Author
Hongying Shen
Bio: Hongying Shen is an academic researcher from Max Planck Society. The author has an hindex of 1, co-authored 1 publications receiving 694 citations.
Papers
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Max Planck Society1, Centre national de la recherche scientifique2, Masaryk University3, University of Navarra4, Drexel University5, Zhejiang University6, Royal Institute of Technology7, Curie Institute8, French Institute for Research in Computer Science and Automation9, Pasteur Institute10, Leiden University11, Chung Yuan Christian University12
TL;DR: Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to notable practical conclusions for users and developers.
Abstract: Particle tracking is of key importance for quantitative analysis of intracellular dynamic processes from time-lapse microscopy image data. Because manually detecting and following large numbers of individual particles is not feasible, automated computational methods have been developed for these tasks by many groups. Aiming to perform an objective comparison of methods, we gathered the community and organized an open competition in which participating teams applied their own methods independently to a commonly defined data set including diverse scenarios. Performance was assessed using commonly defined measures. Although no single method performed best across all scenarios, the results revealed clear differences between the various approaches, leading to notable practical conclusions for users and developers.
819 citations
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TL;DR: TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment and is validated for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells.
2,356 citations
01 Jan 2016
TL;DR: In this paper, the authors present the principles of optics electromagnetic theory of propagation interference and diffraction of light, which can be used to find a good book with a cup of coffee in the afternoon, instead of facing with some infectious bugs inside their computer.
Abstract: Thank you for reading principles of optics electromagnetic theory of propagation interference and diffraction of light. As you may know, people have search hundreds times for their favorite novels like this principles of optics electromagnetic theory of propagation interference and diffraction of light, but end up in harmful downloads. Rather than enjoying a good book with a cup of coffee in the afternoon, instead they are facing with some infectious bugs inside their computer.
2,213 citations
TL;DR: The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization.
Abstract: The spatial regulation of protein translation is an efficient way to create functional and structural asymmetries in cells. Recent research has furthered our understanding of how individual cells spatially organize protein synthesis, by applying innovative technology to characterize the relationship between mRNAs and their regulatory proteins, single-mRNA trafficking dynamics, physiological effects of abrogating mRNA localization in vivo and for endogenous mRNA labelling. The implementation of new imaging technologies has yielded valuable information on mRNA localization, for example, by observing single molecules in tissues. The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization.
472 citations
Masaryk University1, Royal Institute of Technology2, University of Freiburg3, Heidelberg University4, Erasmus University Medical Center5, Stanford University6, Leiden University Medical Center7, Delft University of Technology8, Agency for Science, Technology and Research9, University of Nottingham10, The University of Nottingham Ningbo China11, Pasteur Institute12, City University London13, Karlsruhe Institute of Technology14, University of Porto15, University of Zurich16, Max Planck Society17, Charles III University of Madrid18, University of Navarra19
TL;DR: It is found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the Cell Tracking Challenge.
Abstract: We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challenge displays today's state-of-the-art methodology in the field. We analyzed the challenge results using performance measures for segmentation and tracking that rank all participating methods. We also analyzed the performance of all of the algorithms in terms of biological measures and practical usability. Although some methods scored high in all technical aspects, none obtained fully correct solutions. We found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the challenge.
468 citations
TL;DR: The foundations of SPT are described together with novel optical implementations that nowadays allow the investigation of single molecule dynamic events with increasingly high spatiotemporal resolution using molecular densities closer to physiological expression levels.
Abstract: Optical microscopy has for centuries been a key tool to study living cells with minimum invasiveness The advent of single molecule techniques over the past two decades has revolutionized the field of cell biology by providing a more quantitative picture of the complex and highly dynamic organization of living systems Amongst these techniques, single particle tracking (SPT) has emerged as a powerful approach to study a variety of dynamic processes in life sciences SPT provides access to single molecule behavior in the natural context of living cells, thereby allowing a complete statistical characterization of the system under study In this review we describe the foundations of SPT together with novel optical implementations that nowadays allow the investigation of single molecule dynamic events with increasingly high spatiotemporal resolution using molecular densities closer to physiological expression levels We outline some of the algorithms for the faithful reconstruction of SPT trajectories as well as data analysis, and highlight biological examples where the technique has provided novel insights into the role of diffusion regulating cellular function The last part of the review concentrates on different theoretical models that describe anomalous transport behavior and ergodicity breaking observed from SPT studies in living cells
426 citations