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Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions

M. Unser, C.O.S. Sorzano, P. Thévenaz, S. Jonić, C. El-Bez, S. De Carlo, J.F. Conway, B.L. Trus
2005 Journal of Structural Biology  
Furthermore, the information to build the SSNR can be used to produce a volumetric SSNR (VSSNR). Our method overcomes the need to divide the data set in two.  ...  In this article, we extend the applicability of the spectral signal-to-noise ratio (SSNR) to the evaluation of 3D volumes reconstructed with any reconstruction algorithm.  ...  . 3D Electron Microscopy (3DEM) of single particles is one of the most useful imaging techniques since it allows the visualization of biological macromolecules nearly in their native state without any  ... 
doi:10.1016/j.jsb.2004.10.011 pmid:15721578 pmcid:PMC1464087 fatcat:tdyd7jdomfbqrboh6t2udjjkzu

Deep Learning for Validating and Estimating Resolution of Cryo-Electron Microscopy Density Maps †

Todor Avramov, Dan Vyenielo, Josue Gomez-Blanco, Swathi Adinarayanan, Javier Vargas, Dong Si
2019 Molecules  
However, the resolution value claimed for the reconstructed 3D density map has been the topic of scientific debate for many years.  ...  The model was trained to perform voxel-wise classification of 3D cryo-EM density maps into one of ten resolution classes, instead of a single global resolution value.  ...  In the last few years, cryo-electron microscopy using single particle analysis (termed in the following as cryo-EM or 3DEM) method has gained much attention among structural biologists due to breakthrough  ... 
doi:10.3390/molecules24061181 fatcat:y5zhn2lk6fchtj3rms7mx2tmr4

Seeing is believing – multi-scale spatio-temporal imaging towardsin vivocell biology

Gautier Follain, Luc Mercier, Naël Osmani, Sébastien Harlepp, Jacky G. Goetz
2016 Journal of Cell Science  
Life is driven by a set of biological events that are naturally dynamic and tightly orchestrated from the single molecule to entire organisms.  ...  In addition, we illustrate how these technologies have led to important insights in cell biology, from the molecular to the whole-organism resolution.  ...  imaging Requires manpower Requires access to sophisticated EM technologies for 3DEM DSLM: More suitable for super-resolution technologies PALM/STORM: single- molecule resolution, single- particle  ... 
doi:10.1242/jcs.189001 pmid:27505891 fatcat:2payvmxz5nhqldu6jav4ahxoga

WDR81 Is Necessary for Purkinje and Photoreceptor Cell Survival

M. Traka, K. J. Millen, D. Collins, B. Elbaz, G. J. Kidd, C. M. Gomez, B. Popko
2013 Journal of Neuroscience  
WDR81 is expressed in Purkinje cells and photoreceptor cells, among other CNS neurons, and like the human mutation, the nur5 modification lies in the predicted major facilitator superfamily domain of the  ...  We have used polymorphic marker mapping to demonstrate that affected nur5 mice carry a missense mutation, L1349P, in the Wdr81 gene.  ...  Large electron-dense membrane particles were found in the mutants (B, arrows).  ... 
doi:10.1523/jneurosci.2394-12.2013 pmid:23595742 pmcid:PMC6618862 fatcat:ae76two3ijdqzpdh5vvexqtqna

Serial block face scanning electron microscopy in cell biology: Applications and technology

David Smith, Tobias Starborg
2018 Tissue & Cell  
Serial block face scanning electron microscopy (SBFSEM) is a 3DEM technique, developed in 2004, which has greatly increased the reliability, availability and throughput of 3DEM.  ...  In this review, we will discuss biological SBFSEM from a technical standpoint, with a focus on cellular applications and also subsequent image analysis techniques.  ...  By back projecting the images, it is possible to generate a 3dimensional reconstruction of the tissue in the section.  ... 
doi:10.1016/j.tice.2018.08.011 pmid:30220487 fatcat:skmrwbo3jncrzaavtosgpatbqq

Advances in Electron Microscopy with Deep Learning

Jeffrey Ede
2020 Zenodo  
from single transmission electron micrographs.  ...  Philosophy in Physics is typeset for physical printing and binding.  ...  In addition, part of the text in section 1.2 is adapted from our earlier work with permission 201 under a Creative Commons Attribution 4.0 73 license.  ... 
doi:10.5281/zenodo.4598227 fatcat:hm2ksetmsvf37adjjefmmbakvq

Advances in Electron Microscopy with Deep Learning

Jeffrey Ede
2020 Zenodo  
from single transmission electron micrographs.  ...  Philosophy in Physics is typeset for physical printing and binding.  ...  In addition, part of the text in section 1.2 is adapted from our earlier work with permission 201 under a Creative Commons Attribution 4.0 73 license.  ... 
doi:10.5281/zenodo.4591029 fatcat:zn2hvfyupvdwlnvsscdgswayci

Advances in Electron Microscopy with Deep Learning

Jeffrey Ede
2020 Zenodo  
from single transmission electron micrographs.  ...  in Physics will be typeset for physical printing and binding.  ...  In addition, part of the text in section 1.2 is adapted from our earlier work with permission 201 under a Creative Commons Attribution 4.0 73 license.  ... 
doi:10.5281/zenodo.4399748 fatcat:63ggmnviczg6vlnqugbnrexsgy

Advances in Electron Microscopy with Deep Learning

Jeffrey Ede
2020 Zenodo  
from single transmission electron micrographs.  ...  in Physics will be typeset for physical printing and binding.  ...  In addition, part of the text in section 1.2 is adapted from our earlier work with permission 201 under a Creative Commons Attribution 4.0 73 license.  ... 
doi:10.5281/zenodo.4429792 fatcat:qs6yuapx4vdbdmwna7ix7nnwty

Advances in Electron Microscopy with Deep Learning

Jeffrey Ede
2020 Zenodo  
from single transmission electron micrographs.  ...  in Physics will be typeset for physical printing and binding.  ...  In addition, part of the text in section 1.2 is adapted from our earlier work with permission 201 under a Creative Commons Attribution 4.0 73 license.  ... 
doi:10.5281/zenodo.4413249 fatcat:35qbhenysfhvza2roihx52afuy

Advances in Electron Microscopy with Deep Learning

Jeffrey Ede
2020 Zenodo  
from single transmission electron micrographs.  ...  in Physics will be typeset for physical printing and binding.  ...  In addition, part of the text in section 1.2 is adapted from our earlier work with permission 201 under a Creative Commons Attribution 4.0 73 license.  ... 
doi:10.5281/zenodo.4415407 fatcat:6dejwzzpmfegnfuktrld6zgpiq

Nanoscale synaptic plasticity of aspiny interneuron dendrites with respect to characteristic fine structures [article]

Seth Arthur Weisberg
2018
Heather Smith for reconstructing prowess and fortitude. Dusten, Dakota, and Lyndsey for their kind and helpful comments and suggestions in the preparation of this work.  ...  Hiroshi Nishiyama for kindly sharing their considerable expertise in helping to make sense of this often-complex data. To Dr.  ...  light microscopy were also apparent in 3DEM reconstructions.  ... 
doi:10.15781/t2d21s38k fatcat:fbh3sn7fzrdt3nokvifi4js7ye

Cryo-electron microscopy studies of native cell extracts : elucidating an active pyruvate dehydrogenase complex from Chaetomium thermophilum [article]

Fotios L. Kyrilis, Universitäts- Und Landesbibliothek Sachsen-Anhalt, Martin-Luther Universität, Panagiotis L. Kastritis, Jochen Balbach, Christos Gatsogiannis
2022
Besides visualised folding and binding events an asymmetric reconstruction of a 10-MDa PDHc was illustrated.  ...  In the current work, fully assembled Chaetomium thermophilum α-keto acid dehydrogenase complexes in native cell extracts were identified.  ...  As in crystallography, in the case of in solution NMR spectroscopy biomolecules  ... 
doi:10.25673/86316 fatcat:lnjv5emqdzhh7medu7enfm7bou

Protein kinase dynamics: a multiscale theoretical analysis with Markov Stability

Sarah Louise Byrne, Sophia Yaliraki, David Mann, Mauricio Barahona
2019
The cdks are highly conserved in sequence and structure, especially in their active sites, and it has traditionally been difficult to explain the differences in function between them.  ...  Protein kinases are involved in regulating diverse and essential cellular processes, and their dysfunction is implicated in many diseases, making them key drug targets.  ...  Particles in solution move with Brownian motion, which posits that particles in a system have random direction and average velocity of zero.  ... 
doi:10.25560/74350 fatcat:4xcsgemjxrfzln4paiya3qoqfm