PhotosynQ at Feed the Future Legume Innovation Lab (LIL) Conference in Burkina Faso August 13-18, 2017

Following the PhotosynQ Workshop (see Dan’s post), we had moved to the LIL conference site at Laico Ouaga 2000, a high security hotel/conference venue outside of Ouagadougou city.  “Feed the Future” is a program funded by USAID under the US government’s Global Hunger and Food Security Initiative.  This program has been engaging many universities, institutions and private organizations in the US, Africa and Central/South America to improve the quality and management of legume, and contributing to the well-beings of local people. Michigan State University (http://legumelab.msu.edu/) is one of the leading institutions contributing researches and new technologies to the world.

One of the designated official languages being French, we had a simultaneous translation through headphone at this conference. The last time when I had to use French in daily basis was almost 20 years ago. Listening to the scientific talks was manageable, but my speaking ability was quite embarrassing. Another challenge was internet connectivity. As Dan mentioned, we had to manage the workshop with almost no internet connection. We were hoping to have a better connection at this best hotel in Burkina Faso, but unfortunately, it seemed the system could not handle a large traffic at once. The conference participants expressed that they had never experienced this in the past anywhere in Africa. It seems it was an isolated incidence, but we came up with some better solutions for the future.

  PhotosynQ booth (From right: Dan, Frank and Atsuko)

 Presentation by Dr. Irvin Widders, Director of Legume Innovation Lab, MSU. PhotosynQ was mentioned as one of the highlights of the ‘Feed the Future’ program.

At the last LIL conference held at Livingston, Zambia, Dave Kramer and Dan TerAvest presented the PhotosynQ project using MultispeQ Beta. This year in Burkina Faso, not only the people from Kramer Lab (Dave, Dan, Donghee Hoh, Isaac Osei-Bonsu and me), but also our PhotosynQ collaborators (Dr. Isaac Dramadri in Uganda, Dr. James Kelly with Dr. Jesse Traub and Dr. Wayne Loescher of MSU, and Dr. Kelvin Kamfwa of U of Zambia) presented more detailed and sophisticated data showing the correlations among photosynthesis, plant responses and gene expressions. It was very encouraging for us to see more people started thinking that the PhotosynQ platform and hand-held devices are useful and practical to the broad applications.

We are very excited about the new challenges, collaborations and long-lasting friendships. And we all hope to see you again!

The NPQ(T) Parameter

Measuring non-photochemical quenching in a few seconds without an initial long dark acclimation.

Over the past 3 years, many MultispeQ users have noticed that the NPQ(T) parameter (and ΦNPQ) can be a powerful predictor of plant stress, either biotic or abiotic. The NPQ(T) parameter has also correlated with crop yields in some PhotosynQ projects, like this project from Malawi.

Indeed, one of the big breakthroughs with the MultispeQ is the ability to estimate NPQ (Non-Photochemical Quenching) without a long dark acclimation period, which allows us to develop robust protocols that take less than 20 seconds. So how is the NPQ(T) parameter derived and how does it compare to the established NPQ parameter?

Tietz et al. out of the Kramer Lab have just published a paper in Plant, Cell and Environment describing the parameter and its derivation. Congratulations!

Read the peer reviewed publication or the story on the Michigan State University’s Plant Research Laboratories Website, Protecting plants from the power of sunlight.

Tietz, S., Hall, C. C., Cruz, J. A., Kramer, D. M. (2017) NPQ(T): a chlorophyll fluorescence parameter for rapid estimation and imaging of non-photochemical quenching of excitons in photosystem-II-associated antenna complexes Plant. Cell Environ. 40(8), 1243–1255. doi:10.1111/pce.12924

The MultispeQ beta’s Future

The first version of the MultispeQ, the MultispeQ beta has been a great instrument, workhorse and proof of concept for the PhotosynQ platform and its utility in phenotyping plants outside the lab in large sample sizes. There are still MultispeQ beta instruments out there which are in use. We have decided with a heavy heart to stop the active development for them, since they have already exceeded their anticipated lifespan and focus our limited resources on the new MultispeQ v1.0.

The MultispeQ beta - Our proof of concept instrument that worked longer and produced more results than we expected.
The MultispeQ beta – Our proof of concept instrument that worked longer and produced more results than we ever expected.

So, what does it mean?

You will still be able to use the instruments and use the existing protocols, as well as create your own new ones. If there will be a change that breaks the compatibility with the Platform, we will give you enough of a heads up, so you can finish your experiments before we release the update. Since all the informations about the instrument is open, we hope that fixes or improvements might be made by the community to extend the instrument’s lifetime.

The Hardware

We are no longer supporting hardware fixes, mainly, because we don’t have parts in stock any more. Pieces like the light guides were custom made and can’t be ordered. Electronic parts can be ordered and we are more than happy to point you to where to source the needed parts. Just let us know and write to support@photosynq.org. Otherwise, we advice you to get the new MultispeQ v1.0 for your future data collection.

The Software

There are no more measurement protocols developed for the old MultispeQ beta. The structure and some of the commands have changed when we introduced the new MultispeQ v1.0 and some of the new features would need a complete re-write of the instruments software (firmware).

We are no longer updating the firmware since we want to focus our limited resources on the current instruments and make sure they receive updates and improvements on a regular bases. As long as the communication protocol doesn’t change, the instruments can be used with the apps and submit data to the PhotosynQ platform.

Thank You!

We would like to say thank you again to all the beta testers not only for testing the MultipseQ beta, but the PhotosynQ platform as a whole. We learned a lot and the new MultispeQ v 1.0 has benefitted from those experiences a lot.

~ The PhotosynQ Team

Teachers Workshop at Kellogg Biological Station

I traveled to the MSU K-12 Partnership 2017 Spring Workshop at the Kellogg Biological Station on April 18 with Klara Schnargl. Klara is a Future Academic Scholars in Teaching fellow and she is interested in strengthening the connections between Universities and K-12 education programs. The purpose of the program on this day was to bring graduate students and postdocs from MSU together with middle and high school biology teachers.

Klara and I were going to run a session for teachers who were interested in new, hands on, methods of teaching kids about photosynthesis. We thought that the MultispeQ instrument, combined with the ease of generating simple graphs on the PhotosynQ platform, could be a great way for students to visualize how plants use the light energy they capture and how they respond and regulate photosynthesis in response to their environment.

education blog image

We conducted a really simple experiment with the teachers so they could see PhotosynQ in action. Klara brought along two orchids in small pots and it was a beautiful, sunny spring day. So, we quickly created a project (‘KBS educational module April, 2017’) on www.photosynq.org that asked which session (we had one morning and one afternoon session) was collecting data and whether the plant was inside or outside (2 minutes). Then, after a brief talk about how to connect your phone to the MultispeQ and how to take a quality measurement (4 minutes) the teachers collected some measurements from the orchids in the classroom (5 minutes). Next, we took our orchids out into the sunshine and gave them time to adjust to their new surroundings (2 minutes). After a few more MultispeQ measurements we were heading back into the classroom to check out our data (5 minutes). We logged on to our PhotosynQ project and created a couple of graphs to compare Phi2, PhiNPQ, PhiNO and LEF inside and outside (4 minutes).

In 22 minutes we went from ‘this is MultispeQ’ to ‘look how our orchids regulated incoming light in our experiment.’

The teachers that came to our session were great, with lots of fun ideas on how they could use PhotosynQ in their classrooms and we are looking forward to working with them in the future.

MultispeQs on track to ship

Hi everyone – we’ve had 3 days of production with a pace of 24 finished, boxed, ready to ship units per day!  We should be able to fill the first 200 units over the course of the next 2 – 3 weeks.  With a few exceptions, we will be shipping MultispeQs in the order they were received.

Thank you all for your immense patience as we have worked through this long process.

On a personal note, this is my last week as part of the PhotosynQ project.  My hope is that the project continues to strive for the values of open software, hardware, and data in science, and to create tools which are broadly useful to the both the scientific and non-scientific communities.  I know that these ideals are sometimes hard to hit, but if not us then who, and if not now then when?

Thanks to everyone that I’ve interacted with over the years for your patience, enthusiasm, support, and collaboration.  In the future I’ll be on google plus +GregAustic and twitter @GregAustic.   Hope to see you in my next project!

– Greg

First batch of 24 finished MultispeQs!

Hi everyone – it’s been about 3 weeks working here at Saline Lectronics to get the initial build of 250 MultispeQs underway.  There have been lots of ups and downs, but we finally got the motor running.

We can now make about 24 units per day, which means we can fulfill the initial 250 in about 11 working days.  Here are some pictures of the first 24, ready to be put in a box.

Calibrated, validated devices ready to be boxed

Thank you so much Jared, Paul, Jan, Cathy and everyone else at Lectronics for pushing through and getting 250 units through completion… it would probably surprise people how much we had to touch every single one of these devices to get them out into the world.  Hopefully the next 250 are easier than the first 250 🙂

There’s always lots of problems that need to be fixed…

MultispeQ Assembly and how the sausage gets made

For the manufacturing uninitiated, a manufacturing facility can be pretty impressive. Robots, half-million dollar pick-and-place machines and assembly lines with people diligently working on making stuff produce a lot of ‘ooohs’ and ‘aaahs’.

But, automation is only part of the story. There is a lot of decision-making and little details to make things actually work. Our first week in manufacturing has had some setbacks with a few misplaced parts and similar issues, but our manufacturing partner has beefed up their support and Sean, Dan and I have working side by side with them.  We’re refining our production process and ironing out errors.  In all, we are still making decent time.

All production processes look different, but here’s a peek at ours:

1) Pre-assemble case. Many parts are more efficiently pre-assembled in bulk – placing the small light-blocking o-rings in the main case, for example, or installing the battery. These pre-assembly steps are largely done for all 500 units, so once circuit boards are ready the device will snap together pretty quickly.

Pre-assembled components of the MultispeQ case.

2) Assemble + test circuit boards. The 2 circuit boards are connected, bluetooth and DACs are configured, EEPROM (memory) is zeroed out and lights are tested.

connecting and testing circuit boards.

3) Place boards in case. Circuit boards are installed in the case. The PAR sensor, which contains several very small parts which fit precisely around the TCS light sensor, is assembled at this time as well.

Some very small parts related to the PAR sensor which is put in during this phase.

4) Calibrate + validate.  We have 7 individual calibration steps, as well as a final validation on 3 different plants of varying leaf colors and thicknesses.  All of this data is saved to the website and you (the user) can follow up on your devices factory calibration (if you want).

undergoing PAR calibration!
PAR calibration setup

5) Pack and ship.  Now the final devices are packed in their boxes and shipped to labs around the world.

The box the MultispeQ is shipped in.

As of today (Thursday), we have almost all of the pre-assembly work done, and are in phases (2) and (3) above.  Most of next week will be spent calibrating devices and boxing them up to ship.

We’ll keep you in the loop as we go.

– Greg