Prune¶

Prune/trim tips off a skeletonized image.

plantcv.morphology.prune(skel_img, size)

returns Pruned skeleton image

• Parameters:
  • skel_img - Skeleton image (output from plantcv.morphology.skeletonize)
  • size - How many pixels to trim off
• Context:
  • Iteratively remove endpoints (tips) from a skeletonized image. This "prunes" spurious branches/barbs off a skeleton.
• Important Note:
  • The function prunes all tips of a skeletonized image, and should be used as sparingly as possible since leaves will also get trimmed.

from plantcv import plantcv as pcv

# Set global debug behavior to None (default), "print" (to file), 
# or "plot" (Jupyter Notebooks or X11)
pcv.params.debug = "print"

# The image created for debugging purposes allows for line thickness 
# adjustments with the global line thickness parameter. Try setting 
# pcv.params.line_thickness = 3 for thinner lines (default 5)
pcv.params.line_thickness = 3 

pruned_skeleton = pcv.morphology.prune(skel_img=skeleton, size=14)

Pruned Image (image getting returned)

Debugging Image