CoralspeQ Debut at International Coral Reef Symposium

–This is a belated post about presenting CoralspeQ at the International Coral Reef Symposium where I had a chance to ‘show and tell’ the device and PhotosynQ, the scientific platform.

It was a debut for the CoralspeQ at the International Coral Reef Symposium (13th ICRS) held at the Convention Center in Honolulu, Hawai’i, from June 19 to 24.  About 2,500 participants came from all over the world.  It was sponsored by the International Society for Coral Studies.  There were total of 88 sessions plus plenary talks, workshops, Town Hall meetings, and public sessions (http://sgmeet.com/icrs2016/).

13th ICRS imagesThe Symposium appropriately opened with a performance by a group of native Hawai’ians — songs, dance and the story of genesis of their world (the first creature to appear was a coral polyp!).  The meeting started from 8 AM continued to about 9 PM.  It was indeed jam-packed with events.  There were many interesting talks, but because they were in the concurrent sessions, I had to pick and choose what I wanted to see.

My talk of CoralspeQ/PhotosynQ was presented in the session called “Big Data: Using open access, evolving platforms and the emerging field of data science to improve resource management.” (http://sgmeet.com/icrs2016/sessionschedule.asp?SessionID=52).  All the talks were about open access and data sharing with improved technologies including unmanned vehicles (above and under water).  I was the 3rd presenter among 7 people.  At the starting of the session, the room holding about 250 chairs was rather empty, and I was a little disappointed.  Then, when I stood up to the podium, I was shocked to see the audience — three quarters of the seats were full, and there were standing people at the back.  Wow!  It was worth coming here!!

Content of the talk was explaining PhotosynQ, the scientific platform, and the capability of CoralspeQ.  It was a prelude to the talk given by Peter Ralph (our collaborator/ one of the CoralspeQ project initiators) next day.  Peter’s talk was more focused on how to connect the new technology and the park rangers/managers to help the coral reef conservation .  It was presented on the last day of the Symposium.  Usually, many people start leaving, but the room was filled very well, and some people stayed after the session to talk to us.  CoralspeQ is the first scientific instrument available to the coral scientists, that could measure the fluorescence, coral fluorescent protein signals and reflectance all in one.  In addition, all the data are uploaded to the cloud (data are stored in the smart phone until Wi-Fi is available), and we can share the data globally.  I think the importance of open collaboration became a big theme in the coral reef research community, as the society president, Ruth Gates (she is also our collaborator — please see my past blog: http://blog.photosynq.org/2015/12/04/967-2/), emphasized in her presidential address in plenary presentation.

People might be curious about the prediction of the future coral reefs in the world, particularly after seeing some news articles (e.g. http://www.nytimes.com/2016/04/10/world/asia/climate-related-death-of-coral-around-world-alarms-scientists.html?smid=go-share&_r=0).  The following graph is a prediction of future coral reefs by the end of the century.

Predicted future of coral reefs

In short, if we continue the current practice of land-use, with no further pollution control, over-fishing & etc., coral reefs would disappear by 2070.  With global warming, they would disappear by 2060.  Even with implementation of local pollution control, we could buy time only for a short time, unless we do something about the global warming. (more details in this article: http://www.kewalo.hawaii.edu/images/faculty/Richmond_papers/Richmond_LO_2014.pdf).

The concluding remark at the Symposium was, “It is not too late. We have to tackle the problem of global warming NOW.  In order to do it, we have to mobilize the citizens.”  One thing the 3/5 of participating scientists did at this Symposium immediately was signing a petition for expanding Papahanaumokuakea Marine National Monument (see here — http://civilbeat.org/2016/07/can-1500-scientists-all-be-wrong/).  If you like to see some of the images, go to this link: http://papahanaumokuakea.gov.

Papahanaumokuakea-2

Currently, we are working on a new version of CoralspeQ, based on the new board for the MultispeQ.  The shape of the device will be more like a tube (a diving torch-style).  We are not going to use the non-metal conduit box, because of the size variations (a few mm can be a big deal).

I will post more details of the development later.

— Atsuko

 

PhotosynQ in the news: Malawi

This is a nice story about the potential for collaborative plant research in Malawi, our partners, and the kinds of connections that form in large open research groups.

link: https://prl.natsci.msu.edu/news-and-events/news/photosynq-helping-malawian-farmers-increase-yields/

More Production Delays

Well, it’s July and you still don’t have units.  That’s our fault, we’re learning as we go and you’re the one who is impacted by that process, and we’re sorry.  We have tested several complete working prototype V1.0 devices in the field, thousands of measurements, and they work great (almost better than expected), and I think you’re really going to like them.  So that’s a plus.  But if devices aren’t in your hands when you need them this doesn’t amount to a hill of beans.

Right now, we are still at a minimum a month away, probably more.  We’re doing everything we can to speed up the process – that includes 1) rush ordering circuit boards, 2) working directly with (ie setting up shop at) the manufacturer to try to reduce lag time to troubleshoot questions about the circuit board, 3) and ordering/preparing everything we possibly can before we have final circuit boards are completed.

We’ve been collecting a lot of data here on test plots, and we’ll be sharing what we see so far soon.  I hope this will give you peace of mind – it certainly does for me 🙂

We’re working really hard to get these things out, and we really appreciate your patience and support,

Greg

 

 

Science Fun – Science faire in Ukraine

A science faire was held on May 22nd in Ternopol – IV at Theater Square.  The goal of the event was to popularize science among young people and excite the next generation of scientists in Ukraine.

There were about a dozen tents where schools and universities demonstrated scientific experiments in chemistry, biology and physics to the public.  Students of the Faculty of Chemical and Biological (http://chem-bio.com.ua), part of Ternopil Volodymyr Hnatyuk National Pedagogical University, http://tnpu.edu.ua)  presented PhotosynQ, created by scientists at Michigan State University.

Schoolchildren, students, and young scientists had the opportunity to personally touch science in the truest sense of the word. With the device MultispeQ, anyone could measure the progress of biophysical processes otherwise invisible to the eye in leaves of Phaseolus vulgaris plants and share data throughout the world via the PhotosynQ platform.

The interest and excitement generated at this event shows that science can be very interesting and exciting thing that unites the world.

by Andriy and Nataliia Herts

PhotosynQ software features + fixes

Lots of software changes and improvements, and more on the way.  Here’s a list of what’s going on.

Creating a project has changed!

  • First, we completely revamped how you create a new project.  We’ve consolidated the photosynthesis measurements and chlorophyll content measurement into the same protocol to make it easier to find and order.  This new protocol is called “Leaf Photosynthesis” – please use it!  For existing users – NOTE!  Please use the new protocol, but if you absolutely need to find the old protocols (The One v3.0 and Chlorophyll Content III or any others) you can always go to the ‘advanced’ screen for the old interface.
We combined the old protocols together into a single protocol which measures chlorophyll content and all other photosynthesis parameters.
We combined the old protocols together into a single protocol which measures chlorophyll content and all other photosynthesis parameters.
  • You email invite people  to join your project as collaborators or administrators, and have multiple administrators to share the workload of writing results or adding or editing questions.
Send email invites for collaborators, and add administrators so you can share the project-creation workload!
Send email invites for collaborators, and add administrators so you can share the project-creation workload!
  • You can add multiple images to your project and higher quality descriptions.  And there’s tags and categories so other like-minded people can find you and you find them.
Added Categories to more easily find cool projects and protocols
Added Categories to more easily find cool projects and protocols

 

  • We found that directions was underused, so we removed the directions box.  Don’t worry, we’re going to put directions back in later in a much more useful form, but for now if you have directions for collaborators put that in the “Descriptions” box.

 

Android App bugs fixed + new features

The android app (to be released next week) also has some updates. An improved data display screen, better bluetooth connection screens, and a new history feature.  History keeps track of every data point you have collected, so you can identify mislabelled measurements and track your progress through the field.  In the “settings” tab, you can set the app to wait before sending the measurements to the cloud – giving you the chance to delete bad or mislabelled measurements at the end of a day of collecting data.  Once your confident the data is correct and you’ve remeasured if necessary, you can push the data to the cloud.  No more spending months trying to track mistakes by data collectors you can’t contact anymore!

Bigger, cleaner buttons, history function to ensure your data is correct before pushing to the cloud, and save images + notes to any uploaded data point on the fly.
Bigger, cleaner buttons, history function to ensure your data is correct before pushing to the cloud, and save images + notes to any uploaded data point on the fly.

Finally, both apps now automatically stay up-to-date with the website, so no more syncing when you change a project or protocol!  The entire platform should be up to date, all the time – ensuring that as you and other project partners make improvements everyone data, projects, protocols, and discussions are current.

We have a lot of additional news on the hardware front, but I’m waiting for more data to come in before posting about it – so expect that soon.

PhotosynQ Workshop details + videos

We had our first PhotosynQ day-long workshop on April 22nd at Michigan State. We had over 90 attendees, 9 breakout sessions ranging from education to data analysis, and posters from 12 beta testers.  You can see almost all of the main and breakout sessions on our YouTube Channel.

We discussed everything from abiotic stress, what photosynthesis parameters mean (there’s a nice overview by Professor David Kramer in there which I’d suggest), the new features coming in the MultispeQ V1.0, alternative uses of the platform for microbial detection and measuring coral bleaching, use of the MultispeQ in Africa, and lots lots more.  Definitely check it out!

CoralspeQ Prototype 2.0 update

After the field test in Hawai’i  (updates on g+), we have been working hard to modify both the hardware and software of CoralspeQ. Now five new instruments, PT 2.0, have completed, and distributed. Chris Zatzke has re-joined us after graduated from MSU, and working on every aspect of the instrument construction – electronics, machining, programing and testing.


IMG_0977IMG_0970FullSizeRender (9)

 

 

 

 

Since we are still using the same ready-made case, it looks same as you can see in the photo, but the quality is improved. Chris made a holder for the electronics board that fits snuggly inside of the case, and reorganized the magnetic reed switch and batteries. Therefore, no component would move around inside by the impact of transportation. The light guide is shorter and the distribution of light is more even, thanks to the suggestion by Jeremy Brodersen. Production of light guide was well established now by Geoff Rhodes and Chris Zatzke. Now when the CoralspeQ is turned on and connected through Bluetooth, you can see the LED lighting up through the window. It is more user-friendly.

It took some time to improve the signal quality with light sensor using the light intensity at the sample level. This involved the modification of both protocols and firmware. This part was hugely contributed by Dave Kramer and Greg Austic. Also light calibration was repeatedly done by Chris Zatzke with helps from Dan TerAvest and Robert Zegarac.

As this batch of CoralspeQ is out, we have already started making the next set. We are introducing the inductive charging system, and it will be no longer necessary to open the device for charging the batteries.

Sebastian Kuhlgert informed me that they are implementing the images as a part of the questionnaire when you take a measurement. Even if you do not know the name of the coral you are measuring, you could select and tap the image, and it will be recorded along with the signals. Operating a phone under water is not an easy thing to do, even if you know the name of the coral. Tapping on an image, and pushing one button to start measuring is our goal in the near future.
As I write this blog, one more major improvement is going on. We are trying to add the analysis tool to the PhotosynQ web site. Dave has been compiling the analysis program, and now with his suggestions/guidance, Sebastian and Greg are working to add it so that we could see the Phi2 value and the colors of the coral besides the raw data. This process includes not only the coding, but also yet another firmware change, while we need to re-distribute the memory usage for the device. But we are almost there!

By the way, Global Center for Food Systems Innovation at Michigan State University posted a story about PhotosynQ/CoralspeQ project. That’s right! That’s why there is a picture of Godzilla in this page. Please find our story at their website here.  We also had the first PhotosynQ Workshop on April 22. I am sure Greg will post the story soon.

— Atsuko

MultispeQ V1.0 Testing Results, Production Delays, PhotosynQ Conference, and other news

Lost of updates this week, but for those who pre-ordered make sure to note that we do have some production delays :\ .  But before you get angry, make sure to read about some of the fantastic initial results we have using the new instrument!

– Greg

Production Delays

Well, as with many manufacturing pre-order campaigns, I’m sad to say we have some production delays due to the time it took us to arrange financing.  We have our contract manufacturer (Lectronics, based in Saline, MI) ready to do the board manufacturing and assembly, but our injection molder (Diamond Engineering out of Lansing, MI) has a 12 week lead time on the injection molded case.  The good news is everyone has started work, so the clock is ticking and work is moving forward.  There are no showstoppers as of yet (and if you read below you’ll see we have some pretty exciting results from our initial tests of the v1.0 device) so fingers crossed that there are no additional delays from here on out.

We’re shooting to ship in early July… I know that impacts some of your plans for this year, but please stick with us.  We’ve worked really hard to change the way people use and buy this type of equipment by dramatically lowering the price, building a data management platform based on collaboration (not data silos), all while hitting extremely high bars for measurement quality.  And we’ve done it completely outside of the traditional start-up path… it hasn’t been easy, but we’re getting there, and you early supporters are making it happen.

So thank you thank you thank you for your support and patience.  We’ll keep sharing updates with progress as we go – but for now please read below about the new device, it’ll make you happy 🙂

Results: The Amazing MultispeQ V1.0

Ok, enough with the bad news.  Here’s the good news: the new MultispeQ has, at a minimum, 2 – 5 times better raw signal quality than the Beta MultispeQ.  Ok – so what does that mean?

  • Chlorophyll Fluorescence of dilute algae solutions (1 – 5ug / L) – no problem.
  • Measure Proton Motive Force in the field (the accumulation of protons in the thylakoid) IN UNDER 3 SECONDS!  (read more below about this)
  • All your normal field photosynthesis measurements (Phi(II), Phi(NPQ), Phi(NO), SPAD, LEF, etc. etc.) will be lower noise, higher accuracy, and improved repeatability.
  • Slimmer leaf/cuvette clamp for more accurate PAR readings in complex canopies

At this point, we’re working with bare boards (no case), and the test setup looks like this:

Bare board MultispeQ v1.0 in testing. Note the big fat battery!
Bare board MultispeQ v1.0 in testing. Note the big fat battery!

Not very pretty 🙂 , but in our initial tests show very good results.  We had three technical tests to pass for the MultispeQ V1.0 – a standard chlorophyll fluorescence test (Fv/Fm or Phi2 type measurement) using a leaf, the same using dilute algae solutions, and the Proton Motive Force measurement using a leaf.  The Proton Motive Force and algae chlorophyll content measurements required the highest quality detector response, and neither were sufficiently high quality to be usable on the old beta device.  Here’s some comparisons between the old a new (this is the raw detector response, but notice the signal to noise on the graphs).

ECS comparison, multispeq v1.0 results

algae comparison, multispeq v1.0 results

In the first case (Proton Motive Force) there is a 5.5x improvement in signal to noise, while the second case (Chlorophyl Fluorescence in dilute algae) there is a 2.5x improvement in signal to noise!  That has huge impacts on the ability to collect data quickly and efficiently in the field in a wide range of light conditions.  In addition, these methods are relatively un-optimized, so I expect we can squeak out even better quality by adjusting intensities and timing.  Kudos to our amazing hardware design team which includes Robert Zegarac, Jon Zeeff, and of course David Kramer.

So we can now measure, in a few seconds, Proton Motive Force in the field!  There are no handheld devices that we know of which can collect this data, and certainly none which can do so this quickly.  Only $150k Walz machines, or our own $40k IdeaSpec here in the Kramer Lab, can measure Proton Motive Force at all and they are desktop machines.  We think this is going to add a new set of really important photosynthesis parameters (like ECSt, gH+, vH+…) which may be related to stress, yield, and have broad uses in understanding photosynthetic response.

You can find more about measuring Proton Motive Force, and the new Phi(NPQ) and Phi(NO) parameters here: http://www.ncbi.nlm.nih.gov/pubmed/16228395.

In addition, there are 3 forthcoming papers from the Kramer Lab about the MultispeQ Beta device, PhotosynQ applications in Africa, and the new short method for estimating NPQ (called NPQt).  As soon as they are out, I’ll post them to the blog.

Expect more technical details about MultispeQ V1.0 on our g+ feed as well as in the next blog post.

PhotosynQ Conference, April 22nd!

Selection_611
PhotosynQ users in use in Zambia measuring beans

Register here!

We are organizing the first PhotosynQ conference next month here at Michigan State University in East Lansing, Michigan!  You can sign up via Eventbrite here.  Everyone is invited, but we’ll also livestream the event.  Dan TerAvest (the organizer) will be following up with speakers and topics, but there will be presentations from many beta testers on crop trials, soil measurements, greenhouse and benchtop applications, MultispeQ mods, experimental design and data analysis workshops, and much more.

Well worth the trip for anyone getting a MultispeQ this year, and you’ll save lots of time and improve the quality of your experiments by learning from the experience of the beta testers.

Open Science Hardware Activism

PANO_20160301_132631
more images: https://goo.gl/photos/psoVmrEvBTLMPDeDA

In early March, I helped organize the first Gathering of Open Scientific Hardware, at CERN in Geneva, Switzerland.  Of course I brought the PhotosynQ and talked about our project, but the main goal was to connect with other like-minded developers and scientists who want to make Open Science happen by changing the way we develop tools and technologies used in the lab, the classroom, and field.   A few of my favorite projects (and people!) were Open QCM (a quarts crystal microscope), Safecast (used in Japan to measure radiation during Fukushima disaster), our own MI-based Backyard Brains (neural probes).  In total , there were nearly 50 participants from every corner of the world.

We’re putting together a short manifesto defining Open Science Hardware as a movement, with distinct and important goals related to the broader Open Science community.  If you want to join the discussion, you can find us at the open-science-hardware google group.

Updates, and MultispeQ orders now public!

We had a slew of activity this last week I want to share, so here it is –>

Now anyone can get a MultispeQ

The MultispeQ is now publicly available at www.photosynq.org/buy-multispeq!  So if you’ve been itching to tell people about it but you’ve been holding back, feel free to forward that link along 🙂 .

Solder, test, repeat

Robert soldering a MultispeQ v1.0 board
Robert soldering a MultispeQ v1.0 board

We are testing the new MultispeQ circuit boards right now.  Our hardware team (Robert, Jon, and myself) hope to have a working version ready in the next week or two.  The new board is very similar to the beta in some ways, but has many added components and upgrades – we went from 180 components in the beta to about 275 in the V1.0!  The firmware (written in c++) is also similar but not exactly the same, so we have our work cut out for us in the next month to get everything ready

As soon as we have some outputs from the new board you will receive updates.

PhotosynQ at the Organic Seed Conference

If any group was collaboration-inclined, it’s the community of breeders, both professional and  hobbiest, in the organic seed community.  There are a number of really great projects which I wanted to point out as sources of inspiration for what we feel is coming in the next 10 years both to plant breeding, but also to extension and farmer outreach.  These guys share a vision with our project in terms of expanding involvement in and access to the creation and collection of information in agriculture.

Last year, Nate from Experimental Farm Network organized 300 people to take part in a range of research projects.  EFN acts as a matchmaker, helping to connect individuals who are capable of taking part in research efforts (growing plants, following directions, collecting data, and returning seed) with those who have research.  You can join as a collector or as someone with a research project here – http://experimentalfarmnetwork.org/

 

http://labs.russell.wisc.edu/organic-seed-potato/

I also talked with Dr. Ruth Genger, who runs the Organic Potato Project in Madison Wisconsin.  She’s working with ~25 farmers to both collaboratively select for traits, and build seed stock for, new organic potato varieties.  This is one of the best examples of participatory breeding, a phrase I didn’t know but heard a lot at the conference.  For their blog and more info – http://labs.russell.wisc.edu/organic-seed-potato/

 

I was really impressed by the Culinary Breeding Network, out of Oregon State.  They integrated the opinions of chefs and the public into the breeding program in a way that I’d never seen but which made so much sense.  They brought chef’s to the field, and had tasting parties in Portland, basically anything to better connect consumer to breeder.  This kind of thing should be integrated into any breeding program of crops which are bought and consumed directly by human beings (like not cow corn, but maybe sweet corn 🙂

 

IMG_20160204_165335The folks in the Barley Breeding Program at OSU are passionate about barley in a way I’ve never seen (http://barleyworld.org/) .  They have their own malting machine, and they also have tastings and get lots of public feedback.  I came out pretty convinced that barley is the grain of the future!

 

Overall, I think other land grant universities (*cough* M *cough* S *cough* U *cough*) should follow the lead of these kinds of highly collaborative, integrated breeding programs.

more next time!

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