LCF Reference

Programming Commands

The commands listed in Table 27‑14 can be used in LPL programs (such as AutoPrograms) to perform fluorescence related tasks. For control commands, see Leaf Chamber Fluorometer Control on page 25-21 and LCF Control Functions on page 25-30 in the instruction manual.

Table 27‑14. Fluorescence commands.
Command Description Fct Key Equivalent
FMeas_On Turn on measuring beam f1 level 9
FMeas_Off Turn off measuring beam
DoFlash Do a saturating flash f2 level 9
DoDark Do a dark pulse f3 level 9
DoFm Do a saturating flash, set Fm, com- pute user variables, and Log f2 level 0 (when actinic off)
DoFmp Do a saturating flash, set Fm , and Log f0 level 0 (when actinic on)
DoFoFm Set Fo, then DoFm f3 level 0 (when actinic off)
DoFsFmp Set Fs, do a saturating flash, set Fm , compute user variables, and Log f3 level 0 (when actinic on)
DoFop Do a dark pulse, set Fo , compute user variables, and Log f1 level 0 (when actinic on)
DoFsFmpFop Set Fs, saturating flash, set Fm , dark pulse, set Fo , compute and Log f4 level 0 (when actinic on)
SetZero Uses the current fluorescence sig- nal as a future offset. -none-
SetFs Set Fs to current value of F f2 level 0 (when actinic on)
SetFo Set Fo to current value of F f0 level 0 (when actinic off)
SetFm Set Fm to max F value of latest flash These have no fct key equivalents, but are performed as part of some fct key routines
SetFm_Prime Set Fm to max F value of latest flash
SetFo_Prime Set Fo to min F value during latest dark pulse
Actinic_On Turn on actinic, using current mode and targets. f4 level 9
Actinic_Off Turn off actinic.
FarRed_On Turn on far red LED using current target (farRedTarget). f5 level 0
FarRed_Off Turn off far red LED
FlrRecordingOn Open fluorescence recording (uses current flr recording file name, and appends) -none-
FlrRecordingOff Close fluorescence recording file f5 level 8
FlrRecordingAsk Prompt user to pick a new file for fluorescence recording, and if a file exists, will append.

Fluorescence Compute List

The default LCF compute list is named “Std Flr Comp_6.1”, and is listed below



It essentially links two other compute lists together (this ability is new to OPEN 4.0). The first file, StdComps_6.1, is listed in The Default ComputeList on page 15-38 in the instruction manual. The second file Flr Only adds the fluorescence variables, and it is listed below.

##4201F1 “Fv” “Fm-Fo”

“ flr_m - flr_o “


##4202F3 “Fv/Fm” “Fv/Fm”

“ #4201 / flr_m “


##4205F3 “BlueAbs” “Leaf abs in blue”

“ UCON(0.85) “


##4206F3 “RedAbs” “Leaf abs in red”

“ UCON(0.85) “


##4207F3 “LeafAbs” “Leaf absorptance”

“ (bluePct * #4205 + (100 - bluePct) * #4206)/100 “


##4208F1 “PARabs” “Absorbed PAR” “ parIn_um * #4207 “


##4210F1 “Fv’” “Fm’ - Fo’”

“ flr_mp - flr_op “


##4211F3 “Fv’/Fm’” “Fv’/Fm’”

“ #4210 / flr_mp “


##4212F3 “PhiPS2” “(Fm’-Fs)/Fm’”

“ (flr_mp - flr_s)/flr_mp “


##4213 “Adark” “Dark photo value”

“ UCON(-1) “


##4215F3 “PhiCO2” “(A-Ao)/(aQ)”

“ (#30 - #4213)/(#4208) “


##4216F3 “qP” “(Fm’-Fs)/(Fm’-Fo’)”

“ (flr_mp - flr_s)/(flr_mp - flr_op) “


##4220F3 “qN” “(Fm-Fm’)/(Fm-Fo’)”

“ (flr_m - flr_mp)/(flr_m - flr_op) “


##4221F3 “NPQ” “(Fm-Fm’)/Fm’”

“ (flr_m - flr_mp)/flr_mp “


##4222 “PS2/1” “Photosystem Distribution Factor”

“ UCON(.5) “


##4223F3 “ETR” “Electron Transport Rate”

“ #4212 * #4222 * #4207 * parIn_fs”


##4231F3 “qP_Fo” “(Fm’-Fs)/(Fm’-Fo)”

“ (flr_mp - flr_s)/(flr_mp - flr_o) “


##4232F3 “qN_Fo” “(Fm-Fm’)/(Fm-Fo)”

“ (flr_m - flr_mp)/(flr_m - flr_o) “

Leaf Absorptance

The standard fluorescence ComputeList (Fluorescence Compute List) allows leaf absorptance to be a function of the fraction of blue light. Therefore, two user constants are defined (RedAbs and BlueAbs), and the LeafAbs variable computed from


where α is effective leaf absorptance, αblue and αred are absorptances in the blue and red, and B is the percentage (0-100) of incident light is that is blue. Table 27‑15 shows some a sampling of absorptances. The blue tends to be a bit higher than the red. The values in the table are computed by integrating the product of the spectral irradiance S(λ) of the LED with the spectral absorptivity of the leaf α(λ), and dividing by the integrated spectral irradiance.


Table 27‑15. Leaf absorptances in blue and red for a few species, measured with an LI-1800 spectroradiometer.
Species αblue αred
Maize 0.90 0.85
Bean 0.91 0.83
Jasmine 0.92 0.87
Orange 0.94 0.93

The leaf absorptance variable is used in computing electron transport rate ETR (equation 27‑12) and ΦCO2 (Equation 27‑11.

To set the values of RedAbs and BlueAbs, do one of the following:

  • Config Menu|View/edit, navigate to the node <FlrSettings> <Constants>, or
  • Press Sys&User Consts (f3 level 3) in New Measurements mode, or
  • Press Flr Editor (f2 level 8) in New Measurements mode.

LCF Boundary Layer Conductance

The boundary layer information for the LCF is contained in the file “/Sys/Lib/BlcTable_LCF”, which is listed below:

LCF, broadleaves. 7/19/01

BLCTABLE= 0.48 2

0.58 0.14

3.73 1.92

4.65 2.29

5.36 2.94

5.89 3.39

6.46 3.72

For an explanation of the BLCTable format, see Figure 14-5 on page 14-21 in the instruction manual.

Simultaneous Gas Exchange and Fluorescence

The phrase ‘simultaneous gas exchange and fluorescence measurements’ raises a question: What is happening to the gas exchange measurements while fluorescence measurement events (saturating flash and/or dark pulse) are occurring? Obviously, a flash or several seconds of darkness is not going to leave steady state photosynthesis unaffected, so how are these possible interactions accommodated?

The fundamental fluorescence measurement is the raw, real-time signal (mV) coming from the LCF. This is labelled F, and can be found on display line m. It is measured simultaneously with the gas analyzers, temperatures, and other signals that go into the gas exchange measurements and computations. When a fluorescence event comes along, all gas exchange measurements cease for the duration of the event, while the fluorescence measurement (and the ParIn_μm value) continues. At the end of the event, one final computation is done, and if logging is active, all of the gas exchange and fluorescence computations are written to the log file.

Example: Do Fs Fm’ (f3 level 0)

This keystroke (or the corresponding command in an AutoProgram) is supposed to capture the steady state fluorescence value, the state of the gas exchange parameters, do a saturating flash, and add a data record to the log file (if it is open) that captures all of this information in one line. How does it happen?

Here is the sequence of events:

  1. Fs is set.
  2. System variable Fs (display line o) is set to the current value of F.
  3. Normal events stop
  4. “Normal events” refers to the updating of new raw readings and system variables every second, and computing user variables every 2 seconds. With the exception of raw fluorescence and the parIn_mV value, no raw readings will update until the end of Do Fs Fm’.
  5. Saturating Flash
  6. The system variable Fm’ (display line o) is set to the maximum value of F during the flash.
  7. Compute and Log
  8. If a log file is open (not Fluorescence Recording, but normal data logging), user computations are done prior to the data being written to the file. This effectively updates all fluorescence-related quantities, such as PhiPS2. Every item in the compute list is recomputed, including the gas exchange related values. They will not change, however, since the latest gas exchange related readings haven’t changed since Step 2.
  9. Normal events resume.
  10. Regular readings and computations resume.
  11. Figure 27‑73 shows a sample data file in which data was logged by fluorescence events. In this case, the first observation was made on a dark adapted leaf, and was triggered by DoFoFm, which captures the minimal fluorescence value, does a saturating flash, and assigns the maximal fluorescence to Fm. Note that each of these actions puts one or more remarks into the data file indicating what happened. The gas exchange data (e.g. the photosynthetic rate of -0.73) reflect what was happening just prior to the fluorescence event.

Hint: The LCF generates a lot of remarks. If you do not want these intermingled with your data, they can be routed to a separate file. See Log Options on page 9-15 in the instruction manual.

Figure 27‑73. Sample lines from a data file showing remarks generated by fluorescent measurement events, and data records. At 10:51:31, a DoFoFm was performed, causing Fo to be set. A saturating flash was completed at 10:51:31, and the value of Fm set accordingly. A data record was then logged using gas exchange data from the moment Fo was set. Observations 2 and 3 were each triggered by a DoFsFm’Fo’ event, with a MultiPhase flash used for observation 3.