Bio-Rad EXQuest Spot Cutter - Manual (Page 128)

Detecting and Editing Spots
4-7
Streaks
Protein gels frequently display streaking in areas of high spot concentration. Click the
Streaks tab to access the streak removal settings.
To remove vertical and/or horizontal streaks from your image, select the appropriate
checkbox(es). The disk radius size is determined automatically based on the size of
the largest spot you want to detect (Step 1).
The default disk radius size is conservative. If, after you find spot centers, you would
like to remove more streaking from the image, reduce the size of each disk radius by
about half and find spot centers again.
Background
Click the Background tab to access the settings for subtracting background intensity
from the image.
Background subtraction is required for spot detection. The default method, Floating
Ball, and default ball radius size are highly recommended. Radius size is calculated
automatically based on the largest spot you want to detect (selected in Step 1).
If Floating Ball results in too much background subtraction or undesirable image
artifacts, you can select the Roller Ball method. Typically, the roller ball method
results in more image artifacts than the floating ball.
The Bi-Disk method is slightly faster than the floating or roller balls, and will perform
adequately for images with very smooth, even backgrounds. However, bi-disk will
perform less well for images with uneven backgrounds.
Smoothing
Click the Smoothing tab to access settings for performing smoothing.
Image smoothing in your scans is optional but highly recommended. The default state
of the Perform Smoothing checkbox is checked. To deactivate this function, deselect
the checkbox by clicking in it.
The Filter Type is initially set based on the section of the image you boxed in Step 1.
The Kernel Size is set based on the faintest/smallest spot you want to detect.