scholarly journals SPHIRE-crYOLO: A fast and accurate fully automated particle picker for cryo-EM

2018 ◽  
Author(s):  
Thorsten Wagner ◽  
Felipe Merino ◽  
Markus Stabrin ◽  
Toshio Moriya ◽  
Claudia Antoni ◽  
...  
Keyword(s):  
Image Processing ◽  
Detection System ◽  
Learning Object ◽  
Electron Cryomicroscopy ◽  
High Recall ◽  
Essential Step ◽  
The Past ◽  
General Network ◽  
Manual Selection ◽  
Selection Of

AbstractSelecting particles from digital micrographs is an essential step in single particle electron cryomicroscopy (cryo-EM). Since manual selection of complete datasets typically comprising many thousands of particles is a tedious and time-consuming process, many automatic particle pickers have been developed in the past few decades. However, non-ideal datasets pose a challenge to particle picking. Here, we present a novel automated particle picking software called crYOLO, which is based on the deep learning object detection system “You Only Look Once” (YOLO). After training the network with 500 – 2,500 particles per dataset, it automatically recognizes particles with high recall and precision reaching a speed of up to five micrographs per second. Importantly, we demonstrate a powerful general network trained on more than 40 datasets to select previously unseen datasets, thus paving the way for completely automated “on-the-fly” cryo-EM data pre-processing during data acquisition. CrYOLO is available as a standalone program under http://sphire.mpg.de/ and will be part of the image processing workflow in SPHIRE.

scholarly journals A Wide-Ranging Review on Diabetic Retinotherapy

2020 ◽  
Vol 18 (02) ◽  
pp. 169-187
Author(s):  
Toufique Ahmed Soomro ◽  
Ahsin Murtaza Bughio ◽  
Shahid Hussain Siyal ◽  
Ali Anwar Panwar ◽  
Nasreen Nizamani
Keyword(s):  
Image Processing ◽  
Blood Vessels ◽  
Detection System ◽  
Eye Diseases ◽  
Fundus Images ◽  
The Past ◽  
Retinal Fundus Images ◽  
Retinal Fundus ◽  
Computerized System ◽  
Automatic Algorithm

Diabetic Retinopathy (DR) is one of the major eye diseases that causes damage to retina of the human eye ball due to the rupture of tiny blood vessels. DR is identified by the ophthalmologists on the basis of various specifications i.e., textures, blood vessels and pathologies. The ophthalmologists are recently considering software for eye diseases detection based on image processing designed by the computing techniques and bio-medical images. In the analysis of medical imaging, traditional techniques of image processing and computer vision have played an important role in the field of ophthalmology. From the past two decades, there is a tremendous advancement in the development of computerized system for DR detection. This paper comprises the five parts of analysis on image based retinal detection DR, named as review of low varying contrast techniques of the retinal fundus Images (RFI), review of noise effect in the fundus images, review of pathology detection method from the retinal fundus images, review of blood vessels extraction from the RFI, and review of automatic algorithm for the DR detection. This paper presents a comprehensive detail to each problem in the retinal images. The procedures that are currently utilized to analyze the contrast issue and noise issues are discussed in detail. The paper also explains the techniques used for segmentation. In the end, the recent automated detection system of related eye diseases or DR is described.

Tests of an Improved Rotating Stall Control System on a J-85 Turbojet Engine

1980 ◽  
Vol 102 (4) ◽  
pp. 903-911 ◽  
Author(s):  
G. R. Ludwig ◽  
J. P. Nenni
Keyword(s):  
Control System ◽  
Response Time ◽  
Detection System ◽  
Response Speed ◽  
Rotating Stall ◽  
The Past ◽  
Turbojet Engine ◽  
Design Speed ◽  
Stall Control ◽  
Selection Of

An improved version of a rotating stall control system has been tested successfully on a J-85-B turbojet engine. Past tests had pointed out the desirability of increasing the response speed of the control. In this study, the installation of the stall control on the J-85 was modified so as to decrease the response time of the control by a factor of ten over that attained in the past tests. The modified control was tested to see if the decreased response time improved the ability to clear rotating stall once it has started, and also to see if rotating stall could be anticipated and prevented by proper selection of the variables in the stall control detection system. The performance of the stall control was tested by closing the bleed doors on the engine until rotating stall occurred or until the control anticipated stall and held the bleed doors open. The tests showed that the control is capable of anticipating stall before it occurs and keeping the engine completely clear of stall at speeds up to 80 percent of design speed. No tests were performed above 80 percent of design speed because opening the bleed doors at such speeds might aggravate the stall rather than clear it.

scholarly journals Automatic Particle Picking From Electron Micrographs

1995 ◽  
Vol 3 (3) ◽  
pp. 12-13
Author(s):  
K. Ramani Lata ◽  
P. Penczek ◽  
J. Frank
Keyword(s):  
Single Particle ◽  
Small Area ◽  
Biological Molecules ◽  
The Past ◽  
Local Variance ◽  
Structural Content ◽  
Manual Selection ◽  
Correlation Search ◽  
Substantial Effort ◽  
Selection Of

The present-day interactive manual selection of biological molecules from digitized micrographs for single particle averaging and reconstruction requires substantial effort and time. Thus a computer algorithm capable of recognition of structural content and selection of particles would be desirable. A few approaches have been proposed in the past. The method by Frank and Wagenknecht is based on the principle of correlation search. Van Heel's method is based on the computation of the local variance over a small area around each point of the image field. The method by Harauz and Fong- Lochovsky is based on edge-detection.

A basic introduction to image processing using NIH-Image as a model

1994 ◽  
Vol 52 ◽  
pp. 392-393
Author(s):  
John Mansfield
Keyword(s):  
Image Processing ◽  
Digital Image ◽  
Image Acquisition ◽  
Digital Instrument ◽  
Novice User ◽  
Nih Image ◽  
The Past ◽  
Digital World ◽  
The World ◽  
Instrument Control

Advances in camera technology and digital instrument control have meant that in modern microscopy, the image that was, in the past, typically recorded on a piece of film is now recorded directly into a computer. The transfer of the analog image seen in the microscope to the digitized picture in the computer does not mean, however, that the problems associated with recording images, analyzing them, and preparing them for publication, have all miraculously been solved. The steps involved in the recording an image to film remain largely intact in the digital world. The image is recorded, prepared for measurement in some way, analyzed, and then prepared for presentation.Digital image acquisition schemes are largely the realm of the microscope manufacturers, however, there are also a multitude of “homemade” acquisition systems in microscope laboratories around the world. It is not the mission of this tutorial to deal with the various acquisition systems, but rather to introduce the novice user to rudimentary image processing and measurement.

Three-Dimensional Structure of Rotavirus-Fab Complex

1990 ◽  
Vol 48 (1) ◽  
pp. 238-239
Author(s):  
B.V.V. Prasad ◽  
E. Marietta ◽  
J.W. Burns ◽  
M.K. Estes ◽  
W. Chiu
Keyword(s):  
Image Processing ◽  
Smooth Surface ◽  
Three Dimensional ◽  
Outer Shell ◽  
Dimensional Structure ◽  
Structural Studies ◽  
Cell Penetration ◽  
Electron Cryomicroscopy ◽  
Image Processing Techniques ◽  
Processing Techniques

Rotaviruses are spherical, double-shelled particles. They have been identified as a major cause of infantile gastroenteritis worldwide. In our earlier studies we determined the three-dimensional structures of double-and single-shelled simian rotavirus embedded in vitreous ice using electron cryomicroscopy and image processing techniques to a resolution of 40Å. A distinctive feature of the rotavirus structure is the presence of 132 large channels spanning across both the shells at all 5- and 6-coordinated positions of a T=13ℓ icosahedral lattice. The outer shell has 60 spikes emanating from its relatively smooth surface. The inner shell, in contrast, exhibits a bristly surface made of 260 morphological units at all local and strict 3-fold axes (Fig.l).The outer shell of rotavirus is made up of two proteins, VP4 and VP7. VP7, a glycoprotein and a neutralization antigen, is the major component. VP4 has been implicated in several important functions such as cell penetration, hemagglutination, neutralization and virulence. From our earlier studies we had proposed that the spikes correspond to VP4 and the rest of the surface is composed of VP7. Our recent structural studies, using the same techniques, with monoclonal antibodies specific to VP4 have established that surface spikes are made up of VP4.

Integrated FAHP-VIKOR model for green supplier selection in a Nickle coating SME

2020 ◽  
pp. 133-139
Author(s):  
Sanatan Ratna ◽  
B Kumar
Keyword(s):  
Staff Training ◽  
Supplier Selection ◽  
Fuzzy Ahp ◽  
Research Work ◽  
Supplier Evaluation ◽  
Green Supplier Selection ◽  
The Past ◽  
Coating Industry ◽  
Sustainability Issue ◽  
Selection Of

In the past few decades, there has been lot of focus on the issue of sustainability. This has occurred due to the growing concerns related to climate change and the growing awareness about environmental concerns. Also, the competition at global level has led to the search for the most sustainable route in the industries. The current research work deals with the selection of green supplier in a Nickle coating industry based on certain weighted green attributes. For this purpose, a hybrid tool comprising of Fuzzy AHP (Fuzzy Analytical Hierarchy) and VIKOR (VlseKriterijumska Optimizacija I Kompromisno Resenje) is used. The Fuzzy AHP is used for assigning proper weights to the selected criteria for supplier evaluation, while VIKOR is used for final supplier selection based on the weighted criteria. The three criterions for green supplier selection are, Ecological packaging, Corporate socio-environmental responsibility and Staff Training. The outcome of the integrated model may serve as a steppingstone to other SMEs in different sectors for selecting the most suitable supplier for addressing the sustainability issue.

Traffic incident detection system based on video image processing

2008 ◽  
Vol 28 (7) ◽  
pp. 1886-1889 ◽  
Author(s):  
Qin WANG ◽  
Shan HUANG ◽  
Hong-bin ZHANG ◽  
Quan YANG ◽  
Jian-jun ZHANG
Keyword(s):  
Image Processing ◽  
Detection System ◽  
Video Image ◽  
Incident Detection ◽  
Traffic Incident ◽  
Video Image Processing

Evidence-based Assessment

2010 ◽  
pp. 76-98
Author(s):  
John Hunsley ◽  
Eric J. Mash
Keyword(s):  
Decision Making ◽  
Clinical Assessment ◽  
Assessment Process ◽  
Evidence Based ◽  
The Past ◽  
Specific Assessment ◽  
The Many ◽  
Selection Of ◽  
Made In

Evidence-based assessment relies on research and theory to inform the selection of constructs to be assessed for a specific assessment purpose, the methods and measures to be used in the assessment, and the manner in which the assessment process unfolds. An evidence-based approach to clinical assessment necessitates the recognition that, even when evidence-based instruments are used, the assessment process is a decision-making task in which hypotheses must be iteratively formulated and tested. In this chapter, we review (a) the progress that has been made in developing an evidence-based approach to clinical assessment in the past decade and (b) the many challenges that lie ahead if clinical assessment is to be truly evidence-based.

scholarly journals Standardizing human brain parcellations

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Ross M. Lawrence ◽  
Eric W. Bridgeford ◽  
Patrick E. Myers ◽  
Ganesh C. Arvapalli ◽  
Sandhya C. Ramachandran ◽  
...  
Keyword(s):  
Human Brain ◽  
Coordinate Space ◽  
The Past ◽  
File Storage ◽  
Statistical Inferences ◽  
Standardized Protocol ◽  
Storage Format ◽  
Labeling Scheme ◽  
Selection Of ◽  
Brain Atlases

AbstractUsing brain atlases to localize regions of interest is a requirement for making neuroscientifically valid statistical inferences. These atlases, represented in volumetric or surface coordinate spaces, can describe brain topology from a variety of perspectives. Although many human brain atlases have circulated the field over the past fifty years, limited effort has been devoted to their standardization. Standardization can facilitate consistency and transparency with respect to orientation, resolution, labeling scheme, file storage format, and coordinate space designation. Our group has worked to consolidate an extensive selection of popular human brain atlases into a single, curated, open-source library, where they are stored following a standardized protocol with accompanying metadata, which can serve as the basis for future atlases. The repository containing the atlases, the specification, as well as relevant transformation functions is available in the neuroparc OSF registered repository or https://github.com/neurodata/neuroparc.

Sign in / Sign up

Export Citation Format

Share Document