What's new in version 2.0

This summarizes changes in the latest version. Review this section if you are familiar with older versions of the software and you want to learn what is new.

Some things have moved

Bluestem Version 1

Bluestem Version 2

Figure 1. The previous and new menu structures. Eight items have moved.

In version 2, the top menu reflects the recommended work flow:

  • Preparation - configure the system (chamber, light source, etc.), make sure that things are working (warmup tests, etc.).
  • Verification - take a look at the measured and computed value in Measurements, to make sure they make sense. If there is something wrong here, the remedy is likely to be found in one of the preceding tabs.
  • Operation - once the system is behaving as expected, then you can proceed with collecting measurements (manually or automatically).

Experienced users will notice the absence of a Log button and the presence of a Fluorometry tab. The menu bar adapts as needed:

Range Matching

Range matching screens are now found at Constants > Range Match. To collect range match data, use the Match Utilities screen. To enable or disable, or otherwise configure range matching, use the CO₂ or H₂O screens.

Figure 2. The range match screens.


Most of the screens under Fluorometry are not new, just moved from their old home (Environment) and rearranged a bit.

Figure 3. The old fluorometry pages are arranged under the new Fluorometry tab.


Stability has moved under the Log Setup tab, but its indicator badge showing the fraction of stable items remains on the top menu bar.

Figure 4. The new home of the stability tab.

Need help finding something?

A new feature in version 2 is a way to find where to go to perform various tasks. Tools > Find Task provides a filtered list of things you might need to do, and where to go to do them.

Figure 5. The on-board method of finding where to do a particular task.

Attaching a light source

All spare connectors are configured under Start Up > Peripheral Setup. This includes the light source connectors on the head and console, auxiliary power connector on the head, and the 25-pin console USER I/O connector.

Figure 6. Three screens for configuring spare inputs and outputs to the system.

When a light source is connected, you have the ability right there to test it and check its calibration coefficients.

Figure 7. Helper routines associated with the light source connection pages.

Fluorometer utilities

The Fluorometry > Utilities screen is a new feature, and hosts a number of fluorometry related utility programs.

Figure 8. Fluorometry settings.

The utility screen layout follows a familiar pattern1: Select a task, tap the Start button, and (if appropriate) watch the results unfold on the table and graph. In all cases, tapping Start launches a BP. If you want a peek behind the scenes to see what the program is doing, tap Programs > BP Monitor, and tap the BP entry:

Figure 9. Utility tasks are BPs, and can be monitored while they run, if you are interested.

Test Dark Mod Rates

This test is used to find the optimum dark modulation rate, by measuring the tradeoff between increasing frequency (to increase signal-to-noise) at the risk of the integrated light becoming actinic and inducing photochemistry. The test assumes that you are clamped onto a fully dark adapted leaf. The program will increase the dark mod rate while turning the measuring beam on and off to allow fluorescence to relax before going to a new frequency setpoint.

Figure 10. Testing dark mod rates for a soybean dark adapted for 1 hour.

Figure 10 shows a slight increase in fluorescence at 500 Hz which tells us that the integrated light intensity, 0.05 μmol m-2 s-1, is enough to become actinic. For this soybean, a dark modulation rate of 200 Hz would therefore be optimal.

Test Flash Intensities

This test can help you choose optimum flash intensities and durations for a light adapted leaf. It will run through user specified flash intensities, waiting for fluorescence to stabilize prior to each flash. We are interested in the maximal fluorescence recorded during the flash (Fmax), and the time at which FMax occurred (T@Fmax). The program will build a plot of these as a function of flash intensity. When the program is complete, choose the flash intensity from the graph where Fmax does not significantly increase with higher flash intensities. The second thing to consider is the duration of the flash. If doing rectangular flashes, make sure T@Fmax for the flash intensity you picked is shorter than the duration specified during the test setup. If not, rerun the program with a longer duration or pick a higher flash intensity. If you are using this test to optimize your MPF settings, pick the flash intensity the same way, and use the T@Fmax to set your phase 1 duration.

Prior to running this test, clamp onto and light adapt a leaf of interest to the light intensity you will be making your measurements at.

Figure 11. Testing light adapted flash intensities on a sunflower.

Based on the curve in Figure 11, leveling off around an Fmax of 1950, a red target of 8,000 μmol m-2 s-1 would be a good flash intensity for both the rectangular and MultiPhase flashes. If we did not see the curve reaching a plateau we could either implement an MPF or rerun the test with a higher maximum flash intensity. For the rectangular flash, we can see that T@Fmax occurred at about 300 ms. A duration of 700 ms will then ensure that we capture Fmax during the flash. If we wanted to use the MPF, a good starting point for the phase 1, 2, and 3 durations would be T@Fmax, so about 300 ms each.

Zero Signals

The fluorometer has two detectors that can be zeroed. Their drift is mostly related to temperature.

Figure 12. Zeroing the fluorometer.

View Factory Cal

The View Factory Cal utility lets you view and edit the fluorometer factory calibration coefficients.

Figure 13. Viewing the fluorometer factory calibration.

Fluorometer Square Flash Correction

When the LI-6800 fluorometer is performing a flash, the actinic intensity falls off slightly with time. Figure 14 shows a normalized plot of Q for 7 flashes ranging in intensity from 7,000 to 16,000 µmol/m2/s. The decay for a 16,000 flash is typically less than 2% after a second, and about 0.3% for the 7,000 flash. This also depends on the fluorometer's LED tile temperature; the higher the temperature, the more the falloff.

Figure 14. Flash intensity falloff with time depends on the intensity.

Square Flash Setup

A square flash correction can be implemented by running the Square Flash Setup routine.

Figure 15. Launching the program that collects data for doing square flash corrections.

Figure 16. After collecting the required data, the program present a plot of the residuals, and you can implement the correction function.

Suggested square flash calibration strategy:

Do the calibration with the fluorometer well warmed up, perhaps after leaving the actinic on at 500 or 1000 μmol m-2 s-1 for 30 minutes. Although the calibration does depend on LED tile temperature (FlrLS:Tled), there is a built-in temperature correction that compensates at other temperatures. Use the Square Flash Test (below) to determine how well the calibration is doing at other temperatures, and you can redo the calibration when and if it becomes necessary.

Square Flash Test

A simple way to test how well the square flash correction works is to run the Square Flash Test.

Figure 17. Rectangular and MultiPhase flashes can be tested. The tests simply compares two flashes — with and without correction.

Square Flash Coefficients

You can view the square flash correction coefficients. Note the checkbox that let's you turn them on and off, if you so choose.

Figure 18. Viewing the square flash correction coefficients. They are stored on-board the fluorometer itself.