Threshold ( IAThreshold )

Parameters:

Name	Short Name	Type	Description
Threshold value calculation method	type	string	How is the threshold level calculated: "Pixel value", "Percentile by frames", "Percentile by series", "Percentile by reference", "Otsu by frames", "Otsu by series", "Otsu by reference"
Way	way	string	How is the image modified at the threshold level: Setting values to 1 "Above" or "Below" value; or clipping at "Ceiling" or "Bottom"; or masking by "Mask Above", "Mask Below".
Value	value	real	Pixel value, percentile, or factor times Otsu optimal threshold value (typically 1)
Determine boundaries at	value2	real	This is added to "value" when determining the boundary of local maxima/minima or the boundary is calculated at the given percent of each local maximum when Bound Maxima/Minima locally is selected below.
Threshold from local max/min type	proctype	string	This enables local maximum or minimum search. Set "None" for simple thresholding. Available types: "Bound Maxima uniformly", "Bound Minima uniformly", "Bound Maxima locally", "Bound Minima locally".
Keep original mask	keeporigmask	boolean	Originally masked areas are kept masked if Yes. Otherwise the mask will take zero, ceiling or bottom value.

Description:

Binarizes, masks or clips (ceilings/bottoms) the image at a given or calculated threshold value.
Above sets pixels greater or equal the threshold to 1, while below sets pixels smaller or equal the threshold to 1, the remaining pixels are set to 0.
Ceiling sets pixels greater or equal the threshold to the threshold value, while bottom sets pixels smaller or equal the threshold to the threshold value, the remaining pixels are unaffected.
Mask Above and Mask Below do not binarize the image, but sets corresponding pixels to MASK value.
The Otsu method calculates optimal threshold value. Optionally percentile or Otsu optimal threshold value is calculated from a reference image. To this end set an identical x,y sized image with identical channel number as Histogram reference image using the context menu.
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 given by the threshold value plus the "Determine boundaries at" value. Bound locally will bound local maxima at their given percent compared to the minimum or maximum of the image.
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.
In practice, when local thresholding is used (for maxima) objects brighter than the local background by threshold value will be resulted. Using the "Determine boundaries at" value, the object boundaries can be extended or shrunken. When using "Bound locally" the boundaries are not determined by the threshold level, but taken individually for each local maximum or minimum.
Constraints: Ceiling or Bottom used together with "Bound locally" will ceiling for maxima and bottom for minima at the given percent of the local maximum. Ceiling and bottom are not available for "Bound uniformly" and for "Markers" and above or below thresholding is used instead.
Preexisting masks are kept as mask for Above and Below ways if "Keep original mask" is disabled.