Nika: software for two-dimensional data reduction

2012 ◽  
Vol 45 (2) ◽  
pp. 324-328 ◽  
Author(s):  
Jan Ilavsky
Keyword(s):  
Small Angle ◽  
Data Reduction ◽  
Large Scale ◽  
Grazing Incidence ◽  
Scattering Data ◽  
Two Dimensional ◽  
Saxs Data ◽  
One Dimensional ◽  
Area Detector ◽  
X Ray Scattering

Nikais anIgor Pro-based package for correction, calibration and reduction of two-dimensional area-detector data into one-dimensional data (`lineouts'). It is free (although the user needs a paid license forIgor Pro), open source and highly flexible. While typically used for small-angle X-ray scattering (SAXS) data, it can also be used for grazing-incidence SAXS data, wide-angle diffraction data and even small-angle neutron scattering data. It has been widely available to the user community since about 2005, and it is currently used at the SAXS instruments of selected large-scale facilities as their main data reduction package. It is, however, also suitable for desktop instruments when the manufacturer's software is not available or appropriate. Since it is distributed as source code, it can be scrutinized, verified and modified by users to suit their needs.

scholarly journals A customizable software for fast reduction and analysis of large X-ray scattering data sets: applications of the newDPDAKpackage to small-angle X-ray scattering and grazing-incidence small-angle X-ray scattering

2014 ◽  
Vol 47 (5) ◽  
pp. 1797-1803 ◽  
Author(s):  
Gunthard Benecke ◽  
Wolfgang Wagermaier ◽  
Chenghao Li ◽  
Matthias Schwartzkopf ◽  
Gero Flucke ◽  
...  
Keyword(s):  
Small Angle ◽  
Data Reduction ◽  
Grazing Incidence ◽  
Scattering Data ◽  
Limiting Factor ◽  
Online Data ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

X-ray scattering experiments at synchrotron sources are characterized by large and constantly increasing amounts of data. The great number of files generated during a synchrotron experiment is often a limiting factor in the analysis of the data, since appropriate software is rarely available to perform fast and tailored data processing. Furthermore, it is often necessary to perform online data reduction and analysis during the experiment in order to interactively optimize experimental design. This article presents an open-source software package developed to process large amounts of data from synchrotron scattering experiments. These data reduction processes involve calibration and correction of raw data, one- or two-dimensional integration, as well as fitting and further analysis of the data, including the extraction of certain parameters. The software,DPDAK(directly programmable data analysis kit), is based on a plug-in structure and allows individual extension in accordance with the requirements of the user. The article demonstrates the use ofDPDAKfor on- and offline analysis of scanning small-angle X-ray scattering (SAXS) data on biological samples and microfluidic systems, as well as for a comprehensive analysis of grazing-incidence SAXS data. In addition to a comparison with existing software packages, the structure ofDPDAKand the possibilities and limitations are discussed.

BioXTAS RAW, a software program for high-throughput automated small-angle X-ray scattering data reduction and preliminary analysis

2009 ◽  
Vol 42 (5) ◽  
pp. 959-964 ◽  
Author(s):  
S. S. Nielsen ◽  
K. Noergaard Toft ◽  
D. Snakenborg ◽  
M. G. Jeppesen ◽  
J. K. Jacobsen ◽  
...  
Keyword(s):  
Open Source ◽  
Small Angle ◽  
Data Reduction ◽  
Preliminary Analysis ◽  
Two Dimensional ◽  
One Dimensional ◽  
X Ray ◽  
X Ray Scattering ◽  
Software Program ◽  
Data Files

A fully open source software program for automated two-dimensional and one-dimensional data reduction and preliminary analysis of isotropic small-angle X-ray scattering (SAXS) data is presented. The program is freely distributed, following the open-source philosophy, and does not rely on any commercial software packages.BioXTAS RAWis a fully automated program that,viaan online feature, reads raw two-dimensional SAXS detector output files and processes and plots data as the data files are created during measurement sessions. The software handles all steps in the data reduction. This includes mask creation, radial averaging, error bar calculation, artifact removal, normalization andqcalibration. Further data reduction such as background subtraction and absolute intensity scaling is fast and easyviathe graphical user interface.BioXTAS RAWalso provides preliminary analysis of one-dimensional data in terms of the indirect Fourier transform using the objective Bayesian approach to obtain the pair-distance distribution function, PDDF, and is thereby a free and open-source alternative to existing PDDF estimation software. Apart from the TIFF input format, the program also accepts ASCII-format input files and is currently compatible with one-dimensional data files from SAXS beamlines at a number of synchrotron facilities.BioXTAS RAWis written in Python with C++ extensions.

scholarly journals Guinier peak analysis for visual and automated inspection of small-angle X-ray scattering data

2016 ◽  
Vol 49 (5) ◽  
pp. 1412-1419 ◽  
Author(s):  
Christopher D. Putnam
Keyword(s):  
Small Angle ◽  
Peak Position ◽  
Scattering Data ◽  
Radius Of Gyration ◽  
Automated Inspection ◽  
Elongation Ratio ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

The Guinier region in small-angle X-ray scattering (SAXS) defines the radius of gyration,Rg, and the forward scattering intensity,I(0). In Guinier peak analysis (GPA), the plot ofqI(q)versus q2transforms the Guinier region into a characteristic peak for visual and automated inspection of data. Deviations of the peak position from the theoretical position in dimensionless GPA plots can suggest parameter errors, problematic low-resolution data, some kinds of intermolecular interactions or elongated scatters. To facilitate automated analysis by GPA, the elongation ratio (ER), which is the ratio of the areas in the pair-distribution functionP(r) after and before theP(r) maximum, was characterized; symmetric samples have ER values around 1, and samples with ER values greater than 5 tend to be outliers in GPA analysis. Use of GPA+ER can be a helpful addition to SAXS data analysis pipelines.

Application of Grazing-Incidence Small-Angle X-Ray Scattering Technique to Semiconducting Composite Materials

2005 ◽  
Vol 475-479 ◽  
pp. 1097-1100 ◽  
Author(s):  
T. Ogawa ◽  
H. Niwa ◽  
Hiroshi Okuda ◽  
Shojiro Ochiai
Keyword(s):  
Small Angle ◽  
Grazing Incidence ◽  
Two Dimensional ◽  
Dimensional Model ◽  
X Ray ◽  
X Ray Scattering ◽  
Angle Scattering ◽  
Two Dimensional Model ◽  
Scattering Technique ◽  
Best Fitting

Grazing-incidence small-angle scattering (GI-SAXS) technique was applied to self-assembled Ge islands capped with Si. GI-SAXS has a merit over TEM and AFM that the structure of islands buried in a cap layer for stabilization can be evaluated nondestructively. By analyzing the scattering patterns, the size of Ge islands was estimated to be about 5 nm in height and 26 nm in diameter, with the islands density of 4.2×1014/m2. From the best fitting of two-dimensional model intensity to the experiments, the shape of the islands was deduced

scholarly journals The Diffraction Pattern Calculator(DPC) toolkit: a user-friendly approach to unit-cell lattice parameter identification of two-dimensional grazing-incidence wide-angle X-ray scattering data

2014 ◽  
Vol 47 (6) ◽  
pp. 2090-2099 ◽  
Author(s):  
Anna K. Hailey ◽  
Anna M. Hiszpanski ◽  
Detlef-M. Smilgies ◽  
Yueh-Lin Loo
Keyword(s):  
Crystal Structure ◽  
Grazing Incidence ◽  
Unit Cell ◽  
Lattice Parameters ◽  
Scattering Data ◽  
Wide Angle ◽  
Two Dimensional ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

TheDPCtoolkit is a simple-to-use computational tool that helps users identify the unit-cell lattice parameters of a crystal structure that are consistent with a set of two-dimensional grazing-incidence wide-angle X-ray scattering data. The input data requirements are minimal and easy to assemble from data sets collected with any position-sensitive detector, and the user is required to make as few initial assumptions about the crystal structure as possible. By selecting manual or automatic modes of operation, the user can either visually match the positions of the experimental and calculated reflections by individually tuning the unit-cell parameters or have the program perform this process for them. Examples that demonstrate the utility of this program include determining the lattice parameters of a polymorph of a fluorinated contorted hexabenzocoronene in a blind test and refining the lattice parameters of the thin-film phase of 5,11-bis(triethylsilylethynyl)anthradithiophene with the unit-cell dimensions of its bulk crystal structure being the initial inputs.

scholarly journals Obtaining tertiary protein structures by the ab-initio interpretation of small angle X-ray scattering data

2019 ◽  
Author(s):  
Christopher Prior ◽  
Owen R Davies ◽  
Daniel Bruce ◽  
Ehmke Pohl
Keyword(s):  
Ab Initio ◽  
Small Angle ◽  
Protein Structures ◽  
Scattering Data ◽  
Ab Initio Method ◽  
Primary Sequence ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

ABSTRACTSmall angle X-ray scattering (SAXS) has become an important tool to investigate the structure of proteins in solution. In this paper we present a novel ab-initio method to represent polypeptide chains as discrete curves that can be used to derive a meaningful three-dimensional model from only the primary sequence and experimental SAXS data. High resolution crystal structures were used to generate probability density functions for each of the common secondary structural elements found in proteins. These are used to place realistic restraints on the model curve’s geometry. To evaluate the quality of potential models and demonstrate the efficacy of this novel technique we developed a new statistic to compare the entangled geometry of two open curves, based on mathematical techniques from knot theory. The chain model is coupled with a novel explicit hydration shell model in order derive physically meaningful 3D models by optimizing configurations against experimental SAXS data using a monte-caro based algorithm. We show that the combination of our ab-initio method with spatial restraints based on contact predictions successfully derives a biologically plausible model of the coiled–coil component of the human synaptonemal complex central element protein.SIGNIFICANCESmall-angle X-ray scattering allows for structure determination of biological macromolecules and their complexes in aqueous solution. Using a discrete curve representation of the polypeptide chain and combining it with empirically determined constraints and a realistic solvent model we are now able to derive realistic ab-initio 3-dimensional models from BioSAXS data. The method only require a primary sequence and the scattering data form the user.

PRINSAS– a Windows-based computer program for the processing and interpretation of small-angle scattering data tailored to the analysis of sedimentary rocks

2004 ◽  
Vol 37 (6) ◽  
pp. 1020-1024 ◽  
Author(s):  
Alan L. Hinde
Keyword(s):  
Small Angle ◽  
Scattering Length ◽  
Fractal Model ◽  
Scattering Data ◽  
Arbitrary Distribution ◽  
Geological Samples ◽  
Saxs Data ◽  
X Ray Scattering ◽  
Angle Scattering ◽  
Sample Structure

PRINSASis a Windows program that takes as input raw (post-reduction) small-angle neutron and small-angle X-ray scattering (SANS and SAXS) data obtained from various worldwide facilities, displays the raw curves in interactive log–log plots, and allows processing of the raw curves. Separate raw SANS and ultra-small-angle neutron scattering (USANS) curves can be combined into complete scattering curves for an individual sample. The combined curves can be interpreted and information inferred about sample structure, using built-in functions. These have been tailored for geological samples and other porous media, and include the ability to obtain an arbitrary distribution of scatterer sizes, the corresponding specific surface area of scatterers, and porosity (when the scatterers are pores), assuming spherical scatterers. A fractal model may also be assumed and the fractal dimension obtained. A utility for calculating scattering length density from the component oxides is included in the program.

Wide Angle and Small Angle X-ray Scattering Applications Using a Two-Dimensional Area Detector

1990 ◽  
Vol 34 ◽  
pp. 363-368
Author(s):  
B. G. Landes ◽  
R. A. Newman ◽  
P. R. Rudolf
Keyword(s):  
Dynamic Range ◽  
Scattering Data ◽  
Photographic Film ◽  
Scanning System ◽  
Imaging Plate ◽  
Two Dimensional ◽  
X Ray ◽  
Area Detector ◽  
X Ray Scattering ◽  
Ray Scattering

The traditional medium for collecting two-dimensional x-ray scattering patterns is photographic film. While x-ray film has excellent resolution, several factors make it a poor choice as a detection device: slow speed, limited dynamic range, the “human factor” (developing, fixing, film handling), and the lack of a commercial scanning system designed for reading two-dimensional x-ray films. Until recently, there were no practical alternatives to the use of photographic film for obtaining two-dimensional x-ray scattering data using a conventional x-ray source. In the past few years, two different detection systems have become available for collecting high quality two-dimensional x-ray scattering data: (1) the Siemens (Xentronics) area detector system, which is a gas filled, wire grid detector, and (2) the Fuji imaging-plate system, which utilizes a phosphor storage plate for imaging the x-ray scattering and a laser scanner to process the image.

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