SLAC National Accelerator Laboratory
BL4-2 Biological Small Angle Scattering/Diffraction

SasTool for Solution Data Analysis

SasTool GUI version help
SasTool command line version help

For solution scattering experiments, the scattering of the specimens (sample) in solution and the scattering of the solvent (buffer) are measured. During data analysis, the intensity of buffer scattering is subtracted from that of the sample to obtain the signal responsible by the difference between buffer and sample. At low sample concentrations or larger scattering angles the scattering of the buffer is often nearly as intense as that of the sample. Consequently even small fluctuations of beam intensity can have a big effect on the result if corrections are not applied. In addition, the errors of subtracted scattering patterns have to be determined from the actual intensities in the original data. Since scattering of the sample may change during an experiment due to radiation damage or movement of the beam, it is essential to make several successive measurements on the same sample. Those frames have to be analyzed for differences before they are added up.

When the linear gas proportional detector was used on BL4-2 for solution scattering experiments, the software SAPOKO performed all these tasks. This software cannot be directly used with area detectors; instead, the data would have to be treated with several different programs to obtain the same results, and the user would have to interfere several times during the process. With the routine use of the Mar165 for solution scattering, the need for new automated data reduction software for area detectors became apparent. Our program SasTool integrates the 2-dimensional scattering patterns and reduces them to a 1-dimensional scattering profile. It performs all above mentioned tasks, and more.

There are two versions of SasTool. One is command line version, and the other GUI version. You can download them here.

The command line version is named SasTool.exe while the GUI version SasToolDLG.exe. To run SasTool.exe, the user issues the command from the command line and needs first to create a text file that includes parameters SasTool.exe will use. The parameters include log file name, beam intensity normalization, image file names, beam center position in the images, conversion from pixel size to q values, etc. To run SasToolDLG.exe, the user simply double clicks the application icon. The user can either import a previously generated parameters file, or start from the scratch by specify each and every parameters SasToolDLG.exe will use for data analysis. SasToolDLG.exe also allows the user to select a directory to monitor and process the new image files that are being created. It also has the plotting capability.

While SasToolDLG.exe has more capabilities, it is using SasTool.exe for data processing. SasTool.exe first reads the parameters file and sets the parameters, then processes series of image files based on the parameters. After one or more series are completed, parameters can be changed and more series of images can be processed with the new parameters, within just one parameters file. The image processing proceeds in the following order, read the tiff raw image file, obtain and subtract offsets, normalize for beam intensity, convert 2-D grid data to 1-D distance from beam center, calculate statistics for each image frame (average and standard deviation) (this generates a .dat file for each frame), compare statistics and use them to include or reject frames in the sum of the whole series (this generates a .tot file for each series), and subtract the buffer intensity from the sample intensity (this generates a .sub file for each pair of buffer and sample series). A log file is generated each time SasTool.exe is run, and its file name and location is specified by the user in the parameters file.

SasTool.exe and SasToolDLG.exe can be used on a regular Windows XP PC and performs an analysis of a single frame in less than one second. The output file formats are plain ASCII files which can be read with any text editor and are in a format that is used by other SAXS data analysis program packages. The files have three columns: distance from beam center (in pixels) or q-value, intensity, and error. Currently, SasTool.exe is routinely used to process the Mar165 data, and has improved the quality of the data and the pace of the entire analysis significantly. The newer SasToolDLG.exe will allow users more easily to monitor the progress of data acquisition.

SasTool GUI version help
SasTool command line version help

Download SasTool