scholarly journals Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo

PLoS Biology ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. e3001318
Author(s):  
Stefano Scaramuzza ◽  
Daniel Castaño-Díez
Keyword(s):  
Electron Tomography ◽  
3D Structure ◽  
Processing Technique ◽  
Public Image ◽  
Image Processing Technique ◽  
Computational Aspect ◽  
Virus Like Particles ◽  
Particle Alignment ◽  
Subtomogram Averaging ◽  
The Given

Subtomogram averaging (STA) is a powerful image processing technique in electron tomography used to determine the 3D structure of macromolecular complexes in their native environments. It is a fast growing technique with increasing importance in structural biology. The computational aspect of STA is very complex and depends on a large number of variables. We noticed a lack of detailed guides for STA processing. Also, current publications in this field often lack a documentation that is practical enough to reproduce the results with reasonable effort, which is necessary for the scientific community to grow. We therefore provide a complete, detailed, and fully reproducible processing protocol that covers all aspects of particle picking and particle alignment in STA. The command line–based workflow is fully based on the popular Dynamo software for STA. Within this workflow, we also demonstrate how large parts of the processing pipeline can be streamlined and automatized for increased throughput. This protocol is aimed at users on all levels. It can be used for training purposes, or it can serve as basis to design user-specific projects by taking advantage of the flexibility of Dynamo by modifying and expanding the given pipeline. The protocol is successfully validated using the Electron Microscopy Public Image Archive (EMPIAR) database entry 10164 from immature HIV-1 virus-like particles (VLPs) that describe a geometry often seen in electron tomography.

scholarly journals An Image Processing Based Fungus Detection System for Mangoes

2019 ◽  
Vol 9 (1) ◽  
pp. 3493-3497
Keyword(s):  
Image Processing ◽  
Detection System ◽  
Health Problems ◽  
Processing Technique ◽  
Input Image ◽  
Image Processing Technique ◽  
High Yield ◽  
Data Set ◽  
Different Color ◽  
The Given

Fruits which grow with high yield in many states of India are rich in proteins. But due to addition of excess pesticides and chemicals intake of these fruits lead to serious health problems. It is necessary to identify the presence of chemical in the fruits before consuming it. In this project we have planned to develop an image processing technique to analyze whether the fruit is free from chemicals and fungus. In our paper, we have implemented MATLAB used as well as fungus present in the fruit. We capture the images of the fruit or we use datasets and train the database with different color-based changes that happen after adding chemicals to the fruit. The enhancement process is carried out in the captured image. Then image is segmented to hit the regions with affected spots in the fruit. K-means method is used to carry out the segmentation process. The input image is compared with the given data set for training to identify the images. In this way unhealthy fruits can be identified and the affected spots in the fruit can be detected.

scholarly journals Three-dimensional structure of the basketweave Z-band in midshipman fish sonic muscle

2019 ◽  
Vol 116 (31) ◽  
pp. 15534-15539 ◽  
Author(s):  
Thomas Burgoyne ◽  
John M. Heumann ◽  
Edward P. Morris ◽  
Carlo Knupp ◽  
Jun Liu ◽  
...  
Keyword(s):  
Actin Filaments ◽  
Striated Muscle ◽  
Electron Tomography ◽  
3D Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Band Model ◽  
Type I ◽  
Sonic Muscle ◽  
Subtomogram Averaging

Striated muscle enables movement in all animals by the contraction of myriads of sarcomeres joined end to end by the Z-bands. The contraction is due to tension generated in each sarcomere between overlapping arrays of actin and myosin filaments. At the Z-band, actin filaments from adjoining sarcomeres overlap and are cross-linked in a regular pattern mainly by the protein α-actinin. The Z-band is dynamic, reflected by the 2 regular patterns seen in transverse section electron micrographs; the so-called small-square and basketweave forms. Although these forms are attributed, respectively, to relaxed and actively contracting muscles, the basketweave form occurs in certain relaxed muscles as in the muscle studied here. We used electron tomography and subtomogram averaging to derive the 3D structure of the Z-band in the swimbladder sonic muscle of type I male plainfin midshipman fish (Porichthys notatus), into which we docked the crystallographic structures of actin and α-actinin. The α-actinin links run diagonally between connected pairs of antiparallel actin filaments and are oriented at an angle of about 25° away from the actin filament axes. The slightly curved and flattened structure of the α-actinin rod has a distinct fit into the map. The Z-band model provides a detailed understanding of the role of α-actinin in transmitting tension between actin filaments in adjoining sarcomeres.

scholarly journals Subnanometer-resolution structure determination in situ by a hybrid subtomogram averaging – single particle cryoEM – workflow

2020 ◽  
Author(s):  
Ricardo Sanchez ◽  
Yingyi Zhang ◽  
Wenbo Chen ◽  
Lea Dietrich ◽  
Misha Kudryashev
Keyword(s):  
Single Particle ◽  
Electron Tomography ◽  
Signal To Noise Ratio ◽  
Particle Analysis ◽  
Electron Dose ◽  
Particle Alignment ◽  
Zero Degree ◽  
Subtomogram Averaging

ABSTRACTCryo electron tomography (cryo-ET) combined with subtomogram averaging (StA) enables structural determination of macromolecules in their native context. A few structures were reported by StA at resolution higher than 4.5 Å, however all of these are from viral structural proteins or vesicle coats. Reaching high resolution for a broader range of samples is uncommon due to beam-induced sample drift, poor signal-to-noise ratio (SNR) of images, challenges in CTF correction, limited number of particles. Here we propose a strategy to address these issues, which consists of a tomographic data collection scheme and a processing workflow. Tilt series are collected with higher electron dose at zero-degree tilt in order to increase SNR. Next, after performing StA conventionally, we extract 2D projections of the particles of interest from the higher SNR images and use the single particle analysis tools to refine the particle alignment and generate a reconstruction. We benchmarked our proposed hybrid StA (hStA) workflow and improved the resolution for tobacco mosaic virus from 7.2 to 5.2 Å and the resolution for the ion channel RyR1 in crowded native membranes from 12.9 to 9.1 Å. We demonstrate that hStA can improve the resolution obtained by conventional StA and promises to be a useful tool for StA projects aiming at subnanometer resolution or higher.

scholarly journals Structural organization of the C1b projection within the ciliary central apparatus

2021 ◽  
Author(s):  
Kai Cai ◽  
Yanhe Zhao ◽  
Lei Zhao ◽  
Nhan Phan ◽  
George Witman ◽  
...  
Keyword(s):  
Electron Tomography ◽  
3D Structure ◽  
Protein Composition ◽  
Ciliary Motility ◽  
Cryo Electron Tomography ◽  
Radial Spokes ◽  
Candidate Protein ◽  
Central Apparatus ◽  
Subtomogram Averaging ◽  
Subunit Organization

'9+2' motile cilia contain 9 doublet microtubules and a central apparatus (CA) composed of two singlet microtubules with associated projections. The CA plays crucial roles in regulating ciliary motility. Defects in CA assembly or function usually result in motility-impaired or paralyzed cilia, which in humans causes disease. Despite their importance, the protein composition and functions of most CA projections remain largely unknown. Here, we combined genetic approaches and quantitative proteomics with cryo-electron tomography and subtomogram averaging to compare the CA of wild-type Chlamydomonas with those of two CA mutants. Our results show that two conserved proteins, FAP42 and FAP246, are localized to the L-shaped C1b projection of the CA. We also identified another novel CA candidate protein, FAP413, which interacts with both FAP42 and FAP246. FAP42 is a large protein that forms the peripheral 'beam' of the C1b projection, and the FAP246-FAP413 subcomplex serves as the 'bracket' between the beam (FAP42) and the C1b 'pillar' that attaches the projection to the C1 microtubule. The FAP246-FAP413-FAP42 complex is essential for stable assembly of both the C1b and C1f projections, and loss of any of these proteins leads to ciliary motility defects. Our results provide insight into the subunit organization and 3D structure of the C1b projection, suggesting that the FAP246-FAP413-FAP42 subcomplex is part of a large interconnected CA-network that provides mechanical support and may play a role in mechano-signaling between the CA and radial spokes to regulate dynein activity and ciliary beating.

scholarly journals Combining high throughput and high quality for cryo-electron microscopy data collection

2020 ◽  
Vol 76 (8) ◽  
pp. 724-728
Author(s):  
Felix Weis ◽  
Wim J. H. Hagen
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Data Collection ◽  
Electron Tomography ◽  
3D Structure ◽  
Particle Analysis ◽  
High Resolution Data ◽  
Cryo Electron Microscopy ◽  
Microscopy Data ◽  
Subtomogram Averaging

Cryo-electron microscopy (cryo-EM) can be used to elucidate the 3D structure of macromolecular complexes. Driven by technological breakthroughs in electron-microscope and electron-detector development, coupled with improved image-processing procedures, it is now possible to reach high resolution both in single-particle analysis and in cryo-electron tomography and subtomogram-averaging approaches. As a consequence, the way in which cryo-EM data are collected has changed and new challenges have arisen in terms of microscope alignment, aberration correction and imaging parameters. This review describes how high-end data collection is performed at the EMBL Heidelberg cryo-EM platform, presenting recent microscope implementations that allow an increase in throughput while maintaining aberration-free imaging and the optimization of acquisition parameters to collect high-resolution data.

A New Image Processing Technique for STEM

1974 ◽  
Vol 32 ◽  
pp. 432-433
Author(s):  
Yasushi Kokubo ◽  
Hirotami Koike ◽  
Teruo Someya
Keyword(s):  
Electron Microscopy ◽  
Image Processing ◽  
Scanning Electron Microscopy ◽  
Elastic Scattering ◽  
Field Emission ◽  
Processing Technique ◽  
Image Processing Technique ◽  
Energy Analyzer ◽  
Scanning Microscope ◽  
Scanning Electron

One of the advantages of scanning electron microscopy is the capability for processing the image contrast, i.e., the image processing technique. Crewe et al were the first to apply this technique to a field emission scanning microscope and show images of individual atoms. They obtained a contrast which depended exclusively on the atomic numbers of specimen elements (Zcontrast), by displaying the images treated with the intensity ratio of elastically scattered to inelastically scattered electrons. The elastic scattering electrons were extracted by a solid detector and inelastic scattering electrons by an energy analyzer. We noted, however, that there is a possibility of the same contrast being obtained only by using an annular-type solid detector consisting of multiple concentric detector elements.

A Comparative Study of Ant and Genetic Algorithms in Digital Mammography

2018 ◽  
pp. 194-200
Author(s):  
J. Magelin Mary ◽  
Chitra K. ◽  
Y. Arockia Suganthi
Keyword(s):  
Genetic Algorithm ◽  
Image Processing ◽  
Medical Image ◽  
Medical Image Processing ◽  
Processing Technique ◽  
Input Image ◽  
Image Processing Technique ◽  
Computational Time ◽  
Image Mining ◽  
The Individual

Image processing technique in general, involves the application of signal processing on the input image for isolating the individual color plane of an image. It plays an important role in the image analysis and computer version. This paper compares the efficiency of two approaches in the area of finding breast cancer in medical image processing. The fundamental target is to apply an image mining in the area of medical image handling utilizing grouping guideline created by genetic algorithm. The parameter using extracted border, the border pixels are considered as population strings to genetic algorithm and Ant Colony Optimization, to find out the optimum value from the border pixels. We likewise look at cost of ACO and GA also, endeavors to discover which one gives the better solution to identify an affected area in medical image based on computational time.

An Enhanced Technique for Classification of Fruits using Shape Color and Texture Features

2017 ◽  
Vol 7 (7) ◽  
pp. 408
Author(s):  
Yashpal Jitarwal ◽  
Tabrej Ahamad Khan ◽  
Pawan Mangal
Keyword(s):  
Image Processing ◽  
Texture Features ◽  
Automatic Classification ◽  
Processing Technique ◽  
Image Processing Technique ◽  
Advance Technique ◽  
Time Required ◽  
Fruit Sorting ◽  
Human Inspection

In earlier times fruits were sorted manually and it was very time consuming and laborious task. Human sorted the fruits of the basis of shape, size and color. Time taken by human to sort the fruits is very large therefore to reduce the time and to increase the accuracy, an automatic classification of fruits comes into existence.To improve this human inspection and reduce time required for fruit sorting an advance technique is developed that accepts information about fruits from their images, and is called as Image Processing Technique.

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