scholarly journals Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion

Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6224
Author(s):  
David Strelak ◽  
Amaya Jiménez-Moreno ◽  
José L. Vilas ◽  
Erney Ramírez-Aportela ◽  
Ruben Sánchez-García ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Open Source Software ◽  
Software Package ◽  
Electron Tomography ◽  
New Work ◽  
Cryo Electron Microscopy ◽  
Processing Data ◽  
The World ◽  
Open Source Software Package ◽  
Single Publication

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.

scholarly journals Electron Microscopy (Big and Small) Data Analysis With the Open Source Software Package HyperSpy

2017 ◽  
Vol 23 (S1) ◽  
pp. 214-215 ◽  
Author(s):  
Francisco de la Pena ◽  
Tomas Ostasevicius ◽  
Vidar Tonaas Fauske ◽  
Pierre Burdet ◽  
Petras Jokubauskas ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Data Analysis ◽  
Open Source ◽  
Open Source Software ◽  
Software Package ◽  
Small Data ◽  
Open Source Software Package

scholarly journals Planning, performing and analyzing X-ray Raman scattering experiments

2015 ◽  
Vol 22 (2) ◽  
pp. 400-409 ◽  
Author(s):  
Ch. J. Sahle ◽  
A. Mirone ◽  
J. Niskanen ◽  
J. Inkinen ◽  
M. Krisch ◽  
...  
Keyword(s):  
Raman Scattering ◽  
Open Source ◽  
Open Source Software ◽  
Software Package ◽  
Super Resolution ◽  
Resolution Method ◽  
X Ray ◽  
Imaging Capability ◽  
Processing Data ◽  
Open Source Software Package

A compilation of procedures for planning and performing X-ray Raman scattering (XRS) experiments and analyzing data obtained from them is presented. In particular, it is demonstrated how to predict the overall shape of the spectra, estimate detection limits for dilute samples, and how to normalize the recorded spectra to absolute units. In addition, methods for processing data from multiple-crystal XRS spectrometers with imaging capability are presented, including a super-resolution method that can be used for direct tomography using XRS spectra as the contrast. An open-source software package with these procedures implemented is also made available.

scholarly journals Capturing Enveloped Viruses on Affinity Grids for Downstream Cryo-Electron Microscopy Applications

2013 ◽  
Vol 20 (1) ◽  
pp. 164-174 ◽  
Author(s):  
Gabriella Kiss ◽  
Xuemin Chen ◽  
Melinda A. Brindley ◽  
Patricia Campbell ◽  
Claudio L. Afonso ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Measles Virus ◽  
Influenza A ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Nitrilotriacetic Acid ◽  
Dimensional Structure ◽  
Enveloped Viruses ◽  
Cryo Electron Microscopy ◽  
Human Immunodeficiency Virus Virus

AbstractElectron microscopy (EM), cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) are essential techniques used for characterizing basic virus morphology and determining the three-dimensional structure of viruses. Enveloped viruses, which contain an outer lipoprotein coat, constitute the largest group of pathogenic viruses to humans. The purification of enveloped viruses from cell culture presents certain challenges. Specifically, the inclusion of host-membrane-derived vesicles, the complete destruction of the viruses, and the disruption of the internal architecture of individual virus particles. Here, we present a strategy for capturing enveloped viruses on affinity grids (AG) for use in both conventional EM and cryo-EM/ET applications. We examined the utility of AG for the selective capture of human immunodeficiency virus virus-like particles, influenza A, and measles virus. We applied nickel-nitrilotriacetic acid lipid layers in combination with molecular adaptors to selectively adhere the viruses to the AG surface. This further development of the AG method may prove essential for the gentle and selective purification of enveloped viruses directly onto EM grids for ultrastructural analyses.

scholarly journals Integration of enabling methods for the automated flow preparation of piperazine-2-carboxamide

2014 ◽  
Vol 10 ◽  
pp. 641-652 ◽  
Author(s):  
Richard J Ingham ◽  
Claudio Battilocchio ◽  
Joel M Hawkins ◽  
Steven V Ley
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Package ◽  
Flow Chemistry ◽  
Raspberry Pi ◽  
Step Flow ◽  
Simultaneous Control ◽  
Open Source Software Package

Here we describe the use of a new open-source software package and a Raspberry Pi® computer for the simultaneous control of multiple flow chemistry devices and its application to a machine-assisted, multi-step flow preparation of pyrazine-2-carboxamide – a component of Rifater®, used in the treatment of tuberculosis – and its reduced derivative piperazine-2-carboxamide.

scholarly journals An open source software package for primality testing of numbers of the form p2^n+1, with no constraints on the relative sizes of p and 2^n

2018 ◽  
Author(s):  
Tejas R. Rao
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Software Package ◽  
Primality Testing ◽  
Fermat Number ◽  
Open Source Software Package ◽  
Sierpinski Numbers ◽  
Efficient Software

We develop an efficient software package to test for the primality of p2^n+1, p prime and p>2^n. This aids in the determination of large, non-Sierpinski numbers p, for prime p, and in cryptography. It furthermore uniquely allows for the computation of the smallest n such that p2^n+1 is prime when p is large. We compute primes of this form for the first one million primes p and find four primes of the form above 1000 digits. The software may also be used to test whether p2^n+1 divides a generalized fermat number base 3.

scholarly journals Modelling nonlinear dynamics of interacting tipping elements on complex networks: the PyCascades package

2021 ◽  
Author(s):  
Nico Wunderling ◽  
Jonathan Krönke ◽  
Valentin Wohlfarth ◽  
Jan Kohler ◽  
Jobst Heitzig ◽  
...  
Keyword(s):  
Dynamical Systems ◽  
Open Source Software ◽  
Software Package ◽  
Model Systems ◽  
Stochastic Dynamical Systems ◽  
Moisture Recycling ◽  
Modelling Framework ◽  
Different Types ◽  
Open Source Software Package ◽  
The Individual

AbstractTipping elements occur in various systems such as in socio-economics, ecology and the climate system. In many cases, the individual tipping elements are not independent of each other, but they interact across scales in time and space. To model systems of interacting tipping elements, we here introduce the PyCascades open source software package for studying interacting tipping elements (10.5281/zenodo.4153102). PyCascades is an object-oriented and easily extendable package written in the programming language Python. It allows for investigating under which conditions potentially dangerous cascades can emerge between interacting dynamical systems, with a focus on tipping elements. With PyCascades it is possible to use different types of tipping elements such as double-fold and Hopf types and interactions between them. PyCascades can be applied to arbitrary complex network structures and has recently been extended to stochastic dynamical systems. This paper provides an overview of the functionality of PyCascades by introducing the basic concepts and the methodology behind it. In the end, three examples are discussed, showing three different applications of the software package. First, the moisture recycling network of the Amazon rainforest is investigated. Second, a model of interacting Earth system tipping elements is discussed. And third, the PyCascades modelling framework is applied to a global trade network.

scholarly journals Recent Advances in Transmission Electron Microscopy for Materials Science at the EMAT Lab of the University of Antwerp

Materials ◽  
2018 ◽  
Vol 11 (8) ◽  
pp. 1304 ◽  
Author(s):  
Giulio Guzzinati ◽  
Thomas Altantzis ◽  
Maria Batuk ◽  
Annick De Backer ◽  
Gunnar Lumbeeck ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Materials Science ◽  
Electron Tomography ◽  
High Resolution Imaging ◽  
Rapid Progress ◽  
Transmission Electron ◽  
The World ◽  
Resolution Imaging ◽  
The University

The rapid progress in materials science that enables the design of materials down to the nanoscale also demands characterization techniques able to analyze the materials down to the same scale, such as transmission electron microscopy. As Belgium’s foremost electron microscopy group, among the largest in the world, EMAT is continuously contributing to the development of TEM techniques, such as high-resolution imaging, diffraction, electron tomography, and spectroscopies, with an emphasis on quantification and reproducibility, as well as employing TEM methodology at the highest level to solve real-world materials science problems. The lab’s recent contributions are presented here together with specific case studies in order to highlight the usefulness of TEM to the advancement of materials science.

scholarly journals Development and Evaluation of an Open-Source Software Package “CGITA” for Quantifying Tumor Heterogeneity with Molecular Images

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Yu-Hua Dean Fang ◽  
Chien-Yu Lin ◽  
Meng-Jung Shih ◽  
Hung-Ming Wang ◽  
Tsung-Ying Ho ◽  
...  
Keyword(s):  
Open Source ◽  
Texture Analysis ◽  
Open Source Software ◽  
Software Package ◽  
Tumor Heterogeneity ◽  
Locally Advanced ◽  
Image Texture ◽  
Pixel Intensity ◽  
Open Source Software Package ◽  
Molecular Images

Background. The quantification of tumor heterogeneity with molecular images, by analyzing the local or global variation in the spatial arrangements of pixel intensity with texture analysis, possesses a great clinical potential for treatment planning and prognosis. To address the lack of available software for computing the tumor heterogeneity on the public domain, we develop a software package, namely, Chang-Gung Image Texture Analysis (CGITA) toolbox, and provide it to the research community as a free, open-source project.Methods. With a user-friendly graphical interface, CGITA provides users with an easy way to compute more than seventy heterogeneity indices. To test and demonstrate the usefulness of CGITA, we used a small cohort of eighteen locally advanced oral cavity (ORC) cancer patients treated with definitive radiotherapies.Results. In our case study of ORC data, we found that more than ten of the current implemented heterogeneity indices outperformed SUVmeanfor outcome prediction in the ROC analysis with a higher area under curve (AUC). Heterogeneity indices provide a better area under the curve up to 0.9 than the SUVmeanand TLG (0.6 and 0.52, resp.).Conclusions. CGITA is a free and open-source software package to quantify tumor heterogeneity from molecular images. CGITA is available for free for academic use athttp://code.google.com/p/cgita.

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