RegionsOperatorsmRgnClumpiness Method

Parameters

regions

Type: MediaCy.IQL.FeaturesMcRegions

Return Value

Type: McMeasure

Usage Note

In Visual Basic and C#, you can call this method as an instance method on any object of type McRegions. When you use instance method syntax to call this method, omit the first parameter. For more information, see Extension Methods (Visual Basic) or Extension Methods (C# Programming Guide).

mRgnClumpiness is derived from mRgnHeterogeneity. Heterogeonous pixels are those that vary by more than the McHeterogeneity.IntensityRange property percent (of the full intensity) from the average intensity for the region (mRgnDensity). For the mRgnClumpiness computation, all hetrogenerous pixels are marked as foreground in a temporary image. That image is then eroded by one (the default) or more times using a 5 by 5 octagonal kernel. The ratio of the number of pixels surviving the erosion compared to the number of hetrogenerous pixels is reported as the mRgnClumpiness value for each region. Thus to have a non-zero clumpiness, the region must have fairly large connected areas (greater than about 6 by 6 pixels for a single erode pass) of "hetrodox" (see below) pixels. Subtly or finely textured regions will result in either no heterogeneous pixels or none that will survive the erosion. The largest possible value of mRgnClumpiness approaches 1.0, but never reaches it, because even if all pixels in a region are hetrogenerous the erosion will remove some from the region's edges. The measurement was originally described by Young IT, Verbeek PW, and Mayall BH, Characterization of chromatin distribution in cell nuclei. Cytometry, 1986. 7: p. 467-474. There are three optional parameters that affect mRgnClumpiness: two are shared with mRgnHeterogeneity (i.e., setting the parameter for one measurement also sets it for the other), and one parameter (the number of 5x5 erosions applied before the clumpiness count is made) only applies to mRgnClumpiness. The intensity range parameter determines the offset from the mean intensity outside-which "hetrodox" pixels are identified. The IntensityRange parameter can be set either by assigning to mRgnClumpiness.IntensityRange or by calling mRgnClumpiness.SetParameter(0, NewIntensityRange). The default IntensityRange is 10 percent. By default the test for heterogeneous pixels is bipolar, including pixels that are both sufficiently darker than the mean as well as those sufficiently brighter. The second parameter takes a Bipolar enumeration 0=Both, 1=BrightOnly, 2=DarkOnly. This parameter is set by calling mRgnClumpiness.SetParameter(1, NewBipolarEnum). By default the Bipolar parameter is 0 ("Both"). Givnen the measured image's McImage.RangeMax and RangeMin, the heterogeneity computation is done as follows: LuminanceRange = (RangeMax - RangeMin) * IntensityRange/ 100 Bright hetrodox pixels are those more intense than mRgnDensity+LuminanceRange, while dark hetrodox pixels are those less intense than mRgnDensity-LuminanceRange. If Bipolar is not DarkOnly, bright hetrodox pixels are marked in the mRgnClumpiness pre-erosion map. Similarly, if Bipolar is not BrightOnly, dark hetrodox pixels are marked. Of course if Bipolar is Both (the default), then both bright and dark hetrodox pixels are marked. The IntensityRange parameter is allowed to be negative, which may be useful only in cases where the Bipolar parameter is either DarkOnly or BrightOnly. For example, if the Bipolar parameter is BrightOnly and IntensityRange is minus 10, then hetrodox pixels would be those within each sub-region that are brighter than the mean intensity for that region minus 10% of the full luminance range. This sort of arrangement can be quite useful for mRgnClumpiness where it allows you to have more control over the pixels included in the "hetrodox" mask before the erosion is applied. For example, if the IntensityRange parameter is 0 percent and the Bipolar parameter is BrightOnly, then the clumpiness test (ratio of forground pixels after to before the erosion) would be applied to all pixels brighter than the mean intensity. The third optional mRgnClumpiness parameter is the Number of Erosions, which is set by calling mRgnClumpiness.SetParameter(2, NewNumberOfErosions). Number of Erosions is one by default and is silently constrained to be from one to ten. Each erosion is made with a 5x5 octagonal kernel so that an approximately 3-pixel deep edge is shaved off the boundary of each group of connected hetrodox. With one pass, no group smaller than 6 pixels will survive; with two passes all groups of 10 or fewer pixels will disappear. Stringy groups are eroded more completely that compact groups of pixels. This is a pixel-based measurement. So for regions created by the McThreshold.Execute method or McFeatures.SetFromMask method (features of Type mcftScanList), holes in the blob are significant.