Skeletonize3D ImageJ Plugin

Is it possible to thicken the skeleton after skeletonization? The lines appear very faint.

The skeleton is by definition 1-voxel thick. You can dilate it afterwards if you need something thicker. Have a look at the morphological filters available in MorphoLibJ.

You need to be aware that by dilating you might be changing the topology of the skeleton, for example thickened lines might fill in a ‘hole’ in the skeleton or merge lines which are close.
Perhaps you need a thickening algorithm that at least preserves the topology of the set.

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