September 30, 2020

New and Improved CSR Scanning programs

We have been using our Jaz quite a bit so far this year, and have come a long way.

Firstly, for groups looking at water indices, we recommend going with grating #14, it seems to do a much better job and gives values which align more closely with what is published in the literature. There are also significant differences at the 970 wavelength between genotypes with grating #14, while with grating #4 all of the variability between genotypes seems to be coming from the “correction” wavelength of 880 or 900.

Secondly, we realized while taking 3 measurements per plot that there is a LOT of variability within plots with respect to many of the indices (at least with NDVI indices). There was so much variation within plots that it was almost as great (if not greater) as is was between plots. There was a very low correlation, with an r-square ranging from 0.05 to 0.2 between measurements taken at different spots in a plot. We confirmed that this problem was due to heterogeneity in the plots and not an inconsistency in the Jaz by repeatedly measuring the individual spots on several different plots. There was a very strong correlation (r-square > 0.99) between the measurements on a single spot, and a very low correlation between different spots in an individual plot, along the lines of what was seen before with a low r-square value.

To solve this problem, we modified the script we were using to take a large number of averages (400), and then “scanned” along the plot by holding the fibers level and walking at a constant pace. This allowed us to integrate the entire plot into the reading, as well as reducing the extra bit of noise we were seeing in the new grating #14. This scanning method gives much more repeatable results than taking several point measurements. Although we ran a relatively small test, we had a very strong r-square value of >0.99 between the different scans of the plots, while we obtained very weak r-squared values on those same plots using the point measurement method, and the variation within the same plots with the point method was actually greater than thevariation between different plots with the scanning method.

Attached are the jaz programs that we are currently using, 2 and 3 channel versions are included (you will use one or the other depending on how many channels you have in your jaz unit). It is important that the downwelling channel (the one facing the sky) be channel 0, and upwelling channel be channel 1 (and channel 2 for the 3 channel units), as results are saved differently, and fewer averages are taken for the downwelling channel. If you have a 1 channel jaz and/or do not want to record downwelling measurements, contact me and I can help you make a 1 channel version, or if you are not technically inclined I can just make one for you.

To use these scripts, simply unzip the attached folder, and put its contents directly onto the root drive of your SD card for your Jaz. When you start up your Jaz, it should launch scriptor and you will be able to select the program you want to run.

Here is a quick overview of how to use the program, I tried to make it as foolproof and easy to use as possible though.

After launching the appropriate script (depends on if you are using a 2 or 3 channel Jaz):

Go to More (If you are starting a new round of measurements and have transferred all your data off of the SD card, go to More->Change File#->File reset to reset the file (plot) counter to 0, then go back to the More menu. If you are continuing on a round of measurements do not reset the counter) Go to Reference Menu Position your fiber over your white reference and use Adapt (you will see what the integration times are set to) -If you need to change the integration times (for example adjust the downwelling channel to a shorter time so that it does not saturate as the day gets brighter) go Back->Int Time Adj.-> select the appropriate channel and adjust to desired integration time. We usually set our upwelling channels to 0.003 seconds, but this may vary for you depending on how bright it is and what fibers you are using. After adjusting times go back to the reference menu Position your fiber over your white reference and select White Ref to take your white reference. Once the Jaz says it is saving the reference you do not need to keep the fiber positioned over the reference Cover your fibers and take a dark reference (OK to uncover after Jaz says saving) Go back to the main menu (Back->Back) *If you need to adjust the number of averages you are taking for some reason (probably only if you are doing testing) use the Adjust Averages menu You can now begin taking samples. Position your fiber over the beginning of your plot and select Take Sample. Immediately begin walking to “scan” your plot (about 7 seconds). The amount of time it takes will depend on your number of averages and your integration time. Pause at the end of your plot while the downwelling (Channel 0) measurement is taken *If you are using three channels, when the Jaz begins taking channel 2 scan back over your plot for the second upwelling channel reading Once the Jaz says “processing” or “saving” you can move on to the next plot repeat steps 9-12 after arriving at the next plot. To take new references, go to More->Reference Menu and take white and dark references as in steps 5 and 6 *If you feel the need you can also take a new integration time using adapt at this point, we usually only set integration time at the beginning of the day, and set it to a faster (lower) integration time that will be appropriate for the whole day. Repeat steps 7-14 until finished. Chose Exit to exit the program and close all open files, and then power off the Jaz.

As far as the apparatus we are using to suspend our fibers, we are using  an 80cm segment of PVC joined to a ~50-60cm piece of PVC (1 1/4″ diameter) by a 4-way 90 degree joint (like a plus sign). On the end of the shorter piece is a T-joint with short segments of pipe inserted into each end. We thread the fiber optics through the back of the 4-way joint up to the T-split and then face our downwelling channel (channel 0 for us) up, and the upwelling channel(s) down. We use small pieces of foam to secure the fibers, and have caps for the bottom of the longer piece and the two short pieces on the T-split (for taking dark references and protecting the fiber ends when not in use). We also have a square post bubble level attached to the top so that we can keep it level while scanning plots. The longer piece of PVC has markings on it to indicate distance from the upwelling fiber optics so that we can ensure that we are taking reflectance measurements at a uniform distance. It’s not the most sophisticated design in the world, but it is actually working quite well for us so far and isn’t as cumbersome as the large adjustable pole we were using before (and is also very simple to make). If you need clarifications on the design contact me and I will send pictures and/or better descriptions, I do not have access to a camera at the moment though. This design will probably also change, it gets tiring to hold when the plants are tall.

We have also written a perl script (based off of a script written by Brian Bowman) that will combine together all of the different measurements into a single file, with one file for each channel (as opposed to one file per channel per plot as they are saved in the field). The script is very easy to run, but if you are on a PC you will need to install a perl interpreter such as activeperl, or any other you or your IT department prefers. You will need to set up the SP0, SP1 etc files for use with your particular spectrometer by simply overwriting what is currently saved in the file ( wavelengths values for each channel of my Jaz unit) with values with your Jaz unit. You can do this by opening the SP file with something like text editor or excel, and also opening a file from a previous reading you have taken with your spectrometer (you will need one from each of your different channels), and simply copy and paste your wavelength values over mine, and saving the file again (without an extension). Once you have your wavelength files set up and are ready to go with running perl scripts, just drop the Jaz_data_condenser script as well as the SP0, SP1 and (if you are using three channels) SP2 wavelength files into the folder with your jaz data and run it. It will prompt you with the channel number your would like to process, so just enter the number (0, 1, or 2), and it will run through and process all the files for that channel. You will need to run the script once for each channel (so twice for a two channel, three times for a three channel). After running the script, just open the SP*_processed.txt file for the channel of interest in something like excel, and you can begin calculating indices.

Be aware that the file numbers will be slightly different after running this script, e.g. file SP0.txt.001 as saved by the Jaz will be labeled as SP0.txt.002d in the processed file. This is because this program can also be used to average together multiple point readings from a plot using divider files (hence the “d” at the end of the file name). If you would prefer to take point measurements still, I can send the old Jaz program we were using, it is very simple to use and the data can be processed using the same perl script. I will likely write another version of the script that will not rename the file numbers, and a Jaz script that will not create divider files in the future, it shouldn’t create too much confusion though since you will likely just be looking at the files all together in a relative fashion (e.g. when you paste your plot names/genotype IDs into the file, the first reading will be the first plot no matter what it is named).

Feel free to email me with questions at trhowell@ucdavis.edu. Also, if Jaz users think it would be interested I think it would be good to start up a CSR forum on the PBTN site like we used to have on the TCAP website so that we can all share ideas, problems, and fixes (or if we can get the forum back at the TCAP website that would also be great).

-One last note: We have also received a cropscan unit and our first impressions are that with all the work we have put into creating scripts and protocols for the Jaz, the Jaz is actually easier to use, faster, and more user friendly. This may change if people are still having overheating problems in the summer, we haven’t had a single problem with ours so far this year though (after taking thousands of measurements). The cropscan is much older technology (circa 1990) and is much bulkier. We went to compare cropscan and jaz measures one day last week, but the cropscan was configured incorrectly and didn’t actually take any real measurements, so an analysis of the efficacy of the cropscan vs Jaz is still pending.

I hope this helps!

— Tyson Howell
Genetics Graduate Group
University of California, Davis
trhowell@ucdavis.edu