CoralspeQ Beta, The next generation — a short update

CoralspeQ new boards
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 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/).

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

 

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

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.

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!