Reassign Frame Labels¶

Relabel Fm and Fm' in PSII CropReporter datasets. The photosynthesis subpackage is dependent on a PSII_Data instance file structure as created by photosynthesis.read_cropreporter. Some systems (e.g. CropReporter) output a timeseries of fluorescence images that can be used to calculate a fluorescence induction curve following a saturating light pulse. This function calculates the frame where maximum fluorescence is observed and relabels the Fm or Fm' frame, if needed. This can only be done globally, not on a per-plant basis in a multi-plant image. However, pcv.analyze.yii and pcv.analyze.npq can use this function to identify the optimal frame for each plant in a multi-plant image.

plantcv.photosynthesis.reassign_frame_labels(ps_da, mask)

returns xarray DataArray with updated frame labels

• Parameters:
  • ps_da - photosynthesis xarray DataArray containing multiple post-saturating light pulse fluorescence images
  • mask - binary mask of plant
• Context:
  • Used to assign Fm or Fm' based on observed plant fluorescence.
• Example use:
  • Use In PSII Tutorial

Assign Fm

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 = "plot"

psd = pcv.photosynthesis.reassign_frame_labels(ps_da=ps.ojip_dark, mask=mask)

Assign Fm'

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 = "plot"

psl = pcv.photosynthesis.reassign_frame_labels(ps_da=ps.ojip_light, mask=mask)

Source Code: Here