Countdown to Beta Test

photo by David Kramer

Update

The last 2 months have seen a flurry of activity. We’ve gone through a several more iterations on the hardware, and we’re now pretty happy with the quality of the measurements and the amount of noise in the signal (see more below for specifics on that). We’ve also been working on identifying new partners, especially plant breeders in developing countries who need the tool to improve their breeding lines, and writing proposals. Finally, Sebastian has been working on improving the online graphing and analytics capabilities, which I think is amazing (my guess is the online graphing tool will be good enough that most users won’t need to export their data to open office or excel!). Oh, and we’re buying a pick and place machine (28 slots) so we can populate our own printed circuit boards in small batches… more work but less expensive and more flexible.

We also decided we like PhotosynQ with a big Q… because we want to call the actual measurement device MultispeQ and the Q really just holds the whole concept together…. maybe later we’ll make an AquaspeQ or something and that’ll really solidify things πŸ™‚ . Read on for other PhotosynQ news:

Beta

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Test Status – email coming soon!

Even with all the craziness, January 31st remains the target date for beginning to ship Beta test units. In the few days, beta testers will receive an email with updates on what to do next. We also hope to do a better job of communicating more about the project in the coming month so everyone stays up to date. In total we had almost 50 applicants from Thailand, Japan, Italy, Germany, and all around the US. It included farmers, hackers, engineers, citizen scientists, professors, gardeners, and nature enthusiasts. We are REALLY excited to the cool ideas and research questions that will come out of the initial group.

Open Call: Seeking research questions for PhotosynQ Beta testers to answer

One of the most fun parts of this project is the open ended nature of what a network of sensor-enhanced citizen scientists will actually do – what projects will people create, what questions will they ask and answer? … well, we don’t know!

Over the course of the next month, we’re going to be defining the initial projects available on PhotosynQ. For the Beta test we want projects which can use measurements taken in any location and are fairly easy to perform. For example, tracking a single leaf on a single tree over the course of a growing season to see how photosynthetic efficiency and chlorophyll content fluctuate on a daily basis. If you have any ideas, please shoot me an email at gbathree at msu dot edu .

Updates on hardware – new measurements and specs!

Robert has been working like crazy to get the PhotosynQ a lean, mean, low-noise low-cost measuring machine and they’ve done an amazing job. The most current version has noise of only .03% of a typical signal size… that’s 300 parts per million! We also recently eliminated a few bucks worth of parts and saved some space. Not too shabby, though we’ve got some ideas for making it a lot better down the road.

Ok, so what exactly can this thing do? Here’s the spec list and measurement types (with explanation of how they can be used and links with further explanation):

Main Device:

  • 1 detector – IR filtered, very high accuracy pin photodiode (noise ~.03% of tyipcal signal)
  • 2 measuring LEDs (current draw up to 750mA per LED, <1us rise time to turn on and off)
  • 1 ‘actinic’ LED (current draw up to 750mA per LED, ~2us rise time to turn on and off)
  • 1 ‘calibrating LEDs (lower power IR LED for roughly measuring thickness and/or reflectivity)
  • CO2 sensor, temperature and relative humidity sensors, light intensity and color temperature sensor (RGB).

Measurement capabilities:

  • Pulse Modulated Fluorescence to measure photosynthetic efficiency
  • Chlorophyll content to estimate nitrogen content in leaves (here’s an example study)

    Typical Pulse Modulated Fluorescence trace using PhotosynQ
  • Leaf temperature to estimate stomatal conductance (a key response to drought conditions).
  • Environmental sensors (CO2, temperature, relative humidity, light intensity and color temperature (RGB)

Fluorescence, chlorophyll content, and leaf temperature are very useful and tell us about details about plant health, plant stresses, and the inner workings of photosynthesis itself.

Spectroscopic add-on:

  • 1 detector – unfiltered, very high accuracy pin photodiode (noise ~.03% of tyipcal signal)
  • 2 measuring LEDs (current draw up to 750mA per LED, <1us rise time to turn on and off)
  • 1 ‘actinic’ LED (current draw up to 750mA per LED, ~2us rise time to turn on and off)
  • 1 ‘calibrating LEDs (lower power IR LED for roughly measuring thickness and/or reflectivity)

Measurement capabilities:

  • Photosystem I activity (ie is photosystem 1 active or not?)
  • Absorbance measurements which describe:
  • the electrochromic shift (ECS) due to build-up of hydrogen ions in the thylakoid (example paper here) and
  • dark-induced relaxation kinetics (DIRK) measurements at 850 and 940nm (example paper here).

ECS, PSI activity, and DIRK are a little abstract for the every day user but are very useful measurements which usually cost a lot of money to make and give a unique inside look at exactly what is happening in the process of photosynthesis and what short, medium, and long term changes the plant is making to adjust to it’s environment.

Typical 810 Dirk trace using PhotosynQ

Typical ECS trace using PhotosynQ

ECS, PSI activity, and DIRK are a little abstract for the every day user but are very useful measurements which usually cost a lot of money to make and give a unique inside look at exactly what is happening in the process of photosynthesis and what short, medium, and long term changes the plant is making to adjust to it’s environment.

A little more adjusting and we’ll be ready for prime time (well… beta time at least) –

The greenhouse is the only place tomatoes are alive in Michigan during the winter.
The greenhouse is the only place tomatoes are alive in Michigan during the winter. Photo by Dave Kramer.

Photosynq progress update: boards, beta, add-ons

Contents:
Ways to join the team!
Beta test still open
3rd round of hardware in-process
Been toying around with new ideas – cell phone microscope, and add link, soil moisture tester.
All hardware and software is live on Github

Ways to join the team!

We’ve got this far because of amazing contributions from Talia Selitsky and Pro and the team and Venturit, and we’re ready to identify more collaborators. Sometimes it’s hard to know how to jump in to a project, so here’s some bite-size tasks we’d love you’re help on. If any of these projects tickle your fancy, send us an email at gbathree at msu dot edu and we’ll get you up to speed!

      1. Identify or create a low cost, open source soil moisture measurement tool. (We only need to design the tool itself – not the brain or display. We can hook it up to the Photosynq board, Arduino brain, and smartphone display to output the data). There are branded devices for 140 dollars like these, and there are very cheap units like this. The problem is the cheap units are too small for measuring more than 2 inches into the soil – we need something with longer prongs (1 foot long) that’s sturdy and consistent. This may also be used for measuring moisture in grain (like this) , hay bales, or other moisture-related ag applications. Good fit for someone with experience with electronics and basic product design.
      2. Make the Photosynq mobile app look snazzy! We have a working app, but we’d like to improve the design to make it slick. Good fit for someone with experience with web app design and design skills.
      3. Create clear outlines for plant photosynthesis protocols. A large part of the work is figuring out which method is being used when taking a measurement – there are many different theories, protocols, and methods. Most photosynthesis measurement devices have a variety of protocols that users can choose from – and we need to develop that library. Currently, we have a single, simple protocol for pulsed modulated chlorophyll fluorescence. You do not need experience in programming – just writing the protocol in very clear terms (for example – “Red LED on for 30us for 150 pulses. At pulse 50, also turn on blue LED on for 1 second… take average of values at pulse 50 – 150 and save as Fm, removing top and bottom 2 outliers, etc. etc.”…). We can write the program after the protocol is described. Good fit for someone who understands plant science well and probably has experience using similar handheld devices (LiCOR, etc.).

Beta test still open

Just a reminder that we’re still looking for beta testers for Photosynq. If you are a researcher, hacker, maker, plant enthusiast, professor, gardener, farmer, citizen scientist, grad student or just enthusiastic about this project, go to http://blog.photosynq.org/beta-test-application/ and sign up. From the applications we’ve had so far, I can assure you you’ll be joining an awesome and varied crowd!

3rd round of hardware, added extra board for more measurements

2 boards finished and ready for another round of testing, start alpha tests soon

Photosynq
Main board – ambient temperature, leaf temperature, relative humidity, light intensity, color temperature (RGB), CO2, 4 LEDs, 1 IR pin photodiode detector, built to connect a Teensy 3.0 at base

We’re iterating on the hardware as fast as we can, the most recent circuit board is imaged below. We also created an add-on board which brings us to a grand total of 8 separately controllable high speed LEDs and 2 detectors (one IR detector, and one visible light detector)! It’s designed so that 4 LEDs and one detector are facing across from another 4 LEDs and detector – this allows not only for fluorescence, but also absorbance / transmittance measurements. Absorbance can be used to detect Photosystem 1 activity, ratio of PSI to PSII, and lots of other stuff.

We’ve been toying around with new ideas…

cell phone microscope, and add link, soil moisture tester.

As we’ve got out into the world, we’ve received some great thoughts and advice on additional measurements we could add to the system. One is using Thomas Larson’s simple cell phone microscope lens, which you just stick over the top of your cell phone camera and you can see 15 – 60x zoom! We think it would be useful for close-up comparison of leaf damage, or possibly even seeing the impact of leaf damage on photosynthesis around the damaged area (that’s Rebecca Nelson’s idea from Cornell University and http://ccrp.org/). When I got a few test units from Thomas, I took some images which you can see here. We’ve also had a lot of interest in adding a simple moisture tester. I found this one online for <5 dollars, but it’s very small (3 inches total). For serious moisture field measurements the longer, multi-prong probes are the gold standard.

All hardware and software is live on Github!
https://github.com/Photosynq

It took a while, but we’re now fully version controlled πŸ™‚ Check out our github page where you can see the most recent versions of the hardware, software (mobile app and website), and Arduino Protocols.

Photosynq add-on board
Add-on board: 4 LEDs, 1 pin photodiode detector

Killing plants for fun and science

In getting ready for our trip to the Open Hardware Summit, we wanted to create some short wizbang experiments to show what Photosynq can do. These experiments are focused around measuring pulse modulated fluorescence (find more about it on our ‘how it works‘ page, or this more in depth but accessible summary), which can distinguish between stuff that’s has active photosynthesis (like plants and things that are alive) from stuff that just fluoresces (like white paper and laundry detergents). We also want to create more experiments to show off the CO2 sensor and other stuff, but this is what we’ve got so far.

(Sebastian Kuhlgert and Kent Kovac from Kramer Lab came up with experiments, so thanks!)

Surprise – it’s alive!

Fruits and Veggies… alive or dead?

We wanted to see if fruits and veggies were 1) photosynthetically active at all (meaning, they were absorbing light and doing something with it), and 2) active even after they’ve been picked (sometimes many days after. Sebastian went and got an old pepper and a fresh pepper, an apple, some grapes, and some spinach and we ran some tests. The ‘how alive is it?’ value is called Phi(II) (this is the proportion of light absorbed by PSII which is used for photochemistry – you can read more in depth about chlorophyll fluorescence and ways to quantify it here). The ‘amount of fluorescence’ value is the absolute fluorescence response, which relates to the quantity of chlorophyll (it’s a relative value, not absolute, and it’s not perfect and we’re working on making it better – but let’s work with it for now). Here’s the results:

Blue bars are Phi(II) (ie how efficient is photosynthesis) and red lines are how much chlorophyll is there (these are relative values only)
Blue bars are Phi(II) (ie how efficient is photosynthesis) and red lines are how much chlorophyll is there (these are relative values only)

As expected, the new pepper was more photosynthetically efficient than the old one… but the old one had a higher chlorophyll concentration which was surprising. The grape was reasonably efficient, but didn’t have much chlorophyll (you could have guessed that – grapes aren’t very green and they are mostly water). I was surprised that the spinach didn’t have the highest levels of chlorophyll – it was certainly very green, though it is relatively thin compared to a pepper skin so perhaps that accounts for the difference.

Simple test and simple results, but they raise a lot of questions that even hardened plant scientists will hem and haw about!

Spinach is alive, but chlorophyll by itself is just another protein

Most of plant fluorescence comes from chlorophyll, which is the main component of the antennae which gather light. However, just because something fluoresces doesn’t mean it’s alive! In this experiment, we took a spinach leaf and measured Phi(II) and our relative measure of chlorophyll concentration. Then we mashed up the leaf and mixed it with 80% ethanol (you could use rubbing alcohol or nail polish remover). Then we poured the mixture through a paper towel (coffee filter would also work) so that only a clear green liquid remained. The alcohol removed the chlorophyll and the sieve prevented any whole cells from getting through – so we’re left with a chemical soup containing lots of chlorophyll.

So – what happens if we compare Phi(II) and chlorophyll concentration on the original leaf versus the alcohol/chlorophyll solution?

The spinach leaf is still using the photons to do useful work... the chlorophyll isn't, though they both produces roughly the same fluorescence
The spinach leaf is still using the photons to do useful work… the chlorophyll isn’t, though they both produces roughly the same fluorescence

As you’d expect – the spinach leaf is still using the photons to do useful work (high Phi(II))… but the chlorophyll/alcohol solution isn’t (near zero Phi(II), though they both produces roughly the same fluorescence (red line). This is relevant because fluorescence measurements from satellites can measure absolute fluorescence values, but not photosynthetic efficiency – so it’s valuable to have something like Photosynq to provide additional information on the ground.

Hearing plants cry “Heeeeeelp!”

Plants can’t talk, so when they are stressed (not enough water, too much salt, too hot, too cold, etc.) it’s sometimes hard to tell. Photosynthetic efficiency (Phi(II)) is a good indicator of stress (there’s many papers describing this, see here, here, and here for a few), so it’s a good identified of when plants are in trouble.

So we picked two prickly lettuce plants from the garden and stuck them in water. We added a bunch of salt to the water of one plant, and measured Phi(II) and relative chlorophyll content in both plants over a few days. Here’s the before and after:

In the beginning, there were two prickly lettuce plants…

but Greg and Sebastian smote one with salt!

The results show that not only was the plant wilting, but it’s photosynthetic efficiency was dropping too. It’s like if someone made you drink a bottle of absynthe and then go play in a soccer game – your performance would suffer!

The salt-treated plant (blue line) sees a big drop in photosynthetic efficiency over a couple days
The salt-treated plant (blue line) sees a big drop in photosynthetic efficiency over a couple days

In some ways, this experiment could be a lot more interesting – you can clearly see the plant leaves wilting, so what’s the point of taking the additional measurement with Photosynq, right? In this case that’s true, but out in the field it’s not always obvious that plants are under stress and the visual effects of stress (wilting, loss of color, slow growth) may be delayed by several days. Measuring photosynthetic efficiency directly will identify stresses much sooner.

We’ll have all these experiments plus (if we can get our act together) a few more by OHS on Friday. If you are going, come visit our demo!

Preparing for the Open Hardware Summit

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The Open Hardware Summit is coming up on September 6th at MIT, and we will be presenting our first working beta unit…

… if we get it done on time πŸ™‚Β  There’s so much to do!!! Robert and I are working on the Photosynq device itself – Robert has one iteration of the board finished with lessons learned and are working on the next iteration which we hope to have in next week. I’m working on creating the case, which is tricky because we need tight tolerances on the location of the detector, LEDs and light guide, yet we also need the ability to ‘clamp’ a leaf in front of the detector, and (ideally) the whole design should be easy to assemble, and 3d printable and/or laser cutterable (if that’s a word). For hinges, I’m using standard alligator clips for the hinges and it works pretty darn well! The first design is ugly but basically functional (yes, the board is not populated… we were just using it for layout) – here’s some pictures.

Selection_033

Venturit is working to finish the website and database using Ruby on Rails (similar to Spectral Workbench from Public Labs), so we can store, display, and analyze the data through the web. They’re also creating an API to communicate with the app. They are rocking it out and expect to be done on time.

We handing off a bluetooth enabled prototype to Talia this week, so she can get her app to talk to our device. We’re using Bluesmirf Silver from Sparkfun for the moment, though we’ll go with a cheaper bluetooth unit in the long term. We can already communicate with the device using a smartphone using Blueterm, but that’s just a serial communication and doesn’t look very pretty.

And finally, we need some good experiments to run for the initial beta and to show off the unit at OHS… I put down a few ideas from various folks at the wiki under the heading “Educational Modules” – if you’ve got any other thoughts feel free to send me an email.

If you’re going to OHS please stop by and check us out – hope to see you then!

Measuring algae with the Photosynq

There’s tons of new stuff, but to start here’s a quick list:

1. From Greg’s nerd nite talk we scooped up Talia, a new volunteer helping develop the app! And we spoke at MSU Global‘s Fanning the Flames about our project and the concept of open commercialization generally (click here for a link to the video) – from there we picked up Patrick Hayes who’s going to help us with marketing and social media!

2. We’re laying the groundwork with MSU to figure out how we’re going to get the finished unit out into the world, patent and license free.

3. The Photosynq device can now communicate with some (not all) cell phones and tablets via USB serial port, using a program like Slick Labs USB to Serial program, which allows you to both send a signal and receive a signal to the Photosynq. And we’ve got a few additional interesting protocols which are still under development but show a lot of promise.

4. We’ve got some great looking data by taking photosynthesis measurements of our algae bioreactors. We can clearly see the difference in the rate of photosynthesis from the top of the column (where it’s very bright) to the bottom (where it’s dark). This is information that no one has every really seen in this way. Previously, you had to take individual samples from each level and measure them in an external machine. Now, we can continuously measure photosynthesis throughout the culture in real time.

The setup is a bit messy…

There is actually a photosynq device and a photobioreactor somewhere in this picture
There is actually a Photosynq device and a photobioreactor somewhere among the cord maze…

But the data looks pretty good! Dave and Ben recently presented some initial findings at the International Conference on Algal Biomass, Biofuels, and Bioproducts. You can always keep up with the science end by checking the documents at our project page at Open Design Engine here. Some stuff gets delayed to go to professional journals, but I do the best I can to shovel stuff straight on to ODE as fast as possible!

But we still have a ways to go before it’s as clean as the data from the benchtop fluorescence unit in the lab – in the graph below you can see that the Photosynq signal is much noisier than the benchtop unit called Ideaspec (the detector response is much wigglier — don’t mind that the size is different – the key is the noisiness).

The basic response is similar (low signal, high signal, low signal) but the photosynq line is noisy)
The basic response is similar (low signal, high signal, low signal) but the photosynq line is noisy)

Ok – that’s enough for one post. More soon!

Making Arduino and Android talk

While Robert’s working on the LED controller board / signal processor / micro SC card holder / voltage reference board (yep, definitely multifunctional), it’s my job to see which cell phones will communicate with the Teensy-based Photosynq via the standard USB connection.

Answer: Not many.

Here’s the problem in a nutshell: For two things to talk with each other via USB, one must be a “host” and the other the “slave”. The host is the one in control of the conversation. For example, your PC is a host and your mouse is the the slave. So to connect a Teensy microcontroller to your phone, your phone has to be the host. Android operating system has allowed your phone to act as a host since version 3.1 using a special USB OTG (On The Go) cable, but many (dare I say most) equipment manufacturers are not creating phones which work with this standard. For example, a Nexus 4 does not communicate via Serial with our Teensy (at least not without a lot of fooling around), but a Toshiba Excite tablet does. There’s a big list here of what is and what is not USB host compatible.

I was impressed with the variety of Android Apps available for those devices which do work when you have the right device. I found 3 great apps which allow you to send and receive data via the Serial port to the Teensy (just like the standard Arduino IDE Serial Monitor): USB Serial Monitor Lite, UsbTerminal, Slick Labs (regular and pro). All worked very well with some minor differences and little glitches, but overall I was impressed – too bad so few devices are USB Host compatible.

In addition, only a portion of those OTG compatible devices actually supply the full 500mA power (as per USB 2.0 standards) to the USB device. This is a problem for us, considering we would like to have small bursts of potentially significant current to run the LEDs.

So, my dreams of a simple, universal, plug-and-play device appear shattered!

No matter – it’s time to look into Bluetooth and wireless options (like Eye-Fi and/or Sparkfun’s bluetooth module) and add a battery. Hope to get them in in the next few days and test them out. More updates then!

Yay! My Teensy said Hello to my Excite Tablet via the USB port. Too bad it couldn’t take to the Nexus, or 99% of other useful cell-based devices out there. Argh.
Nice data Serial output from the Teensy-based Photosynq

 

 

 

 

Look mom – no cords! … well, almost

In the last few weeks we’ve been working diligently on getting the photosynq handheld device actually handheld. Until now we had taken data using the standard Ideaspec hardware but with the new LEDs, detectors, and light guide setup. Now it’s time to shed the Ideaspec hardware totally and go completely cordless.

We’re almost there.

Ideaspec (box + computer) versus early version of Photosynq handheld (little unit sitting on top of box)

Robert is in the process of creating a shield (to use arduino-ish terminology) for the Teensy 3.0. This shield does a lot of important stuff – it contains an SD card reader, provides AC filtering of the detector signal, creates a high quality / low noise analog reference signal for the ADC, and includes full brightness control over all of the LEDs. It’s a work in progress, but we hope to have an early version in a few weeks before he goes on vacation of Croatia for the summer, where nice beaches and family time will probably out-compete time spent on this project πŸ™‚

I’ve been writing the Arduino code to run a basic fluorescence measurement – and it’s pretty much done. It interfaces through the serial port and has a simple program for user input before sampling (“do you want to create a new file y/n?” and “would you like to run a calibration?”… etc). It also saves the data on an SD card, which will make sending the data to a cell phone a piece of cake later. I’m working on getting the code on github, but for now I’m just posting to the Teensy forum at PJRC (Teensy is the arduino-based microcontroller that we’re using) located here.

Though the code itself works like a champ, the signal quality is not quite as good as when we use the Ideaspec signal processing hardware. It looks like we’ve got a lot of noise as you can see in the graphs below (the left is Ideaspec, the right is the handheld). But we’re pretty sure we understand the source of the noise and Robert’s on it – you can read about the source of the noise here, and expect to see more posts on PJRC from Robert which describes how we’re dealing with it.

ideaspec v handheld comparison

The last big “cords” left to get rid of is the main power and the 12V power which is pushed through the detector. Once those are gone, we’ll be truly cordless… I can’t wait!

Wireframing the Photosynq App

We’ve made good progress in the last week – we have a basic wireframe for the Photosynq Android app! The Android app is one of the most important parts of the system – it connects the Teensy arduino-based sensor to the backend database and web, and provides immediate feedback to the user as to how things are goinSelection_010g. Here’s a screenshot of the app’s main page. As users create research projects, they may want only data in a certain area (for example, if I’m studying unique plants in Borneo, I don’t want someone adding data from Lansing), or in a specific season, or a specific time of day. The main page helps sort some of these things automatically, and identifies research opportunities that apply to you: ie you are in the right place and right time to take part in. Any user can create their own research through the web page, and it be searchable via the app. I modelled this roughly after the Google Play store.

If you’d like to give us some feedback, feel free to download the whole wireframe and walk through it. It’s located on our project management page at Open Design Engine here (you’ll also have to install Pencil from here).

We also managed to address one of the primary problems with the actual measurement device itself – correct calibration. For measurement instruments, it’s often easy to get any old signal, but very hard to get a very accurate signal. In our case, we want to measure very very small levels of fluorescence (in our case fluorescence is infra-red (IR) light in the 700 – 800nm range) which is emitted by the plant. However, there’s lots of IR light coming from light, sun, and reflections in the room – so we have to filter that out to drill down the signal coming from the plant.

Robert came up with a clever way of getting rid of all of the static IR light from the sun or lights in the room, but we still had some left over which was coming from the very LEDs we were using to stimulate the plant with. In our large scale bench units, this is most often done with a series of optical filters which removes any non-desirable wavelengths from the measuring LED. But we don’t really want those in a tiny handheld unit – too expensive, too big, too easy to misplace. After looking through about 30 different LEDs, we finally identified a few which produced much much less IR – this significantly reduced the impact of a bad calibration and was a big improvement.

But that wasn’t enough πŸ™‚ We really want to use this tool even on very very weak or dilute samples, like Ben’s algal bioreactors. In this case, the sample being tested could be a very dilute solution of algae, which produces a really weak signal. With signals that small, even a very small amount of interfering IR can overwhelm the signal. In our tests, even with our fancy new low IR LED, the interfering IR was 2 – 3x larger than the signal itself. We even tried using lasers, which have very very specific emissions, with the hope you could eliminate this IR all together, but no dice.

Current unit in action (obviously the final version will have much fewer wires… and a cover

Soooo…. we decided to pursue a software solution. We decided to flash the plants with a very very weak 800nm light, which doesn’t cause them to fluoresce at all. BUT, our de

tector can measure the amount of the 800nm light reflected from the sample. Then, assuming that the IR generated by our measuring LEDs produces a similar level of reflection off the plant, we can estimate the interfering IR and remove it. Each sample will reflect IR differently, so by measuring every sample’s reflection using our 800nm light we can calibrate each sample as accurately as possible. Initial tests showed that the results were in fact more accurate than previously calibrations or no calibration at all. Yay! You can find that research report here (IR calibration method.odt is the openoffice text file) which goes into more detail.

Now we’re ready to dig into the Teensy and move away from the big and bulky LED and detector controller systems we currently use. More on that in the next post!

Greg

 

Measuring plant health across the world

Welcome!

Photosynq is a big project — we aim to create an open access database of plant health information from around the world by enabling researchers, educators, and citizen scientists to collect field data using their cell phones. Here’s how it works. We think we will be able to understand photosynthesis better, help plant breeders in developing countries improve their local varieties, create interesting and meaningful research opportunities to engage students and teachers, and enable bio-prospecters and travelers to find novel plants that might just help us solve our food and energy problems. I know, that’s a pretty expansive list, but check out a few examples of why this is a really neat idea.

We also have big dreams about the types of measurements we’d like to take – we already have a hand-held unit which can measure continuous or pulse modulated fluorescence (learn more about the science behind it here and here), but we plan also to measure other things which tell us more precisely how and where a plant is utilizing energy from the sun. Professor Kramer’s lab has been developing equipment to make these and many other measurements for over 15 years, so most of our efforts will be spent shrinking bench-top sized units to something that fits into the palm of your hand.

The current unit we’re working on now looks like this:

IMG_20130326_162036And here’s one on an algae bio-reactor.
Here’s a close up

It’s small enough, but it’s not quite designed correctly to be used with leaves and plants, and exposed electronics is never a good idea πŸ™‚ So we’re working on V0.2, which will be designed for use with plant leaves specifically, and will have a much smaller footprint. We’re using a Arduino clone called Teensy as the microcontroller (the thing that controls the LEDs and detectors) and any Android phone to display and collect the data. We’re hoping to use the framework developed by www.funf.org to pull the sensor information off the Teensy, store it, and display and analyze it in interesting ways on your phone and on the web. Hopefully, V0.2 looks something like this (except replace the iPhone with an Android phone):

 

handheld v0.11 with annotations If your really serious, you can track all the nitty gritty details here.

More soon,

Photosynq Team