EXTRAX : an ImageJ plug-in for electron diffraction intensity extraction (original) (raw)
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Ultramicroscopy, 2000
A new software package for quantitative electron di!raction data treatment of unknown structures is described. No`a prioria information is required by the package which is able to perform in successive steps the 2-D indexing of digitised di!raction patterns, the extraction of the intensity of the collected re#ections and the 3-D indexing of all recorded patterns, giving as results the lattice parameters of the investigated structure and a series of data "les (one for each di!raction pattern) containing the measured intensities and the relative e.s.d.s of the 3-D indexed re#ections. The software package is mainly conceived for the treatment of di!raction patterns taken with a Gatan CCD Slow-Scan Camera, but it can also deal with generic digitised plates. The program is designed to extract intensity data suitable for structure solution techniques in electron crystallography. The integration routine is optimised for a correct background evaluation, a necessary condition to deal with weak spots of irregular shape and an intensity just above the background.
ELD — a computer program system for extracting intensities from electron diffraction patterns
Ultramicroscopy, 1993
A computer program system, ELD, for extracting intensities from electron diffraction (ED) patterns has been developed. ELD runs on a personal computer (PC). Electron diffraction patterns are digitized using a CCD camera, and the data is transferred to the PC via a frame grabber. The lattice vectors and the shape and size of the diffraction spots are first determined, and based upon this information the strategy for extracting the electron diffraction intensities is decided by ELD. It is possible to merge several diffraction patterns taken with different exposure times, whereby both very strong and very weak reflections can be measured. Quantified electron diffraction data can be useful both for chemical applications, such as refining crystal structures, previously solved by crystallographic image processing (CIP), in materials science and for physical applications.
TexPat – a program for quantitative analysis of oblique texture electron diffraction patterns
Zeitschrift für Kristallographie, 2004
We have developed a program – TexPat for quantification of texture patterns in order to facilitate, speed up and improve the accuracy of this analytical method. The program introduces new approaches for automated detection of centre and symmetry axes and simplifies the process of indexing and calculating the unit cell parameters. The main algorithm of the program uses the symmetry properties of the texture pattern images. The successive steps help to process the reflections of the pattern using the peak shape extracted from well-separated peaks. The program generates a list of unit cell parameters, all processed reflections with Miller indices and their integrated intensities. The quality of the results obtained by TexPat is compatible with published data.
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Journal of Structural Biology, 2007
Bsoft is a software package written for image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image processing. The code is modularized to allow for rapid testing and deployment of new processing algorithms, while also providing sufficient infrastructure to deal with many file formats and parametric data. The design is deliberately open to allow interchange of information with other image and molecular processing software through a standard parameter file (currently a text-based encoding of parameters in the STAR format) and its support of multiple image and molecular formats. It also allows shell scripting of processes and allows subtasks to be distributed across multiple computers for concurrent processing. Bsoft has undergone many modifications and advancements since its initial release [Heymann, J.B., 2001. Bsoft: image and molecular processing in electron microscopy. J. Struct. Biol. 133,[156][157][158][159][160][161][162][163][164][165][166][167][168][169]. Much of the emphasis is on single particle analysis and tomography, and sufficient functionality is available in the package to support most needed operations for these techniques. The key graphical user interface is the program bshow, which displays an image and is used for many interactive purposes such as fitting the contrast transfer function or picking particles. Bsoft also offers various tools to manipulate atomic structures and to refine the fit of a known molecular structure to a density in a reconstruction. Published by Elsevier Inc.
XMIPP: a new generation of an open-source image processing package for electron microscopy
X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. This public-domain software package was introduced to the electron microscopy field eight years ago, and since then it has changed drastically. New methodologies for the analysis of single-particle projection images have been added to classification, contrast transfer function correction, angular assignment, 3D reconstruction, reconstruction of crystals, etc. In addition, the package has been extended with functionalities for 2D crystal and electron tomography data. Furthermore, its current implementation in C++, with a highly modular design of well-documented data structures and functions, offers a convenient environment for the development of novel algorithms. In this paper, we present a general overview of a new generation of Xmipp that has been re-engineered to maximize flexibility and modularity, potentially facilitating its integration in future standardization efforts in the field. Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community.
Quantitative electron diffraction — new features in the program system ELD
Ultramicroscopy, 1993
Accurate quantitative intensities from electron diffraction patterns can be obtained by the program system ELD. Such data is needed for solving or refining crystal structures. ELD runs on a personal computer. The quality of normal (i.e. not slow-scan) CCD cameras is sufficient for giving quite accurate structure factor amplitudes from electron diffraction patterns. Several factors which affect the intensity evaluation are discussed and some algorithms in ELD concerned with the problems of extracting high quality quantitative structure factors from electron diffraction patterns are described.
Xmipp: An Image Processing Package for Electron Microscopy
Journal of Structural Biology, 1996
We present in this article a specialized suite of image processing programs primarily aimed at obtaining the three-dimensional reconstruction of biological specimens from large sets of projection images obtained by transmission electron microscopy. The programs are written in ANSI-C and use X-Windows for graphical output. A number of parallel extensions using PVM and PARMACS are provided. The programs are freely available by anonymous ftp at ftp.cnb.uam.es.
Iplt—image processing library and toolkit for the electron microscopy community
Journal of Structural Biology, 2003
We present the foundation for establishing a modular, collaborative, integrated, open-source architecture for image processing of electron microscopy images, named iplt. It is designed around object oriented paradigms and implemented using the programming languages C++ and Python. In many aspects it deviates from classical image processing approaches. This paper intends to motivate developers within the community to participate in this on-going project. The iplt homepage can be found at http:// www.iplt.org.
Journal of Applied Crystallography, 2013
Implementation of a computer program package for automated collection and processing of rotation electron diffraction (RED) data is described. The software package contains two computer programs:REDdata collection andREDdata processing. TheREDdata collection program controls the transmission electron microscope and the camera. Electron beam tilts at a fine step (0.05–0.20°) are combined with goniometer tilts at a coarse step (2.0–3.0°) around a common tilt axis, which allows a fine relative tilt to be achieved between the electron beam and the crystal in a large tilt range. An electron diffraction (ED) frame is collected at each combination of beam tilt and goniometer tilt. TheREDdata processing program processes three-dimensional ED data generated by theREDdata collection program or by other approaches. It includes shift correction of the ED frames, peak hunting for diffraction spots in individual ED frames and identification of these diffraction spots as reflections in three dimen...