So now that production is in process (moving along, we had a minor hardware patch to apply so we’re waiting for a new shipment of boards, but we’re all ready to crank out boards otherwise) and we feel good about the core measurements of the MultispeQ, we decided it was time to see if we could easily slap on other sensors into the PhotosynQ framework. First up – the YwRobot’s Soil Moisture sensor (actually, soil conductivity, but we’ll get into that later. Let’s start by talking about how to connect to MultispeQ and what tools can be connected —
2 digital pins and 1 analog pin through-hole pins.
10+ analog pads which are not through hole
3.3V line and ground
So the simplest device to connect is anything which outputs a 0 – 5V signal. Our YwRoboto sensor does just that!
Soil Moisture Background and Experiment
Measuring soil moisture can be approximated by measuring soil conductivity. Conductivity is influenced by the movement of ions in the material between the electrodes – see image below for what the device looks like. So for a given soil type, more water increases the movement of ions. However, it is very difficult to compare different soil types, because they will have different concentrations of ions and therefore different results. So this is useful for relative soil moisture changes in a single location (like your house plant), not in different locations (like different fields in different soil types).
In our quick and dirty test, we made a matrix of 4 soil types x 3 moisture levels (from high to none) which you can see in the image below. We connected the pins between the moisture sensor and the MultispeQ as follows:
MultispeQ (Teensy 3.1) Pin
The communication protocol between the PhotosynQ chrome app (or Android app) and the MultispeQ is in a JSON format. In order to request the information from pin A14 (also referred to as pin 40), just add it to the JSON. Below is an example simple JSON which requests temperature, relative humidity, and the analog read from pin 40. It also specifies to take 2t00 measurements with a 2 second delay between them:
You can also create this protocol using menu-based drag-and-drop tools through the Chrome app, but I thought I’d give the details here so you could see it.
Initially, I compared soil moisture in each of 12 samples above. Here’s what I got:
As you can see, the 6.5ml water addition versus dry doesn’t show a consistent positive correlate, which doesn’t make sense. I think it may be due to the fact that I had to take out and put back in the probe each time. So I just tried placing the probe in soil, and adding moisture to the surface without affecting the probe. These results were much closer to what I would have expected:
Overall, this sensor definitely relates to soil moisture, and the completely saturated cases of different soil types even show similar absolute response (about 45k counts). However, at less than saturated levels, soil conductivity varies quite a bit between the different soil types at least from this quick little introductory test so probably soil moisture can be accurately measured at a single location.
In terms of integrating this sensor into PhotosynQ, it was pretty easy. Connect 3 pins, add one small line to tell the device to look for it, and vioala – graphs!
The next step is to actually stick this thing into my yard and see what happens. We’ve been talking about trying to pull in weather data into PhotosynQ so you can correlate and analyze that in addition to the sensor data, which would be particularly fun here. Also, I think there is a new version which is gold plated and therefore much more robust which I’ve already ordered to play with. Finally, I should create a real research project (which others can join and participate in) out of this, instead of just taking one off measurements. Then we can see how the PhotosynQ online analysis tool could be useful to analyze the resulting data (see here for example of recent data taken in bean fields in North Dakota – please be patient while the data loads!).
If you’re a beta tester I know you’ve been waiting forever, but believe me when I say we’re making great progress. We now have the capacity (human and machine, for details keep reading) to make the 80-odd required devices for the beta. We also have the quality specs necessary to make those units useful for you (calibration and comparison to known devices, for details keep reading). We also have some great software tools for analyzing and sharing data quickly, easily, and (dare I say) beautifully. Now we just have to crank them out. Stay patient, we’ll get there soon.
Detroit Maker Faire
PhotosynQ was on display at the Detroit Maker Faire! We took about a hundred measurements all around the faire, and had our very own tee shirts (see picture). We met all kinds of folks, including educators like Melissa from Tinker Tailor, the guys putting together a new makerspace in Lansing called Innovation 5, and we were located right next to Josh and the fabulous folks at All Hands Active where he had is Soil Cam 9000 on display – I absolutely love that thing. We are just itching to get our first real beta units out into the world to folks like this to see what we can discover together!
3D printer up and running!
We recently bought a SeeMeCNC Rostock Max V2, and it is awesome! It took some adjusting and Jake’s been working on it for about 3 weeks now, but I’m very pleased with the quality and relative simplicity. That beings aid, let me share some lessons with you:
First things first – adjust the z thickness to it’s as big as possible but still sufficient for your project, and make sure the first layer is fairly thick to help it stick to the bed.
Make sure you include the big circle of abs around your part first, so the abs has a chance to stick to the plate (we smear glue on the plate as suggested by SeeMeCNC to get it to stick, that works well).
For anything more than the smallest, simplest parts, you ABSOLUTELY MUST enclose the machine to prevent heat loss. The bed will heat up to only about 90C, which just isn’t hot enough to prevent warping of parts. It’s not shown in the picture, but we’re building a plexiglass case to completely enclose the whole unit – this helps the bed get up to 105 – 110 AND it keeps the printed piece itself warm so that warping isn’t an issue. We struggled with this for a while. We tested it by covering it in cardboard, so if you don’t want to get plexiglass don’t worry, there are cheaper options:)
We’ll be using this to print the cases for the beta units. We’ve tested making all of the different case components and have successfully achieved the necessary tolerances, so now it’s off to the races!
Pick and Place machine up and running!
FINALLY. The pick and place saga has ended. We initially attempted to order a Madell Technologies DP2006-3 way back in DECEMBER OF 2013! It has room for up to 100 parts, separate machine vision on the pick and the place, runs at ~2000 parts per hour and is under 20k with all the bells and whistles. MSU purchasing took forever to approve the purchase, then once we got it over a month ago our great undergrads Chris and Jake have been pulling their hair out to get it installed and working. It hasn’t been easy. We’ve had numerous issues setting up the machine, some our fault and some their fault, and while it’s taken a long time to get this thing working I can’t say Madell hasn’t been responsive – in fact their customer service is amazing. However, the number of bugs and issues with the device has definitely required that support, especially as it relates to the software and computer vision system. For anyone thinking about buying this machine, two things: 1) just get everything preinstalled including computer and vacuum pump (unless your time is worth $1 per hour, just let them do it, trust me here), 2) lights, lights, lights, get lights everywhere, pretend your creating a photobox to take product photos, no shadows and super bright lights, the machine vision system is finicky and the most lights the better! and 3) expect at least 3 weeks for install and testing.
ANYWAY, it works and now we can produce at a minimum 10 boards per day, so that is no longer the limiting step in our production chain.
Calibration, calibration, calibration!
Note: For your calibration nerds out there, there’s no graphs below – sorry about that. We’re just now at the point that it’s worthwhile to start really graphing our calibrations and comparisons to commercial instruments. Expect to see that data in the near future.
One of the big reasons for delay in releasing the MultispeQs is the process of properly calibrating the outgoing units. Initially in our zeal to hit self-imposed deadlines, we sent about 15 units of varying quality stages of development to beta testers. While we did learned some important lessons, we felt they were very time consuming both for us and the users. So the next 15 units that go into the world are going to be calibrated to commercial equipment AND calibratable (ie users can recalibrate as needed). We’re focused on the two most demanded measurements – chlorophyll fluorescence (that includes calculating fv/fm, fs, fm’, Phi2, qE, qI, NPQ, and all the other related acronyms), and SPAD (a measure of greenness similar to NDVI originally created by Minolta).
Chlorophyll Fluorescence Phi2
In our initial comparisons with LiCOR 64 (a top of the line fluorometer costing about 50k), LiCOR would say .85 and we would say .74 or so… this was too large of an offset to be acceptable. We made some adjustments and added a new offset due to electronic noise and addressed some background IR light which was bumping our signal higher than it should have been. After that, we were within about .02 of the LiCOR… I wanted to improve more, until one day during testing the LiCOR itself decided to show values about .05 higher than it had the day before for no apparent reason. Jesse Traub, my partner in calibrating, couldn’t figure out the issue, but said after looking back at his data that this kind of variation wasn’t uncommon. After that, I decided that .02 is easily within the variation of any given instrument.
We’ve been measuring SPAD successfully for 8 months, but we have this persistent issues of showing a little more than double the ‘normal’ SPAD meter value (SPAD shows 45, we show 110, for example). The correlation with Minolta SPAD values is excellent, but the raw values are always about double. So last week, we tried to get to the bottom of this. First, what is SPAD? It measures absorbance through a leaf at two wavelengths: 650 (red) and 940 (infrared) (see here for Minolta meter and description and here for manual). To calculate SPAD, you have to take a blank value (no leaf) as a baseline. If we call the blank absorbance 650 and 940 and the leaf absorbance 650′ and 940′ respectively, then you calculate SPAD in the following way:
SPAD = Log ( 940′ / 940) / (650′ / 650 )
So, we tried getting these values using a normal spectrometer – surely that would give us Minolta-esque SPAD values… but no! It was consistent with our values (in the 130 range)… we tried many other things I won’t go into here (using Ln instead of Log, reducing lost light in the MultispeQ, etc etc) but kept getting the same answer. Then Sebastian looked into the original SPAD manual from Minolta to confirm how they are calculating SPAD, and here’s the description:
The values obtained in steps 1 and 2 (940′, 940, 650′, and 650) are processed to calculate the SPAD value, which corresponds to the amount of chlorophyll present in the sample leaf.
In other words, they don’t say!! Argh! So who knows what they do or how they calculate it, but it sure seems that for some reason they are multiplying the actual value by some factor to get it to land in the 20 – 60 range. So, we’ll do the same thing, and we’ll have great, consistent SPAD values!
Finally, there’s actually immensely more to the calibration thing than I’ve mentioned here. Once things have settled and we’re sure we’re not going to be changing things a lot more, I’ll document exactly what gets calibrated when and how in more detail.
Light Intensity PAR (Photosynthetically Active Radiation)
In order to measure Phi2 (photosynthetic efficiency), it’s important to have an accurate light sensor. PAR is only the portion of the spectrum which plants can absorb – about 400nm – 700nm. This is surprisingly tricky to measure! There are many very good and accurate light meters available, like the TCS light sensor available as a breakout board from Adafruit. However, their either measure too light (from 420 – 650) or too much in the case of the other TCS sensors (from 400 – 1200). So decided to go with the TCS 34715, which has a broad range from 400 – 1200nm, then adding a hot mirror to eliminate any light from 700 – 1200nm. This, combined with a tighter case design, resulted in a pretty accurate PAR sensor, which if you compare to LiCOR is currently within about 10% accuracy (LiCORs PAR sensor alone costs $500!). Users can recalibrate the sensors if they change over time.
Using the MultispeQ with the Chrome app
Our initial idea for using a MultispeQ fluoromoter was an Android app, so that people can use the device in the field. However, we quickly realized that we also needed a desktop solution so we began working on a Chrome app. Now, 76 commits later, we almost have a version, we feel comfortable with, so you can use it. The developer version is on Github (https://github.com/Photosynq/PhotosynQ-ChromeApp). We spent a lot of time on the UI, to make it as easy as possible to work with the app. It not only includes measurements, but also the tools to give you the ability to design your own measurement and programming little code snippets called macros to evaluate your measurements. Right now we are trying to finish the help section, the script generator and the missing communication pieces with the database. And of cause, we are trying to catch as many bugs as possible before the first release. Almost a 1000 test measurements have been done with the very early units and saved to our website, using the chrome and the android app. We’d like to thank everyone testing the software at this very early stage and helping us improving it. — Sebastian
Here’s some key features in the Chrome app (also see images below):
Taking measurements for projects, including user specific answers.
Selecting measurement protocols available from photosynq and run them.
Using the console to communicate with the device if you’re getting an expert
Manual control for instant measurements, recording environmental parameters with just one click.
Drag ‘n drop tool to build measurement scripts
Programming tool to build macros to evaluate measurements
Data viewer to look at locally saved data.
Measurement and image caching for offline work
User sign in Notification log
Location service Device information
We’re redesigning the Android App to be more user friendly and faster, especially for breeders and those performing hundreds of measurements per day
Expect to see a complete redesign of the website, and the merging of our database site and landing page. Finally, we’ll have a coherent face to present to the world – thanks Venturit!
We’re hiring Geoff Rhodes to manage the assembly and shipping of MultispeQs to beta testers and collaborators. He’s also going to be working on calibrating devices and developing new methods. Expect to hear more from him in the future. Also, we’ve had Jake Nuremberg and Chris Zatske working on the project, and we’ve added all these fells to our collaborators page if you want details on their awesomeness.
Phew… 48 hours normal hours and 24 standing-on-your-feet-talking hours later and Maker Faire is over. We met hundreds of people, got to use the MultispeQ about 200 times (good opportunity to test the heck out of it), saw lots of other awesome projects like Manylabs, Nerds for Nature, Fusion, Pinoccio and others, met some good potential partners, and got editors choice aware (see picture)!
I could go on about a lot of aspects of the Faire, but my favorite part was the sheer number of ideas people about what to do with a MultispeQ. For example:
“Hey, could you stick this thing on a drone” (a very common one, people want to stick everything on a drone nowadays)
“You should sell these things to Lowes so they can check the quality of their nursery stock as they come through the door, so they can reject bad plants that may, visibly, still look ok”
(from developer at Pinnocio) “What if you put a plant on a wheeled robot, and as the plant became stressed the robot moved it to higher or lower light – it’s like bionic limbs for plants!!!”
“What if you could measure toxins with it? Then, you could crowd-source identification of plants which are particularly good at absorbing toxins from the ground to use for environmental remediation”
(and many many others)
Still have lots of follow up to do, but overall it was great.
In other news — 15 units have shipped! …
We have shipped 15 units to Costa Rica, NYC, Mexico, Kansas, and even Malawi! They have all been hand assembled, which is a serious effort (takes about 1 day to assemble and test 1 unit) so we don’t really want to go full steam ahead until we have the pick and place machine up and running. That’s on the docket for this week. Once that’s complete, we should be shipping much faster.
Next time we’ll go more in depth about the online analysis tool, the data collaborators have collected so far, and maybe some data on new measurements we’re working on.
Robert, Sebastian and I are here at the Bay Area Maker Faire in San Mateo. We spent the day today getting our PhotosynQ booth ready, and putting last minute touches (well… more like frantic last minute working) on the experiments we’re running during the Faire. Since it’s late and I’m sleepy, I’m not going to write much but just show a bunch of images from our day. Tomorrow and Sunday we’ll have more data from the measurements inside the Faire itself.
If you want to follow us tomorrow, check google plus for #photosynq, we’ll try to post throughout the day.
Sorry for the long delay between posts. There’s lots of expectant beta testers waiting for us to get units out so we need to keep up good communication.
Though a bit late, we have shipped the first few beta (very beta) units! One took measurements of wheat fields in Mexico as part of the Poland Lab, while one is on its way to the Arctic, with two more staying behind at Columbia University for testing by the Griffin Lab. These units were a bit rushed, because of time constraints, but overall we learned a lot from the experience. The pick and place machine has FINALLY been delivered (see image), so that will dramatically speed up our production of the circuit boards and therefore shipments of the MultispeQ. Will have more news on that soon.
Also, I want to let everyone know that we’ll be at many a Maker Faire this summer, starting with the Ann Arbor mini Maker Faire May 10th (already happened, it was awesome), then the Bay Area Maker Faire in SF May 17th and 18th, and finally the Detroit Maker Faire July 26th and 27th. We’ll have devices on hand and we’re going to try to run mini experiments at the Faire which should be a lot of fun. If you live nearby, please come and check it out!
Ok – here’s a recap of what we’ve been working on since the last post:
1) Power consumption and power on/off. Yes, the devices need an on/off switch (duh), and we didn’t really plan for that until recently. Robert (on the second try) designed a very nice switch, which also includes the ability to shut down power via bluetooth or serial communication, which will allow the unit to save power and prevent users from draining the battery. It has another switch for a low power mode which further saves power.
So I’m very happy to say that we’ve done it! Rather than write about it, I put together a quick video showing the different components, and how they connect. Note – the UI for most of this stuff isn’t completely finished, but all the key connections in place so that projects, measurements, macros, and users truly synq together.
3) Data caching – no need to always be web-connected. All of our first few users required that the device would still work even when not connected to the web. We knew this was important, but were planning to push it off down the road – needless to say we got it done. Now, if you’re in the Amazon rain forests and you want to still take measurements as part of your “Bioprospecting for amazing plants!” project but you have no internet, not problem – the data you collect is cached in the phone and sent to the database once you arrive back at camp (or wherever you have wifi).
4) Improving chlorophyll fluorescence measurements. Making better measurements and calibrating the device will be an ongoing process, but we made some important improvements to the Phi(II) measurement, which is often used in other comparable instruments including the ‘gold standard’ LiCOR. Phi(II) requires that the ambient light is measured, and then that light intensity is mimicked inside the leaf chamber, so the leaf can’t tell that you just clamped it receiving the same amount of light. We calibrated the light intensity sensor and actinic lights and managed to get it working. It’s fairly rough, with only about 20 light levels between 0 – 2000 uE and some minor variation between devices, but it works pretty well.
On the horizon
1) Finishing touches on the data analysis tool. Sebastian made an awesome data analysis tool that we can’t wait to get into the world, but it’s been slow integrating it into the new website.
2) GPS data for all measurements. Right now, GPS data is not included in the Android app – so you can’t make awesome maps of everyone you’ve taken measurements. Obviously, we need to fix that.
3) Enabling users to create custom measurements. Currently, only admin users can create custom measurements (aka protocols) and macros.
4) Easy measurement creation tool. If users will be able to create their own protocols and macros, then we need a nice UI to make it simple and intuitive, as the syntax of communication with the device is, well, not very pretty or intuitive. Sebastian cranked one out last week, and it’s a really good start. Here’s a quick snapshot of what it looks like so far. You drag and drop the variables, change the settings, and viola! you have a protocol JSON which you can use in your next project. This is pre-release but it’s moving fast, hope to have it up in a month.
5) Real-time data logging for environmental measurements. Though designed primarily as a handheld device, you can do long-term data logging with the MultispeQ. As such, Sebastian included a real-time data logging feature in the Chrome app. So if you’re measuring CO2 over the course of a day, you can see each measurement as soon as it’s created and graphed before your eyes, instead of having to wait until the very end of the day.
6) More direct applications for MultispeQ measurements. As a lab of researchers who study photosynthesis all day, the question of “so what can I DO with all these measurements?” sometimes falls on deaf ears. But we’re working to change that by identifying more concrete and clear use cases for chlorophyll fluorescence, SPAD, and other measurements taken by MultispeQ. Professors Dave Kramer and Wayne Loescher have identified a pretty clear relationship between drought tolerance in beans and a special type of chlorophyll fluoresence measurement which is pretty easy to take. This
could be extremely useful for breeding applications, as you could select for varieties of interest much earlier in their life cycle.
Finally, I want to say thanks to Chris and carrythewhat.com who’s been shipping us MultispeQ cases he’s been 3D printing, and has helped make sure that our cases are 3D printable on a standard plastic extrusion printer (rep rap, maker bot, etc.).
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.
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
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,
compact dispenser Washing brush into, after buy viagra online noticed 15-20 than on of leave numerous.
and whatever else he thinks you may find interesting. You can see his RSS feed here, or follow him on Google
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 –>
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!
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.