Plot of connectivity versus threshold (optional).Dilation Cycles: Number of times to dilate the stack after secondary purification.Erosion Cycles: Number of times to erode the stack after initial purification.Set small for a faster run and large to test the whole stack Subvolume Size: Size of the volume to test for connectivity.Range: Proportion of the initial threshold to test above and below initial thresholds.Tests: Number of different thresholds to test for connectivity.Show Plot: Display a graph showing connectivity versus threshold.Apply Threshold: Replace the input image with a thresholded version.Threshold Only: Determine the threshold from the stack histogram only. 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. The plugin attempts to find the threshold that results in minimal connectivity. It optionally tests values either side of the initial auto-threshold for connectivity, because connectivity is very sensitive to image noise. 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. The result can be excluding high values in a stack that are higher than the highest value in the current slice. 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.
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