CF-SAXSbot V.1.0 BETA


About:
      This program was created for the manual and automated data analysis of continuous flow small angle x-ray scattering data (CF-SAXS), post-data reduction by radial averaging of the scattering TIFF detector images to a 2D data format. The motivation for this software comes from the unique data sets that CF-SAXS data produces. As CF-SAXS technology was an ongoing development within our lab (C. Robert Matthews and Osman Bilsel) there were no efficient existing software platforms for the analysis. CF-SAXS experiments rapidly mix protein solutions and flow the mixture through a microfluidic channel that is translated across a micro-focused SAXS beam. The translation of the channel across the beam results in ~90 data points per scan, with 30 or more scans being typical of 1 experimental run. These ~300 images per single kinetic run have to be analyzed in the correct order, taking into consideration channel position, buffer and simple scans, scan number, and method of collection cycle as it relates to translation. CF-SAXS bot permits these ordering relations and the individual trace analyses to be accomplished quickly and effortlessly.
      This program has many functions apart from the aforementioned book keeping capabilities. Simple transformations of the data can be accomplished simultaneously to any number of traces with arbitrary selections. Singular value decomposition, guinier analysis, data binning, error propagation, and file import/export are also similarly arbitrarily invoked for maximum flexibility in the analysis. The same flexibility is extended to the automated guinier analysis, which drastically enhances the productivity of the software.

Interface and Use:
      The interface is kept very simple. On the left the each data set is stored as a "Buffer" which can be arbitrarily selected. Selected Buffers are automatically plotted in the right pane and subjected to the invoked data manipulation processes. A small command terminal in the lower left will eventually be used for command line operation and macro scripting. Output from the fitting routines is displayed in the console window. Below is an example of the general GUI layout.



      A universal integrated data import panel (see below)is included in this software package. Most ASCII data format can be described using the panel for fast data import. Import and export of files also has a binary mode compatible with Savuka legacy formats. A filelist panel is also accesible which allows for filelists of directories of files to be custom sorted by any characters in the file names. These file lists can be used to seamlessly import the data through the below panel.



      The below image demonstrates the customization panel for the automated Guinier analysis. This process includes capabilities for averaging, buffer subtraction, and removal of outlier traces. The maximum Guinier region is specified by the user (constraints are checked for validity) and every possible window size specified by a user-defined step size is used to calculate the Rg from the Guinier approximation. The program is hard- coded to maximize Rg*Qmax to 1.3 for the most reliable results with our data quality and Q range.



Controls:

Within Menu:

File/Create File List      =       Opens FileList make for easy organization and creation of File List.
File/Import File List      =       Opens file manager to select File List.
File/Import Matrix      =       Imports SAXSbot binary matrix.
File/Import Matrix/Savuka.Y      =       Imports binary files in Savuke .Y legacy format.
File/Save.../Write Matrix      =       Saves all Buffers in SAXSbot binary file.
File/Save.../Save As Txt/All      =       Saves each Buffer as an individual txt file (tab delim.) for all Buffers.
File/Save.../Save As Txt/Selection      =       Saves each Buffer as an individual txt file (tab delim.) for all selected Buffers.
File/Exit      =       Closes the program

Options/Add XR Data/Fill with interval      =       Opens parameter panel for parameter specifications. Set XR value or each buffer by increment value(second dependent variable).
Options/Set Data Limits      =       Opens parameter panel for parameter specifications. Set plot limits based on point values. Toggle on/off.
Options/Trim Data Points      =       Opens parameter panel for parameter specifications. Set plot limits based on point number. Toggle on/off.

Functions/Guinier Fit      =       Opens parameter panel for parameter specifications. Fits selected Buffers.

Transforms/SAXS/Guinier      =       Transforms selected Buffers to Guinier plots. Output are new Buffers appended to the current list.
Transforms/SAXS/Kratky      =       Transforms selected Buffers to Kratky plots. Output are new Buffers appended to the current list.
Transforms/SAXS/Auto Reduce      =       Shows auto reduction panel. Set options to automatically average, subtract, and remove outliers from selected Buffers.


Within Buffer List:

Double Left Click      =       Displays FileViewer window to show/edit selected Buffer's data in table view.
Right Click      =       Displays manipulation options for selected Buffers (average, subtract, add, transform, & clear options).
arrow 'up'      =       Select one cell position up.
arrow 'down'      =       Select one cell position down.
'delete'      =       Deletes selected buffers and renumbers the current Buffer values beginning with 1.


Within Plot Area:

Right Click      =      Displays menu for plot options.



Dependencies:

The fitting and SVD routines are dependent on the ALGLIB library.
The plotting requires GigaSoft Proessentials
All calculations are from current literature.



Copyright © 2013 Paul Nobrega