Optimise Threshold

Several histogram-based methods exist for automatic determination of threshold for binary segmentation, but in ImageJ these are currently limited to pixel values in a single slice. The result can be excluding high values in a stack that are higher than the highest value in the current slice. This plugin uses all the pixels in a stack to construct a histogram and uses ImageJ's built-in isodata algorithm to determine the threshold. It optionally tests values either side of the initial auto-threshold for connectivity, because connectivity is very sensitive to image noise. The plugin attempts to find the threshold that results in minimal connectivity. Purification, erosion and dilation can improve the connectivity estimate, so Purify is always called, and erosion and dilation are applied as part of a sequence: purify, erode, purify, dilate.

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