Analyze FLU Signal

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

fluor_fvfm(fdark, fmin, fmax, mask, device, filename, bins=1000, debug=None)

returns device, FLU channel histogram headers, FLU channel histogram data

  • Parameters:
    • fdark - image object, grayscale
    • fmin - image object grayscale
    • fmax - image object, grayscale
    • mask - binary mask of selected contours
    • device - Counter for image processing steps
    • 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
    • debug - None, "print", or "plot". Print = save to file, Plot = print to screen. Default = None
  • Context:
    • Used to extract fv/fm per identified plant pixel.
    • Generates histogram of fv/fm data.
    • Generaes 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


import plantcv as pcv

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

Histogram of Fv/Fm values


Pseudocolored output image based on Fv/Fm values