undergoing PAR calibration!

Validation of MultispeQ v1.0 – Chlorophyll, thickness, PAR

We have been validating the 10 – 15 MultispeQ v1.0 devices we received from the factory.  It’s going extremely well, in some ways better than I had imagined, and I want to share our results:

Relative Chlorophyll (SPAD)

  • The MultispeQ relative chlorophyll correlates well to the industry standard Minolta SPAD 502+ (Minolta = MultispeQ * 1 – .93, r2 = .987, using 11 devices and 68 measurements).
  • Validation was performed on Ficus, Basil, Banana Tree of varying thickness (.07 – .62mm) and greenness levels (Minolta SPAD values from 24.5 – 60.8).
  • Very thick (aloe) or very small leaves may require adjustments to measure consistently, but the measurement range is similar to the Minolta SPAD 502+.

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Keep reading! Link to the full results below
https://photosynq.org/projects/arrakis-relative-chlorophyll/results

Leaf Thickness

  • The MultispeQ leaf thickness is an accurate (thickness = multispeqThickness * 99 + .01, across 11 devices and 209 measurements), inexpensive, and simple field based leaf thickness measurement.
  • Strong magnets or large pieces of metal close to the device can impact thickness calibration.
  • Leaf veins should be avoided when clamping if a very accurate leaf thickness measurement is desired.

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Keep reading! Link to the full results below
https://photosynq.org/projects/arrakis-leaf-thickness-and-compass-test/results

Ambient PAR

  • The MultispeQ ambient PAR correlates well to a LiCOR LI-250A PAR meter (LiCOR = MultispeQ * 0.95 + 3.99, r2 = .996, using 13 devices with 206 measurements). Devices showed some offsets from the actual PAR, but the noise at any given light level for each device is relatively low (high r2).
  • Validation included measurements in different spectral conditions: cloudy day, sunny day, LED, and fluorescent lights.
  • Additional spectral conditions (for example, inside a dense canopy) should be added to improve the quality of the validation.

Keep reading! Link to the full results below https://photosynq.org/projects/arrakis-par-confirmation/results

Ambient PAR to Leaf Chamber PAR

The MultispeQ has to replicate ambient PAR inside the measurement chamber.  This is quite tricky because there is some error in measuring ambient PAR and some error in converting ambient PAR to a defined LED intensity.  Those two errors combine to increase total error.

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  • The MultispeQ’s conversion of ambient PAR to LED light inside the leaf chamber is ActualPAR = 0.94*LEDPAR + 12.17 (r2 0.979) using 10 devices, across a range of spectral conditions and intensities, with a total of 253 measurements).
  • MultispeQ LED PAR tended to be shifted higher slightly compared to the actual ambient PAR.
  • Green, red, and blue LEDs (lights 1,2, and 4) correlated the best with the LiCOR LI-250A. The orange LED (light 3) performed the worst.

Keep reading! Link to the full results below https://photosynq.org/projects/arrakis-licor-par-actinic-licor/results

We’re going to continue to validate and check devices as we produce them, and post it through these same projects so everyone can see it.  Expect another update regarding production status in the next few days.

MultispeQ Beta publication in Royal Society for Open Science

Check out the first publication from the Kramer Lab about the MultispeQ Beta!

You will find comparisons to commercial devices, calibration, and use and application in the field in collaboration with Beta test partners.

It’s important to note that this is paper is about the MultispeQ Beta device, NOT the MultispeQ v1.0 which we’re working on currently.  The MultispeQ v1.0 will have its own publication.  While the v1.0 has many improved features, better quality, and higher accuracy, the v1.0 is otherwise pretty similar to the Beta and this publication is a useful starting point for understanding either device.

Congratulations to Sebastian, Dave, Dan, Marty, Robert, Isaac, Donghee, Mitch, Kevin, and Pro for their hard work on getting this paper out into the world and the many sponsers which supported us along the way.

 

First 20 MultispeQ devices delivered from factory!

We are continuing to make progress on shipping the MultispeQ v1.0.  We now have the first 20 devices from the factory.  These are exactly (!) like the ones we’ll ship to those who pre-ordered.  And we now have all parts in stock to complete all orders and then some.

We are now evaluating these initial 20 devices, adjusting our existing calibration routines, and field testing them to make they hit our high standards.  We did as much of the testing as possible prior to receiving these 20 devices on hand-built versions with 3D printed cases, but due to small changes in manufacturing it wasn’t possible to finish all calibration routines and test all tolerances. Here’s two such examples: 1) 3D printed cases are notoriously slopped in comparison to injection molded ones, so mechanical components needs to be retested (like the bushings for the clamp mechanism); 2) the case material (ABS) has a different light absorptivity than the 3D printed cases we used before, and that changes the absorption and chlorophyll content calibrations.

In addition, we’re fixing some good old fashioned errors, like we ordered a bluetooth module but were shipped the wrong one (currently being reordered), and the USB 3.0 port wasn’t soldered on the board completely, causing confusion during initial calibration (a new soldering routine is being developed by the factory).

These aren’t excuses, but hopefully give you a sense of the kind of troubleshooting and persistence that’s required to get something that works consistently 🙂

Once we’re comfortable with these 20 devices, we will manufacture the remaining devices and ship.  We have about 2 more weeks until the final parts we had to re-order come in, and it will probably take a few more weeks to complete the calibration and final testing before shipping.  But we won’t ship anything until we’re completely comfortable with the device and it’s efficacy.

We apologize for the long delays, we know it can be both nerve racking and frustrating.  We are getting there, and we think you’ll be happy with the result.  Thanks for your patience and support!

MultispeQ v1.0 up close

MultispeQ v1.0 Workshop

Learn the MultispeQ v1.0 and the PhotosynQ platform.

This is a 3 day intensive workshop to learn and share best practices, experimental design, data analysis, and hardware modification on devices in the PhotosynQ platform with a focus on the MultispeQ v1.0 device.

  • Dates: Oct 14 – 16, 2016
  • Location: East Lansing MI

We already have a great group of attendees with backgrounds in plant breeding, plant science, arboriculture, and citizen science from academia and the private sector.  Join us!

To keep the workshop small and personal, tickets are limited so sign up soon.

Sign up now!

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

MultispeQ Production Update

We have some updated numbers on manufacturing.  I’m providing these in an overabundance of sharing, but recognize (if you don’t already) that manufacturing numbers are never that tight.  Things come up.  Things break.  Shit happens.  So take this with a healthy dose of scepticism and a small dash of hope.  That’s what I do.

  1. All circuit board and case designs are finalized (ie no more changes!).
  2. Our mold maker estimates 3 weeks for case molds, + 1 week for testing
  3. Our printed circuit board manufacturer estimates 5 weeks for completed, tested, populated circuit boards.
  4. Other parts with long lead times are down to 8 business days (~2 weeks), including light guides and 2 rubber molded parts.
  5. From final assembly, It will take us at least a week to test a small batch (~20) of these devices to confirm our calibration routines are working as expected, and determine if the variation is within out specifications.
  6. From that point, it will take another week or two to produce, pack, and ship the first 500 devices.
  7. Our software (desktop app, android app, and website) are working with the new device, so no limitations there.

What does this all mean?  It means we are at a minimum 6 weeks to shipping devices.   Argh…

It’s not all gloom and doom though.  Next post I’m going to show our progress, how quickly you can take measurements, and how effective those measurements can be.  It’s exciting stuff.  Stay tuned.

– Greg

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