SPAD measurement for chlorophyll content

[Greg Austic]

<-- also post this to the blog, FYI but wanted to make sure you all saw it too...

I made several improvements to the Arduino code in the last few days so that it'll be easier for Bruno and others to create new protocols!  We'll have a training video about how to create a protocol as well, which should help make that process pretty straightforward.

I'm also working on implementing chlorophyll content measurements before the start of the Beta.  Often called SPAD, this measurement was first commercialized by Minolta and they remain a big seller of chlorophyll content measurement instruments, specifically the SPAD 502 meter (http://www.specmeters.com/nutrient-management/chlorophyll-meters/chlorophyll/spad502p/). 

SPAD measurement

Chlorophyll content can be a proxy for N levels in plants, and therefore indicate when additional fertilization is required.  Here's a quick little paper which uses SPAD measurements on 2 crops to predict N application: http://www.hort.cornell.edu/uhi/research/articles/horttech12%284%29.pdf.  This technique is particularly proven in corn and several other major commercial crops - so pretty darn useful!

How it works

The SPAD meter measures transmission of 2 wavelengths (650nm and 940nm) through the leaf.  The 650nm correlates with the presence of chlorophyll, while the 940 measures the leaf thickness.  The ratio of the two tells you roughly how much chlorophyll is in the leaf (measured in SPAD units).  This is a relatively easy measurement because neither light sources need bandpass filters (a bandpass filters out light outside of a narrow spectral band, for example from 640 to 660, to provide a more pure light source).   

Other companies have developed other techniques, like opti-sciences, which are a bit better (they don't require that you clamp on both sides, they don't require that the leaf completely cover the light guide, can wider range of chlorophyll concentration, etc.).  That technique compares 700nm with 730nm which also correlates to chlorophyll content - however, this technique requires bandpass filters which are expensive.  Read more about it here: http://optisci.com/ccm300.htm . 

So we're going with the good old SPAD measurement because we can do it with out current device setup and, most of the time, it's just as good as the newer method.

Help make PhotosynQ SPAD-tastic

We are looking for any beta testers interested in helping us correlate our SPAD measurements with Minolta (or other brand's) SPAD readings.  If you're interested, please shoot me an email!

Greg

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Greg Austic

2198 Seminole Dr.

Okemos, MI 48864

(919) 545 1083

www.austiclabs.com

[Bruno Hay Mele]

Il giorno venerdì 27 dicembre 2013 23:26:24 UTC+1, Greg Austic ha scritto:

I made several improvements to the Arduino code in the last few days so that it'll be easier for Bruno and others to create new protocols!  We'll have a training video about how to create a protocol as well, which should help make that process pretty straightforward.

Thanks, Greg. The video could prove extremely useful for training students in protocol creation.

[CUT]

Help make PhotosynQ SPAD-tastic

[CUT] 

Unfortunately, we do not have SPAD meters in our lab. But we can do almost all the PSII photochemistry, that is:

*) electron trasport rate (ETR)

*) quantum yield of PSII linear electron transport (ΦPSII)

*) yield of regulated energy dissipation (ΦNPQ)

*) non-regulated energy dissipation in PSII (ΦNO) 

*) maximalPSII photochemical efficiency (Fv/Fm)

*) non-photochemical quenching (NPQ)

*) photochemical quenching (qP)

Data retrieval and elaboration - wise, I usually work with R, so I expect to use the Arduino Serial Connection for collecting the output and the rjson package (http://cran.r-project.org/web/packages/rjson/index.html) for importing the dataset in R. How hard it is to tell photosinQ to output in .csv? 

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Bruno Hay Mele

asf-cf lab | +39 081 679 102

Dipartimento di Biologia, Federico II University

Via Cinthia, Naples(80126), Italy

[Greg Austic]

Comparison for the PSII photochemistry would also be great - we have a lot of the same benchtop tools in our lab also, so we should get a lot of good data from multiple sources.

In terms of using R, right now we're looking towards using something like this for data visualization and analysis:  http://explorer.okfnlabs.org/#rgrp/e3e0b0f18dfe151f9f7e/view/grid .  It's called Data Explorer, and it's a very simple way to quickly compare, graph and map different variables in a dataset.  Plus, you can create macros in Javascript (in the upper right corner) which can run additional calculations on the variables (for example, calculate Fs/Fm, or determine the best fit of a curve)...

So if it is possible to access R from Javascript, then perhaps R could be used there (?).  Sebastian (who's creating the data display component) may have more to say on that -

Greg

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[Bruno Hay Mele]

2014/1/1, Greg Austic <gbat...@gmail.com>:

> In terms of using R, right now we're looking towards using something like
> this for data visualization and analysis:
> http://explorer.okfnlabs.org/#rgrp/e3e0b0f18dfe151f9f7e/view/grid . It's
> called Data Explorer, and it's a very simple way to quickly compare, graph
> and map different variables in a dataset.

Yeah, I think that is a good choice, consistent with the aims of your project.

> So if it is possible to access R from Javascript, then perhaps R could be
> used there (?).

Actually I saw that Data explorer data can be saved in csv. That is more than
enough for my needs. Accessing R from data explorer would make things
unnecessarily complicated.

Happy new year to everyone,