Particle Data Analysis

  1. Load a particle stack "particles.mrc" into Image Stack Editor.
  2. Browse the image stack with arrow-buttons in the Display Parameters box.
  3. Image filtering: set band-limits, click the Filter button in Image Processing box.
  4. Image normalization: set the mean and s.t.d. values, click the Norm button.
  5. Invert intensity contrast by setting Multiplier to –1 and click the Scale button.
  6. Image frame cropping and padding with the Crop function.
  7. Image frame selection: position the mouse cursor inside the image frame, press CTRL and left-click
  8. Image frame Extract and Delete: applicable to the selected frames.
  9. Switch to Menu : Function : Digital Gel Filtration. Set Masking Radius to 0.75 and click Apply in Mass Distribution box to generate the density mass statistics.
  10. Use mouse to drag the red and green bars in the histogram display to define an appropriate band of usable particles. Then click Apply in Threshold Parameters box. The number of selected particles will be counted. Press Commit Selection to accept the selection. The Image Stack Editor will show up again, with selected particles marked in blue frames. Accept the selection by clicking the Extract button. A new image stack will be formed.
  11. Browsing through the resulting image stack. Should some particle be removed, highlight it by pressing CTRL and left-click. At the end, apply the Delete button to remove those selected frames. Save the images by clicking the Save button to finalize the particle quality inspection.