Measure Width of Segments¶

Measure the average width of segments.

plantcv.morphology.segment_width(segmented_img, skel_img, labeled_mask, n_labels=1, label=None)

returns labeled_image

• Parameters:
  • segmented_img - Segmented image (output either from plantcv.morphology.segment_skeleton or plantcv.morphology.segment_id), used for creating the labeled image.
  • Skeleton image (output from plantcv.morphology.skeletonize or output from plantcv.morphology.prune)
  • labeled_mask - Labeled mask of segments/objects to get analyzes (output from plantcv.morphology.fill_segments, pcv.create_labels, or pcv.roi.filter)
  • label - Optional label parameter, modifies the variable name of observations recorded. (default = pcv.params.sample_label)
• Context:
  • Calculates the average width of each segment with a distance transformation.
• Output data stored: Data ('segment_width') automatically gets stored to the Outputs class when this function is ran. Width measurements can be scaled to real world units (e.g. mm) using the unit, px_height, and px_width parameters. These data can always get accessed during a workflow (example below). For more detail about data output see Summary of Output Observations

Reference Image: Images of copper wires with various diameters for validating root image analysis

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"
# Optionally, set a sample label name
pcv.params.sample_label = "wire"

labeled_img = pcv.morphology.segment_width(segmented_img=segmented_img, skel_img=skel, labeled_mask=labeled_mask, n_labels=5)

# Access data stored out from segment_width
seg_widths = pcv.outputs.observations['wire']['mean_segment_width']['value']

Labeled Image

Source Code: Here