journal menu
![[Figure 1]](mo5305fig1mag.jpg)
|
|
Figure 1
General flow of operations in MuscleX-DI. The rectangles on the left indicate individual workflow steps and a description and/or purpose of that step is described in the rectangle next to it. All analyses begin in `Single Image' mode. By default, all rings are identified and displayed on the image that is loaded on into MuscleX-DI. The instrument information (sample-to-detector distance, X-ray wavelength, detector type) can be applied by selecting a calibrant diffraction pattern (lanthanum borate, silver behenate etc.) and choosing the ring that denotes the principal repeat, or by manually entering these parameters. A blank image (typically a diffraction pattern from the matrix in which the sample section is embedded within the sample holder) can be used to subtract the `instrumental' background. Masks can be applied to exclude specific areas of images, particularly around the beamstop. All diffraction features (rings) are identified by default and users can then select target rings to analyze across datapoints through selection on the user interface. The complete diffraction sequence is then analyzed in `Folder Mode'. Total ring intensity, d-spacing of each ring and fiber alignment are calculated for each diffraction pattern in the sequence and are written to output files (see sections below). The 2D heatmap interface is then used to display a stitched map where each pixel can denote one of the parameters that was calculated. Fiber orientation can be toggled on or off using the respective buttons. The heatmap can then be exported in various formats for further analyses and representation. |
![[Figure 1]](mo5305fig1.jpg)
 | JOURNAL OF SYNCHROTRON RADIATION |
ISSN: 1600-5775
Open 
access
access
