Analyze FLU Signal¶

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

fluor_fvfm(fdark, fmin, fmax, mask, device, filename, bins=1000, debug=False)

returns device, FLU channel histogram headers, FLU channel histogram data, normalized color slice 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 - Default value is False, if True, intermediate image with boundary line will be printed
• 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

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=True)

Histogram of Fv/Fm values

Pseudocolored output image based on Fv/Fm values