MultispeQ in Malawi

As the development team focuses on manufacturing the MultispeQ v1.0, we’ll have a series of articles from project partners and developers we hope you find interesting. We’ve had a great response to the pre-release, so thanks to everyone! – Greg

malawi multispeq users
(left) Masters student Hellen Mwale and Kareem Longwe practice data collection with the MultispeQ to get ready for data collection on FRN’s in Central Malawi. (right) Frank Mnthambala and Margaret Chiipanthenga collect data on soybeans in a greenhouse in Bvumbwe, Malawi to identify drought tolerant cultivars.

Over the past year we have partnered with a number of researchers in Malawi who have collected over 30,000 measurements on 15 different projects using PhotosynQ. Our partners in Malawi include researchers from the Department of Agricultural Research Services (DARS), Lilongwe University of Agricultural Research Services (LUANAR), and a private seed company (Global Seeds). I just got back from 2 weeks in Malawi meeting with them and getting their feedback on PhotosynQ.

Access to high quality laboratory equipment is lacking in Malawi, so researchers are very excited about what information MultispeQ can provide to them. In many cases, field based plant breeding and cropping systems research has been limited to data that can be recorded with a scale and tape measure. With PhotosynQ, they can see beyond what happened (e.g. how the crop yielded) and can start to understand the reasons why crops performed the way they did (e.g. how plants regulated photosynthesis to adapt to their conditions).

Despite a lot of enthusiasm, there are some real challenges that need to be overcome to collect quality data. Internet infrastructure in Malawi is very poor and the internet is often too slow to work effectively on-line or doesn’t work at all. This makes it difficult for users to create projects and analyze results. But it also means that users don’t update their mobile app very often. So they may still be trying to work around bugs in an older version of the app that we have already fixed in a newer release.

Another challenge to using PhotosynQ in Malawi is frequent ‘brown-outs.’ Partners can’t count on the electricity being on when they need to recharge their phones or MultispeQ batteries. Some partners in Malawi have responded by using ‘power banks.’ A power bank is a small extra battery that can hold enough charge to recharge your phone 2-3x. They will plug it right into their phone or tablet’s usb port in the field and recharge their mobile device while taking measurements. It’s one more thing to hold onto in the field, but it solves a problem.

malawi battery pack
A student uses a power bank to keep his mobile device working in the field.

This coming year our partners have even more interesting projects planned. Everything from variety trials of soybean, sweet potato, maize, common beans, and pigeonpea to studies analyzing the effects of cropping systems on crop performance (click here to see a list of existing projects + data). These projects will take place on research stations and smallholder farms all around Malawi.

Two Master’s students from LUANAR will be using PhotosynQ on Farm Research Networks (FRN’s) to assess how different legume-based cropping systems can increase production on smallholder farms. FRN’s are research trials that are located on smallholder farms, instead of research stations, and are managed by the farmers themselves. As such, they paint a much more accurate picture of how ‘new’ cropping systems affect crop production on smallholder farmers. What’s really exciting is that these 2 students will be collecting data on FRN’s that include over 300 farms in 3 districts in Malawi. Even if they only collect PhotosynQ data on 1/3 of the farms, it will be the largest on-farm data collection using PhotosynQ to date! And it will take place with poor internet connectivity and frequent power outages!

More Malawi Projects

Dan TerAvest

Who’s using the MultispeQ? Let’s see…

As we approach the next version of the MultispeQ, I wanted to share stories from a few of our beta testers – Matt, Karen, and Kay from the MSU Kellogg Biological Station, Jeremy Harbinson from the University of Wageningen, and Jesse Traub from Michigan State University.  You can find even more stories here.  Hope this sparks some interesting ideas for applications in your lab, home, farm, work, or play 🙂

Kellogg Biological Station

Matthew Carey (REU student), Karen Stahlheber (postdoc) and Kay Gross (KBS director), Ecologists

Matthew Carey, measuring grass at Kellogg Biological Station
Matthew Carey, measuring grass at Kellogg Biological Station

Our group is interested in the response of switchgrass (Panicum virgatum) varieties to drought, and how that interacts with fertilizer use. We installed rain reduction shelters on fields planted with switchgrass ~6 years ago and managed either with or without fertilizer. These shelters reduce available soil moisture and simulate drought conditions that might occur with future global change. Throughout the summer, we monitored plant growth, chlorophyll fluorescence, xylem tension, and the abundance/diversity of mycorrhizae (fungi that live in symbiosis with plant roots). The eventual goal (after several field seasons) is to understand how the interactions between fertilizer application and arbuscular mycorrhizae diversity affect ecosystem services such as productivity, pathogen tolerance, drought tolerance, and soil carbon storage.PhotosynQ has been a great asset to our project because it allows us to measure any stress the plants may experience due to high light/low water conditions throughout the summer. By measuring Fv/Fm in the early hours of the morning we can understand if plants underneath the shelters have suffered damage to their photosynthetic machinery compared to control plants receiving ambient rainfall. We also can use the devices during the day to assess general photosynthetic performance and see if that differs between varieties or is changed by fertilizer use.

If PhotosynQ is successful, it could allow farmers of cellulosic biofuel crops like switchgrass to use the same tools to monitor their plants for stress or for responses to fertilizer.

Plant Sciences Department, University of Wageningen

Jeremy Harbinson, Plant Physiologist / University Lecturer

Jeremy Harbinson
Jeremy Harbinson

We try to understand better the operation, regulation and limitation of photosynthesis in vivo, both from physiological and genetic perspectives. We plan to use the PhotosynQ in teaching and as a tool for the more or less routine monitoring of leaf-level photosynthesis of plants in the field. The PhotosynQ concept opens many doors. In terms of eco or environmental physiology – or phenotyping, particularly that of photosynthesis, it enables large scale data collection in a way that has previously not been possible. It helps close the gap between the diversity for physiological responses encountered in the field due to environmental and genetic reasons and the time required to get good data relating to these responses. Low-cost, fast, and measuring a large number of processes makes many things possible that cannot be done with existing instruments which are expensive, often slow and limited in what they can measure. It is a revolutionary concept.

Department of Horticulture, Michigan State University

Jesse Traub, PhD candidate

Jesse Traub, MSU Horticulture
Jesse Traub, MSU Horticulture

We are investigating physiological differences among contrasting dry bean genotypes in their response to drought and heat stress. We are especially focusing on the response of photosynthetic parameters to these stresses. The PhotosynQ platform enabled us to screen large amounts of germplasm to determine at what severity of stress different bean genotypes started to become damaged.  If PhotosynQ became a standard tool for my discipline of plant physiology and plant breeding, it would provide an easy way to compare otherwise unrelated experiments and sets of data. This would be great for the reproducibility of experiments! I admire that the PhotosynQ project has been committed to making their hardware, software, and data freely accessible to all to use, learn from, and modify. I hope such sentiments continue to grow in the academic world.

This is just a few of the 100 or so people who used the MultispeQ Beta

You can find a few more stories about using PhotosynQ to develop tools for corals, identify agricultural best practices in Malawi, optimizing light in greenhouses in the Ukraine, and detect disease in soybeans in Michigan.  Next time, a progress report on the MultispeQ v1.0!

CoralspeQ Prototype 1.5 Update – Ready to go for the field test!

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

CoralspeQ two prototypes(1)

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+.

Stay tuned!

– Atsuko Kanazawa

PS – And don’t forget you can go here to support the next version of the device to help us better understand the coral bleaching process.

Hawaii-Institute-of-Marine-Bilogy-Kaneohe-Bay(1)

CoralspeQ Update — “Global Coral Bleaching Project”

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

-Atsuko Kanazawa

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.

Photo by Aaron Florn
Photo by Aaron Florn

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.

You can help support this important research by supporting our crowd-funding campaign here at this link

Prof. Peter Ralph using a modified MultispeQ on corals at Heron Island, Great Barrier Reef
Prof. Peter Ralph using a modified MultispeQ on corals at Heron Island, Great Barrier Reef

CoralspeQ Technical Updates

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.

Figure 1, 2A, 2B
Figure 1, 2A, 2B

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.

MultispeQ v1.0 cometh!

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).

Enjoy!

 

v1.0 Hardware / Design

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Redesigned exterior for MultispeQ v1.0 from Barry Hutzel at Bazza Designs.
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Recent evolution of the MultispeQ. The current beta device is on the far side of the desk, while the new design provided by Barry is on the near side. The other components were 3D printed or milled ABS used to test hand fit, as well as mechanical action of the clamp.
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MultispeQ v1.0 early mechanical design. The initial case design needs to define all of the hard requirements relating to the clamp mechanism, location of components (PAR sensor, batteries, circuit boards, etc.). Once this is complete, then Barry can build a beautiful exterior around it. You can see that the new design can measure very thick items like cuvette’s by default (no need to take apart the unit to measure algae!). This is just one of many improved features.

 

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.

CASE

  • 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.

SENSORS

  • 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!

USABILITY

  • 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

SOFTWARE

  • 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!!!

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Updates: CoralspeQ/ AquaspeQ to measure coral bleaching

Shrink-wrapped devices
Shrink-wrapped devices

coral picture

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).

I will post more updates when available!

 

Updates: Devices available and progress during Beta

Devices Available!

10 devices without CO2 sensors (so no soil respiration measurements) are available on publiclab.org (http://store.publiclab.org/products/multispeq-handheld-fluorometer).  We have quite a few more in the works, so if you miss this batch you can catch the next.

New ways to get a MultispeQ

 

PhotosynQ Share

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.

Mobile Phenotyping Group

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.

Project highlights

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:

BS 172 US15 Photosynthetic Activity – [Beta]
Tree Age influence on Photosynthetic rates. – [Beta]
Sugar Tyme Efficiency Sum 15 – [Beta]
I’m going to improve the quality of the projects and the results pages, so keep an eye out for more highlighted projects in the future.

Improvements to Forum

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).

 

 

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Go to your user profile and click Manage Subscriptions to join a forum. Any projects you join or create you are automatically included in the forum.
Screenshot from 2015-06-08 08:12:35
Forums are located in the Forums tab.

v1.0 update

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.