Fig. 3
From: Image analysis for the automatic phenotyping of Orobanche cumana tubercles on sunflower roots
Steps for image analysis for automatic counting of the number of tubercles. To facilitate the visualization of the various image analysis steps toward the identification of tubercles, a 4-week-old inoculated sunflower root was used instead of a 3-week-old root. First, the scale was defined in mm (1100 pixels = 50 mm in this example). Tubercles were identified thanks to the tubercle orange color and defined size. a Cropping of the image. b The cropped image. c, d Color threshold window to define HSB parameters (hue = 0–57, saturation = 171–255, brightness = 92–255 in this case) and resulting image (c). e Binary mask showing the tubercle in black, with filled holes. f Original image with drawing of counted particles. g Table of the number of particles with their position (center of mass) and area (parameters previously defined in the ImageJ interface: analyze-set measurements)