scatterBrain First Steps

Owned by SAXS Cluster (Unlicensed)
Nov 09, 2021
6 min read

Page Index


This 'First Steps' section provides a guide to the various files that scatterBrain uses to correctly display SAXS images and calculate integrated SAXS profiles. It also provides a guide to starting the program and loading SAXS data ready for further work. Information on using the various features of scatterBrain for displaying, reducing and analysing data are given further in the manual: Using The Plot Window and Using The Image Window 

All of the screenshots shown in this section were taken from the Windows version of the scatterBrain software. The appearance of scatterBrain on the Linux and OS X platforms may be different, due to an underlying issue with IDL.


Starting scatterBrain

The files required to start scatterBrain are detailed as the final points of the Recommended Installation and Alternative Installation. The Recommended Installation allows the straightforward use of a .exe, .sh or .app file to open scatterBrain, while the Alternative Installation requires IDL and the .sav file.

  • Upon starting scatterBrain after the Recommended Installation method, the user is greeted with a confirmation window
  • Click on the 'scatterBrain Analysis' button to continue loading scatterBrain
  • The IDL splash screen will then appear, click anywhere on this screen to continue loading scatterBrain
    • The IDL splash screen appears due to using the IDL virtual machine. Purchasing a full IDL licence is the only way to remove this

  

 scatterBrain Welcome Screen                                       IDL Virtual Machine Splash Screen       

If the Alternative Installation method has been used these windows do not appear and scatterBrain will simply open as two windows.

scatterBrain will then open as two screens, as shown below. The Image Window is used for selecting the files required by scatterBrain, loading images and setting parameters required for calculation of SAXS profiles. The Plot Window is used for data manipulation, e.g. applying normalisation or background subtraction, and exporting data for more detailed analysis in other programs.

  

The Image Window                                                                              Plot Window


Default File Tree

When a new Experiment is created using scatterBrain a series of folders are created using the default file tree structure. The Experiment File, Live Log File and Images are all set in locations that scatterBrain will reference by default. The overview here can be used to assist in locating a specific file. If files or folders are moved or renamed scatterBrain may no longer automatically locate files

  • The Experiment File, xxx.xml, (see below) is saved in the base directory of the experiment
  • Raw data, i.e. .tif files, is in the folder called "images"
  • The Log File, livelog.log, (see below) is in the folder called "images"
  • It is recommended to save 1-D data you have processed manually in scatterBrain into the folder "manual"
  • The other folders contain various stages of automatically processed 1-dimensional data
    • Automatically processed data is usually only relevant to protein scattering experiments
    • For protein experiments the beamline setup and calibration is likely to be correct during the experiment, meaning the 1D automatically processed data is usually correct
    • For non-protein samples it is not recommended to use the autoprocessed data as the automated processing system was not designed with other samples in mind and should not be relied upon.


Experiment File

The Experiment File contains all of the configuration parameters required to calculate radially averaged, 1-D SAXS profiles. This includes the position of the direct beam, camera length, wavelength, masks, pixel size, normalisation, etc... The Experiment File is created at the start of the experiment by the beamline scientists. However, it can also be created or modified at a later date using parameters determined from calibration SAXS data. The Experiment File has a file name specified at the time of data collection. Extensible Markup Language (XML) is used as the format of the Experiment File, a section of which is shown below:



As the configuration parameters are required for scatterBrain to interpret SAXS images, it is necessary to load the Experiment File prior to examining any SAXS data.


To load an Experiment File

  • Select the File tab of the top menu in the Image Window
  • Select the Get Experiment option in the sub-menu. A window will pop up to allow a choice of which file to load
  • Select the desired Experiment File


The Experiment File is overwritten whenever it is saved in scatterBrain. However, there is no automatic saving implemented in scatterBrain, this must be done manually. To avoid losing any important calibration details it is recommended to save a new Experiment File after making modifications to an existing one.


To save the existing Experiment File

  • Select the File tab of the top menu in the Image Window of scatterBrain
  • Select the Save Experiment option in the sub-menu

To save current parameters in a new Experiment File

  • Select the File tab of the top menu in the Image Window of scatterBrain
  • Select the Save As Experiment option in the sub-menu
  • Use the pop-up window to name and save the new Experiment File

Initially the experiment file doesn’t contain any information about the SAXS images or beamline parameters for a particular exposure. During data collection this information is stored in the Live Log File as detailed below. However, whenever the Experiment File is saved, the currently loaded Log information is also saved into the Experiment File. If the Experiment File and full Log File are loaded prior to saving the Experiment File, it will no longer be necessary to load that Log File again. The Experiment File also contains the normalisation parameters for <Link>Summed Images<Link> when this has been performed in scatterBrain.


Live Log File

The Live Log File, typically referred to as the Log File, is generated during data acquisition to record the state of any variables of relevance to a sample. Many parameters are logged, including the filename, exposure time, normalisation parameters, the position of various motors on the beamline, temperatures, etc... Although a large number of parameters are tracked in the Log File, it does not contain any information regarding the set-up of the SAXS camera. The parameters required for interpreting the SAXS images are stored in the Experiment File. The Log File uses the XML format, although it typically has the filename 'livelogfile.log' to prevent confusion with the Experiment File. Due to the large number of parameters in the Log File, each line tends to be quite long as in the sample below:

Data is only ever appended to the Log File and it is never overwritten by the control system. A new line is added to the Log File with every exposure SAXS exposure collected with all parameters being logged for each exposure. During data acquisition at the SAXS beamline the Log File is constantly updated, and scatterBrain displays these updates in real time. Unless the Log information is saved into the Experiment File, when working off-line it is necessary to explicitly load the Log File into scatterBrain. Otherwise it is not possible to access details such as the normalisation parameters.


To load a Log File

  • Acquire tab (top menu) in the Image Window
  • Select Live Log (sub-menu)
    • A pop-up window will appear to allow choice of Log File
    • Navigate to and select the desired Log File

If the Experiment File is saved after a Log File has been loaded all of the Log File will be included in the newly saved Experiment File. This means that the Log information will subsequently be loaded into scatterBrain whenever the Experiment File is loaded. This can simplify data analysis as it is no longer necessary to load the Log File.

Loading Data

Once the Experiment File (and Log File if necessary) have been loaded the left side of the Image Window will show a list of filenames. This is populated by a list of all files for which Log information is present. This provides a straightforward interface for selecting and loading a SAXS image that will be displayed in the Image Window and added to the Plot Window. Multiple files may be selected and loaded into the Plot Window, however only the lost one in the selection is shown in the Image Window.

 

To load a SAXS image:

·       Double-click on the filename in the list to to the left of the Image Window

OR

·       Select the filename in the list to the left of the Image Window. Drag and drop the filename into the Plot Window

·       Shift-select or Ctrl-select can be used to plot multiple files in the Plot Window

Once an image (or images) have been loaded the raw SAXS image will be shown in the Image


Window and the radially averaged, 1-D SAXS pattern (or patterns) will be displayed in the Plot Window. If a subsequent file is loaded it will replace the one displayed in the Image Window but will be added as an additional trace in the Plot Window. An example of what the scatterBrain windows may look like after sequentially loading two images is shown below:

 


Averaging Data / Summing Images

The Image Window of scatterBrain may be used to sum a selection of SAXS images in a similar manner to loading them individually. Rather than averaging the images, scatterBrain sums the individual frames and sums the normalisation data. The normalisation data allows the summed image to be viewed in a similar manner to an average, with less calculation error.

  • Use Shift-select or Ctrl-select in the File Tree to select all of the images to be averaged
  • Right-Click one of the selected file.
  • In the menu that pops up, select 'Sum Images'.
  • A further pop up menu will open to select a location to save the summed file.
  • The saved file will be added to the File Tree.