What you can measure with your MultispeQ

Production line, located in the Plant Research Lab Dungeon!
PhotosynQ production line, located in the Plant Research Lab dungeon!

Production of the MultispeQ has begun in earnest!  We have all the parts (except the circuit boards which are coming next week) to build 250 beta MultispeQ devices, and we’ve got Geoff full time on production to make it happen.  The hardware version is locked, device calibrations are known, the software platform is stable and works in the lab and in the field,  and we have a suite of high quality methods for measuring plant and soil health.  It’s been a long journey, but we feel good that we’re finally ready to let go 🙂

I’d like to take this post to give more detail about just what the heck you’re going to be able to do with your MultispeQ device once you get it.  Next to each measurement you’ll see a comparable commercial device, though it’s important to note in some cases the MultispeQ is more accurate, and in some cases less accurate.  Combined, the commercial cost of devices which measure everything described below is 10s of thousands of dollars so we think we’re doing pretty good!

Measurements

The machinery of photosynthesis! The red circled items are areas which can be measured using the MultispeQ.
The machinery of photosynthesis! The red circled items are areas which can be measured in some way using the MultispeQ.

Light Levels

LiCOR PAR meter

Photosynthetically Active Radiation (PAR)

PAR is the range of wavelengths of light which are actually absorbed by plants to do photosynthesis.  This range is 400nm (purple) to 700nm (dark red).  Standard light meters are influenced by infra-red and UV, which are not used in photosynthesis.  We use PAR, combined with the other measurements below, the figure out the flow of energy via electrons and H+ ions which ultimately produce sugar and plant tissues.

Chlorophyll content

spad 502 plus
Minolta SPAD meter

SPAD

Chlorophyll content in the leaf has been shown to relate to overall plant health, and NDVI (a similar measurement taken using reflectance instead of transmittance) is used commercially to determine the timing of nitrogen application in corn and other crops.  This measurement is very short (about 1/2 a second) and can be calibrated easily in a few seconds in the field.  SPAD measurement was initially popularized by Minolta and they continue to produce most of these types of handheld devices.

Efficiency of Photosynthesis

Pulse modulated chlorophyll fluorometer

Photosystem II and Photosystem I efficiency

Photosystem II (PSII) is where most the energy gets captured from the sun which is used by plant to make food.  Tracking it’s activity, efficiency, and regulation tells us a lot about the condition of the plant.  For example, PSII efficiency changes based on stresses (like drought or lack of nutrients) quite quickly – in fact it is possible to spot a under-watered plant using PSII efficiency before the change is noticeable by eye.  We can calculate PSII efficiency by measuring infra-red chlorophyll fluorescence under various conditions – here’s a cool infra-red filtered time-lapse showing fluorescing plants in a growth chamber!

Photosystem I (PSI) also captures energy from the sun, but it’s role is a bit more complex and not worth diving into here.  But, knowing both PSII and PSI together can tell us linear and cyclic electron flow (the flow rate of the very electrons which ultimately produce ATP and sugars)… that’s kind of like measuring the pulse of a human being.  The faster our pulse, the harder we’re working or more stressed we are.

There are lots more details about these measurements and the mechanisms linked below:

http://www.advancedaquarist.com/2004/7/aafeature
http://en.wikipedia.org/wiki/Photosynthetic_efficiency
http://jxb.oxfordjournals.org/content/51/345/659.full.pdf
http://blog.our-sci.net/wp-content/uploads/2013/03/photosynthesis-state-of-the-art-2007.pdf (warning – very in depth but lots of good information!)
See page 1112 in this article “PSI Electron Flux” for a description of PSI measurement using 850nm

ATP production

Benchtop spectrometer

Proton Motive Force (PMF)

We are quite proud of this measurement, because we are the only handheld device that we know of capable of taking it!  The Proton Motive Force (PMF) is the energy produced by the flow of H+ ions out of the thylakoid membrane (see picture above).  What does that mean?  If we imagine that photosynthesis is like a hydro-electric dam then PMF is the energy produced by the water flowing through the turbines.   But for plants, instead of turbines producing electricity, it’s the ATP synthase producing ATP.  We can estimate PMF by measuring something called electrochromic shift (ECS).

This is a very new measurement so we don’t have a lot of clear applications in the field as of yet, but we hope the PhotosynQ community will help us find more!

Photosynthetic regulation

Non Photochemical Quenching (NPQ)

Plants spend a lot of time dissipating energy from the sun because too much light can damage plant tissue.  Chlorophyll fluorescence is one way to dissipate that energy (fancy term for this is photochemical quenching), but the plant can also turn excess light into heat.  This dissipation as heat is called non-photochemical quenching, or NPQ for short.  Normally, it takes about 10 minutes or more to accurately measure NPQ, but Dave and Stefi have been working on a new measurement called NPQt which cuts that time down to about 10 seconds… which means plant breeders, ag extension agents, and others can take this measurement in the field, in real time!

Combining photosynthesis measurements

One measurement to rule them all!

We’re working on combining PSI, PSII, and NPQ described above into a single measurement which takes 10 – 15 seconds to complete.  This is possible because these measurements all share similar components, like a saturating light, a measuring light, far red, etc.  In fact, combining them is potentially better than performing them separately because the measurements themselves disturb the plant – so the fewer times you flash lights at the plant, the more accurate your readings will be.  Expect to see a blog post detailing this measurement soon.

Soil biological activity

Solvita CO2- Burst Soil
Soil biological activity by CO2 accumulation

Soil CO2 production

Soil health is hard to measure because there are so many different components – nitrogen, phosphorus, potassium (NPK), micro-nutrients, the presence or absence of toxic chemicals, and other factors.  So measuring overall biological activity in a soil can give us a general indication of the soil health by measuring the CO2 produced by micro-organisms in the soil.  The rate of this CO2 production tells us the amount of biological activity.  Here’s an graph of some recent measurements we took showing the CO2 production of swamp, forest, and grassland soils taken in the field – swamp was the most active (fastest increase in CO2), as expected.

Soil organic carbon (humus)

Product image for Colorimeter
Standard small colorimeter

Permangenate oxidizable carbon

Organic carbon in the soil helps maintain pH, reduces leeching of nutrients, and increases water holding capacity.  It can be measured by using a potassium permangenate solution according to this protocol.  We have done initial successful testing but can’t wait to get more feedback from the community on this method!

Soil moisture and ion concentration

Soil EC meter and display

Electrical Conductivity (EC)

While the MultispeQ itself doesn’t have a conductivity meter attached, you can purchase a conductivity meter and hook it into the MultispeQSoil conductivity, i.e. passing an electrical current through the soil and measuring it’s resistance, is influenced by the presence of ions like nitrates, potassium, sodium, sulfate, and ammonia as well as the presence of water.  It’s a tricky measurement, because it’s influenced by soil type and moisture levels.  However, we’re particularly excited about this because if we can collect global soil EC data, and correlate it with soil type and weather information, we think we could eventually predict soil ion concentrations.

 

Other ideas

Polyphenol concentration in grapes, relates to taste for wine makingBrix (sugar concentration), relates to taste and readiness for picking

Anthocyanin content in leaves, a measure of stress

Pulse oxymetry, not plants, but hey why not

Seed mold, seed storability by measuring temperature, CO2, and relative humidity

We can’t wait to get these devices out into the field, and see what you guys come up with… expect more updates soon!

World Tour

We’ve been on a PhotosynQ world tour of sorts in the last month, starting with Mozfest in London, PhenoDays in France, TechCon in Berkeley, and now Public Lab’s Barnraising in Louisiana!  And, of course, we’ve been doing more method development and Geoff and Robert even managed to whip out a few more units on our march towards 100 to ship to beta testers.  Our media stream from these events are on our g+ page

Explore our data!

Where do I find the data for all these projects? Click here! Expect some nice tutorial videos on how to explore the data soon!
Where do I find the data for all these projects? Go to the project’s main page and click on the dashboard button. Expect some nice tutorial videos on how to explore the data soon!

We recently reskinned our website (www.photosynq.org) and made our initial alpha and beta testing data available to all!

A lot of it is old, performed on old instruments which we’ll clean up before we send out new devices.  Be gentle – we know there’s lots of bad data points, and that the data itself isn’t well documented – we’re working on that!  Also, expect a full video tutorial on this in the next few weeks.  But given all those caveats, here’s some cool ones to check out:

North Dakota State Bean Variety Trials: We measured 150 different crosses of the common bean this summer with Juan Osorno’s lab at NDSU.  You can see clear differences in photosystem 2 efficiency and SPAD.  Definitely some error in the data also – one of the devices was way out of range for PAR light intensity!

MSU North Campus Tree Phenology Research Project: about 20 students from Michigan State University tracked the color and photosynthetic efficiency of 6 different trees on campus over the course of 2 months.  Are red leaves still doing photosynthesis?  What about yellow leaves?  You’ll have to check the data to find out!

Malawi Bean Variety Trials: These were several different fields of different management methods on beans over the course of about 7 weeks.

Assaying Sampling Techniques using Beans: This is an ongoing project where we’re trying to figure out how each leaf on a common bean stalk is responding to light.  We’re measuring every leaf (about 11 or so in these 5 week old beans) for photosystem 2 efficiency, SPAD (greenness), and ECS (measures proton motive force).  We may switch the project as we change and adjust the protocols and user questions, but the data is quite interesting!

World Tour!

MozFest logo copy

 

MozFest in London.

Met folks from Zooniverse, Open Knowledge Foundation, and got Professor Grey from CERN excited about the idea of making a open scientific hardware conference (hope to post more about that later – if you’re interested in helping to organize please contact me!).  Hooked up with some awesome guys from Chicago Hive who will make great educational partners, and had a long and very educational talk with a gaggle of 14 year old British girls in a workshop about teens and citizen science.  Coolest of all – a DIY atomic force microscope for ~100 bucks… holy mackrel.

Also learned about some really neat tools Mozilla have developed to help the next generation be creators in the open web (instead of consumers in the ‘shopping mall’ web, as they describe it).   Check it out.

 

https://i0.wp.com/www.phenodays.com/fileadmin/templates/images/top-banner.jpg

PhenoDays in Beaune, France.

PhenoDays is a conference put on by LemnaTec, a company which makes very large scale plant phenotyping systems, focused mainly on imaging technologies for estimating biomass, though it also does chlorophyll fluorescence and even (as we saw in a nearby facility) measures root growth (see picture).

I met lots of great folks here, including a contingent from the Danforth Center, the Australian Phenotyping Center and the UK one (in Wales, the land of no vowels),

I wasn’t sure how we would be received, given that we are kind of the opposite of everyone else there (open data/software/hardware, low cost, measure the field not the greenhouse, uncontrolled conditions).  But actually, everyone loved the concept of an public database of plant health measurements in the field, and in fact we complement (not compete) with the existing plant phenotyping platforms like Lemnatec and Phenospex, because the data we collect can feed interesting ideas, phenotypes, outcomes, and questions into the more controlled chamber-type systems.

Also, we were thoroughly wined and dined. One night we had dinner here… in a ‘chateau’… pretty much a 1000 year old castle.

 

 

USAID’s TechCon in Berkeley CA.

TechCon is intended to bring together non-profits (including USAID), universities, for profits, and venture capital to help solve the toughest problems in the developing world.  The venture capital is there to help successful small projects to take it to the next level, as scale up is a big problem in development.

We met more interesting folks than I could mention, though the coolest thing I saw was Planet Labs, who want to take an image of the entire earth once per day.

Chris giving his pitch in the Innovation Marketplace
Chris Zatzke (of pick and place troubleshooting fame) presented the PhotosynQ project in the Innovation Marketplace, a competition among 49 teams funded through USAID. We won the Audience Choice award and we were chosen to take part in Venturewell’s development process (which leads to further funding and possible investment down the road). Basically, Chris rocked it!

 

Public Lab

Publiclab.org ‘s barnraising in Cocodrie Louisiana.

Actually, this is happening as we speak – Robert and Geoff are there learning and teaching and having fun.  We’ll be presenting the PhotosynQ platform to the Public Lab community, and hopefully we can get some interest in folks using, forking, or otherwise contributing to our pretty robust data collection, sharing, and analysis backend.

We’re also talking with Public Lab as a distribution partner through their Kits Initiative.  That saves us time in packing/shipping/fulfillment and gets us access to the amazing community that is Public Lab.

Other News

While we spent a lot of time on the road, we have also managed to develop some new and interesting methods.  The next blog post will have lots more detail, but we have successfully implemented the soil biological activity measurement using our CO2 sensor, and a spectroscopic measurement of proton motive force (using ECS).  This is actually kind of a big deal – no other handheld device IN THE WORLD can measure proton motive force, in part because of the accuracy required (an example measurement is shown below).  Our goal is to make sure short enough that people can take the measurement in the field.  More detail in the future, but we’re really excited about this.

measuring proton motive force using electrochromic shift caused by chlorophyll absorbption at 520ishnm
measuring proton motive force using electrochromic shift caused by chlorophyll absorbption at 520ishnm

 

We’ve also managed to make another 3 units, and we will STOP AT NOTHING until we have 100 units in hand!  Nothing is holding us up except all this traveling (which ends this weekend) and hand wringing so we will get it done!

Fun with PhotosynQ: Cuvette Holder

So while I had some down time (we are going through a slight board re-design to decrease noise and cross-talk) I worked on the ability of the PhotosynQ platform to gather non-plant data. I present to in all its glory, the MultispeQ cuvette holder attachment!

Here is the obligatory “action shot”. In reality the light pulses are so fast/short you can’t see anything.

IMG_1522   IMG_1520

 

Since a cuvette holder is basically useless without established methods that use it, I decided to adapt an assay designed to measure active soil carbon (carbon that is readily available for use by microbes) to the PhotosynQ platform. This assay is already in use by the USDA & many Universities ( Ohio, Missouri, etc).

The cuvette holder and PhotosynQ platform can (with a little work) be used for any of your standard absorbance assays that use wavelengths close to what the MultispeQ has available. For example, you could do Bradfords assay, or OD590 (the MultispeQ’s version of OD600). I am also working on a right angle cuvette holder for turbidity and fluorescence measurements.

The method is described here http://lter.kbs.msu.edu/protocols/133 (it is pretty close to what I did) and I’ve got my own procedure that I will put out shortly (once I make a how to guide).

The MultispeQ in its natural habitat (the MSU Horticulture Gardens http://www.hrt.msu.edu/our-gardens/).

IMG_1533

The basic idea is that you can go outside, collect a soil sample, oxidize it with permanganate for 10 minutes, find the absorbance of the sample, compare it to a standard curve/plug some numbers into a formula, and then get a mg/kg amount of active carbon in your soil.

Here is a picture of my standard solutions (in the falcon tubes) and my soil sample (in the cuvette). Don’t worry, even though it looks like my soil sample will fall outside of the standard curve it doesn’t.

IMG_1532

So after some troubleshooting I developed a protocol that works pretty well with the MultispeQ as it is now (once the new boards are in I might have to redo it, but its only going to get better).

Sadly as of now you have to calculate the absorbance manually (we are working on fixing that).

As you can see the standard deviation for the MultispeQ is higher than the labs spectrophotometer, but we expect that to go down significantly with the new boards.

Screen Shot 2014-10-06 at 2.10.31 PMScreen Shot 2014-10-06 at 2.10.40 PM

This is a graph of the stand curve as done on the MultispeQ and the standard curve produced by the labs spectrophotometer.

Screen Shot 2014-10-06 at 2.08.10 PM

 

Once the new boards are in I will work on optimizing this protocol so that the MultispeQ reports values that are closer to the labs spectrophotometer. I also have grand plans to integrate this assay into the PhotosynQ app, so you won’t need to plug anything into formulas or excel. As shown above, the deviation between the two becomes greater as adsorption rises. This will cause the MultispeQ to report values that can be ~30% greater than our control spectrophotometer. However, absorbances this large only occur in very poor soils, and as soil quality increases the error between the MultispeQ and the control spectrophotometer goes down considerably (in laymans terms we are able to very accurately calculate the absorbance of dilute solutions, even with the cross-talk and noise problems that we are correcting).

 

Hello Fargo, I’ve come for your beans!

Project: Bean Variety Trials at North Dakota State University
Project Leads: Juan Osorno and Ali Soltani, North Dakota State University
Goal: Collect photosynthesis and plant health data on 150 varieties of common bean for eventual QTL (genetic) mapping.

Project Page
View and analyze the data (create a login if necessary)
Juan Osorno’s NDSU page

 

Hello Fargo!
Hello Fargo!

This week I went to Fargo, North Dakota to meet with Professor Juan Osorno and post-doc Ali Soltani, bean breeders at North Dakota State University. I bet you didn’t know that NDSU has one of the premier bean breeding programs in the US – well they do!

On my flight in, I told the guy next to me I’d never been to North Dakota before, and his response was “You’re going to love it”… Love it? North Dakota? Well, yes, I did love it. People were nice, and it appeared that everyone was there because they wanted to be, which makes sense, you don’t end up in North Dakota for no reason. Agriculture is booming, and the the fields are gigantic (at least in comparison to the ones I was used to growing up in central New York). So, what were we doing there? I’ll let Ali give a recap:

So our goal is to show that you can correlate photosynthetic outcomes to actual genes or groups of genes.   This has so far proven difficult and slow to achieve for breeders especially in comparison with the dizzying pace of mapping the genome, which has been automated and has come down in cost many orders of magnitude over the last 15 years. We took measurements of 150 different varieties with 6 replicates each (900 measurements total).  Each measurement included two protocols: SPAD (a measure of leaf greenness which correlates to Nitrogen content) and Phi2 (a measure of photosynthetic efficiency).

Stephan collecting data using the Android app
Stephan collecting data using the Android app

It took us some time to get ready to collect data.  We had to go to a coffee shop to get internet to make sure everyone had an account at PhotosynQ.org and their cell phones had the PhotosynQ android app installed correctly.  But once we got to the field (a full 1.5 hours away!), taking measurements was a snap.  The only technical problems we had were swapping batteries as they needed to be recharged – that was a big success for us, and shows we’re ready to do real work with this thing!

MultispeQs charging their batteries after a hard days work.
MultispeQs charging their batteries after a hard days work.

So let’s look at some preliminary results using the online analysis tool (so you can view and play with the data too!  Note that you may have to create a login first). This tool is intended to be a Swiss Army knife of sorts – it can do lots of quick analysis, but none of them too deeply.  If you need to do multiple regression analysis… you’ll probably have to just download the data 🙂  We might to see more data in this project this week, as Ali and Stephan go back to a second field, we’ll see.  Also, Ali is working on more in depth device comparisons, to try to use statistics to parse out the variation coming from the device versus that coming from the varieties themselves.

 

We can also compare two variables on the X and Y axis. Here we have LEF (linear electron flow) a measure of energy from photosynthesis compared to light intensity. Each device has a separate series. These differences may be due to calibration, or differences in plants, hard to know yet.
We can also compare two variables on the X and Y axis. Here we have fluorescence in the steady state (normal light) versus that from a saturated state (very high light).  These differences may be due to calibration, or differences in plants, hard to know yet.
SPAD (a measure of greenness) was fairly consistent across devices as you can see. Some variation is due to the fact that each device only measured 60 of the 150 varieties, so there's not perfect overlap there.
SPAD (a measure of greenness) was fairly consistent across devices as you can see. Some variation is due to the fact that each device only measured 60 of the 150 varieties, so there’s not perfect overlap there.
The most important outcome from this trial was to determine if 6 devices could produce consistent results. As you can see here, device 43 was reading too high on light intensity PAR - we'll have to investigate that!
The most important outcome from this trial was to determine if 6 devices could produce consistent results. As you can see here, device 43 was reading too high on light intensity PAR – we’ll have to investigate that!
This is a simple average of Phi2 for 15 varieties. The black bars are 1 standard deviation.
This is a simple average of Phi2 for 15 varieties. The black bars are 1 standard deviation.  Anything statistically significant here?… mmm… not quite yet.
Histogram showing Phi2 (photosynthetic efficiency) for the entire sample - distribution isn't too bad!
Histogram showing Phi2 (photosynthetic efficiency) for the entire sample – distribution isn’t too bad!  Not a lot of outliers which means the MultispeQs worked ok.
temperature by time
This graph doesn’t show much from a plant health perspective, but it does show how temperature in the device varied over time. In general we’ve found that people’s hands heat up the device the longer they hold it. You can see that effect here for each device (each series snakes upwards), and you can see how long it took us to take all our measurements. This is something else we need to address in the next version.
Here's a map of the field colored by device ID. The entire field is offset to the left by about 10 meters. However, you can see that each user measured from left to right over only a few rows, which was correct - cool!
Here’s a map of the field colored by device ID. The entire field is offset to the left by about 10 meters. However, you can see that each user measured from left to right over only a few rows, which was correct – cool!

 

 

Attaching sensors to MultispeQ part 1: YwRobot soil moisture sensor

So now that production is in process (moving along, we had a minor hardware patch to apply so we’re waiting for a new shipment of boards, but we’re all ready to crank out boards otherwise) and we feel good about the core measurements of the MultispeQ, we decided it was time to see if we could easily slap on other sensors into the PhotosynQ framework.  First up – the YwRobot’s Soil Moisture sensor (actually, soil conductivity, but we’ll get into that later.  Let’s start by talking about how to connect to MultispeQ and what tools can be connected —

What can connect to MultispeQ?

The MultispeQ is built around a Teensy 3.1, so please see the Teensy’s capabilities here for details.  The lights, detectors, and existing sensors already use most of the existing pins (see here for Teensy pinout), but there are a few extra available pins:

  • 2 digital pins and 1 analog pin through-hole pins.
  • 10+ analog pads which are not through hole
  • I2C line
  • DAC
  • 3.3V line and ground

So the simplest device to connect is anything which outputs a 0 – 5V signal.  Our YwRoboto sensor does just that!

Soil Moisture Background and Experiment

Measuring soil moisture can be approximated by measuring soil conductivity.  Conductivity is influenced by the movement of ions in the material between the electrodes – see image below for what the device looks like.  So for a given soil type, more water increases the movement of ions.  However, it is very difficult to compare different soil types, because they will have different concentrations of ions and therefore different results.  So this is useful for relative soil moisture changes in a single location (like your house plant), not in different locations (like different fields in different soil types).

In our quick and dirty test, we made a matrix of 4 soil types x 3 moisture levels (from high to none) which you can see in the image below. We connected the pins between the moisture sensor and the MultispeQ as follows:

through-hole locations to connect to the MultispeQ
through-hole locations to connect to the MultispeQ
YwRobot Pin MultispeQ (Teensy 3.1) Pin
GND GND
VCC 3.3V
OUT A14

 

The YwRobot Moisture Sensor attached to a MultispeQ in potting soil
The YwRobot Moisture Sensor attached to a MultispeQ in potting soil
4 types of soil (3 potting mixes and 1 clay dense dirt from outside) with 3 levels of moisture (no moisture, 6ml moisture, and completely drenched)
4 types of soil (3 potting mixes and 1 clay dense dirt from outside) with 3 levels of moisture (no moisture, 6ml moisture, and completely drenched)

The communication protocol between the PhotosynQ chrome app (or Android app) and the MultispeQ is in a JSON format.  In order to request the information from pin A14 (also referred to as pin 40), just add it to the JSON.  Below is an example simple JSON which requests temperature, relative humidity, and the analog read from pin 40.  It also specifies to take 2t00 measurements with a 2 second delay between them:

[{“environmental”:[[“temperature”,0],[“relative_humidity”,0],[“analog_read”,0,40]],”measurements”:100,”measurements_delay”:2}]

You can also create this protocol using menu-based drag-and-drop tools through the Chrome app, but I thought I’d give the details here so you could see it.

Initially, I compared soil moisture in each of 12 samples above.  Here’s what I got:

Measured soil conductivity of the 12 different soil samples. The two lowest moisture levels are not that different and sometimes opposite of expected
Measured soil conductivity of the 12 different soil samples. The two lowest moisture levels are not that different and sometimes opposite of expected

As you can see, the 6.5ml water addition versus dry doesn’t show a consistent positive correlate, which doesn’t make sense.  I think it may be due to the fact that I had to take out and put back in the probe each time.  So I just tried placing the probe in soil, and adding moisture to the surface without affecting the probe.  These results were much closer to what I would have expected:

Kept the probe in a single soil mix, and sprayed water onto surface to simulate rain. This makes much more sense, though even wiggling the probe slightly significantly changes the signal.
Kept the probe in a single soil mix, and sprayed water onto surface to simulate rain. This makes much more sense, though even wiggling the probe slightly significantly changes the signal.

Conclusions

Overall, this sensor definitely relates to soil moisture, and the completely saturated cases of different soil types even show similar absolute response (about 45k counts). However, at less than saturated levels, soil conductivity varies quite a bit between the different soil types at least from this quick little introductory test so probably soil moisture can be accurately measured at a single location.

In terms of integrating this sensor into PhotosynQ, it was pretty easy. Connect 3 pins, add one small line to tell the device to look for it, and vioala – graphs!

Next Steps

The next step is to actually stick this thing into my yard and see what happens. We’ve been talking about trying to pull in weather data into PhotosynQ so you can correlate and analyze that in addition to the sensor data, which would be particularly fun here. Also, I think there is a new version which is gold plated and therefore much more robust which I’ve already ordered to play with. Finally, I should create a real research project (which others can join and participate in) out of this, instead of just taking one off measurements. Then we can see how the PhotosynQ online analysis tool could be useful to analyze the resulting data (see here for example of recent data taken in bean fields in North Dakota – please be patient while the data loads!).

Mid-Summer PhotosynQ update: Maker Faires, Pick ‘n Place, 3D Printer

Beta Testers Update

If you’re a beta tester I know you’ve been waiting forever, but believe me when I say we’re making great progress.  We now have the capacity (human and machine, for details keep reading) to make the 80-odd required devices for the beta.  We also have the quality specs necessary to make those units useful for you (calibration and comparison to known devices, for details keep reading).  We also have some great software tools for analyzing and sharing data quickly, easily, and (dare I say) beautifully.  Now we just have to crank them out.  Stay patient, we’ll get there soon.

Detroit Maker Faire

PhotosynQ was on display at the Detroit Maker Faire!  We took about a hundred measurements all around the faire, and had our very own tee shirts (see picture).  We met all kinds of folks, including educators like Melissa from Tinker Tailor, the guys putting together a new makerspace in Lansing called Innovation 5, and we were located right next to Josh and the fabulous folks at All Hands Active where he had is Soil Cam 9000 on display – I absolutely love that thing.  We are just itching to get our first real beta units out into the world to folks like this to see what we can discover together!

Robert talking plants and electronics with his new very green PhotosynQ shirt at the Detroit Maker Faire. On the back it says “Plant Medic” 🙂
Geotagging of MultspeQ measurements at the Detroit Maker Faire using the PhotosynQ online data analysis tool (I guess Google's last image was when it was just a lonely parking lot :)
Geotagging of MultspeQ measurements at the Detroit Maker Faire using the PhotosynQ online data analysis tool (I guess Google’s last image was when it was just a lonely parking lot 🙂

3D printer up and running!

We recently bought a SeeMeCNC Rostock Max V2, and it is awesome!  It took some adjusting and Jake’s been working on it for about 3 weeks now, but I’m very pleased with the quality and relative simplicity.  That beings aid, let me share some lessons with you:

  1. First things first – adjust the z thickness to it’s as big as possible but still sufficient for your project, and make sure the first layer is fairly thick to help it stick to the bed.
  2. Make sure you include the big circle of abs around your part first, so the abs has a chance to stick to the plate (we smear glue on the plate as suggested by SeeMeCNC to get it to stick, that works well).
  3. For anything more than the smallest, simplest parts, you ABSOLUTELY MUST enclose the machine to prevent heat loss.  The bed will heat up to only about 90C, which just isn’t hot enough to prevent warping of parts.  It’s not shown in the picture, but we’re building a plexiglass case to completely enclose the whole unit – this helps the bed get up to 105 – 110 AND it keeps the printed piece itself warm so that warping isn’t an issue.  We struggled with this for a while.  We tested it by covering it in cardboard, so if you don’t want to get plexiglass don’t worry, there are cheaper options:)

We’ll be using this to print the cases for the beta units.  We’ve tested making all of the different case components and have successfully achieved the necessary tolerances, so now it’s off to the races!

SeeMeCNC Rostock Max V2

Pick and Place machine up and running!

FINALLY.  The pick and place saga has ended.  We initially attempted to order a Madell Technologies DP2006-3 way back in DECEMBER OF 2013!  It has room for up to 100 parts, separate machine vision on the pick and the place, runs at ~2000 parts per hour and is under 20k with all the bells and whistles.  MSU purchasing took forever to approve the purchase, then once we got it over a month ago our great undergrads Chris and Jake have been pulling their hair out to get it installed and working.  It hasn’t been easy.  We’ve had numerous issues setting up the machine, some our fault and some their fault, and while it’s taken a long time to get this thing working I can’t say Madell hasn’t been responsive – in fact their customer service is amazing.  However, the number of bugs and issues with the device has definitely required that support, especially as it relates to the software and computer vision system.  For anyone thinking about buying this machine, two things: 1) just get everything preinstalled including computer and vacuum pump (unless your time is worth $1 per hour, just let them do it, trust me here), 2) lights, lights, lights, get lights everywhere, pretend your creating a photobox to take product photos, no shadows and super bright lights, the machine vision system is finicky and the most lights the better! and 3) expect at least 3 weeks for install and testing.

ANYWAY, it works and now we can produce at a minimum 10 boards per day, so that is no longer the limiting step in our production chain.

Pick and place running all by itself for the first time with a joyous but nervous Chris at the helm

 

Now we’re cooking with solder paste – we should be able to make 10 boards a day with relative ease.

Calibration, calibration, calibration!

Note: For your calibration nerds out there, there’s no graphs below – sorry about that.  We’re just now at the point that it’s worthwhile to start really graphing our calibrations and comparisons to commercial instruments.  Expect to see that data in the near future.

One of the big reasons for delay in releasing the MultispeQs is the process of properly calibrating the outgoing units.  Initially in our zeal to hit self-imposed deadlines, we sent about 15 units of varying quality stages of development to beta testers.  While we did learned some important lessons, we felt they were very time consuming both for us and the users.  So the next 15 units that go into the world are going to be calibrated to commercial equipment AND calibratable (ie users can recalibrate as needed).  We’re focused on the two most demanded measurements – chlorophyll fluorescence (that includes calculating fv/fm, fs, fm’, Phi2, qE, qI, NPQ, and all the other related acronyms), and SPAD (a measure of greenness similar to NDVI originally created by Minolta).

Chlorophyll Fluorescence Phi2

In our initial comparisons with LiCOR 64 (a top of the line fluorometer costing about 50k), LiCOR would say .85 and we would say .74 or so… this was too large of an offset to be acceptable.  We made some adjustments and added a new offset due to electronic noise and addressed some background IR light which was bumping our signal higher than it should have been.  After that, we were within about .02 of the LiCOR… I wanted to improve more, until one day during testing the LiCOR itself decided to show values about .05 higher than it had the day before for no apparent reason.  Jesse Traub, my partner in calibrating, couldn’t figure out the issue, but said after looking back at his data that this kind of variation wasn’t uncommon.  After that, I decided that .02 is easily within the variation of any given instrument.

Minolta SPAD

We’ve been measuring SPAD successfully for 8 months, but we have this persistent issues of showing a little more than double the ‘normal’ SPAD meter value (SPAD shows 45, we show 110, for example).  The correlation with Minolta SPAD values is excellent, but the raw values are always about double.  So last week, we tried to get to the bottom of this.  First, what is SPAD?  It measures absorbance through a leaf at two wavelengths: 650 (red) and 940 (infrared) (see here for Minolta meter and description and here for manual).  To calculate SPAD, you have to take a blank value (no leaf) as a baseline.  If we call the blank absorbance 650 and 940 and the leaf absorbance 650′ and 940′ respectively, then you calculate SPAD in the following way:

SPAD = Log ( 940′ / 940) / (650′ / 650 )

So, we tried getting these values using a normal spectrometer – surely that would give us Minolta-esque SPAD values… but no!  It was consistent with our values (in the 130 range)… we tried many other things I won’t go into here (using Ln instead of Log, reducing lost light in the MultispeQ, etc etc) but kept getting the same answer.  Then Sebastian looked into the original SPAD manual from Minolta to confirm how they are calculating SPAD, and here’s the description:

The values obtained in steps 1 and 2 (940′, 940, 650′, and 650) are processed to calculate the SPAD value, which corresponds to the amount of chlorophyll present in the sample leaf.

In other words, they don’t say!!  Argh!  So who knows what they do or how they calculate it, but it sure seems that for some reason they are multiplying the actual value by some factor to get it to land in the 20 – 60 range.  So, we’ll do the same thing, and we’ll  have great, consistent SPAD values!

Finally, there’s actually immensely more to the calibration thing than I’ve mentioned here.  Once things have settled and we’re sure we’re not going to be changing things a lot more, I’ll document exactly what gets calibrated when and how in more detail.

Light Intensity PAR (Photosynthetically Active Radiation)

In order to measure Phi2 (photosynthetic efficiency), it’s important to have an accurate light sensor.  PAR is only the portion of the spectrum which plants can absorb – about 400nm – 700nm.  This is surprisingly tricky to measure!  There are many very good and accurate light meters available, like the TCS light sensor available as a breakout board from Adafruit.  However, their either measure too light (from 420 – 650) or too much in the case of the other TCS sensors (from 400 – 1200).  So decided to go with the TCS 34715, which has a broad range from 400 – 1200nm, then adding a hot mirror to eliminate any light from 700 – 1200nm.  This, combined with a tighter case design, resulted in a pretty accurate PAR sensor, which if you compare to LiCOR is currently within about 10% accuracy (LiCORs PAR sensor alone costs $500!).  Users can recalibrate the sensors if they change over time.

Using the MultispeQ with the Chrome app

Our initial idea for using a MultispeQ fluoromoter was an Android app, so that people can use the device in the field.  However, we quickly realized that we also needed a desktop solution so we began working on a Chrome app.  Now, 76 commits later, we almost have a version, we feel comfortable with, so you can use it.  The developer version is on Github (https://github.com/Photosynq/PhotosynQ-ChromeApp).  We spent a lot of time on the UI, to make it as easy as possible to work with the app. It not only includes measurements, but also the tools to give you the ability to design your own measurement and programming little code snippets called macros to evaluate your measurements. Right now we are trying to finish the help section, the script generator and the missing communication pieces with the database. And of cause, we are trying to catch as many bugs as possible before the first release. Almost a 1000 test measurements have been done with the very early units and saved to our website, using the chrome and the android app. We’d like to thank everyone testing the software at this very early stage and helping us improving it.      — Sebastian

Here’s some key features in the Chrome app (also see images below):

  • Taking measurements for projects, including user specific answers.
  • Selecting measurement protocols available from photosynq and run them.
  • Using the console to communicate with the device if you’re getting an expert
  • Manual control for instant measurements, recording environmental parameters with just one click.
  • Drag ‘n drop tool to build measurement scripts
  • Programming tool to build macros to evaluate measurements
  • Data viewer to look at locally saved data.
  • Measurement and image caching for offline work
  • Project preview
  • User sign in Notification log
  • Location service Device information
Chrome App displaying a project we created for the maker faire. Project includes directions to user, user questions, and what measurements will be taken
Chrome App displaying a project we created for the maker faire. Project includes directions to user, user questions, and what measurements will be taken
This is the PhotosynQ macro creation tool. Use simple Javascript to calculate values from a detector response. We use this to calculate fv/fm, but you could use it to calculate most anything.
This is the PhotosynQ macro creation tool. Use simple Javascript to calculate values from a detector response. We use this to calculate fv/fm, but you could use it to calculate most anything.
This is the Protocol creation tool. Instead of writing raw JSON code to tell the MultispeQ when and how to flash lights or read sensors, we put together this drag and drop tool to simplify your life (and reduce errors). It also tells you when inputs are out of range or incorrectly formatted.
This is the Protocol creation tool. Instead of writing raw JSON code to tell the MultispeQ when and how to flash lights or read sensors, we put together this drag and drop tool to simplify your life (and reduce errors). It also tells you when inputs are out of range or incorrectly formatted.

 

Other News

  • We’re redesigning the Android App to be more user friendly and faster, especially for breeders and those performing hundreds of measurements per day
  • Expect to see a complete redesign of the website, and the merging of our database site and landing page.  Finally, we’ll have a coherent face to present to the world – thanks Venturit!
  • We’re hiring Geoff Rhodes to manage the assembly and shipping of MultispeQs to beta testers and collaborators.  He’s also going to be working on calibrating devices and developing new methods.  Expect to hear more from him in the future.  Also, we’ve had Jake Nuremberg and Chris Zatske working on the project, and we’ve added all these fells to our collaborators page if you want details on their awesomeness.
Chris Zatske, conquerer of the DP2006-3 pick and place machine
Chris Zatske, conqueror of the DP2006-3 pick and place machine
Jake Nuremberg, master of the Rostock Max V2 Delta 3D printer
Jake Nuremberg, master of the Rostock Max V2 Delta 3D printer
Geoff Rhodes is new to the team but we can already tell he's in it to win it!
Geoff Rhodes is new to the team but we can already tell he’s in it to win it!

Make Faire wrap-up and updates

Maker Faire wrap-up

Phew… 48 hours normal hours and 24 standing-on-your-feet-talking hours later and Maker Faire is over. We met hundreds of people, got to use the MultispeQ about 200 times (good opportunity to test the heck out of it), saw lots of other awesome projects like Manylabs, Nerds for Nature, Fusion, Pinoccio and others, met some good potential partners, and got editors choice aware (see picture)!

Yay a ribbon!

I could go on about a lot of aspects of the Faire, but my favorite part was the sheer number of ideas people about what to do with a MultispeQ. For example:

“Hey, could you stick this thing on a drone” (a very common one, people want to stick everything on a drone nowadays)

“You should sell these things to Lowes so they can check the quality of their nursery stock as they come through the door, so they can reject bad plants that may, visibly, still look ok”

(from developer at Pinnocio) “What if you put a plant on a wheeled robot, and as the plant became stressed the robot moved it to higher or lower light – it’s like bionic limbs for plants!!!”

“What if you could measure toxins with it? Then, you could crowd-source identification of plants which are particularly good at absorbing toxins from the ground to use for environmental remediation”

(and many many others)

Still have lots of follow up to do, but overall it was great.

It seems friendly… but those girders are made of children’s bones!

In other news — 15 units have shipped! …

2 fully assembled, and 2 boards only. We use the bare boards for environmental measurements only.

We have shipped 15 units to Costa Rica, NYC, Mexico, Kansas, and even Malawi! They have all been hand assembled, which is a serious effort (takes about 1 day to assemble and test 1 unit) so we don’t really want to go full steam ahead until we have the pick and place machine up and running. That’s on the docket for this week. Once that’s complete, we should be shipping much faster.

Next time we’ll go more in depth about the online analysis tool, the data collaborators have collected so far, and maybe some data on new measurements we’re working on.