Hey guys – another interesting update from Atsuko about the CoralspeQ, currently raising funds for early stage testing on corals. MultispeQ V1.0 updates coming soon, till then enjoy! — Greg
Now the CoralspeQ PT 1.5 is complete! As you can see, it became a bit of a monster (compared with PT 1.0 right next to it). Inside, it houses a modified electronics board from MultispeQ, light sensor, and heavy-duty rechargeable AA batteries (that‘s right! They are no longer AAAs!).
We did our best to water-proof it– PVC glue is permanent, and silicon glue attached to the light guide and the fiber cable for the light sensor is impressive. A magnetic reed switch is installed inside, and you can turn on and off the instrument from outside using a magnet. Both Geoff and Robert are telling me that it has been sufficiently water-proofed. But as Dave Kramer pointed out, oceanographers have been working hard to figure out how to water-proof their expensive equipment. There is a reason why those water-proofed cases/ vessels are expensive. The ‘proof of pudding’ is in eating it. At one point in the field, I will hand this to a diver, and we will find out the truth.
We still have to open the box to recharge batteries. The PVC lid is replaced with a Plexiglas with gasket to increase the sealing capacity. I know it does not look pretty, but we are just being ‘MacGyver’ here. As long as it works, we are happy right now. There is a saying among us, scientists who do instrumentation (making own instruments), — if the instrument breaks right AFTER you took the last measurement, it is ok.
I am leaving for Hawaii this Saturday, Dec. 5. Dr. Ruth Gates, a coral scientist at Hawaii Institute of Marine Biology, kindly agreed with my visit for the field test. I am looking forward to meeting with her team. I am going to post my blog on Google+.
Hey guys – as an interlude to updates about the MultispeQ v.1.0 device, here’s an exciting post from Atsuko Kanazawa about the CoralspeQ – a different PhotosynQ-connected device which measures coral bleaching. The CoralspeQ team is currently raising money to alpha test their device and concept. If you’re passionate about our oceans and understanding them better, go support their efforts! More MultispeQ updates next time. Till then, enjoy! — Greg
Global Coral Bleaching Project
Some of you have already read recent news articles (see the Washington Post and the New York Times) about the severe effect of El Niño in 2015 and 2016.
Termed “Godzilla El Niño,” a weather pattern that will warm the oceans where many coral reefs live, leading to a catastrophic coral bleaching event would be the worst in 20 years. On October 8, 2015, National Oceanic and Atmospheric Administration (NOAA) announced “third ever global coral bleaching event on record” (see NOAA news for details).As the oceans warm and acidify, corals bleach, losing the photosynthetic algae that give them energy. Bleaching then leads to loss the diverse and beautiful life that lives in the coral reefs.
The Godzilla El Niño may also be our best chance to understand why some corals are more sensitive, why some recover and other can’t, and thus what we can do, if anything, to fix the problem. A major problem is that the tools needed to probe corals have not been available to most of the world.
The “Global Coral Bleaching Project” was first conceived by Prof. Peter Ralph at University of Technology at Sydney in Australia, Prof. David Kramer at Michigan State University, and Dr. Atsuko Kanazawa also at MSU, who saw the potential of PhotosynQ – engaging the local community world-wide to monitor and to collect the vast on-site data. To respond to the proposed project, the Kramer Lab at MSU, and our colleagues around the world, are developing a first-of-its-kind technology that will allow researchers, park rangers and citizen scientists all over the world to probe coral health and the factors that may affect bleaching. Data from field sites is instantly uploaded to the cloud where people around the world can access and analyze it. This data will help to understand the coral bleaching process, and lead to new coral conservation approaches.
The current CoralspeQ prototype version 1.5 has micro spectrometer, various LEDs and BGR light sensor, controlled by Teensy 3.1. At this stage, we are still using a store-bought non-metal electrical conduit box that is larger than the first prototype to house a full-size board and batteries (see Figure 1).
We have tested how well it was water-proofed. It could withstand in the depth of 4.3 m/ 14 ft for at least 30 min with sealer/gasket/rid modifications. CoralspeQ is controlled by an Android phone with Bluetooth. We found a reasonably-priced water-proofed case for the phone. It is claimed to withstand to the depth of 100 ft. It worked well in 14 ft. Figure 2 (A and B) shows a device strapped to a broom at the bottom of 14 ft diving pool. A black square at the bottom corner is a phone in a water-proof case.
Additionally, we have tested the Bluetooth function in salt water. The Android phone screen covered with a bag of baby oil could send signal to CoralspeQ 1.5 and activate the measurement. Same as MultispeQ, CoralspeQ also needs to be turned on by pushing a start button, but under water. Magnetic reed switch is installed inside of the box, and therefore, it can be turned on from outside using a magnet without opening the box.
The next step is to test them in the field. Currently, 6 different LEDs are installed in different combinations in 3 devices. The field measurements will tell us which wavelengths would be more useful to identify the conditions of both coral and symbiotic algae. Also, we are expecting the modifications of device based on the field trial for the next version.
Hey everyone, I know it’s been radio silence from the PhotosynQ team for a while. We’ve been working our tails off learning lessons from the beta test, designing the v1.0 MultispeQ, and beta testing the CoralspeQ device. But it’s time to reconnect…
New MultispeQ v1.0 pre-orders will start sometime in 2015 ( !!!! ), and I wanted to show you what we’ve been up to. Our goal is to hit an April 1 deadline for shipping devices, so that you can be ready to collect data in the Northern Hemisphere’s growing season. If you missed out on the MultispeQ beta test which occurred this summer (which I know a lot of people did) don’t worry, a new and much improved MultispeQ is coming.
Let’s dive in to pics and specs, but please note — these are preliminary and this is all a work in progress, so things may change slightly as we get to manufacturing. We’ve got Hardware / Design updates this time, but we’ll be following in a few days with updates about new applications and some interesting scientific outcomes from MultispeQ projects, and the some information about CoralspeQ, a device to measure coral bleaching (still in beta testing phase, not part of the April 1 release).
v1.0 Hardware / Design
We learned a lot from this summer’s beta test, both by using the device ourselves and from the feedback of our many amazing beta testers. Here’s a partial list of improvements in v1.0 for the April 1st launch.
3x bigger internal battery – Recharges via USB just like your phone, no more replacing AAA batteries!
Improved PAR sensor – Achieves an r-squared linear fit of .98 with same light conditions using a LiCOR PAR sensor. Light conditions tested were highly varied (full sun, in canopy, LED, fluorescent)
Thinner design – easier to measure very small leaves (like arabidopsis) and get into tight spaces
Form fits hand, right or left handed
Measure cuvette or leaf without modification – changed the clamp mechanism so you can measure anything from .1mm to 13mm thick – no need to unscrew or add anything (or mess up the calibration) to measure leaves or cuvettes!
White case heats up less, more accurate ambient temperature and relative humidity – Your hand and the black case make the current temp and rh kind of useless… in the new version, these measurements should be significantly more accurate.
Contactless leaf temperature – using IR sensor, accuracy of .1 degrees C
Leaf thickness sensor – no guarantee but we’re trying to include this. Measures leaf thickness to an accuracy of 10 microns
Leaf angle and cardinal direction – gives you leaf wilt angle, and what direction the leaf is facing
Reduced noise by 5 – 10x – we’re still verifying, but based on some improvements in the circuit we’re expect to see a big jump here. We’re hoping this will allow you to measure proton motive force (ECS) quickly and effectively in the field, and improve fluorescence measurements with weak signals (like dilute algae).
10 LEDs instead of 8 – more options for spectroscopic measurements
External sensor connector – we’ll have a connector so you can plug in any sort of sensor with analog or digital outputs to read using the MultispeQ (soil moisture sensors, pH probes, etc.). Connector includes power, ground, and 16 bit analog pins. This is a developer option right now – so you’ll have to do some hacking to make it work but we really hope you do!
Automatic firmware updates – firmware will update automatically over USB or bluetooth from the PhotosynQ apps – no more following complicated directions, and it means you’re always up to date!
Bluetooth 4.0 – fewer dropped measurements, simpler to connect
Fixed annoying bugs! – we (and our lovely, patient, hard working beta testers) identified lots of bugs with the Android and Chrome apps, especially dropped connections and aggravating user experiences – these are being fixed. Beta testers know what I’m talking about here :
Clearer selection of measurements – we know that not everyone is a photosynthesis researcher – v1.0 will be much clearer about what the measurements do (or do not do), and try to provide reference projects which can help you identify what measurements are most useful for your project.
More flexible project creation – now change anything (questions, protocols, their order, whatever) in a project whenever you want without losing data.
Shorter loading times when viewing your data on the website
iPhone app – it’s on our to do list, but can’t guarantee we’ll have it done by April – but we’re sure going to try.
That’s it for this time – next time we’ll walk through some of the advances we and the community have made on the science and applied end of things – some exciting stuff going on there too.
Oh – and I want to congratulate Veronica Greeve – she just broke the 10,000 measurement mark. Congratulations Veronica… you’ve contributed about 5% of all data to the platform… pretty amazing!!!
We have been working on the modification of MultispeQ for the under-water use.
In order to establish the connection between an Android phone and a MultispeQ, they have to be very close, meaning they have to be in the same enclosure—a plastic bag. However, phone’s touch-screen does not work in salt water. Venny (Vanessa) found out that placing a thin plastic bag, containing baby oil, on the screen solved this problem.
Kathryn and Geoff R. tested the inductive charging set (5V kit from Adafruit), and yes, it can charge the phone. This way, we do not need a USB cable hanging out from the phone. We could seal the instruments completely inside of e.g. a plastic bag. So the next step is modifying the MultispeQ charging system.
We also tried different plastic bags/ tubes to encase the entire device. The best material we found so far is the polyethylene heat-sealable shrink film. We still need to perfect the sealing, but the initial test showed being water-tight, and minimal air space (=minimal buoyancy).
We’ve learned two important things so far in the Beta: 1) We suck at making MultispeQ devices quickly and 2) Most people just need a device for a short time (a month or so). So we decided to make a lending library for MultispeQs. Just click on this link, fill out the form, and we’ll let you know if and when we can get you a device.
Also, we started a crew of fearless data collectors to work with partners here at Michigan State University. We call these guys the Mobile Phenotyping Group. We’re working with folks like Marty Chilvers on pest management in corn, soybeans, and wheat, Jim Kelly on selection of the common bean, and a whole bunch of other folks on everything from photosynthesis research to forest management. If you are at Michigan State and you’d like our help designing, implementing, and analyzing data collected using the MultispeQ please go apply here.
We realize that the site is a bit messy, and sometimes it’s hard to find really interesting projects, so I thought I’d list a few to check out. Click on ‘dashboard’ to see the raw data and play with it, or the discussion button to see what people have been saying about the project.
Nitrogen Management in CA systems in Malawi (Plant) 11. – This was data collected in Malawi comparing 5 different crop rotation systems with some surprising results (farmer recommendations on which treatment is optimal would NOT be the same for each location!) . If you click on ‘dashboard’ and map you can see the 3 site’s where the data were collected from.
Testing Parents for Genetic Variation -Jared Crain from Kansas State University was able to identify very small (<3%) differences in photosynthetic efficiency of photosystem 2 between two elite wheat lines.
MSU’s Sonya Lawrence is having her summer biology students create projects – here’s a few:
The website forum has been updated, and many problems are now fixed. You can communicate with other collaborators within your project using the forum, get tech support (we trawl the tech support forum so you’ll get an answer as fast or faster than emailing me directly!) or find others with similar interests. You can adjust your forum settings in the “Manage Subscriptions” part of your user profile page (see image below).
We are furiously working on the next version of the MultispeQ, v1.0. We’re getting the first test PCBs out soon, and the case is being redesigned with some important improvements like integrated cuvette measurements (so no separate cuvette holder to install) and integrated leaf thickness sensor and leaf temperature. At some point in the next 3 months, we’ll give a more significant update on the features of this next version, so stay tuned.
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!
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 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
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:
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!
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
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.
While the MultispeQ itself doesn’t have a conductivity meter attached, you can purchase a conductivity meter and hook it into the MultispeQ. Soil 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.
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!
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!
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!
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!
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.
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 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.
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.
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.
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.
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!