Data Processing and Analysis

HDF5 files

Opening and viewing HDF5 files

To open the HDF5 files, this requires a specific HDF5 file viewer. We recommend the following options:

• Visual Studio Code – with H5Web extension, can open files up to 2GB

  • Note the SEC-SAXS data files are >2GB so will not open in this software

• myHDF5 website (developed and maintained by ESRF) - View HDF5 files of all sizes

Navigating HDF5 files

Open

Reduced data

The 2D scattering data is reduced by a script written in-house by the beamline scientists using pyFai. The reduction algorithm outputs ASCII files (.dat) containing the values of the scattering angle [q (Å^-1)], intensity [I(cm^-1)] and uncertainty (cm^-1).

Specific details relating to each reduction can be found within each reduced file by opening in a text-editing software (e.g. TextPad, Notepad).

SEC-SAXS uv absorbance data

Calculated absorbance values can be found in the subfolder “absorbances” within your experiment folder produced during the beamtime. The absorbance values are written as .csv files containing the timestamps, calculated absorbances and time (minutes).

Absorbances are calculated from the raw intensities on the spectrometer for the specified wavelengths. The default wavelengths are 260 nm and 280 nm.

Recommended software for data processing/analysis

• SAS-View: https://www.sasview.org/

• ATSAS Software package: https://www.embl-hamburg.de/biosaxs/download.html

• BioXTAS RAW (relies on some ATSAS programs): https://bioxtas-raw.readthedocs.io/en/latest/