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Spatially Adaptive Colocalization Analysis in Dual-Color Fluorescence Microscopy [article]

Shulei Wang, Ellen T. Arena, Jordan T. Becker, William M. Bement, Nathan M. Sherer, Kevin W. Eliceiri, Ming Yuan
2019 arXiv   pre-print
strategy for utilizing spatial information to detect colocalization in a spatially adaptive fashion.  ...  The framework, referred to as spatially adaptive colocalization analysis (SACA), integrates a pixel-wise local kernel model for colocalization quantification and a multi-scale adaptive propagation-separation  ...  Related Work In literature, there are methods which also incorporate spatial information of microscopy images into colocalization analysis.  ... 
arXiv:1711.00069v2 fatcat:nragmm5s3re4hkcr25aqivkaxq

Novel Tools to Measure Single Molecules Colocalization in Fluorescence Nanoscopy by Image Cross Correlation Spectroscopy

Simone Pelicci, Laura Furia, Mirco Scanarini, Pier Giuseppe Pelicci, Luca Lanzanò, Mario Faretta
2022 Nanomaterials  
Single Molecule Localization Microscopy (SMLM) reaches a spatial resolution less than 50 nm with a precision in calculating molecule coordinates between 10 and 20 nanometers.  ...  We propose new tools based on Image Cross Correlation Spectroscopy (ICCS) to quantify the colocalization of fluorescent signals at single molecule level.  ...  S.P. and M.F. want to thank Francesco Nuti for technical assistance in microscope set-up. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/nano12040686 pmid:35215014 pmcid:PMC8875509 fatcat:yl3vpcsehvg57bb6h34lf27e2e

Coaligned Dual-Channel STED Nanoscopy and Molecular Diffusion Analysis at 20 nm Resolution

Fabian Göttfert, Christian A. Wurm, Veronika Mueller, Sebastian Berning, Volker C. Cordes, Alf Honigmann, Stefan W. Hell
2013 Biophysical Journal  
Stimulated emission depletion pulses of nanosecond duration and 775 nm wavelength are used to silence two fluorophores simultaneously, ensuring offset-free colocalization analysis.  ...  We report on a fiber laser-based stimulated emission-depletion microscope providing down to~20 nm resolution in raw data images as well as 15-19 nm diameter probing areas in fluorescence correlation spectroscopy  ...  The situation is exacerbated when implementing pairs of excitation and STED beams for dual-color colocalization studies (5, 6) .  ... 
doi:10.1016/j.bpj.2013.05.029 pmid:23823248 pmcid:PMC3699760 fatcat:w4u6qtrxkzg2xib7yjq3tmcmty

Statistical analysis of molecule colocalization in bioimaging

Thibault Lagache, Nathalie Sauvonnet, Lydia Danglot, Jean-Christophe Olivo-Marin
2015 Cytometry Part A  
The quantitative analysis of molecule interactions in bioimaging is key for understanding the molecular orchestration of cellular processes and is generally achieved through the study of the spatial colocalization  ...  Colocalization methods are traditionally divided into pixel-based methods that measure global correlation coefficients from the overlap between pixel intensities in different color channels, and object-based  ...  [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.] Figure 2 . Principles of colocalization analysis in fluorescence microscopy.  ... 
doi:10.1002/cyto.a.22629 pmid:25605428 fatcat:ueiaynkj7bbohebxa6uy2fkghi

Resolving the spatial relationship between intracellular components by dual color super resolution optical fluctuations imaging (SOFI)

Maria Elena Gallina, Jianmin Xu, Thomas Dertinger, Adva Aizer, Yaron Shav-Tal, Shimon Weiss
2013 Optical Nanoscopy  
Results: In this work, we demonstrate dual-color Super Resolution Optical Fluctuations Imaging (SOFI) using a standard far-field fluorescence microscope and different color blinking quantum dots.  ...  While still very challenging, important SR colocalization results have been reported in recent years using STED, PALM and STORM techniques.  ...  Work in the lab of YST is supported by the European Research Council (ERC).  ... 
doi:10.1186/2192-2853-2-2 pmid:24324919 pmcid:PMC3855418 fatcat:yxy7mfkmy5gvxphlbjqvepmeya

Super-resolution Microscopy Reveals Compartmentalization of Peroxisomal Membrane Proteins

Silvia Galiani, Dominic Waithe, Katharina Reglinski, Luis Daniel Cruz-Zaragoza, Esther Garcia, Mathias P. Clausen, Wolfgang Schliebs, Ralf Erdmann, Christian Eggeling
2016 Journal of Biological Chemistry  
This compartmentalization, which was less evident in cases of strong colocalization, indicates dynamic protein reorganization linked to changes occurring in the peroxisomes.  ...  Here, we present the use of super-resolution optical stimulated emission depletion microscopy to investigate with sub-60-nm resolution the heterogeneous spatial organization of the peroxisomal proteins  ...  Acknowledgments-We thank the Wolfson Imaging Centre Oxford and Christoffer Lagerholm for providing microscope facility support for data acquisition and analysis.  ... 
doi:10.1074/jbc.m116.734038 pmid:27311714 pmcid:PMC5016101 fatcat:z4whajze3nduzdm2yptiq4o7le

COPII proteins exhibit distinct subdomains within each ER exit site for executing their functions

Miharu Maeda, Kazuo Kurokawa, Toshiaki Katada, Akihiko Nakano, Kota Saito
2019 Scientific Reports  
Here, we used super-resolution confocal live imaging microscopy (SCLIM) to investigate the localization of endogenous proteins, and we identified domains abundant in transmembrane complexes (TANGO1/cTAGE5  ...  However, the detailed spatial organization of mammalian ER exit sites is yet to be revealed.  ...  Acknowledgements This work was supported in part by research grants from Japan Society for the Promotion of Science (JSPS) (grant numbers 17J07885 to M.M.; 25221103, 16HD05419, 17H06420, 18H05275 to K.K  ... 
doi:10.1038/s41598-019-43813-3 pmid:31089171 pmcid:PMC6517409 fatcat:qeyuyeigkrgxzcupqvu7tdusju

Spatial Association of Signaling Proteins and F-Actin Effects on Cluster Assembly Analyzed via Photoactivation Localization Microscopy in T Cells

Chih-Jung Hsu, Tobias Baumgart, Alejandro Almarza
2011 PLoS ONE  
We first determined the photophysical rate constants of Dronpa and tdEos fluorescence probes, which allowed us to optimize our dual-color PALM imaging method.  ...  We showed that this spatial segregation at the cell periphery occurred in parallel with the reduction of MC phosphorylation levels.  ...  We begin with an analysis of the photophysical reaction kinetics of our fluorescent probes, as is required for our dual-color PALM method.  ... 
doi:10.1371/journal.pone.0023586 pmid:21887278 pmcid:PMC3160965 fatcat:hiy7b4mv6bb5da35t2k4i2eqau

Nanoscale distribution of nuclear sites by super-resolved image cross-correlation spectroscopy

M. Oneto, L. Scipioni, M.J. Sarmento, I. Cainero, S. Pelicci, L. Furia, P.G. Pelicci, G.I. Dellino, P. Bianchini, M. Faretta, E. Gratton, A. Diaspro (+1 others)
2019 Biophysical Journal  
In this context, super-resolution microscopy has gained considerable interest because it can be used to probe the spatial organization of functional sites in intact single-cell nuclei in the 20-250 nm  ...  Here, we combine dual-color stimulated emission depletion (STED) nanoscopy with ICCS (STED-ICCS) to quantify the nanoscale distribution of functional nuclear sites.  ...  The simplest approach to study spatial organization of two labeled molecules consists in the analysis of dual-color images for the presence of colocalized signal, i.e., signal that overlaps within the  ... 
doi:10.1016/j.bpj.2019.10.036 pmid:31732142 pmcid:PMC6895719 fatcat:xikazruhxjczdf52ev7tbyopme

Dual color localization microscopy of cellular nanostructures

Manuel Gunkel, Fabian Erdel, Karsten Rippe, Paul Lemmer, Rainer Kaufmann, Christoph Hörmann, Roman Amberger, Christoph Cremer
2009 Biotechnology Journal  
The dual color localization microscopy (2CLM) presented here is based on the principles of spectral precision distance microscopy (SPDM) with conventional autofluorescent proteins under special physical  ...  This technique allows us to measure the spatial distribution of single fluorescently labeled molecules in entire cells with an effective optical resolution comparable to macromolecular dimensions.  ...  These make the light-optical analysis of biological Research Article Dual color localization microscopy of cellular nanostructures Manuel Gunkel 1 , Fabian Erdel 2 , Karsten Rippe 2 , Paul Lemmer 1  ... 
doi:10.1002/biot.200900005 pmid:19548231 fatcat:gasgly2srbbe5b6fkrhrxczc2q

High resolution, fluorescence deconvolution microscopy and tagging with the autofluorescent tracers CFP, GFP, and YFP to study the structural composition of gap junctions in living cells

Matthias M. Falk, Undine Lauf
2001 Microscopy research and technique (Print)  
In addition, we give a simple description of the principal mechanisms of DV microscopy, name advantages and disadvantages, and discuss issues such as dual-color imaging using CFP and YFP, spatial resolution  ...  Such gap junction plaques were examined by single, dual, and triple-color DV microscopy.  ...  Dual-Color Live Cell Microscopy Using CFP and YFP To obtain more detailed information on the structural composition of gap junction plaques assembled from two different connexin isotypes, ␣ 1 (Cx43), ␤  ... 
doi:10.1002/1097-0029(20010201)52:3<251::aid-jemt1011>3.3.co;2-r pmid:11180618 fatcat:g4ltkabwyfg35j3enzkqromk3y

High resolution, fluorescence deconvolution microscopy and tagging with the autofluorescent tracers CFP, GFP, and YFP to study the structural composition of gap junctions in living cells

Matthias M. Falk, Undine Lauf
2001 Microscopy research and technique (Print)  
In addition, we give a simple description of the principal mechanisms of DV microscopy, name advantages and disadvantages, and discuss issues such as dual-color imaging using CFP and YFP, spatial resolution  ...  Such gap junction plaques were examined by single, dual, and triple-color DV microscopy.  ...  Dual-Color Live Cell Microscopy Using CFP and YFP To obtain more detailed information on the structural composition of gap junction plaques assembled from two different connexin isotypes, ␣ 1 (Cx43), ␤  ... 
doi:10.1002/1097-0029(20010201)52:3<251::aid-jemt1011>3.0.co;2-# pmid:11180618 fatcat:maa4cxf5m5cddeaipvrr6ym3mi

Differential submitochondrial localization of PINK1 as a molecular switch for mediating distinct mitochondrial signaling pathways

Dana Fallaize, Lih-Shen Chin, Lian Li
2015 Cellular Signalling  
Dual-color 3D-SIM imaging analysis revealed that PINK1 resides in the cristae membrane and intracristae space but not on the outer mitochondrial membrane (OMM) of healthy mitochondria.  ...  Under normal physiological conditions, PINK1 colocalizes with its substrate TRAP1 in the cristae membrane and intracristae space.  ...  We thank Emory Integrated Cellular Imaging Core Facility (supported in part by NIH grant NS055077) for providing instrumentation and support.  ... 
doi:10.1016/j.cellsig.2015.09.020 pmid:26436374 pmcid:PMC4684445 fatcat:4mkpifrm3bdj7atjehcugoo53m

Characterization of Differential Toll-like Receptor Responses below the Optical Diffraction Limit

Jesse S. Aaron, Bryan D. Carson, Jerilyn A. Timlin
2012 Small  
This study reports the first visualizations of TLR4 distributions on intact cells at image resolutions of <30 nm using a novel, dual-color stochastic optical reconstruction microscopy (STORM) technique  ...  Importantly, we also show that LPS derived from immuno-stimulatory bacteria resulted in significantly higher LPS-TLR4 cluster sizes and a nearly two-fold greater ligand/receptor colocalization as compared  ...  In addition, we would like to thank Mr. Quinton Smith for assistance in characterization of the imaging system.  ... 
doi:10.1002/smll.201200106 pmid:22807232 pmcid:PMC3613986 fatcat:iftkgwnjyzhsxchualele2hlbi

Protein Diffusion in the E. coli Cytoplasm and Periplasm under Osmotic Stress

James C. Weisshaar, Michael C. Konopka, Kem A. Sochacki, Benjamin P. Bratton, Colin Ingram
2009 Biophysical Journal  
We have used single-molecule fluorescence spectroscopy to characterize the efficacy of four known peptide-based inhibitors toward preventing or reversing association in the earliest Ab oligomers (n ¼ 2  ...  Spatially resolved monomers and oligomers are examined, one at a time; the number of associated peptides in each species is determined based on quantized photobleaching of the individual dye molecules.  ...  The structure of P-Selectin influences its mobility in the WPB and PM. 156-Pos 157-Pos Board 158-Pos Board B37 Quantitative Analysis of Spatial Protein-protein Proximity in Fluorescence Confocal  ... 
doi:10.1016/j.bpj.2008.12.049 fatcat:islu5q2pundlbb45iyzqryyahq
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