Filter on calculated object properties¶

Calculates properties of objects in a binary image. Keeps objects that are either above or below a specified threshold for a specified property. When debug set to "plot," also prints the min, max, and mean of the specified property.

plantcv.filters.obj_props(bin_img, cut_side = "upper", thresh=0, regprop="area")

returns filtered_mask

• Parameters:
  • bin_img - Binary image containing the connected regions to consider
  • cut_side - "upper" or "lower", side to keep when objects are divided by the "thresh" value
  • thresh - Threshold for keeping objects.
  • regprop - Which object property to filter on
• Context:
  • Used to isolate objects of interest in a binary image based on their features. The output mask can be used for further analysis.
• Example use:
  • Below

Input binary mask

from plantcv import plantcv as pcv

# Set global debug behavior to None (default), "print" (to file),
# or "plot" 
pcv.params.debug = "plot"

# Apply filter on solidity
filtered_solidity = pcv.filters.obj_props(bin_img=binary_img, cut_side="upper", thresh=0.6, regprop="solidity")

# Apply filter on eccentricity
filtered_eccentricity = pcv.filters.obj_props(bin_img=binary_img, cut_side="lower", thresh=0.99, regprop="eccentricity")

# Apply filter on area
filtered_area = pcv.filters.obj_props(bin_img=binary_img, cut_side="lower", thresh=6000, regprop="area")

Mask of objects with solidity > 0.6

Mask of objects with eccentricity < 0.99

Mask of objects with area < 6000

Source Code: Here