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

```python

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

Screenshot

Image 2 with identified stem characteristics

Screenshot

Source Code: Here