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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  ...  and works presented in this paper.  ... 
doi:10.1109/jstsp.2015.2505402 fatcat:fgbrxtuhsfbobluogllqll6q2e

Single-molecule fluorescence microscopy review: shedding new light on old problems

Sviatlana Shashkova, Mark C. Leake
2017 Bioscience Reports  
Improvements in detector and dye technologies coupled to advances in image analysis methods have fuelled recent development towards single-molecule fluorescence microscopy, which can utilise light microscopy  ...  For example, the discovery of green fluorescent protein (GFP), initiating the so-called 'green revolution', has pushed experimental tools in the biosciences to a completely new level of functional imaging  ...  using probabilistic methods of single particle tracking.  ... 
doi:10.1042/bsr20170031 pmid:28694303 pmcid:PMC5520217 fatcat:w4ygpdkfu5cd3c6xlyxhvmle5u

Live-cell imaging of viral RNA genomes using a Pumilio-based reporter

Jens Tilsner, Olga Linnik, Nynne M. Christensen, Karen Bell, Ian M. Roberts, Christophe Lacomme, Karl J. Oparka
2009 The Plant Journal  
Therefore, a wide number of RNA imaging strategies have been designed (reviewed in Rodriguez et al., 2007); however, the majority of these techniques for viral RNA tracking are based on fluorescence in  ...  This may be especially problematic for viral RNA tracking also as large insertions of non-viral fragments are likely to result in alteration of viral function.  ... 
doi:10.1111/j.1365-313x.2008.03720.x pmid:18980643 fatcat:n7vf6lil5jbdzlkbbj2jg37apm

Real-time visualization and quantification of human Cytomegalovirus replication in living cells using the ANCHOR DNA labeling technology [article]

Bernard Mariamé, Sandrine Kappler-Gratias, Martin Kappler, Stéphanie Balor, Franck Gallardo, Kerstin Bystricky
2018 bioRxiv   pre-print
Here we present the first application of the ANCHOR DNA labeling system to a herpes virus, allowing real time imaging and direct monitoring of HCMV infection and replication in human living cells.  ...  If OR protein is fused to GFP, this accumulation results in a site specific fluorescent focus.  ...  When merging fluorescence and 437 electron microscopy images, fluorescent spots and viral capsids nicely superimposed at the 438 periphery of the RC(Fig.8d).  ... 
doi:10.1101/300111 fatcat:b5kfaoychzalrgemdxw7hneop4

Single Molecule Fluorescence Approaches Shed Light on Intracellular RNAs

Sethuramasundaram Pitchiaya, Laurie A. Heinicke, Thomas C. Custer, Nils G. Walter
2014 Chemical Reviews  
ACKNOWLEDGMENTS This work was supported by NIH Grants GM081025 and GM098023 to N.G.W.  ...  Nuclear diffusion data for each construct are summarized in Table 2. (B) Deconvolved time-series images of nuclear Cerulean-1/2 mini-Dys + intron mRNP diffusing in the nucleoplasm (green tracks).  ...  Her previous experience working with in vitro RNA folding intermediates, RNA− protein interactions, and cell culture has facilitated a smooth transition into using single molecule fluorescence microscopy  ... 
doi:10.1021/cr400496q pmid:24417544 pmcid:PMC3968247 fatcat:sqog4jvjafb6zhrfegawtiygta

2013 Index IEEE Transactions on Biomedical Engineering Vol. 60

2013 IEEE Transactions on Biomedical Engineering  
-that appeared in this periodical during 2013, and items from previous years that were commented upon or corrected in 2013.  ...  The primary entry includes the coauthors' names, the title of the paper or other item, and its location, specified by the publication abbreviation, year, month, and inclusive pagination.  ...  ., +, TBME Jan. 2013 55-62 Optical microscopy A Fully Constrained Optimization Method for Time-Resolved Multispectral Fluorescence Lifetime Imaging Microscopy Data Unmixing.  ... 
doi:10.1109/tbme.2013.2295159 fatcat:kjadiysea5h55hjr7i3o6vstlm

Thirty-seventh Annual Meeting February 14–18, 1993 Washington Convention Center Washington, D.C

1993 Biophysical Journal  
Cells were incubated with LaCI3 for 10 min. (1 mM) or 30 min (0.1 mM). and intracellular calcium distributions were imaged by ion microscopy.  ...  Our Interptaon of these data is that there are different neuraminic acid requirements for a virus partice to infect a oell by fusion of the viral envelpe with the piasma membrane than forfusion of an infected  ...  Do the viral proteins form oligomeric complexes at the site at which fusion is to occur? Can we identify in fusion steps or structures?  ... 
doi:10.1016/s0006-3495(93)81403-6 fatcat:aghpptcx7jh55dha23w336z7cu

Poster Presentations

2014 Acta Physiologica  
In this study, we used livecell spinning disc confocal microscopy, superresolution structured illumination microscopy and scanning electron microscopy to image how macrophages, isolated from wt-mice and  ...  This data may help in understanding the functional role of the proteasome in platelets, its role for platelet functions and platelet-related diseases.  ...  This work was supported by the "Stiftung Rheinland-Pfalz für Innovation" (961-386261/957) and the "Research Initiative Membrane Biology".  ... 
doi:10.1111/apha.12270 fatcat:jeilsxhrmbddlkur2fpfckliwm

Thirty-first Annual Meeting 22–26 February 1987 Rivergate Convention Center, New Orleans, Louisiana

1987 Biophysical Journal  
It appears that the behavior of the toxin at low pH and high temperature can be partly explained in terms of the behavior of its individual subunits.  ...  The B subunit of the toxin does not show a significant change in Trp emission wavelength at low pH or high temperature.  ...  We studied the structure of negatively stained filaments by electron microscopy and image reconstruction. The diffraction pattern indexes on an approximate repeat of 1/570 i-1.  ... 
doi:10.1016/s0006-3495(87)83345-3 fatcat:y7lbrtqgvzgfjl76na4x7kw6xq

7thESACP Congress in Caen April 1–5, 2001

2001 Analytical Cellular Pathology  
Spectral imaging is used extensively for spectral karyotyping analysis in fluorescence microscopy, and makes use of full spectral information.  ...  In routine fluorescence microscopy the image contrast is often better than with transmitted-light microscopy.  ...  Pairs of images of any diagnosis, magnification and staining  ... 
doi:10.1155/2001/414753 fatcat:7vxekd2dbjherbnpv5q7dshpsu

ABSTRACTS OF PAPERS AT THE SEVENTY-FIRST ANNUAL MEETING OF THE SOCIETY OF GENERAL PHYSIOLOGISTS: The Optical Revolution in Physiology: From Membrane to Brain

2017 The Journal of General Physiology  
Ca 2+ transients in ICC-DMP activate inward currents that can regulate the excitability of the small intestine provides a signaling mechanism responsible for transduction of enteric neuronal input. 3.  ...  These observations demonstrate direct innervation and postjunctional responsiveness of ICC-DMP in intestinal muscles.  ...  Increase in Recording Neural Activity in Freely Behaving Animals With 3D Tracking Two-Photon Microscopy.  ... 
doi:10.1085/jgp.149.9.889 fatcat:nplsscsocfcpdntcc7wfv6pn4i

Index [chapter]

2016 Encyclopedia of Cell Biology  
probes 2:52 see also fluorescent proteins breaking diffraction barrier 2:56 competing parameters for optimal imaging 2:58F imaging cells in whole organisms 2:54-56 technical considerations for live imaging  ...  microscopy 2:55, 2:55F as probes for function 2:52-54 single-particle tracking with 2:57F super-resolution imaging 2:58F fluoxetine 1:248 flux connectivity theorem 4:28-29 flux control coefficient 4:27  ...  populations within a heterogeneous sample 2:9-11 image acquisition 2:6 image processing in 2:6-7 of macromolecular complexes 2:5-13 model building and model validation 2:8-9 preferred orientation 2:6,  ... 
doi:10.1016/b978-0-12-394447-4.09001-5 fatcat:p5gwgrhzjjgyziy6x6cxvcfo6u

Second International Meeting of ISEV 2013: Boston, USA, April 17th-20th, 2013

2013 Journal of Extracellular Vesicles  
Here we demonstrate and compare two methods of tracking exosomes in vivo in real time, utilizing the IVIS imaging system.  ...  Reproductive tissues were imaged by confocal and electron microscopy.  ...  The collected MVs were evaluated for size and morphology by electron microscopy and nanoparticle tracking analysis.  ... 
doi:10.3402/jev.v2i0.20826 pmid:26082317 pmcid:PMC3760629 fatcat:fzccutscpnasrkcokd4wuckeba

Probabilistic Tracking and Behavior Identification of Fluorescent Particles

William J. Godinez
2013
This thesis deals with the problem of extracting symbolic representations of the dynamical behavior of fluorescent particles from fluorescence microscopy image sequences.  ...  Explicit and tractable characterizations of the dynamical behavior of virus particles are pivotal for a thorough understanding of the infection mechanisms of viruses.  ...  Lehmann, and K. Rohr, "Analysis of viral surfing based on fluorescence microscopy imaging and automatic tracking," in Proc. 9th IEEE Internat.  ... 
doi:10.11588/heidok.00015343 fatcat:byn7mi5ikffwrayx6n7hoq3lju

Thirty-seventh Annual Meeting February 14-18, 1993 Washington Convention Center Washington, D.C. Monday Symposia and Posters, Part III

1993 Biophysical Journal  
We have obtained evidence, utilizing three color fluorescence in situ hybridization and computer imaging microscopy, for the non-random spatial arrangement of chromosomes 7, 11 and 17 in interphase nuclei  ...  Three stacks of 32 images were collected for each nucleus using filter combinations for red, blue and green fluorescence.  ...  Scanning electron microscopy showed these cysts to be relatively smooth thus making the apical surface area and volume measurements very accurate.  ... 
doi:10.1016/s0006-3495(93)81402-4 fatcat:24ko6otkrrfypo7t6fl2sbkuqu
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