Plot Histogram

This is a plotting method used to examine the distribution of signal within an image.

plantcv.visualize.histogram(gray_img, mask=None, bins=256, color='red', title=None)

returns hist_header, hist_data, fig_hist

  • Parameters:
    • gray_img - Grayscale image data, the original image for analysis.
    • mask - Optional binary mask made from selected contours (default mask=None)
    • bins - Number of class to divide spectrum into (default bins=256)
    • color - The color of the line plot in the histogram (default color='red'). Users can input and color that is accepted by plotnine ggplot.
    • title - The title for the histogram (default title=None)

Context: - Examine the distribution of the signal, this can help select a value for binary thresholding.

Grayscale image




from plantcv import plantcv as pcv

# Examine signal distribution within an image
# prints out an image histogram of signal within image
header, hist_data, hist_figure = pcv.visualize.histogram(gray_img, mask=mask, bins=256, color='red', title=None)

Histogram of signal intensity