10. Spot ID
Spot ID detects, fits, and indexes diffraction spots from experimental electron diffraction images.
Displays the diffraction image. Load images by drag & drop or from the File menu. Right-click or right-drag to zoom.
| Operation | Action |
|---|---|
| Single left click | Select a spot |
| Double left click | Add a spot |
| Ctrl + left double-click | Add direct spot |
| Ctrl + right single click | Remove spot |
| Setting | Description |
|---|---|
| Min / Max | Brightness range (also adjustable via track bar) |
| Gradient | Positive or Negative |
| Scale | Linear or Log |
| Colour | Grey scale or Cold-Warm |
| Dust & Scratch | Remove exceptional bright/dark pixels (set range and threshold) |
| Gaussian blur | Apply blur (range in pixels) |
Enter the incident source, energy/wavelength, camera length, and detector pixel size.
If a dm3/dm4 file (Gatan Digital Micrograph) is loaded, these values are set automatically.
Press Detect & fit spots to automatically detect diffraction spots and fit them with a 2D Pseudo-Voigt function. Results appear in the table.
| Parameter | Description |
|---|---|
| Number | Maximum number of spots to detect |
| Nearest neighbour | Minimum distance between detected spots |
| Fitting range | Radius (pixels) around each spot for fitting |
| Button | Action |
|---|---|
| Reset range | Re-set fitting range for all spots |
| Show label/symbol | Overlay labels/symbols on the image |
| Clear all spots | Remove all spots |
| Save / Copy | Export table in tab-separated (Excel) format |
| Re-fit all | Re-fit all spots |
Check the box to open a detail window showing the selected spot (left) and profiles in four directions (right). Blue = observed data, red = fit.
Press Identify spots to index detected spots against the crystal selected in the Main window.
| Setting | Description |
|---|---|
| Acceptable error | Tolerance for indexing |
| Single grain / Multi grains | Index as single crystal or multiple grains (set max grain count) |
| Show label/symbol | Overlay indexed labels on image |
| Refine thickness and direction | Apply dynamical theory (Bethe method) to refine sample thickness and crystal orientation that best matches the detected intensities |