Otsu Auto Threshold

Creates a binary image from a gray image based on the threshold values.

plantcv.threshold.otsu(gray_img, object_type="light")

returns thresholded/binary image

  • Parameters:

    • gray_img - Grayscale image data
    • 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.
  • Context:

    • Used to help differentiate plant and background

Grayscale image (green-magenta channel)

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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"

# Create binary image from a gray image based on threshold values. 
# Targeting dark objects in the image.
threshold_dark = pcv.threshold.otsu(gray_img=gray_img, object_type='dark')

Thresholded image

Screenshot

Grayscale image (blue-yellow channel)

Screenshot


# Create binary image from a gray image based on threshold values. 
# Targeting light objects in the image.
threshold_light = pcv.threshold.otsu(gray_img=gray_img, object_type='light')

Thresholded image (inverse)

Screenshot

Source Code: Here