Survey measurement considerations

The goal of survey measurements is usually to characterize a population, which means sampling a lot of leaves in a short period of time. This means spending a minimal amount of time (no more than 60 to 90 seconds) on any one leaf in order to maximize the sample size.

If your ultimate goal is to be able to say something about a community, or at least a number of plants, it follows that each leaf needs to be measured in similar conditions. The conditions in the chamber should be as close as possible to what the leaf was experiencing prior to the measurement. This saves time as well; you will only be waiting for the chamber to equilibrate (flush out), rather than waiting for the leaf to equilibrate.


Light is the most important variable, so be careful how it changes before and during the measurement. Avoid shading the leaf as much as possible as you move it into the chamber. During the measurement, keep the chamber orientation constant. Be cognizant of the recent light history of the leaf. If you are measuring sunlit leaves, don't select one that happens to be in a small sunfleck, or one that became sunlit when you moved some stems out of the way. When you put a leaf into a clear-top chamber, the light incident on the leaf will be reduced by about 10%. Photosynthesis may respond fairly quickly to that reduction, and should equilibrate in a few seconds. Stomatal responses take longer, but 10% light reduction will usually not cause a measurable change in conductance.

Avoid large changes of light. A common error is to reorient the chamber during a measurement. Whether you do it inadvertently (distracted by your Twitter feed) or intentionally (avoiding shade), it's bad.

For outdoor survey measurements, clear days are a blessing and partly cloudy days are a curse. With only short periods of uninterrupted sun, the leaves will be in perpetual disequilibrium. Measurements taken under these conditions will be nearly impossible to interpret, and therefore meaningless. The use of a light source will guard against the odd cloud shadow interrupting a measurement on a nearly clear day. With more abundant clouds, the most a light source can offer is the chance to let each leaf equilibrate for 10 or 15 minutes in constant light, and that makes for very slow survey work.


Since photosynthesis is a function of CO2, it is important to have the chamber CO2 as consistent as possible. To accomplish this, set the instrument to control CO2 on sample and set the target to near ground-level ambient conditions, so the leaf draws CO2 down to ambient levels. Consider controlling on CO2_r for faster survey measurement. To find ambient CO2, make sure flow is turned on then turn the CO2 and H2O controls off and step away from the console so you aren’t exhaling near the instrument’s air inlet. Look at CO2_r to see approximate ambient CO2. Enter that value as the setpoint.


If doing survey measurements on soybean in a greenhouse and the instrument is set to control CO2_s at 400 µmol mol-1, clamp onto a leaf and note the CO2_r concentration when things are stable. If it requires 422 µmol mol-1 to keep the chamber at 400 µmol mol-1, the expected delta is 22 µmol mol-1. Set the instrument to control on CO2_r = 422 µmol mol-1 for subsequent measurements.

The benefit of using this method is that there are no feedback control loops involved for CO2_r and hence the system will reach steady state more quickly. The drawback is that it only works when measuring plants with similar assimilation rates. You probably would not do this if you have large variations in assimilation rates since you want CO2_s to be about the same for each measurement.


Set the humidity between 50% and 80% RH. You want conditions that are familiar to the plant, but be aware that the mixing fan will decrease the thickness of the leaf boundary layer, so you need a setting that is higher than ambient humidity to maintain stable conditions for the leaf and ensure that the plant does not significantly change its stomatal opening after being enclosed in the chamber. Consider controlling on H2O_r for faster survey measurements. To find the setpoint, clamp onto an example leaf and find an H2O_r setpoint that gives 50 to 85% RH in the chamber. Use that setpoint for the next measurements. Controlling on VPD is not recommended for survey measurements.


Flow should be set to a moderate level so the chamber flushes quickly when you clamp on a new leaf (500-600 µmol s-1 is good, typically). However, you also want to be mindful of your ΔCO2 and ΔH2O. If you are working with stressed leaves and are measuring low fluxes, lower the flow rate (200-300 µmol s-1) in order to increase the deltas to have a better signal-to-noise ratio and more confidence in the flux measurements.


There are two schools of thought about the temperature control and survey measurements: one is that you shouldn't use the cooler so that your batteries last longer. The other maintains that you should use the cooler to maintain ambient temperature so that the chamber doesn't get hot from being in the sun. You decide.

Be aware that a large change in temperature will have an effect on photosynthesis, so if the temperature is changing rapidly or these survey measurements are part of a diurnal curve, temperature control is advised. Tleaf is not recommended for rapid survey measurements. Instead, control on Tair or Txchg if anything at all. A second thermocouple can be attached to the vacant T1 or T2 connector to monitor ambient temperature.

Matching the IRGAs

Match once on the first leaf (or a "trial leaf"), and perhaps every 30 minutes or so after that, especially if temperature is changing.

Logging considerations

You will need to decide some other logging considerations, as well:

  • Leaf Area?
  • Does the leaf fill the chamber aperture, or is it changing from leaf to leaf? How and when will it be measured? Do you wish to be prompted for leaf area as you go, or enter leaf area into the spreadsheet later?
  • Extra Data?
  • Are there extra data you wish to record, such as plant numbers or remarks, to help identify the data later? If so, consider configuring the user constants and activate the Prompt on log option under Log Files > Logging Options.
  • How Many Log files? Log Options? Are all the measurements destined for one file, or should there be several? If several, what's the rationale for the grouping? Does it matter in which order the measurements are done?
  • The simplest approach is to log all the data into one file. If, for some reason, you desire multiple files, then make your measurements so that File1 is finished before File2 is started.
  • Use Stability criteria?
  • You can guess when to log or use some objective criterion, such as stability.