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Scanning Transmission Electron Microscopy Facility


PCMass Manual: Tutorial 7

Tutorials >>  1 2 3 4 5 6 7

Filament Trace
  1. If you are interested in the twisting or curvature of filaments, select an appropriate image. (Note this does not give much additional information for TMV.) Read in an image, run background, select a cylinder model, and position the cursor near the center of the filament of interest.
  2. After the model 'locks on' (difference image shows only noise), strike the <7> key. The program should trace the centerline to one end of the filament, then return to the starting point and trace to the other end. During the tracing, a plot should appear in the bottom left on 1024x1280 displays and middle right on 768x1024 displays. The curves are: local radius of curvature or twist angle (blue) relative to offset zero (gray), local RMS difference between model and LA data (white/red), local peak signal (green) and local M/L (yellow). The x-coordinate is the distance from the end of the filament. Note that the plot reverses when the search returns to the starting point and goes in the other direction.
  3. After the first pass is complete, a second pass averages the radial profiles for segments passing RMS and BKG_RMS tests. A final pass re-plots the traces with solid lines. The 'Total Length' printed is the contour length of trace (both white & red in RMS plot).
  4. Inspect the plot by holding down the <SPACE> bar and moving the mouse pointer over the plot area. Cursors should indicate the position being read and the value at that point. Note that for long filaments on a small screen (1024x768) the rightmost portion of the trace may be cut off. The left and right arrow keys also move along the trace.
  5. Save the data by holding down <CONTROL> and striking <7>. This writes a file NKXXXXYYRadPro_xxx_yyy.txt in the MassMeas directory. The values xxx and yyy are coordinates of one end of the filament. The average radial profile appears first, followed by the data as a function of distance from the end. The 'radius of curvature' plot is actually 1000/Radius in pixels, in order to have straight filaments = 0.
  6. Save the entire screen to the clipboard by holding down <ALT> while hitting PrintScreen, then paste into Paint, PowerPoint, or Photoshop and clip off unwanted information or save as a jpg file.

 

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Last Modified: June 12, 2009
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