Fill Segments¶

Propagate the labels of a segmented skeleton to fill the mask.

plantcv.morphology.fill_segments(mask, objects)

returns filled_img

• Parameters:
  • mask - Binary mask
  • objects - Segment objects (output from either plantcv.morphology.prune, plantcv.morphology.segment_skeleton, or plantcv.morphology.segment_sort).
• Context:
  • Uses the watershed algorithm to fill the mask propagating the objects' labels.
• Output data stored: Data ('segment_area') automatically gets stored to the Outputs class when this function is ran. These data can always get accessed during a workflow (example below). For more detail about data output see Summary of Output Observations

Reference Image: mask, objects drawn as labels

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"

filled_img = pcv.morphology.fill_segments(mask=plant_mask, objects=obj)

# Access data stored out from fill_segments
segments_area = pcv.outputs.observations['segment_area']['value']

Filled Image

Source Code: Here