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find_spots_detail.md

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Find Spots (detail)

Input

Output

The output of spot finding shows the number of strong pixels found on every image and then at the end shows an overall summary:

Extracted 42922 spots
Removed 18801 spots with size < 3 pixels
Removed 16 spots with size > 1000 pixels
Calculated 24105 spot centroids
Calculated 24105 spot intensities
Filtered 23081 of 24105 spots by peak-centroid distance

Histogram of per-image spot count for imageset 0:
23081 spots found on 500 images (max 457 / bin)
                   *                                       *
**     **   **  ** ** *** *  ****               * *    *   *
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1                         image                          500

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Saved 23081 reflections to strong.refl

This "ascii-art" graph can be useful to give you an overall indication of how the data look. If, as here, the graph is approximately constant you may assume that the sample has not suffered substantial radiation damage and was reasonably well centred. If there are sinusoidal variations this may indicate either a variation in diffraction strength (e.g. anisotropy) or a significant variation in the unit cell lengths (i.e. when a long axis is perpendicular to the beam there are more spots.)

This summary also shows how many reflections were excluded for being too small or too large - usually the defaults are sensible however, but you can adjust these with min_spot_size and max_spot_size.