Analyze Stem Objects

Primary, or stem, objects identified during workflows that examine the morphology of plants or plant organs can have specific characteristics measured about the stem segments of a skeleton.

plantcv.morphology.analyze_stem(rgb_img, stem_objects)

returns labeled_img

  • Parameters:
    • rgb_img - RGB image data for plotting.
    • stem_objects - List of stem segments (output from segment_sort function)
  • Context:
    • Used to output stem morphological characteristics, including height, angle, and length.
  • Example use:

  • Output data stored: Data ('stem_angle', 'stem_height', and 'stem_length') automatically gets stored to the Outputs class when this function is ran. All data stored in the Outputs class gets printed out while running print_results but these data can always get accessed during a workflow. For more detail about data output see Summary of Output Observations


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"

stem_debug_img1 = pcv.morphology.analyze_stem(rgb_img=img1, stem_objects=stem_objects1) stem_debug_img2 = pcv.morphology.analyze_stem(rgb_img=img2, stem_objects=stem_objects2)

Access data stored out from analyze_object

stem_angle = pcv.outputs.observations['stem_angle']['value']


Image 1 with identified stem characteristics


Image 2 with identified stem characteristics


Source Code: Here