![]() 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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