User guide

Quantity One User Guide

14-8

Minimum Density

When Normalization is turned off, this is the lowest signal intensity value

that will be counted as a band.

Before entering a value for Min. Density, use the Lane > Plot Lane command

to plot a trace of a lane that includes some faint bands. Then enter a value that

is lower than the intensity of the peak of a faint band but is still above the

background.

If faint bands are still being missed after applying this parameter, double-

check the intensity of faint bands on the lane trace and/or consider increasing

the Sensitivity setting.

If Normalize is turned on, Min. Density is converted from an absolute value

to a percentage. This percentage is the fraction of the signal intensity of the

darkest band in the lane that will be detected as a band. For example, if the

darkest band in a lane is 50,000 counts and the Min. Density is set to 25,000

counts, when you turn on Normalize, the Min. Density will switch to 50%. In

other words, for a band to be detected it must be at least half as dark as the

darkest band in the lane.

Noise Filter

The Noise Filter can be used to minimize the number of small ﬂuctuations in

the image (i.e., noise) that are called bands while still recognizing larger

features (i.e., real bands). This distinction becomes increasingly critical the

higher the Sensitivity parameter is set.

The Noise Filter value refers to the size of the ﬁlter in pixels (e.g., a value of

2.50 equals a ﬁlter size of 2.50 x 2.50 pixels). Features smaller than the ﬁlter

size will not be recognized as bands. Entering a noise ﬁlter size of zero turns it

off completely. The default value is 4.00.

If band detection calls a doublet a single band, decrease the Noise Filter

setting and/or increase the Sensitivity.

You can also try decreasing the Size Scale parameter instead of the Noise

Filter to improve the detection of closely-spaced bands. Be wary of decreasing

both the Noise Filter and the Size Scale, as this may result in the fuzziness

around bands being mistakenly detected as separate bands.