Spot refinement is needed to generate an initial reference map for cross correlation in the unbending steps. Automatic spot detection is based on the local signal to noise ratio of the peak to the surrounding background. The step arguably requires the highest level of user-interaction due to the subjective nature of the points being considered.
The spot list may be viewed at any time via the Navigator menu or by pressing the keyboard shortcut p. When the primary lattice is also displayed, the ring-display of the spots changes to X-display across their associated lattice nodes. The dimensions of the rings or crosses can be adjusted in the parameter pane (accessible via letter d).
To manually refine the spot list select the menu Lattice Refinement and the sub-option Enter Lattice Refinement Mode. This will display both the lattice and the current spot selection, either of which may still be toggled using the Navigator menu or keyboard shortcuts. To add spots select the appropriate node, to remove them select the appropriate spot. Spots selected when the lattice is hidden are still constrained to lattice nodes, but selection in this manner can make identifying spots easier as high-contrast ellipses are no longer present.