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Spot ID v2

Spot ID v2 is the enhanced version of Spot ID with improved spot detection, fitting algorithms, and a more powerful indexing engine.

Spot ID v2

Keyboard & mouse shortcuts

You build the spot list directly on the loaded image. The image pane uses ReciPro's standard image-view navigation for pan/zoom; spot editing adds the combinations below.

Shortcut Action
F1 Open this page of the online manual
Left double-click the image Add a spot at that point (peak-fitted)
CTRL + Left double-click Add a spot and mark it as the direct (000) beam
Left-click a spot Select the nearest spot
CTRL + Right-click a spot Delete the nearest spot
CTRL + arrow keys Nudge the selected spot by one pixel
Left-drag / Middle-drag (empty area) Pan the image
Mouse wheel Zoom in / out at the cursor
Right-drag a box Zoom in to the selected region
Right double-click Zoom out
Double-click a spot's row header (table) Zoom to that spot (×2)

The main-window CTRL+SHIFT+T opens/closes this window.

→ See 21. Keyboard & mouse shortcuts for every window at a glance.

File menu

Open / save a diffraction image. The same drag-and-drop loading as Spot ID v1 is supported, and Gatan DM3/DM4 metadata (camera length, wavelength, pixel size) is honoured automatically.

Optics

Optics

Incident source

Select the radiation type (X-ray / electron / neutron) and set the energy or wavelength.

Camera length / Pixel size

The camera length (mm) and detector pixel size (mm or nm⁻¹). When a Gatan DM file is loaded, these values are populated from the file header.

Spot information

Spot information

  • Detect & Fit Spots: Automatic spot detection using local maxima and background subtraction.
  • Number: The maximum number of spots to detect.
  • Nearest neighbour: The minimum separation (px) allowed between detected spots. Peaks closer than this are merged, preventing double-detection of the same spot.
  • Fitting range (radius): The radius (px) of the circular region used to fit each spot's peak. Pixels inside this circle are fitted with a pseudo-Voigt function.
  • Apply to All: Sets the fitting radius of every spot to the current Fitting range (radius) value.
  • Delete spot / Clear spots: Remove individual or all detected spots.
  • Copy to clipboard: Copy spot positions and intensities to the clipboard.
  • Details of the spot: When checked, opens a window showing detailed information about the currently selected spot.

Details of the spot

Index

Index

  • Identify Spots: Run the indexing algorithm to find the best-matching crystal and zone axis.
  • Acceptable error: Set the acceptable deviation in d-spacing and angle for a match.
  • Ignore prohibited reflections: When checked, reflections forbidden by screw axes and glide planes are treated as not necessarily satisfied while searching for the zone axis.
  • Single Grain / Multiple Grains: Search for a single orientation (single crystal), or for several orientations (a polycrystalline / multi-grain region). For multiple grains, Max. num. of grains sets the upper limit on the number of grains to search for.
  • Results: The best matches are displayed with crystal name, zone axis [uvw], and individual spot indices (hkl).

Improvements over v1

  • Better noise handling in spot detection.
  • More robust fitting algorithms with multiple profile shapes.
  • Faster indexing with optimized search algorithms.
  • Support for overlapping spots and satellite reflections.

See also