Segment a Skeleton

Turn a skeletonized image into separate pieces.

plantcv.morphology.segment_skeleton(skel_img, mask=None)

returns Segmented image, segment objects

  • Parameters:
    • skel_img - Skeleton image (output from plantcv.morphology.skeletonize)
    • mask - Binary mask for debugging (optional). If provided, debug image will be overlaid on the mask.
  • Context:
    • Breaks skeleton into segments. Performs the exact same process as plantcv.morphology.prune when size=0. If the prune function is performed, using plantcv.morphology.segment_skeleton is redundant.

Reference Images



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 = "plot"

# Adjust line thickness with the global line thickness parameter (default = 5),
# and provide binary mask of the plant for debugging. NOTE: the objects and
# hierarchies returned will be exactly the same but the debugging image (segmented_img)
# will look different.
pcv.params.line_thickness = 3 

segmented_img, obj = pcv.morphology.segment_skeleton(skel_img=skeleton)

segmented_img2, obj = pcv.morphology.segment_skeleton(skel_img=skeleton, 

Segmented Image without Mask


Segmented Image with Mask


Source Code: Here