Journal ArticleDOI
Measurement of co-localization of objects in dual-colour confocal images
TLDR
The co‐localization coefficients can provide relevant quantitative information about the positional relation between biological objects or processes, and are tested on images of real biological specimens.Abstract:
A method to measure the degree of co-localization of objects in confocal dual-colour images has been developed. This image analysis produced two coefficients that represent the fraction of co-localizing objects in each component of a dual-channel image. The generation of test objects with a Gaussian intensity distribution, at well-defined positions in both components of dual-channel images, allowed an accurate investigation of the reliability of the procedure. To do that, the co-localization coefficients were determined before degrading the image with background, cross-talk and Poisson noise. These synthesized sources of image deterioration represent sources of deterioration that must be dealt with in practical confocal imaging, namely dark current, non-specific binding and cross-reactivity of fluorescent probes, optical cross-talk and photon noise. The degraded images were restored by filtering and cross-talk correction. The co-localization coefficients of the restored images were not significantly different from those of the original undegraded images. Finally, we tested the procedure on images of real biological specimens. The results of these tests correspond with data found in the literature. We conclude that the co-localization coefficients can provide relevant quantitative information about the positional relation between biological objects or processes.read more
Citations
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Journal ArticleDOI
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.
Robert B. Best,Xiao Zhu,Jihyun Shim,Pedro E. M. Lopes,Jeetain Mittal,Michael Feig,Alexander D. MacKerell +6 more
TL;DR: The results indicate that the revised CHARMM 36 parameters represent an improved model for the modeling and simulation studies of proteins, including studies of protein folding, assembly and functionally relevant conformational changes.
Journal ArticleDOI
Mitofusin 2 tethers endoplasmic reticulum to mitochondria
TL;DR: It is shown that mitofusin 2, a mitochondrial dynamin-related protein mutated in the inherited motor neuropathy Charcot–Marie–Tooth type IIa, is enriched at the ER–mitochondria interface, and that it tethers ER to mitochondria, a juxtaposition required for efficient mitochondrial Ca2+ uptake.
Journal ArticleDOI
A practical guide to evaluating colocalization in biological microscopy.
TL;DR: A guide to analyzing colocalization in cell biology studies is provided, emphasizing practical application of quantitative tools that are now widely available in commercial and free image analysis software.
Journal ArticleDOI
Automatic and Quantitative Measurement of Protein-Protein Colocalization in Live Cells
Sylvain V. Costes,Dirk Daelemans,Edward H. Cho,Zachary C. Dobbin,George N. Pavlakis,Stephen J. Lockett +5 more
TL;DR: A novel statistical approach that quantifies, for the first time, the amount of colocalization of two fluorescent-labeled proteins in an image automatically, removing the bias of visual interpretation is introduced.
Journal ArticleDOI
Quantifying colocalization by correlation: the Pearson correlation coefficient is superior to the Mander's overlap coefficient.
Jeremy Adler,Ingela Parmryd +1 more
TL;DR: The MOC is a confusing hybrid measurement that combines correlation with a heavily weighted form of co‐occurrence, favors high intensity combinations, downplays combinations in which either or both intensities are low and ignores blank pixels, and is not suitable for making measurements of colocalization either by correlation or co-occurrence.
References
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