GISAXS - User contributions [en]

Software

2015-06-01T21:52:05Z

Strzalka: Updates reference for GISXGUI article

A common question for new [[GISAXS]] users is: "What software can I use to analyze my data?" Unfortunately, there is no single package that will allow you to perform any possible analysis. This is in part due to the diversity of possible kinds of data analysis one might want to do on [[GISAXS]] or [[GIWAXS]] images. The following lists a variety of packages that are available.

==Data Viewing, Reduction, and Simple Analysis==
These packages provide ways to view data, and perform simple operations (linecuts, etc.).
===Geared towards 2D data===
* '''Fit2D''': A well-known package for treatment and conversion 2D scattering images.
** [http://www.esrf.eu/computing/scientific/FIT2D/ Official site.]
** [http://staff.chess.cornell.edu/~smilgies/D-lineNotes/GISAXS-at-D-line/fit2d-GIXS-primer.html Fit2D primer.]
** [http://g-line.chess.cornell.edu/G-lineStatus/G-lineManuals/CheatSheets/FIT2D_MAIN.html Fit2D hints page.]
* '''Datasqueeze''': Graphical tool for analyzing 2D detector images.
** [http://www.datasqueezesoftware.com/ Official site.]
* '''ImageJ''': A generic tool for image treatment and analysis. Can be used to open and process x-ray detector images.
** [http://rsb.info.nih.gov/ij/ Official site.]
* '''[[view.gtk]]''': A simple interface for viewing 2D data, calibrating your data into ''q''-space, and extracting linecuts. Written by Lin Yang for the [[X9]] beamline at [[NSLS]]. Installation requires (free) GTK libraries.
* '''[[pyXS]]''': Python scripts (with C++ backend) for performing analysis of 2D data.
** [http://www.bnl.gov/ps/x9/software/pyXS.asp Official site.]
* '''[[GIXSGUI]]''': Visualization and reduction package for GISAXS. Requires the commerical Matlab software. Written by Zhang Jiang ([[APS]]).
** Citation: Z. Jiang [http://scripts.iucr.org/cgi-bin/paper?S1600576715004434 GIXSGUI: a MATLAB toolbox for grazing-incidence X-ray scattering data visualization and reduction, and indexing of buried three-dimensional periodic nanostructured films] ''J. Appl. Cryst.'' '''2015''', 48, 3, 917-926. [http://dx.doi.org/10.1107/S1600576715004434 doi: 10.1107/S1600576715004434]
** [https://www1.aps.anl.gov/Sectors/Sector-8/8-ID/Operations-and-Schedules/Useful-Links/Sector-8-GIXSGUI Official site.]
* '''[[GISAXSshop]]''': 2D visualization and reduction for GISAXS. Requires the Igor (Wavemetrics). Written by Byeongdu Lee ([[APS]]).
** [https://sites.google.com/site/byeongdu/software Official site.]

===Geared towards 1D data===
* '''NCNR SANS/USANS Package''': Set of tools for reducing SANS and USANS data. Requires the commercial IgorPro software.
** Citation: S.R. Kline [http://www.ncnr.nist.gov/programs/sans/pdf/publications/0569.pdf Reduction and Analysis of SANS and USANS Data using Igor Pro], ''J. Appl. Cryst.'' '''2006''', 39, 6, 895. [http://dx.doi.org/10.1107/S0021889806035059 doi:10.1107/S0021889806035059]
* '''Nika''': Conversion of 2D images into 1D for SAS. Requires commercial IgorPro software.
** [http://usaxs.xray.aps.anl.gov/staff/ilavsky/nika.html Official site.]
* '''Indra 2''': Reduction of USAXS data. Requires the commercial IgorPro software. Written for the 15ID instrument at [[APS]].
** [http://usaxs.xray.aps.anl.gov/staff/ilavsky/indra_2.html Official site.]
* '''DPDAK''': Open-source Python tool for analyzing large sets of SAXS data. Works on Linux and Windows.
** [https://dpdak.desy.de/index.php/Hauptseite Official site.]

==Data Modeling and Fitting==
These packages can predict scattering curves for various possible nano- or molecular- structures. Some of the packages allow fitting of experimental data.
===[[SAXS]]===
* '''NCNR SANS/USANS Package''': Can model form factors for many common object shapes in solution. Requires the commercial IgorPro software.
** Citation: S.R. Kline [http://www.ncnr.nist.gov/programs/sans/pdf/publications/0569.pdf Reduction and Analysis of SANS and USANS Data using Igor Pro] ''J. Appl. Cryst.'' '''2006''', 39, 6, 895. [http://dx.doi.org/10.1107/S0021889806035059 doi:10.1107/S0021889806035059]
* '''Irena''': Multiple tools for analyzing [[SAXS]], [[SANS]], [[USAXS]], and [[USANS]] data. Allows modeling of [[diffuse scattering]], form factors, reflectivity, etc. Requires the commercial IgorPro software.
** [http://usaxs.xray.aps.anl.gov/staff/ilavsky/irena.html Official site.]
* '''Scatter''': Targeted towards analysis of transmission-mode [[SAXS]] and [[SANS]]. Allows modeling of nano- and meso-structure materials (surfactants, lipids, micelles, vesicles, block-copolymers, etc.).
** Citation: S. Förster, L. Apostol and W. Bras [http://scripts.iucr.org/cgi-bin/paper?S0021889810008289 Scatter: software for the analysis of nano- and mesoscale small-angle scattering] ''J. Appl. Cryst.'' '''2010''', 43, 639. [http://dx.doi.org/10.1107/S0021889810008289 doi: 10.1107/S0021889810008289]
** [http://www.pci.uni-bayreuth.de/rg_foerster/en/Software/index.html Official site.]
* '''SASFit''': Combined fitting of 1D scattering curves.
** [https://kur.web.psi.ch/sans1/SANSSoft/sasfit.html Official site.]
* '''BayesApp.org''': Online tool for estimating distribution functions from SAS data.
** [http://www.bayesapp.org/ Official site.]
** Citation: Hansen [http://scripts.iucr.org/cgi-bin/paper?S1600576714013156 Update for BayesApp: a web site for analysis of small-angle scattering data] ''J. Appl. Cryst.'' '''2014''' [http://dx.doi.org/10.1107/S1600576714013156 doi: 10.1107/S1600576714013156]
* '''SCT''': Software to predict/fit [[SAS|small-angle scattering]] data from atomistic models of molecules and proteins.
** Citation: D. W. Wright and S. J. Perkins [http://scripts.iucr.org/cgi-bin/paper?po5031 SCT: a suite of programs for comparing atomistic models with small-angle scattering data] ''J. Appl. Cryst.'' '''2015''', 48 [http://dx.doi.org/10.1107/S1600576715007062 doi: 10.1107/S1600576715007062]
** [https://github.com/dww100/sct Official site.]

===[[BioSAXS]]===
* '''ScÅtter''': Java-based application for SAXS analysis. Developed by Robert Rambo (Diamond Light Source); previously developed at the SIBYLS beamline (12.3.1) of the [[ALS]].
** [http://www.bioisis.net/tutorial/9 Official site.]
* '''BioXTAS RAW''': Simple program for performing 1D [[Guinier plot|Guinier analysis]] for [[BioSAXS]] data. (Provided by [[CHESS]].)
** [http://bioxtasraw.sourceforge.net/ Official site], [http://sourceforge.net/projects/bioxtasraw/ download].
* '''ATSAS''': A suite of tools for small-angle scattering data of biological macromolecules.
** Citation: P. V. Konarev, M. V. Petoukhov, V. V. Volkov and D. I. Svergun [http://scripts.iucr.org/cgi-bin/paper?S0021889806004699 ATSAS 2.1, a program package for small-angle scattering data analysis] ''J. Appl. Cryst.'' '''2006''', 39, 277. [http://dx.doi.org/10.1107/S0021889806004699 doi: 10.1107/S0021889806004699]
** Citation: M. V. Petoukhov, D. Franke, A. V. Shkumatov, G. Tria, A. G. Kikhney, M. Gajda, C. Gorba, H. D. T. Mertens, P. V. Konarev and D. I. Svergun [http://scripts.iucr.org/cgi-bin/paper?S0021889812007662 New developments in the ATSAS program package for small-angle scattering data analysis] ''J. Appl. Cryst.'' '''2012''', 45, 342, [http://dx.doi.org/10.1107/S0021889812007662 doi: 10.1107/S0021889812007662]
** [http://www.embl-hamburg.de/biosaxs/software.html Official site.]
* '''Biomachina''': Visualization of low-resolution bead-based models of proteins from SAXS data.
** [http://situs.biomachina.org/tutorial_saxs.html#visual Official site.]
* '''ScatterBrain''': Cross-platform (Windows, OSX, Linux) IDL software, provided by Australian Synchrotron.
** [http://www.synchrotron.org.au/index.php/aussyncbeamlines/saxswaxs/software-saxswaxs Official site.]

===[[GISAXS]]===
* '''IsGISAXS''': GISAXS analysis and simulation software. Enables prediction of 2D scattering patterns, including the effects of [[DWBA]] and its variants. Written by Rémi Lazzari.
** Citation: R. Lazzari [http://scripts.iucr.org/cgi-bin/paper?S0021889802006088 IsGISAXS: a program for grazing-incidence small-angle X-ray scattering analysis from supported islands] ''J. Appl. Cryst.'' '''2002''', 35, 406-421. [http://dx.doi.org/10.1107/S0021889802006088 doi: 10.1107/S0021889802006088]
** [http://ln-www.insp.upmc.fr/axe4/Oxydes/IsGISAXS/isgisaxs.htm Official site.]
* '''FitGISAXS''': DWBA modeling. Requires commercial IgorPro software.
** [http://www.pprime.fr/?q=fr/nanoparticules-nanostructures Official site.]
* '''NANOCELL''': Simulates 2D diffraction patterns from single-crystals for GISAXS/GISANS geometry
** [http://faculty.washington.edu/h2/simulation.html Official site.]
** Citation: Tate MP, Urade VN, Kowalski JD, Wei TC, Hamilton BD, Eggiman BW, Hillhouse HW [http://pubs.acs.org/doi/abs/10.1021/jp0566008 Simulation and interpretation of 2D diffraction patterns from self-assembled nanostructured films at arbitrary angles of incidence: from grazing incidence (above the critical angle) to transmission perpendicular to the substrate] ''J. Phys. Chem. B'' '''2006''', 110 (20), 9882–9892. [http://dx.doi.org/10.1021/jp0566008 doi: 10.1021/jp0566008]
* '''[[BornAgain]]''': Python/C++ implementation of DWBA modeling (similar to IsGISAXS, but more modern and with lots of extensions). Allows for polarized [[GISANS]] and GISAXS simulation and fitting. Available on Linux, MacOS and Windows. Written by the [http://apps.jcns.fz-juelich.de/doku/sc/start Scientific Computing Group] at [http://www.mlz-garching.de/ MLZ Garching].
** Citation: C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke (2015), BornAgain - Software for simulating and fitting X-ray and neutron small-angle scattering at grazing incidence, http://www.bornagainproject.org
** [http://www.bornagainproject.org/ Official site.]
* '''[[HipGISAXS]]''': A high-performance (massively parallel) C++ software for simulating GISAXS data.
** Citation: S. Chourou, A. Sarje, X.S. Li, E. Chan, A. Hexemer, [http://scripts.iucr.org/cgi-bin/paper?nb5076 HipGISAXS: A High Performance Computing Code for Simulating Grazing Incidence X-Ray Scattering Data] ''Journal of Applied Crystallography'' '''2013''', 46, 6, 1781-1795. [http://dx.doi.org/10.1107/S0021889813025843 doi: 10.1107/S0021889813025843]
** Citation: A. Sarje, X.S. Li, S. Chourou, E. Chan, A. Hexemer, [http://dl.acm.org/citation.cfm?id=2389059 Massively Parallel X-ray Scattering Simulations] in Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (Supercomputing, SC'12), no. 46, pp. 46:1-46:11, November '''2012'''.
** [http://portal.nersc.gov/project/als/hipgisaxs/ Official site.]
* '''SimDiffraction''': Simulation of diffraction patterns.
** May be obtained by contacting [http://www.ntnu.edu/employees/dag.breiby Dag Werner Breiby], Dept. Physics, NTNU.
** Citation: D. W. Breiby, O. Bunk, J. W. Andreasen, H. T. Lemke and M. M. Nielsen [http://scripts.iucr.org/cgi-bin/paper?S0021889808001064 Simulating X-ray diffraction of textured films] ''J. Appl. Cryst.'' '''2008''', 41, 262-271. [http://dx.doi.org/10.1107/S0021889808001064 doi: 10.1107/S0021889808001064]
* '''Diffraction Pattern Calculator (DPC) toolkit''': User-friendly GUI for determining [[unit-cell]] [[lattice]] parameters in [[GIWAXS]] data.
** Citation: A.K. Hailey, A.M. Hiszpanski, D.-M. Smilgies and Y.-L. Loo [http://scripts.iucr.org/cgi-bin/paper?fs5084 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] ''Journal of Applied Crystallography'' '''2014''', 47. [http://dx.doi.org/10.1107/S1600576714022006 doi: 10.1107/S1600576714022006]
** [http://www.princeton.edu/cbe/people/faculty/loo/group/software Official site.]

===[[Reflectivity]]===
* '''Reflfit''': NIST software for fitting neutron (or x-ray) reflectivity curves.
** [http://www.ncnr.nist.gov/programs/reflect/data_reduction/software/ Official site.]
* '''Motofit''': Co-refinement of multiple contrast reflectometry data (x-ray or neutron). Written by Andrew Nelson, ANSTO, Australia.
** Citation: Nelson, A. [http://www.iucr.org/cgi-bin/paper?ce5001 Co-refinement of multiple contrast neutron / X-ray reflectivity data using MOTOFIT] ''Journal of Applied Crystallography'' '''2006''', 39, 273-276. [http://dx.doi.org/10.1107/S0021889806005073 doi: 10.1107/S0021889806005073]
** [http://motofit.sourceforge.net/ Official site.]
* '''Yanera''': "Yet Another NEutron Reflectivity Analyzer", provides an open-source C++ implementation of the [[Parratt formalism]]. Written by Thad Harroun (Brock University), with contributions from [[Kevin Yager]].
** [http://www.physics.brocku.ca/~tharroun/yanera/index.html Official site.]
* '''GA refl''': Simultaneous fitting of x-ray and neutron polarized reflectometry data.
** [http://www.ncnr.nist.gov/programs/reflect/data_reduction/software/garefl.html Official site.]
* '''Simulreflec''': Calculate reflectivity of magnetic multiplayer systems.
** [http://www-llb.cea.fr/prism/programs/simulreflec/simulreflec.html Official site.]
* '''AFIT''': Fitting of reflectometry data. ([http://physchem.ox.ac.uk/%7erkt/AFit.zip download])
* '''Parratt32''': Windows GUI implementing the Parratt formalism. ([http://www.hmi.de/bensc/instrumentation/instrumente/v6/refl/parratt_en.htm link])
* '''Drydoc and Wetdoc''': Multiple contrast data fitting. ([http://www.studsvik.uu.se/research/NR/drydoc.htm link])
* '''Surface''': Analysis of specular reflectivity. ([http://www.isis.rl.ac.uk/largescale/SURF/technical/surface.htm link])
* '''Polly''': Polarized neutron reflectometry. ([http://www.isis.rl.ac.uk/largescale/CRISP/downloads/POLLY/reg_form.htm link])
* '''Superfit''': Specular and diffuse neutron reflectivity. ([http://www.mf.mpg.de/en/abteilungen/dosch/software/software_en.shtml link])
* '''GenX''': Parratt formalism combined with genetic algorithm.
** Citation: Matts Björck and Gabriella Andersson [http://journals.iucr.org/j/issues/2007/06/00/aj5091/aj5091bdy.html GenX: an extensible X-ray reflectivity refinement program utilizing differential evolution] ''J. Appl. Cryst.'' '''2007''', 40, 1174-1178. [http://dx.doi.org/10.1107/S0021889807045086 doi: 10.1107/S0021889807045086 ]
** [http://genx.sourceforge.net/ Official site.]

===[[Crystallography]]===
* [http://www.iucr.org/resources/other-directories/software IUCr Crystallographic software list]
* [http://biophysics.med.jhmi.edu/cgi-bin/software/software_list?category=crystallography X-ray Lab Crystallography Software list]
* '''Sir2014''': Crystal structure solving for small/medium structures, from [[x-ray]] or [[electron]] diffraction data.
** [http://wwwba.ic.cnr.it/content/sir2011-v10 Official site.]
** Citation: M. C. Burla, R. Caliandro, B. Carrozzini, G. L. Cascarano, C. Cuocci, C. Giacovazzo, M. Mallamo, A. Mazzone and G. Polidori [http://scripts.iucr.org/cgi-bin/paper?kk5193 Crystal structure determination and refinement via SIR2014] ''J. Appl. Cryst.'' '''2015''', 48, 306-309. [http://dx.doi.org/10.1107/S1600576715001132 doi: 10.1107/S1600576715001132]
* '''SynchWeb & ISPyB''': Web interface for tracking samples and data (focused on [[MX]]).
** Citation: S. J. Fisher, K. E. Levik, M. A. Williams, A. W. Ashton and K. E. McAuley [http://scripts.iucr.org/cgi-bin/paper?fs5101 SynchWeb: a modern interface for ISPyB] ''J. Appl. Cryst.'' '''2015''', 28. [http://dx.doi.org/10.1107/S1600576715004847 doi: 10.1107/S1600576715004847]

==Computing [[Materials]] Properties==
* '''X-Ray Interactions With Matter''': CXRO/LBL web-portal with various calculators for x-ray interaction parameters.
** [http://henke.lbl.gov/optical_constants/ Official site].
* '''NCNR''': NIST Center for Neutron Research web-based calculator for Neutron [[SLD|Scattering Length Density]] and [[Absorption]].
** [http://www.ncnr.nist.gov/resources/activation/ Official site].
* '''pyFPRIME and ABSORB''': [[APS]] software for computing approximate x-ray scattering cross sections.
** [https://subversion.xor.aps.anl.gov/trac/pyFprime/ Official site].

==Custom==
It is of course possible to code your own software for modeling or fitting scattering data. This is not as difficult as it may at first seem. The fundamental scattering equations are well-known (c.f. [[scattering]], [[Fourier transform]], [[Form Factor]], [[Structure Factor]], [[Lattice Factor]]), and can be brute-force solved numerical. Or, they can be solved (or simplified) analytically for a particular case. Many modern programming languages provide libraries for numerical integration, fitting, minimizing multi-dimensional parameter spaces, etc. (e.g. [[Python]] is particularly clean and powerful).

==See Also==
* [http://smallangle.org/content/software#Reduction-Visualisation SAS Portal Software List]
* [http://www.ccp14.ac.uk/recomm/ Resources for Crystallographic Software Developers]
* [[Data formats]]
** [[NeXus data format]]

Software

2015-06-01T21:37:33Z

Strzalka: Updated link for GIXSGUI official site.

A common question for new [[GISAXS]] users is: "What software can I use to analyze my data?" Unfortunately, there is no single package that will allow you to perform any possible analysis. This is in part due to the diversity of possible kinds of data analysis one might want to do on [[GISAXS]] or [[GIWAXS]] images. The following lists a variety of packages that are available.

==Data Viewing, Reduction, and Simple Analysis==
These packages provide ways to view data, and perform simple operations (linecuts, etc.).
===Geared towards 2D data===
* '''Fit2D''': A well-known package for treatment and conversion 2D scattering images.
** [http://www.esrf.eu/computing/scientific/FIT2D/ Official site.]
** [http://staff.chess.cornell.edu/~smilgies/D-lineNotes/GISAXS-at-D-line/fit2d-GIXS-primer.html Fit2D primer.]
** [http://g-line.chess.cornell.edu/G-lineStatus/G-lineManuals/CheatSheets/FIT2D_MAIN.html Fit2D hints page.]
* '''Datasqueeze''': Graphical tool for analyzing 2D detector images.
** [http://www.datasqueezesoftware.com/ Official site.]
* '''ImageJ''': A generic tool for image treatment and analysis. Can be used to open and process x-ray detector images.
** [http://rsb.info.nih.gov/ij/ Official site.]
* '''[[view.gtk]]''': A simple interface for viewing 2D data, calibrating your data into ''q''-space, and extracting linecuts. Written by Lin Yang for the [[X9]] beamline at [[NSLS]]. Installation requires (free) GTK libraries.
* '''[[pyXS]]''': Python scripts (with C++ backend) for performing analysis of 2D data.
** [http://www.bnl.gov/ps/x9/software/pyXS.asp Official site.]
* '''[[GIXSGUI]]''': Visualization and reduction package for GISAXS. Requires the commerical Matlab software. Written by Zhang Jiang ([[APS]]).
** Citation: Z. Jiang [http://scripts.iucr.org/cgi-bin/paper?S1600576715004434 GIXSGUI: a MATLAB toolbox for grazing-incidence X-ray scattering data visualization and reduction, and indexing of buried three-dimensional periodic nanostructured films] ''J. Appl. Cryst.'' '''2015''', 48. [http://dx.doi.org/10.1107/S1600576715004434 doi: 10.1107/S1600576715004434]
** [https://www1.aps.anl.gov/Sectors/Sector-8/8-ID/Operations-and-Schedules/Useful-Links/Sector-8-GIXSGUI Official site.]
* '''[[GISAXSshop]]''': 2D visualization and reduction for GISAXS. Requires the Igor (Wavemetrics). Written by Byeongdu Lee ([[APS]]).
** [https://sites.google.com/site/byeongdu/software Official site.]

===Geared towards 1D data===
* '''NCNR SANS/USANS Package''': Set of tools for reducing SANS and USANS data. Requires the commercial IgorPro software.
** Citation: S.R. Kline [http://www.ncnr.nist.gov/programs/sans/pdf/publications/0569.pdf Reduction and Analysis of SANS and USANS Data using Igor Pro], ''J. Appl. Cryst.'' '''2006''', 39, 6, 895. [http://dx.doi.org/10.1107/S0021889806035059 doi:10.1107/S0021889806035059]
* '''Nika''': Conversion of 2D images into 1D for SAS. Requires commercial IgorPro software.
** [http://usaxs.xray.aps.anl.gov/staff/ilavsky/nika.html Official site.]
* '''Indra 2''': Reduction of USAXS data. Requires the commercial IgorPro software. Written for the 15ID instrument at [[APS]].
** [http://usaxs.xray.aps.anl.gov/staff/ilavsky/indra_2.html Official site.]
* '''DPDAK''': Open-source Python tool for analyzing large sets of SAXS data. Works on Linux and Windows.
** [https://dpdak.desy.de/index.php/Hauptseite Official site.]

==Data Modeling and Fitting==
These packages can predict scattering curves for various possible nano- or molecular- structures. Some of the packages allow fitting of experimental data.
===[[SAXS]]===
* '''NCNR SANS/USANS Package''': Can model form factors for many common object shapes in solution. Requires the commercial IgorPro software.
** Citation: S.R. Kline [http://www.ncnr.nist.gov/programs/sans/pdf/publications/0569.pdf Reduction and Analysis of SANS and USANS Data using Igor Pro] ''J. Appl. Cryst.'' '''2006''', 39, 6, 895. [http://dx.doi.org/10.1107/S0021889806035059 doi:10.1107/S0021889806035059]
* '''Irena''': Multiple tools for analyzing [[SAXS]], [[SANS]], [[USAXS]], and [[USANS]] data. Allows modeling of [[diffuse scattering]], form factors, reflectivity, etc. Requires the commercial IgorPro software.
** [http://usaxs.xray.aps.anl.gov/staff/ilavsky/irena.html Official site.]
* '''Scatter''': Targeted towards analysis of transmission-mode [[SAXS]] and [[SANS]]. Allows modeling of nano- and meso-structure materials (surfactants, lipids, micelles, vesicles, block-copolymers, etc.).
** Citation: S. Förster, L. Apostol and W. Bras [http://scripts.iucr.org/cgi-bin/paper?S0021889810008289 Scatter: software for the analysis of nano- and mesoscale small-angle scattering] ''J. Appl. Cryst.'' '''2010''', 43, 639. [http://dx.doi.org/10.1107/S0021889810008289 doi: 10.1107/S0021889810008289]
** [http://www.pci.uni-bayreuth.de/rg_foerster/en/Software/index.html Official site.]
* '''SASFit''': Combined fitting of 1D scattering curves.
** [https://kur.web.psi.ch/sans1/SANSSoft/sasfit.html Official site.]
* '''BayesApp.org''': Online tool for estimating distribution functions from SAS data.
** [http://www.bayesapp.org/ Official site.]
** Citation: Hansen [http://scripts.iucr.org/cgi-bin/paper?S1600576714013156 Update for BayesApp: a web site for analysis of small-angle scattering data] ''J. Appl. Cryst.'' '''2014''' [http://dx.doi.org/10.1107/S1600576714013156 doi: 10.1107/S1600576714013156]
* '''SCT''': Software to predict/fit [[SAS|small-angle scattering]] data from atomistic models of molecules and proteins.
** Citation: D. W. Wright and S. J. Perkins [http://scripts.iucr.org/cgi-bin/paper?po5031 SCT: a suite of programs for comparing atomistic models with small-angle scattering data] ''J. Appl. Cryst.'' '''2015''', 48 [http://dx.doi.org/10.1107/S1600576715007062 doi: 10.1107/S1600576715007062]
** [https://github.com/dww100/sct Official site.]

===[[BioSAXS]]===
* '''ScÅtter''': Java-based application for SAXS analysis. Developed by Robert Rambo (Diamond Light Source); previously developed at the SIBYLS beamline (12.3.1) of the [[ALS]].
** [http://www.bioisis.net/tutorial/9 Official site.]
* '''BioXTAS RAW''': Simple program for performing 1D [[Guinier plot|Guinier analysis]] for [[BioSAXS]] data. (Provided by [[CHESS]].)
** [http://bioxtasraw.sourceforge.net/ Official site], [http://sourceforge.net/projects/bioxtasraw/ download].
* '''ATSAS''': A suite of tools for small-angle scattering data of biological macromolecules.
** Citation: P. V. Konarev, M. V. Petoukhov, V. V. Volkov and D. I. Svergun [http://scripts.iucr.org/cgi-bin/paper?S0021889806004699 ATSAS 2.1, a program package for small-angle scattering data analysis] ''J. Appl. Cryst.'' '''2006''', 39, 277. [http://dx.doi.org/10.1107/S0021889806004699 doi: 10.1107/S0021889806004699]
** Citation: M. V. Petoukhov, D. Franke, A. V. Shkumatov, G. Tria, A. G. Kikhney, M. Gajda, C. Gorba, H. D. T. Mertens, P. V. Konarev and D. I. Svergun [http://scripts.iucr.org/cgi-bin/paper?S0021889812007662 New developments in the ATSAS program package for small-angle scattering data analysis] ''J. Appl. Cryst.'' '''2012''', 45, 342, [http://dx.doi.org/10.1107/S0021889812007662 doi: 10.1107/S0021889812007662]
** [http://www.embl-hamburg.de/biosaxs/software.html Official site.]
* '''Biomachina''': Visualization of low-resolution bead-based models of proteins from SAXS data.
** [http://situs.biomachina.org/tutorial_saxs.html#visual Official site.]
* '''ScatterBrain''': Cross-platform (Windows, OSX, Linux) IDL software, provided by Australian Synchrotron.
** [http://www.synchrotron.org.au/index.php/aussyncbeamlines/saxswaxs/software-saxswaxs Official site.]

===[[GISAXS]]===
* '''IsGISAXS''': GISAXS analysis and simulation software. Enables prediction of 2D scattering patterns, including the effects of [[DWBA]] and its variants. Written by Rémi Lazzari.
** Citation: R. Lazzari [http://scripts.iucr.org/cgi-bin/paper?S0021889802006088 IsGISAXS: a program for grazing-incidence small-angle X-ray scattering analysis from supported islands] ''J. Appl. Cryst.'' '''2002''', 35, 406-421. [http://dx.doi.org/10.1107/S0021889802006088 doi: 10.1107/S0021889802006088]
** [http://ln-www.insp.upmc.fr/axe4/Oxydes/IsGISAXS/isgisaxs.htm Official site.]
* '''FitGISAXS''': DWBA modeling. Requires commercial IgorPro software.
** [http://www.pprime.fr/?q=fr/nanoparticules-nanostructures Official site.]
* '''NANOCELL''': Simulates 2D diffraction patterns from single-crystals for GISAXS/GISANS geometry
** [http://faculty.washington.edu/h2/simulation.html Official site.]
** Citation: Tate MP, Urade VN, Kowalski JD, Wei TC, Hamilton BD, Eggiman BW, Hillhouse HW [http://pubs.acs.org/doi/abs/10.1021/jp0566008 Simulation and interpretation of 2D diffraction patterns from self-assembled nanostructured films at arbitrary angles of incidence: from grazing incidence (above the critical angle) to transmission perpendicular to the substrate] ''J. Phys. Chem. B'' '''2006''', 110 (20), 9882–9892. [http://dx.doi.org/10.1021/jp0566008 doi: 10.1021/jp0566008]
* '''[[BornAgain]]''': Python/C++ implementation of DWBA modeling (similar to IsGISAXS, but more modern and with lots of extensions). Allows for polarized [[GISANS]] and GISAXS simulation and fitting. Available on Linux, MacOS and Windows. Written by the [http://apps.jcns.fz-juelich.de/doku/sc/start Scientific Computing Group] at [http://www.mlz-garching.de/ MLZ Garching].
** Citation: C. Durniak, M. Ganeva, G. Pospelov, W. Van Herck, J. Wuttke (2015), BornAgain - Software for simulating and fitting X-ray and neutron small-angle scattering at grazing incidence, http://www.bornagainproject.org
** [http://www.bornagainproject.org/ Official site.]
* '''[[HipGISAXS]]''': A high-performance (massively parallel) C++ software for simulating GISAXS data.
** Citation: S. Chourou, A. Sarje, X.S. Li, E. Chan, A. Hexemer, [http://scripts.iucr.org/cgi-bin/paper?nb5076 HipGISAXS: A High Performance Computing Code for Simulating Grazing Incidence X-Ray Scattering Data] ''Journal of Applied Crystallography'' '''2013''', 46, 6, 1781-1795. [http://dx.doi.org/10.1107/S0021889813025843 doi: 10.1107/S0021889813025843]
** Citation: A. Sarje, X.S. Li, S. Chourou, E. Chan, A. Hexemer, [http://dl.acm.org/citation.cfm?id=2389059 Massively Parallel X-ray Scattering Simulations] in Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (Supercomputing, SC'12), no. 46, pp. 46:1-46:11, November '''2012'''.
** [http://portal.nersc.gov/project/als/hipgisaxs/ Official site.]
* '''SimDiffraction''': Simulation of diffraction patterns.
** May be obtained by contacting [http://www.ntnu.edu/employees/dag.breiby Dag Werner Breiby], Dept. Physics, NTNU.
** Citation: D. W. Breiby, O. Bunk, J. W. Andreasen, H. T. Lemke and M. M. Nielsen [http://scripts.iucr.org/cgi-bin/paper?S0021889808001064 Simulating X-ray diffraction of textured films] ''J. Appl. Cryst.'' '''2008''', 41, 262-271. [http://dx.doi.org/10.1107/S0021889808001064 doi: 10.1107/S0021889808001064]
* '''Diffraction Pattern Calculator (DPC) toolkit''': User-friendly GUI for determining [[unit-cell]] [[lattice]] parameters in [[GIWAXS]] data.
** Citation: A.K. Hailey, A.M. Hiszpanski, D.-M. Smilgies and Y.-L. Loo [http://scripts.iucr.org/cgi-bin/paper?fs5084 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] ''Journal of Applied Crystallography'' '''2014''', 47. [http://dx.doi.org/10.1107/S1600576714022006 doi: 10.1107/S1600576714022006]
** [http://www.princeton.edu/cbe/people/faculty/loo/group/software Official site.]

===[[Reflectivity]]===
* '''Reflfit''': NIST software for fitting neutron (or x-ray) reflectivity curves.
** [http://www.ncnr.nist.gov/programs/reflect/data_reduction/software/ Official site.]
* '''Motofit''': Co-refinement of multiple contrast reflectometry data (x-ray or neutron). Written by Andrew Nelson, ANSTO, Australia.
** Citation: Nelson, A. [http://www.iucr.org/cgi-bin/paper?ce5001 Co-refinement of multiple contrast neutron / X-ray reflectivity data using MOTOFIT] ''Journal of Applied Crystallography'' '''2006''', 39, 273-276. [http://dx.doi.org/10.1107/S0021889806005073 doi: 10.1107/S0021889806005073]
** [http://motofit.sourceforge.net/ Official site.]
* '''Yanera''': "Yet Another NEutron Reflectivity Analyzer", provides an open-source C++ implementation of the [[Parratt formalism]]. Written by Thad Harroun (Brock University), with contributions from [[Kevin Yager]].
** [http://www.physics.brocku.ca/~tharroun/yanera/index.html Official site.]
* '''GA refl''': Simultaneous fitting of x-ray and neutron polarized reflectometry data.
** [http://www.ncnr.nist.gov/programs/reflect/data_reduction/software/garefl.html Official site.]
* '''Simulreflec''': Calculate reflectivity of magnetic multiplayer systems.
** [http://www-llb.cea.fr/prism/programs/simulreflec/simulreflec.html Official site.]
* '''AFIT''': Fitting of reflectometry data. ([http://physchem.ox.ac.uk/%7erkt/AFit.zip download])
* '''Parratt32''': Windows GUI implementing the Parratt formalism. ([http://www.hmi.de/bensc/instrumentation/instrumente/v6/refl/parratt_en.htm link])
* '''Drydoc and Wetdoc''': Multiple contrast data fitting. ([http://www.studsvik.uu.se/research/NR/drydoc.htm link])
* '''Surface''': Analysis of specular reflectivity. ([http://www.isis.rl.ac.uk/largescale/SURF/technical/surface.htm link])
* '''Polly''': Polarized neutron reflectometry. ([http://www.isis.rl.ac.uk/largescale/CRISP/downloads/POLLY/reg_form.htm link])
* '''Superfit''': Specular and diffuse neutron reflectivity. ([http://www.mf.mpg.de/en/abteilungen/dosch/software/software_en.shtml link])
* '''GenX''': Parratt formalism combined with genetic algorithm.
** Citation: Matts Björck and Gabriella Andersson [http://journals.iucr.org/j/issues/2007/06/00/aj5091/aj5091bdy.html GenX: an extensible X-ray reflectivity refinement program utilizing differential evolution] ''J. Appl. Cryst.'' '''2007''', 40, 1174-1178. [http://dx.doi.org/10.1107/S0021889807045086 doi: 10.1107/S0021889807045086 ]
** [http://genx.sourceforge.net/ Official site.]

===[[Crystallography]]===
* [http://www.iucr.org/resources/other-directories/software IUCr Crystallographic software list]
* [http://biophysics.med.jhmi.edu/cgi-bin/software/software_list?category=crystallography X-ray Lab Crystallography Software list]
* '''Sir2014''': Crystal structure solving for small/medium structures, from [[x-ray]] or [[electron]] diffraction data.
** [http://wwwba.ic.cnr.it/content/sir2011-v10 Official site.]
** Citation: M. C. Burla, R. Caliandro, B. Carrozzini, G. L. Cascarano, C. Cuocci, C. Giacovazzo, M. Mallamo, A. Mazzone and G. Polidori [http://scripts.iucr.org/cgi-bin/paper?kk5193 Crystal structure determination and refinement via SIR2014] ''J. Appl. Cryst.'' '''2015''', 48, 306-309. [http://dx.doi.org/10.1107/S1600576715001132 doi: 10.1107/S1600576715001132]
* '''SynchWeb & ISPyB''': Web interface for tracking samples and data (focused on [[MX]]).
** Citation: S. J. Fisher, K. E. Levik, M. A. Williams, A. W. Ashton and K. E. McAuley [http://scripts.iucr.org/cgi-bin/paper?fs5101 SynchWeb: a modern interface for ISPyB] ''J. Appl. Cryst.'' '''2015''', 28. [http://dx.doi.org/10.1107/S1600576715004847 doi: 10.1107/S1600576715004847]

==Computing [[Materials]] Properties==
* '''X-Ray Interactions With Matter''': CXRO/LBL web-portal with various calculators for x-ray interaction parameters.
** [http://henke.lbl.gov/optical_constants/ Official site].
* '''NCNR''': NIST Center for Neutron Research web-based calculator for Neutron [[SLD|Scattering Length Density]] and [[Absorption]].
** [http://www.ncnr.nist.gov/resources/activation/ Official site].
* '''pyFPRIME and ABSORB''': [[APS]] software for computing approximate x-ray scattering cross sections.
** [https://subversion.xor.aps.anl.gov/trac/pyFprime/ Official site].

==Custom==
It is of course possible to code your own software for modeling or fitting scattering data. This is not as difficult as it may at first seem. The fundamental scattering equations are well-known (c.f. [[scattering]], [[Fourier transform]], [[Form Factor]], [[Structure Factor]], [[Lattice Factor]]), and can be brute-force solved numerical. Or, they can be solved (or simplified) analytically for a particular case. Many modern programming languages provide libraries for numerical integration, fitting, minimizing multi-dimensional parameter spaces, etc. (e.g. [[Python]] is particularly clean and powerful).

==See Also==
* [http://smallangle.org/content/software#Reduction-Visualisation SAS Portal Software List]
* [http://www.ccp14.ac.uk/recomm/ Resources for Crystallographic Software Developers]
* [[Data formats]]
** [[NeXus data format]]

Tutorials

2014-06-04T14:32:20Z

Strzalka: Fixed typo in Zhang's name.

This page provides tutorials (basic and advanced) to help [[GISAXS]] users with experiment design, data analysis, and data modeling:

==Slides from Presentations==
* '''[http://gisaxs.com/files/gisaxs_jiang_ACA.pdf Theory of GISAXS]''', Zhang Jiang ([[APS|Advanced Photon Source]], Argonne National Laboratory): Introduction to the theoretical methods required for correctly analyzing and modeling GISAXS data, including the [[DWBA]] and [[X-ray waveguiding|waveguide effects]].
* '''[http://gisaxs.com/files/Strzalka.pdf GIXS: hands-on data analysis]''', Joe Strzalka ([[APS|Advanced Photon Source]], Argonne National Laboratory): An introduction to practical aspects of interpreting and analyzing grazing-incidence data, including the use of [[GIXSGUI]] software.
* '''[http://gisaxs.com/files/YagerACA_05.pdf GISAXS/GIWAXS Data Analysis: Thinking in Reciprocal-Space]''', [[Kevin Yager]] ([[National Synchrotron Light Source]] and Center for Functional Nanomaterials, [[BNL|Brookhaven National Laboratory]]): An introduction to the interpretation and basic analysis of GISAXS data, in particular in relation to the concept of how the experiment probes a slice through the 3D [[reciprocal-space]].
* '''[http://gisaxs.com/files/Van%20Herck_DataAnalysisWithBA.pdf GISAS Data Analysis with BornAgain]''', Walter Van Herck (Jülich Centre for Neutron Science JCNS, Germany): Description of how to use the [[BornAgain]] software for quantitatively modeling and fitting GISAXS data.
* '''[http://gisaxs.com/files/2014_Hexemer.pdf High performance GISAXS]''', Alexander Hexemer ([[ALS|Advanced Light Source]], Lawrence Berkeley National Laboratory): Description of recent developments in the high-throughput and high-performance modeling of GISAXS data, in particular describing the [[HipGISAXS]] software.