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

3 more days until beta test is officially closed!

Hey everyone, we’re still accepting new signups for the beta test, but we’re going to close applications pretty soon as we begin purchasing parts. So if you’ve been waffling now’s the time to make a move (link to signup page)!

Dave and Robert’s work on the detector (show pictures)

Dave Kramer and Robert Zegarac have been working on improving the signal quality on the MultispeQ (the handheld measurement device used in the PhotosynQ platform). Previously, we achieved a peak to peak noise of about 300 ppm which enabled us to easily and effectively measure things like plant fluorescence, but when it came to measuring smaller signals like absorbance at 940nm or 520nm the signals were acceptable but not great. See below for some examples of leaf absorbance at 940 and 520.

Dave and Robert

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came up with some new ideas for filtering the electronic signal and increasing the number of averages in the ADC to effectively increase the resolution from 13ish bits to 16 bits or higher. Using the same photodiode (ie the part that absorbs the light), we

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prototype. That low noise is is on par with even the best benchtop units for measuring photosynthesis (and those cost 100k!). This noise reduction will not have a dramatic effect on the basic measurements like photosynthetic efficiency and chlorophyll content, but it may open up additional measurements which require that level of precision that we’re not yet aware of.

Updates from Dave

Dave Kramer, who’s been working on the methods, equipment and science around measuring plant photosynthesis for last 20 years and who’s benchtop equipment morphed into the MultispeQ instrument, is now on social media! He posts thoughts, articles, and links related to the PhotosynQ project, plant science,

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and whatever else he thinks you may find interesting. You can see his RSS feed here, or follow him on Google

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Plus here. The Kramer Lab website is here if you want to learn more about his past and current work.

Updates from Chlorophyll Content (SPAD) measurements

In the last post I talked about the chlorophyll content measurement (aka SPAD aka Soil Plant Analysis Development coined by Minolta who developed the first handheld device) and why it’s useful. Well, we’ve managed to make the MultispeQ measure absorbance at 650 and 940nm necessary for measure chlorophyll content and the initial results are promising. We have not yet correlated actual chlorophyll content measured using extraction with our handheld device (that’s the next step), we have used some Rosco gel filters which have known transmittance values at 650nm (basically plastic sheets of varying colors of green) to see if we are getting values we’d expect. Well – looks pretty good –>

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Initial chlorophyll content results using SPAD measurements scale

As one would expect, the light green (high transmission) has higher values while dark green (lower transmission) have lower values, with a y-intercept very near zero. I also measured a couple of leaves of varying greenness (just measured by eye) and the values came out to about what one would expect, which is promising.

If anyone is interested in running a calibration of our device to a Minolta or other SPAD meter, we’d love to see it! If we have time, we’ll do a correlation to actual chlorophyll content sometime before the beta.

Pick and place machine ordered!

No outsourcing for us! We’re doing small batches which will change frequently, and we have other projects in the lab which could use it, so a small-scale pick and place makes sense. We’re getting the slightly larger (28 reel) version of this one, which was demoed by the guys at Dangerous Prototoypes . We’re hoping that it won’t take too long to set up, though we all have a sinking feeling it may be a bit finicky to get started – we will see soon enough!

Progress Update – boards,

News highlights

  • Purchase pick and place machine for in-house circuit board assembly – will arrive within 2 weeks
  • Ordered final circuit boards (170, 2 boards per device) – will arrive in 5 business days and we can start hand-assembling at that point
  • Chrome app, android app, and website all in basic working order
  • Chlorophyll fluorescence and SPAD (chlorophyll content) up and running (NDVI just around the corner), and temperature, relative humidity, CO2, and light intensity (with PAR filter so it’s measuring only photosynthetically active radiation or pretty close) also working
  • Previous design was a complete power hog (160ish mA)… now we have an auto-shutdown feature and low power mode to increase battery life, and switched to standard AAA batteries with battery holder on the device.

 

PhotosynQ demo at Mach 30 Hangout this Thursday @ 8:30

Though we’re a bit behind schedule, we’re making great progress. We officially closed the beta last week with a total of 35 participants and 74 devices! We have every kind of user and location in there – here’s a partial list:

high school teachers, citizen scientists, organic and conventional farmers, agronomists, plant scientists and professors, hardware engineers…

Switzerland, Brazil, Kansas, Wyoming, Ghana, Japan, NYC, Florida, Colorado, Australia, Alaska, Siberia, California, Idaho, Italy, Canada…

I really can’t wait to see all the amazing data that people generate, and hopefully some great collaborations as well.

In other news, we’re going to show off what we’ve got so far this Thursday at 8:30pm at the Mach Hangout taking place on Google plus. You can join us at this link – it’ll include a look at the hardware, online analysis tool, and measurements types that PhotosynQ and MultispeQ can do. Below is a quick preview of what we’ll have in more detail Thursday.

Hardware

Robert and Dave have dramatically improved the detector quality, and we’ve got rid of some little blips in the signal which happen during bright actinic or saturating lights, and we’ve included a signal gain system which allows those creating new protocols to really zoom in on the signal of interest. We just received the most recent (and hopefully last) prototype board which is being built now, so it’s likely we’ll have that one to show off Thursday. We’ve also put in the final parts order for 85 units worth of parts mostly to Digikey, so that should be in pretty soon.

New board in progress… soldering 0402s (less than 1mm x 1mm) by hand takes some time…

Measurements and Protocols

Up until now, the only way to add a new measurement to the system was to upload it to the firmware (the arduino code loaded onto the handheld device)… this sucks, to put it mildly. Imagine if you created a new measurement, you’d have to get everyone else who wants to use that measurement to update their firmware, which involves downloading Arduino IDE, teensyduino, and all associated libraries… booo! Now, all of the information needed to run a program is transferred to the device from the web or mobile app every time the measurement is called. The information is in the form of a JSON, a nice standard format which can be parsed by the firmware. That means you can create a new measurement in a nice online form and everyone can use that measurement immediately, no firmware updates needed – yaaay! In order to have an effective and robust scientific community and people creating their own measurements, this was a critical feature to add and I’m happy we finished it.

Data analysis tool

Sebastian’s been making amazing progress on the online analysis tool. We have all sorts of features, too many to mention here, but needless to say we’ll go through it on Thursday. He’s also created a chrome app, which like the phone app, communicates with the handheld device to initiate measurements and capture the data. That means if you’re taking measurements at your bench, you can use your computer instead of a phone.

tool in action – you can select any outputs from the measurement and plot them against each other – in this case Phi2 (photosynthetic efficiency) and SPAD (chlorophyll content)

The new Chrome app – you login to the database, select your experiment, answer the relevant user questions describing your sample, and then run the protocol and BAM! you see the raw signal and calculated values and environmental variables!

More to see on Thursday, hope to see you there!

The PhotosynQ team