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Motion Analysis of Live Objects by Super-Resolution Fluorescence Microscopy

Chunyan Yao, Jianwei Zhang, Guang Wu, Houxiang Zhang
2012 Computational and Mathematical Methods in Medicine  
This paper briefly reviews the developments in this area mostly in the recent three years, especially for cellular analysis in fluorescence microscopy.  ...  The tasks of motion analysis include detection and tracking of objects, as well as analysis of motion behavior, living activity, events, motion statistics, and so forth.  ...  However, reconstruction of subcellular structures from images remains a major challenge in the field [19] .  ... 
doi:10.1155/2012/859398 pmid:22162725 pmcid:PMC3227432 fatcat:pjlhy4ehbzfp5i3lhctqhwfvji

Intravital imaging of cardiac function at the single-cell level

A. D. Aguirre, C. Vinegoni, M. Sebas, R. Weissleder
2014 Proceedings of the National Academy of Sciences of the United States of America  
Here we describe a microscopy method for subcellular resolution and motion-artifact-free imaging of contracting cardiomyocytes in vivo in the native mouse heart.  ...  cardiac gating approach using cardiac pacing, and (iv) an image processing algorithm, prospective sequential segmented microscopy (PSSM), for motion-artifact-free subcellular imaging at any point in the  ...  The project was funded by National Institutes of Health (NIH) Contracts HHSN268201000044C and R01EB006432. A.D.A. was funded by NIH Training Grant T32HL094301.  ... 
doi:10.1073/pnas.1401316111 pmid:25053815 pmcid:PMC4128110 fatcat:vle26ngxzzeprbbixafga3ybbu

A framework for generating realistic synthetic sequences of total internal reflection fluorescence microscopy images

Seyed Hamid Rezatofighi, William T. E. Pitkeathly, Stephen Gould, Richard Hartley, Katarina Mele, William E. Hughes, James G. Burchfield
2013 2013 IEEE 10th International Symposium on Biomedical Imaging  
Since generation of reliable ground truth annotation of fluorescence microscopy sequences is usually a laborious and expensive task, many proposed detection and tracking methods have been evaluated using  ...  In this paper, we present a framework for generating realistic synthetic sequences of total internal reflection fluorescence microscope (TIRFM) through simulation of the image formation process and accurate  ...  Fluorescence microscopy images are distorted by two main sources of noise; namely, photon noise (Poisson) and readout noise (Gaussian).  ... 
doi:10.1109/isbi.2013.6556436 dblp:conf/isbi/RezatofighiPGHMHB13 fatcat:k2n4aznfknbf3hdaom7j5kmykm

Fluorescence microscopic imaging and image analysis of the cytoskeleton

Gerlind Herberich, Thomas Wurflinger, Antonio Sechi, Reinhard Windoffer, Rudolf Leube, Til Aach
2010 2010 Conference Record of the Forty Fourth Asilomar Conference on Signals, Systems and Computers  
The dynamic behaviour of these subcellular structures in living cells can be analysed by fluorescence microscopy yielding series of 2D or 3D images.  ...  Towards a quantitative analysis, we present methods for the segmentation and motion estimation of cytoskeletal filaments as well as for the tracking of adhesion sites, allowing the quantification of cytoskeletal  ...  ACKNOWLEDGMENTS The work was supported in part by the German Research Council (WI 731/6-1) and by the excellence initiative of the German federal and state governments.  ... 
doi:10.1109/acssc.2010.5757755 fatcat:le6bqjc62rc2vlrxabimfajhwa

Fluorescence and SEM correlative microscopy for nanomanipulation of subcellular structures

Zheng Gong, Brandon K Chen, Jun Liu, Chao Zhou, Dave Anchel, Xiao Li, Ji Ge, David P Bazett-Jones, Yu Sun
2014 Light: Science & Applications  
In nanomanipulation of sub-cellular structures, a key step is to identify targets of interest through correlating fluorescence and SEM images.  ...  This paper presents an affine scale-invariant feature transform (ASIFT) based method for correlating SEM images and fluorescence microscopy images.  ...  Fluorescence imaging permits convenient visualization of subcellular structures, many of which are not contrasted by SEM imaging.  ... 
doi:10.1038/lsa.2014.105 fatcat:yhilxd6jsrgchfl4wcvv7yc6oy

Particle Filtering for Multiple Object Tracking in Molecular Cell Biology

Ihor Smal, Wiro Niessen, Erik Meijering
2006 2006 IEEE Nonlinear Statistical Signal Processing Workshop  
Motion analysis of subcellular structures in living cells is currently a major topic in molecular cell biology, for which computerized methods are desperately needed.  ...  In this paper we adopt and tailor particle filtering techniques for this purpose and present the results of robust and accurate tracking of multiple objects in real fluorescence microscopy image data acquired  ...  Motion analysis of subcellular structures such as microtubules or proliferating cell nuclear antigen-like proteins ( Fig. 1 ) requires tracking of hundreds of bright spots in noisy image sequences [1  ... 
doi:10.1109/nsspw.2006.4378836 fatcat:hyc7b766ejenfbcmapidegg3oy

A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy

Charles Kervrann, Carlos Oscar Sanchez Sorzano, Scott T. Acton, Jean-Christophe Olivo-Marin, Michael Unser
2016 IEEE Journal on Selected Topics in Signal Processing  
Microscopy imaging, including fluorescence microscopy and electron microscopy, has taken a prominent role in life science research and medicine due to its ability to investigate the 3D interior of live  ...  In this paper, we present recent advances in fluorescence and electron microscopy and we focus on dedicated image processing and analysis methods required to quantify phenotypes for a limited number but  ...  The authors thank the members of the "Space-time imaging of cellular dynamics of organelles and endomembranes" research team (UMR 144 CNRS Institut Curie) and S.  ... 
doi:10.1109/jstsp.2015.2505402 fatcat:fgbrxtuhsfbobluogllqll6q2e

Imaging In Vitro on the Nanometer Scale with Ultrasound

Stephen W. Carmichael, James F. Greenleaf
2018 Microscopy Today  
By controlling amplitude and detecting frequency, or phase, they produced an image dependent on the out-of-phase motion of the AFM probe.  ...  EBSD 2018 -Electron Backscatter Diffraction Conference There have been impressive advances in recent years in electron microscopy and light microscopy, but imaging molecular structures in vitro under physiological  ... 
doi:10.1017/s1551929518000214 fatcat:cvkgtnugwrdhbps7wfsbnupr4e

Combining optical tweezing and confocal microscopy for the study of cell mechanics

Ze'ev Bomzon, Kim Pham, Daniel Day, Sarah Russell, Min Gu
2007 2007 Conference on Lasers and Electro-Optics - Pacific Rim  
We have developed a system combining an optical tweezers and a confocal microscope for the study of cell mechanics.  ...  In passive microrheology, tracer particles are embedded into the cell, and their Brownian motion is tracked using either a laser beam and a quadrant detector, or fluorescence video microscopy and a multiple  ...  The limitation of measuring the bulk deformation of a cell is that it does not resolve the mechanical behavior on a subcellular level.  ... 
doi:10.1109/cleopr.2007.4391166 fatcat:x4ngh2snozf47ilnn5c4xr7g74

High Resolution Intravital Imaging of Subcellular Structures of Mouse Abdominal Organs Using a Microstage Device

Liqin Cao, Satoru Kobayakawa, Atsushi Yoshiki, Kuniya Abe, Kurt I. Anderson
2012 PLoS ONE  
We demonstrate that this technique allows for the quantitative analysis of subcellular structures and gene expressions in cells, the tracking of intracellular processes in realtime as well as three-dimensional  ...  Intravital imaging of brain and bone marrow cells in the skull with subcellular resolution has revolutionized neurobiology, immunology and hematology.  ...  Kiyotsugu Kojima of Olympus Corporation for microscopy technical support, Dr.  ... 
doi:10.1371/journal.pone.0033876 pmid:22479464 pmcid:PMC3313950 fatcat:2sl5tw3rn5dw7hferlifi6q32q

A new detection scheme for multiple object tracking in fluorescence microscopy by joint probabilistic data association filtering

Ihor Smal, Wiro Niessen, Erik Meijering
2008 2008 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro  
Index Terms-Kalman filtering, Bayesian estimation, multiple object tracking, fluorescence microscopy.  ...  Tracking of multiple objects in biological image data is a challenging problem due largely to poor imaging conditions and complicated motion scenarios.  ...  INTRODUCTION Current biological studies using time-lapse fluorescence microscopy imaging require analysis of huge amounts of image data.  ... 
doi:10.1109/isbi.2008.4540983 dblp:conf/isbi/SmalNM08 fatcat:h3j543pfubbnljpjw3vzvv36qy

Digital correction of motion artefacts in microscopy image sequences collected from living animals using rigid and nonrigid registration

K. S. LORENZ, P. SALAMA, K. W. DUNN, E. J. DELP
2011 Journal of Microscopy  
Intravital microscopy introduces the additional problem of motion artifacts, resulting from respiratory motion and heartbeat from specimens imaged in vivo.  ...  Digital image analysis is a fundamental component of quantitative microscopy. However, intravital microscopy presents many challenges for digital image analysis.  ...  O'Brien Award from the National Institutes of Health NIH/NIDDK P50 DK 61594.  ... 
doi:10.1111/j.1365-2818.2011.03557.x pmid:22092443 pmcid:PMC3856233 fatcat:xcporyoroncllmua3kv7jrqs6m

Imaging and Optical Microscopy - III

2008 Biophysical Journal  
(TIRF), and confocal laser scanning microscopy (CLSM) allow researchers to obtain images of fluorescently labeled components of cell membranes.  ...  The technique does not rely on spatial correlations, which frees it from biases due to subcellular compartmentalization that can be problematic for spatial image correlation based approaches.  ...  Imaging Subcellular Structure by Using 4Pi Confocal Fluorescence Microscopy Karen Deuschle, Sylvia Glaschick, Carlheinz R€ ocker, Franz Oswald, Joerg Wiedenmann, Gerd U.  ... 
doi:10.1016/s0006-3495(08)79032-5 fatcat:ojsdoxw6qbamhlu6va5oe23amu

Dynamic super-resolution structured illumination imaging in the living brain

Raphaël Turcotte, Yajie Liang, Masashi Tanimoto, Qinrong Zhang, Ziwei Li, Minoru Koyama, Eric Betzig, Na Ji
2019 Proceedings of the National Academy of Sciences of the United States of America  
We optimized image acquisition and reconstruction to combat sample motion and applied adaptive optics to correcting sample-induced optical aberrations in super-resolution structured illumination microscopy  ...  However, to apply it to in vivo brain imaging, we must address the challenges of 3D imaging in an optically heterogeneous tissue that is constantly in motion.  ...  We thank Rongwen Lu for his assistance with the initial design of the optical setup and David P. Hoffman for helpful discussions. The Howard Hughes Medical Institute supported this work.  ... 
doi:10.1073/pnas.1819965116 pmid:31028150 pmcid:PMC6511017 fatcat:n64eumwekffr3lqxj3cwfx44ie

Short Communication: Subcellular Motion Compensation for Minimally Invasive Microscopy, In Vivo: Evidence for Oxygen Gradients in Resting Muscle

J. L. Schroeder, M. Luger-Hamer, R. Pursley, T. Pohida, C. Chefd'Hotel, P. Kellman, R. S. Balaban
2010 Circulation Research  
A primary limitation of optical microscopy in vivo is tissue motion, which prevents physiological time course observations or image averaging.  ...  Rationale: In vivo microscopy seeks to observe dynamic subcellular processes in a physiologically relevant context.  ...  (D) Lookup table of percentage change image from +100% (top) to -100% (bottom). Net motion, filtered image data, and survey of percent change (A) Graph of total motion, ! !  ... 
doi:10.1161/circresaha.109.211946 pmid:20167928 pmcid:PMC3209509 fatcat:dyg3jj6ukzg4tp2opy6slezkcm
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