Identify Segment Ends¶

Find segment tip and inner branch-point coordinates, and sort segments by the y-coordinates of the branch points

plantcv.morphology.segment_ends(skel_img, leaf_objects, mask=None, label=None)

returns Re-ordered leaf segments, list of branch point coordinates, list of leaf tip coordinates

• Parameters:
  • skel_img - Skeleton image (output from plantcv.morphology.skeletonize)
  • leaf_objects - Secondary segment objects (output from plantcv.morphology.segment_sort).
  • mask - Binary mask for plotting. If provided, the debugging image will be overlaid on the mask (optional).
  • label - Optional label parameter, modifies the variable name of observations recorded. (default = pcv.params.sample_label)
• Context:
  • Aims to sort leaf objects by biological age. This tends to work somewhat consistently for grass species that have the youngest leaves emerge at the top of the plant.

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 point thickness with the global line_thickness parameter (default = 5)
pcv.params.line_thickness = 3 

sorted_obs, bp, tips = pcv.morphology.segment_ends(skel_img=skeleton,
                                         leaf_objects=leaf_objs,
                                         mask=plant_mask,
                                         label="leaves")

segmented_img, leaves_labeled = pcv.morphology.segment_id(skel_img=skeleton, 
                                                          objects=leaf_objs,
                                                          mask=plant_mask)
# With ID re-assignment
segmented_img, leaves_labeled = pcv.morphology.segment_id(skel_img=skeleton, 
                                                          objects=sorted_obs,
                                                          mask=plant_mask)

Segment End points Debug

Leaf tips are green, branch points are red.

Source Code: Here