Abstract
Single particle imaging (SPI) is a promising method of native structure determination, which has undergone fast progress with the development of x-ray free-electron lasers. Large amounts of ...data are collected during SPI experiments, driving the need for automated data analysis. The necessary data analysis pipeline has a number of steps including binary object classification (single versus non-single hits). Classification and object detection are areas where deep neural networks currently outperform other approaches. In this work, we use the fast object detector networks YOLOv2 and YOLOv3. By exploiting transfer learning, a moderate amount of data is sufficient to train the neural network. We demonstrate here that a convolutional neural network can be successfully used to classify data from SPI experiments. We compare the results of classification for the two different networks, with different depth and architecture, by applying them to the same SPI data with different data representation. The best results are obtained for diffracted intensity represented by color images on a linear scale using YOLOv2 for classification. It shows an accuracy of about 95% with precision and recall of about 50% and 60%, respectively, in comparison to manual data classification.
An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular ...and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.
Interventional cardiology practice puts forward a problem of analysis of the coronary arteries 3D structure. One of the most commonly utilized method is X-ray coronary angiography. To reconstruct a ...three-dimensional image of the coronary arteries tree for an individual patient from several 2D X-ray angiography projections one needs to make use of mathematical modelling approach.
In this paper we propose an approach to the reconstruction of centerlines of the coronary arteries, based on epipolar geometry. We choose mutually correlated projections of an unknown 3D point on the centerline. Then we restore its 3D coordinates, using epipolar constraints and simple linear equations.
We present an annual international Young Scientists Conference (YSC) on computational science http://ysc.escience.ifmo.ru/, which brings together renowned experts and young researchers working in ...high-performance computing, data-driven modeling, and simulation of large-scale complex systems. The first YSC event was organized in 2012 by the University of Amsterdam, the Netherlands and ITMO University, Russia with the goal of opening a dialogue on the present and the future of computational science and its applications. We believe that the YSC conferences will strengthen the ties between young scientists in different countries, thus promoting future collaboration. In this paper we briefly introduce the challenges the millennial generation is facing; describe the YSC conference history and topics; and list the keynote speakers and program committee members. This volume of Procedia Computer Science presents selected papers from the 4th International Young Scientists Conference on Computational Science held on 25 June − 3 July 2015 in Athens, Greece.
In this paper we present an approach to the on-the-fly Cryo-EM data acquisition and analysis using High Performance Data Analysis concept. An analysis of bottlenecks in the currently used data ...processing is presented, and the new iterative scheme for near real time implementation of the Cryo-EM data processing is discussed. The on-the-fly approach is proposed that will considerably reduce the time required for the protein (or other biological objects, e.g. viruses) 3D structure determination and allow eliminating manual interventions in the data processing.
This study aimed to evaluate the suitability of two bioaerosol generation systems (dry and wet generation) for the aerosolization of microorganisms isolated from the International Space Station, and ...to calibrate the produced bioaerosols to fulfill the requirements of computational fluid dynamics model (CFD) validation. Concentration, stability, size distribution, agglomeration of generated bioaerosol and deposition of bioaerosols were analyzed. In addition, the dispersion of non-viable particles in the air was studied. Experiments proved that wet generation from microbial suspensions could be used for the production of well-calibrated and stabile bioaerosols for model validation. For the simulation of the natural release of fungal spores, a dry generation method should be used. This study showed that the used CFD model simulated the spread of non-viable particles fairly well. The mathematical deposition model by Lai and Nazaroff could be used to estimate the deposition velocities of bioaerosols on surfaces, although it somewhat underestimated the measured deposition velocities.
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We present a concept of the information system for intensive work with metadata in heterogeneous data store to modify dynamically both the data and the metadata models by user. This concept is ...illustrated by example of such information system for the project where the digital registrar is developing for the culture heritage of Old Russian paintings, namely Dionisius frescoes in the Cathedral of the Nativity of the Virgin at the Ferapontov Monastery painted in 1502.
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