Report Size Marker¶

Get and record the size of a size marker or set an area as a size marker.

plantcv.report_size_marker_area(img, roi, marker='define', objcolor='dark', thresh_channel=None, thresh=None, label=None)

returns analysis_image

• Parameters:
  • img = An RGB or grayscale image to plot the marker object on
  • roi = A region of interest (e.g. output from pcv.roi.rectangle or other methods)
  • marker = 'define' (default) or 'detect'. If 'define' it means you set an area, if 'detect' it means you want to detect within an area
  • objcolor = Object color is 'dark' (default) or 'light' (is the marker darker or lighter than the background)
  • thresh_channel = 'h', 's', or 'v' for hue, saturation or value, default set to None
  • thresh = Binary threshold value (integer), default set to None.
  • label = Optional label parameter, modifies the variable name of observations recorded. (default = pcv.params.sample_label) In PlantCV v4.9 and later, the 'label' parameter is no longer utilized, since size marker is now metadata.
• Context:
  • Allows user to add size marker data, so that shape data can be normalized between images/cameras
• Output metadata stored: Data ('marker_area', 'marker_ellipse_major_axis', 'marker_ellipse_minor_axis', 'marker_ellipse_eccentricity') automatically gets stored to the Outputs class when this function is ran. These data can always get accessed during a workflow (example below). These measurements can be used with known size of the marker and the unit, px_height, and px_width parameters to scale length and area outputs to real world units (e.g. mm and mm²). Summary of Output Observations

Object (green) that is identified as partially inside ROI

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"

# Define an ROI for the marker
roi = pcv.roi.rectangle(img=img1, x=3550, y=850, h=500, w=500)

# Detect and Measure Size Marker
image = pcv.report_size_marker_area(img=img1, roi=roi, marker='detect', 
                                    objcolor='light', thresh_channel='s', 
                                    thresh=120)

# Access data stored out from report_size_marker_area
marker_area = pcv.outputs.metadata['marker_area']['value']

# Scale length & area Outputs collected downstream by
# updating size scaling parameters if the marker is detected
# E.G. Given a square size marker, (3cm x 3cm) in size
if image: # function returns None if no marker detected
    pcv.params.unit = "cm"
    pcv.params.px_width = 3 / marker_area**(1/2) 
    pcv.params.px_height = 3 / marker_area**(1/2)

# E.G. Given a circular size marker, 2cm in Diameter 
# by averaging ellipse axis lengths detetcted
marker_diameter_cm = 2
if image: # function returns None if no marker detected
    pcv.params.unit = "cm"
    marker_diameter_px = (pcv.outputs.metadata['marker_ellipse_major_axis']['value'] + \
        pcv.outputs.metadata['marker_ellipse_minor_axis']['value']) / 2 
    pcv.params.px_width = marker_diameter_cm / marker_diameter_px
    pcv.params.px_height = marker_diameter_cm / marker_diameter_px

Area selected to detect size markers

Object (green) that is identified as size marker

Source Code: Here