Analyze FLU Signal¶

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

plantcv.fluor_fvfm(fdark, fmin, fmax, mask, filename, bins=1000)

returns 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
  • 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
• 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:
  • Use In PSII Tutorial

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 = pcv.fluor_fvfm(fdark, fmin, fmax, kept_mask, filename, 1000)

Histogram of Fv/Fm values

Pseudocolored output image based on Fv/Fm values