Otsu Auto Threshold¶
Creates a binary image from a gray image based on the threshold values.
plantcv.threshold.otsu(gray_img, max_value, object_type="light")
returns thresholded/binary image
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Parameters:
- gray_img - Grayscale image data
- max_value - Value to apply above threshold (255 = white)
- object_type - "light" or "dark" (default: "light"). If object is lighter than the background then standard thresholding is done. If object is darker than the background then inverse thresholding is done.
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Context:
- Used to help differentiate plant and background
Grayscale image (green-magenta channel)
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"
# Create binary image from a gray image based on threshold values.
# Targeting light objects in the image.
threshold_light = pcv.threshold.otsu(gray_img, 255, 'dark')
Thresholded image
Grayscale image (blue-yellow channel)
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"
# Create binary image from a gray image based on threshold values.
# Targeting dark objects in the image.
threshold_dark = pcv.threshold.otsu(gray_img, 255, 'light')
Thresholded image (inverse)