithms [cs.DS], 0211 other engineering and technologies, 0102 computer and information sciences, 02 engineering and technology, Bang-bang robot, linear search, 01 natural sciences, Article, Computer Science::Robotics, Position (vector), mobile robots, 0202 electrical engineering, electronic engineering, information engineering, Cartesian coordinate robot, Point (geometry), Computer vision, [INFO]Computer Science [cs], Online algorithm, Simulation, Linear search, 021103 operations research, business.industry, Applied Mathematics, Mobile robot, Computer Science Applications, 010201 computation theory & mathematics, group search, Moment (physics), Line (geometry), Robot, 020201 artificial intelligence & image processing, Artificial intelligence, [INFO.INFO-DC]Computer Science [cs]/Distributed, Parallel, and Cluster Computing [cs.DC], business
Abstract

Two mobile robots are initially placed at the same point on an infinite line. Each robot may move on the line in either direction not exceeding its maximal speed. The robots need to find a stationary target placed at an unknown location on the line. The search is completed when both robots arrive at the target point. The target is discovered at the moment when either robot arrives at its position. The robot knowing the placement of the target may communicate it to the other robot. We look for the algorithm with the shortest possible search time (i.e. the worst-case time at which both robots meet at the target) measured as a function of the target distance from the origin (i.e. the time required to travel directly from the starting point to the target at unit velocity). We consider two standard models of communication between the robots, namely wireless communication and communication by meeting. In the case of communication by meeting, a robot learns about the target while sharing the same location with a robot possessing this knowledge. We propose here an optimal search strategy for two robots including the respective lower bound argument, for the full spectrum of their maximal speeds. This extends the main result of Chrobak et al. (in: Italiano, Margaria-Steffen, Pokorný, Quisquater, Wattenhofer (eds) Current trends in theory and practice of computer science, SOFSEM, 2015) referring to the exact complexity of the problem for the case when the speed of the slower robot is at least one third of the faster one. In the wireless communication model, a message sent by one robot is instantly received by the other robot, regardless of their current positions on the line. For this model, we design a strategy which is optimal whenever the faster robot is at most \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\sqrt{17}+4\approx 8.123$$\end{document}17+4≈8.123 times faster than the slower one. We also prove that otherwise the wireless communication offers no advantage over communication by meeting.

Published
2019