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[2DE] Configuration Settings

Objetive

Description of configuration settings of the 2DE spot detection engine.

Configuration
Name
Category
Suggested Values.
(default value in bold)
Implementation
minimum signal %Blob detection3 5 10 20 30 35 40 50 60 70 75 80 90 95 99SpotsDetector class>>#minimumSignalIntensity:
background %Blob detection3 5 10 20 30 40 50 60 70 75 80 90 95 99SpotsDetector class>>#backgroundPercent:
distributionBlob detection0 none,1 linear,2 x*x,3 x*x*xSpotsDetector class>>#distributionIndex
MAF: minimum area factorBlob detection50 only big points are valid
75 100 200 300 500 750 1000
10000 small points are valid
DetectedBlob class>>#minimumAreaFactor
levels of watermarkingBlob detection3 less presition and faster
5 7 10 15 17 20 25 30
more time and resources 50
SpotsDetector class>>#signalLevels
signal enhancementBlot detection and preparationnone smooth verticalSmoothBlotDetector class>>#enhancement

Configuration
Name
Comments
minimum signal %When the pixels of the image are scanned for spots detection, the lighter pixels are not analyzed and considered "the background". This threshold has a default value in 35% of black.
Bigger % values let you exclude from processing dark pixels. Big values can be used for dark images (with blind/flash spots).
Smaller values increase sencibility to light pixels and can be used for "washed images".
background %The background is detected computing the ligher colors in the image. Th epixels that covers at least the "background%" of the image are considered background and are not considered in spot detection.
distributionThe image is analyzed cutting the signal map in slides (shashimi) and building contours. The interval at wich the signals are cut can be defined by a function.
The best known function for shashimi y simply cutting at regular intervals, but it can be changed for beter results (using curves) if the images is known to have high saturation.
MAF: minimum area factorDetected spots with an area below MAF will be disabled automatically.
By default a value of 200 force the spots of <0.5% of image extent to be disabled.
This parameter limits the spots that will be considered noise or dust in image.
levels of watermarking During shashimi process the image is cutted in slices. The number of slices is defined by this parameter.
A value of 10 is an empirical optimum. This parameter defines also the perfomance (resources and time spent) of spot detection process.
signal enhancementAll Dye detectors can perform a pre-processing effect during image preparation.
The default enhancement is vertical smoothing to reduce noise.
It is not recommended to change this parameter.