In memory of Prof. Ruth Gates

Prof. Ruth Gates, one of the prominent coral scientists in the world, the director of Hawai’i Institute of Marine Biology, and the president of the International Society for Reef Studies (ISRS), passed away on October 25 after a battle with cancer (In Memory of Ruth Gates – The Atlantic).

Her recent works include breeding heat tolerant corals or “super corals”, for the effort to save the coral reefs from severe bleaching, and holding the public forums to make the communities aware the benefit of saving the reefs and what kind of actions the normal citizens can take. She was one of the PhotosynQ/CoralspeQ collaborators. You could find her detailed scientific works, news articles and contributions elsewhere. Here, I would like to write about brief but memorable interactions with her.

It started in summer of 2015. Prof. Peter Ralph at University of Technology, Sydney, visited us in Michigan, telling us about the upcoming monstrous El Nino… officially called Godzilla El Nino. Peter, our long time collaborator and early adopter of PhotosynQ, proposed us if we could make a field deployable instrument like MultispeQ (it was Beta type back then) to monitor corals. It was a challenge, because it has to work under water. Thus, CoralspeQ was born. Peter strongly suggested Ruth Gates as a collaborator, because not only she was a respected coral expert, but also she constantly touted the importance of collaboration and data sharing. We had also contacted several other scientists who are marine biologists and spectroscopists, and received a positive response.

When we finally built a prototype in November when the damages from El Nino had already started, we needed a field test instead of the lab test. It was Ruth who emailed me directly and said, “What can I do for you?” I flew to her Institute in Coconut Island with 2 instruments in December, 2015 (CoralspeQ Prototype 1.5 Update – Ready to go for the field test!), and took measurements with captive corals with a help from Jennifer Davidson, and in the reef with a help from Elizabeth Lenz. This field test was crucial to see what we could tell about the coral conditions in the real environment.

In the following summer, at the 13th International Coral Reef Symposium in Honolulu, I finally had an opportunity to talk to her in person (CoralspeQ Debut at International Coral Reef Symposium). Being the president of the ISRS and one of the Symposium organizers, she had people lined up to have a brief private conversation. I was fortunate to have an interaction, and was totally flattered by her saying “Thank you for doing this!” She meant that making inexpensive instrument and sharing the data through the cloud-connected scientific platform would benefit everybody. Her closing plenary talk was about the need of scientists and communities working together and coming up with the solutions to save the reef ecosystem. I think she had been inspiring many people with her optimistic open-minded attitude. Now she has passed a baton to the next generation. CoralspeQ is a difficult long-term project, but equipped with Ruth’s optimism, we will get there.

CoralspeQ Beta, The next generation — a short update

New boards!

We have just received the brand new boards!  We have been working on this since last year.  It took longer than we anticipated, because both Dave and I kept adding the features (“we want a laser,” “more LEDs,” “we need longer wavelengths,” “I found this cool LED. Can you use it?” & etc.).  I truly appreciate the patience of Robert and Chris.  We surfed through the wave of holidays, and finally, the initial trial electronics boards are here.

The new board is largely modified from the MultispeQ V.1 board, and the idea is that it will be used not only for the CoralspeQ, but also for other instruments currently under development. GrainspeQ is one of them.

It will still take time to build a complete CoralspeQ Beta. I hope I could update again soon.

CoralspeQ featured in Nature magazine

CoralspeQ is featured in the article called “Computers on the reef: Software tools that digitize and annotate underwater images are transforming marine ecology” in Nature magazine today ( here for the link: http://www.nature.com/news/computers-on-the-reef-1.20497 ).

This article is describing the advancement of technologies in the field of marine science. It is great that our effort is being noticed. Now, we have to get back to work!

— Atsuko

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/).

The 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: https://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.

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.

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 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.


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

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)