Secondary Watershed Segmentation ( IAAdvSegmentSepSeed )

Secondary Watershed Segmentation (formerly Advanced Segmentation Sep.Seed). Watershed segmentation using separate, primary seed image (Image B) to segment Image A. Use this function to determine cell boundaries based on a nuclear marker and a cell stain.
Use #1: Both Image A and B are grayscale images. This routine obtains seeds with morphological reconstruction. Image A is segmented by the Watershed method.
Use #2: If Image B is already segmented the segments will be used as seeds, and the intensities of pixels in Image A corresponding to segments in Image B will seed the Watershed algorithm. No threshold values are calculated, but the Mean, Max or Min intensities are taken within the segments according to the setting of "Threshold value calculation method", "Mean, Max or Min of marks" and the boundaries are determined by flood filling "Bound locally" from this value. In practice this widens the segments in Image B according to the pattern in Image A.
Watershed Segmentation (formerly Advanced Segmentation). Segments grayscale images using the Watershed algorithm. The threshold value calculation methods are identical to the ones used for the Threshold function.
Way: Above segments bright details, Below segments dark details as objects
Segmentation is performed from local maxima or minima for "Above" or "Below" setting, respectively at the "Way" parameter.
Threshold from local max/min: "None" calculates simple threshold according to the threshold value, "Bound uniformly" calculates segment boundary with morphological reconstruction using a cap value modified by the "Determine boundaries at" value. Bound locally will bound local maxima at their given percent compared to the minimum or maximum of the image. This is performed by flood filling from the local maximum or minimum, respecting the boundaries of the Watershed segments.
Determine boundaries at: when "Bound uniformly" is selected above, given in the same units and additive to the threshold value, and sets how far from the local maximum will the boundary of the object drawn. When "Bound locally" is selected, it is a value in percents of local maximum or minimum.
Method: "Mark Seed" shows local maxima or minima by each as a single pixel. "Mark Shape" shows the boundaries of the objects, undivided by the watershed algorithm. Watershed divides bounded segments propagating from local maxima or minima.
The number of segments is limited only by the available memory.
Note: the segmentation algorithm has integer core, and does not work properly if the image consist of small, fractional values. Use Scalar Arithmetic to set a proper range, where pixel values are >>1.
The "Keep original mask" is not applicable here; masked areas are ignored during threshold calculation, but substituted by zeros in the segmented images.