Fluorescence

options.calc_fluor

Definition

Light reaching a leaf (pretty much any object) can be reflected, transmitted or absorbed. In plants absorbed light can be spent on three different processes:

  1. photochemistry (assimilation CO2)

  2. non-photochemical quenching (NPQ): heat dissipation

  3. chlorophyll fluorescence excitation

../_images/aPAR_destiny.png

Source: http://spie.org/newsroom/4725-remote-sensing-of-terrestrial-chlorophyll-fluorescence-from-space?SSO=1

>>> Fluorescence is light emitted by chlorophyll molecules in the range 640-800 nm.

SCOPE

Fluorescence light (pretty much as any light) can be absorbed and scattered on its way to a sensor.

SCOPE model simulates 3 hemispherical fluorescence quantiles:

  1. fluorescence emitted by all photosystems without any scattering / re-absorption neither within leaf, nor withing canopy

  2. fluorescence emitted by all leaves without any scattering / re-absorption within canopy or from soil

  3. fluorescence emitted by canopy (all leaf layers) accounting for all scattering / re-absorption events

../_images/fluorescence.png

Note

Notice the difference in ranges and units between directional and hemispherical fluorescence.

SCOPE model simulates directional fluorescence (the one that actually reaches a sensor) and its components coming from:

  1. sunlit leaves

  2. shaded leaves

  3. scattered by leaves and soil

It is also possible to partition directional fruorescence between photosystem I and II (PSI, PSII) with options.calc_PSI, not recommended though.

../_images/fluorescence_contributors.png

Note

There are much more outputs of biochemical() related to Pulse-Amplitude-Modulation (PAM) Fluorometry quantiles that are stored in internal structure biochem_out.