Data reduction

To make your data processing easier, we provide the essential software tools for data reduction.

  • SAXS images are "reduced" by performing a number of necessary corrections (intensity normalization, background subtraction, q-calibration, ...), followed by an azimuthal integration. The data formats currently supported are: BSL, edf, tiff, and hdf5/nexus.
  • WAXS data are processed in order to correct the geometrical distortion due to detector's position, and to calculate the diffracted intensity via azimuthal integration. The correction steps are performed using matlab based macros (see short presentation bellow).

The User's survival manual explains in detail how to use these procedures.

The data reduction programs will be set up by your local contact at the beginning of your experiment.

If however you prefer to perform data reduction by yourself, here are a few links that might be useful:

FIT2D

FIT2D is both a general purpose and specialist 1 and 2 dimensional data analysis program, quite popular among ESRF users. It can be used for both interactive and "batch" data processing.

You may need to enter the detector pixel size: 172 µm (square) for the Pilatus detectors

pyFAI

pyFAI-calib can be used to calibrate the diffraction setup geometry based on Debye-Sherrer ring images without much a priori knowledge of your setup, but you must correctly identify the diffraction rings based on a calibrant or a “d-spacing” file (containing the spacings of Miller planes in Ångstroms of your calibrant; largest first). Ring 0 corresponds to the largest d-spacing in the file, but is not always the first you can see on the detector - the program needs to be told the right number! You also need to know the X-ray wavelength. Inside the ESRF the program can be called from a LINUX window.

Example use for SAXS Pilatus 1M detector at 12keV (1.033Å) with silver behenate calibrant: pyFAI-calib -w 1.033 -D pilatus1m -c AgBh.D datafilename.edf

If using the WAXS Pilatus 300K-W detector use: -D pilatus300kw

pyFAI-saxs uses the parameters obtained with pyFAI-calib (output as a file with extension .poni) to perform azimuthal integrations with output by default in Intensity vs q (in nm-1)  giving a file with extension .dat. Output is possible with units of A-1 or as I vs scattering angle 2theta (degrees) or with a user defined extension.  The mask can be generated using FIT2D

Example use: pyFAI-saxs -m maskfile.msk -p calibrantFilename.poni -n 2000 dataFilename.edf

ConeX ConeX is a program for the angular calibration of flat 2D detectors in the context of scattering by isotropic samples, notably of X-rays. The purpose of the software is to average the 2D images recorded by the detector into 1D scattering patterns.
Follow the link to get the software package.

More details here: data reduction

 

Data analysis

Scatter We have been involved in the development of the program Scatter that is able to analyse small-angle X-ray (SAXS) and neutron scattering (SANS) curves and patterns of nano- and mesoscopically structured materials such as surfactant, lipid and polymeric micelles and vesicles, lyotropic phases, block copolymers, core/shell-nanoparticles, nanocomposites and mesoporous materials. It in particular can model and fit 2-dimensional scattering patterns and allows the automated, non-interactive analysis of large series of data files.
Follow the link to read more and to get the software package.
OMIC tools A suite of programs particularly useful for analysing SAXS data from biological macromolecules
Information content How much information do you have in your SAXS profile? When is your model a good fit to the data?  Rob Rambo's information theory led analysis is worth reading. doi: 10.1038/nature12070

 

Detector response

When you proceed to data reduction, you may need the response of the detector you used:

Pilatus detectors do not require correction for detector response (they do require a mask for dead and obstructed areas)

Other links

CCP13 CCP13 is the Collaborative Computational Project for fibre diffraction.
The project has been refunded to support research fellows working on data extraction from diffraction patterns recorded at x-ray and neutron beam sources.
The CCP13 suite has been installed on a variety of platforms running UNIX based operating systems.
canSAS Collective Action for Nomadic Small-Angle Scatterers