Analyze PSII Signal

Extract Fv/Fm data of objects and produce pseudocolored images.

plantcv.fluor_fvfm(fdark, fmin, fmax, mask, filename, bins=256)

returns Fv/Fm histogram headers, Fv/Fm histogram data, PSII analysis images list

  • Parameters:
    • fdark - image object, grayscale
    • fmin - image object grayscale
    • fmax - image object, grayscale
    • mask - binary mask of selected contours
    • filename - False or image name. If defined print image.
    • bins - number of grayscale bins (0-256 for 8-bit images and 0 to 65,536), if you would like to bin data, you would alter this number (default bins=256)
  • Context:
    • Used to extract fv/fm per identified plant pixel.
    • Generates histogram of fv/fm data.
    • Generates pseudocolored output image with fv/fm values per plant pixel.
  • Example use:

  • Output Data Units:

    • Bin-number - number of bins set by user
    • FV/FM Bins - bin values based on number of bins set by user
    • FV/FM Histogram - histogram of FV/FM ratio values for object
    • FV/FM Histogram Peak - bin value of histogram peak (greatest number of pixels)
    • FV/FM Median - bin value of histogram median
    • F-Dark Passed QC - Check (True or False) to determine if Fdark image does not have pixel intensity values above 2000.

Fdark image


Fmin image


Fmax image


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 = "print"

# Analyze Fv/Fm    
 fvfm_header, fvfm_data, fvfm_images = pcv.fluor_fvfm(fdark, fmin, fmax, kept_mask, filename, 1000)

Histogram of Fv/Fm values


Pseudocolored output image based on Fv/Fm values