Bio-Rad EXQuest Spot Cutter - Manual (Page 127)

PDQuest User Guide
4-6
Min Peak
If increasing the Sensitivity setting or selecting a new Faint Spot still fails to find
some faint spots, you can lower the Min Peak value. This is the minimum peak
intensity that a spot must have to be identified. Again, image noise may be detected as
spots if the Min Peak is too low.
Size Scale
The Size Scale field helps distinguish trends in signal intensity (spots) from random
intensity fluctuations (noise). It uses the size of objects in the image (in pixels) to
determine the nature of those objects. The initial size scale setting is based on the
Small Spot you selected in Step 1.
If a gel image has noticeable noise features, a larger size scale may be preferable. If
smoothing has adequately removed noise, small values are preferred so that small
spots will be detected. You can enter odd values from 3 to 9 in the field or adjust the
value using the arrow buttons.
Gaussian Model During Test
If the Gaussian Model During Test checkbox is selected, two-dimensional Gaussian
fitting will be performed on all spots when you find spot centers. It will take longer to
detect spots; however, spot detection will be more accurate for overlapping spots.
Note: Fewer spots may be found if Gaussian Model During Test is selected, because
large spots that would be identified as overlapping spot clusters can be correctly
resolved with Gaussian modeling.
4.1.c Advanced Tab
Most of the background removal and smoothing settings under Optional Controls are
set automatically based on your selections in Step 1. You should try to Find Spot
Centers first before adjusting these controls.
Note: If your image has streaks, you should select streak removal under the Streaks tab
when finding the spot centers.