PhotosynQ | Website Update

As we get ready to release the MultispeQ v1.0 we have been working hard in the background to provide an improved user experience. This includes visible changes, as well as a lot of changes in the background. Over the last couple of months we have updated the website, adding and updating features. Here is a brief summary of the biggest changes to https://photosynq.org.

1. Search

Now you can search not only through Projects, but also through Protocols, Macros, Discussions and Users. The searchable content is scored, so we can hopefully provide more relevant search results at the top of the list for you.
Further you can filter your search results for Projects, Protocols and Macros by their associated category.
Go to https://photosynq.org/search to try it out.

2. Discover

If you are new to PhotosynQ or you don’t know what to search for, take a look at the improved Discover page. Now you can browse Projects, Protocols, Macros and Users, and filter the results by category.
Go to https://photosynq.org/discover and get inspired by the work of others.

3. Help Getting Started

We have added a lot of content that we hope will help users get started with PhotosynQ and collect quality data. This content includes new and updated tutorials, a help center, and frequently asked questions.

A. Tutorials

Over the summer we started to make some new tutorial videos, helping you to get started with the platform and the new MultispeQ v1.0 instrument. We added some advanced tutorials on how to create a measurement Protocol, a Macro and how to do a basic analysis outside the platform, using R. Also, check out the ‘further information’ sidebar for downloadable pdf tutorials.
Go to https://photosynq.org/tutorials to see what we recorded for you.

B. Help Center

Along with providing more detailed tutorials, we have added a new help center that will guide you through: managing your account settings, creating a project, viewing your data, creating and editing protocols and macro’s and much more. We have also moved the blog over to the ‘learn more’ tab of the menu bar and replaced it with a link to the help center.

Changes in the navigation menu

C. Frequently Asked Questions

We often get asked questions directly by email and not through the forum. Because of that, we have started a collection of the most frequent and pressing questions. Over time we will add more questions and answers. Go to https://photosynq.org/faq to check out what we have gathered so far.

4. Data Viewer

We worked on the Data Viewer, improving existing features and adding new ones including adding thresholds and adding custom data in addition to the measurements you have already submitted.

Plotting data in the data viewer

  1. Now you can use create plots with up to four dimensions, adding marker size and marker color. The second y-axis has proven to be less helpful has been removed.
  2. Thresholds allow you to look into a subset of data, after you have filtered your dataset into different series. You can select thresholds for one or multiple parameters.
  3. The parameters are now sorted into Primary Parameters, Project Questions, Custom Parameters (if available) and Advanced Parameters, making it easier to find the parameter you are interested in among the many provided. Furthermore, this order of the parameters applies now to the columns in the spreadsheet view as well.
  4. New range sliders and a calendar are available to allow you to select a specific time and date range more precisely, especially when you have long term projects, or a lot of data over a short period of time.
  5. If you are looking at a single measurement, you can now easily navigate to the next / previous one. The small map indicating the measurement location now shows a bigger section with topography as well as latitude and longitude.
  6. New data types can be used, allowing you to display arrays as sparklines when you are looking at a single measurement. Furthermore, colors can now be defined as hexadecimal, RGB and RGBa, allowing you to use them as coloration in your plots or for your map.

5. Additional Data

Some experiments are going beyond data collection in the field with the MultispeQ or other instruments. Now you can add more information to each measurement after you took them (e.g. yield), as long as you are the project lead. This data is kept separate from the original measurements and can be altered at any time, in case you want to change, remove or add information.

additional data upload

6. User Activity

Previously, your user profile mainly presented a number of stats about your activity on PhotosynQ and the Projects you are involved in, either as a Project Lead or a Collaborator. Now we have an Activity feed, which displays the last 100 important events relevant to you on PhotosynQ. You can see if others contributed to your Project, if somebody posted a comment or question to one of the Projects you are involved in and of course everything you did, so you can more easily navigate to what is important for your workflow.

7. In the Background

One of the biggest changes is the work done in the background. Before the update, the original data for a Project was loaded into the Data Viewer and processed on your computer. Now, we do this step on our server and send you only the results from the calculations. As a result, the amount of data sent to you is reduced to 10–15% of its original size, allowing faster access to Project results.
Updating the calculations for a parameter? No problem, since your data gets re-analyzed when you view it after the changes, so you are always up to date.

Production progress: 250 units

Today we started producing the first 250 of our 500 initial production batch at Saline Lectronics, a contract manufacturing company out of Saline MI.  No major hiccups, though we had one or two LEDs which were switched and a filter which was incorrectly sized, but those are fixable in the next day.  Luckily we found them after the first 30 units, and not after the first 500 🙂

We spent most of today prepping the case itself (as you can see in the picture), and did a dry run of a single unit through the entire process (from assembly to calibration) to ensure we had everything we needed.  Bluetooth continues to be challenging (connecting mostly), and it’s now my least favorite communication standard by far!  But once you get it connected once it gets easier after that.

Expect to see more updates in the next few days as we continue to move forward.  The current estimated ship date is March 3rd.  If there are problems or setbacks I will update you as soon as they happen.

Thanks,

Greg

Production Update

I was hoping to have more specific information for you guys before creating this post, but we need to provide an update either way.  Here’s the update:

  • The bluetooth module was mis-shipped again (yep, not kidding).  So we managed to find a local supplier.  This time we confirmed it’s the right part by ordering it and installing and testing it first.  The expected delivery date for the full quantity we need is Feb 10th.
  • We are waiting on a response from the factory on when we fit into their schedule once those modules are delivered.  We have been planning on late January, so they’ll need to adjust their schedule to get us in in mid February instead.
  • Everything else is in place to fulfill all of the pre-orders.  Specifically, we have:
    • All parts except the bluetooth module
    • Factory calibration process for each device
    • Factory Assembly instructions
    • Other packaging (instructions, box, etc.)
    • Confirmed precision and range of key measurements on a a subset of 10 – 15 devices
    • Updated website and android app

As soon as we begin manufacturing, I’ll update the blog again with details, progress and pictures.

Thanks everyone for your patience and support.

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+.

Selection_999(121).png

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.

Selection_999(108).png

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.

Selection_999(158).png

  • 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 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 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

 

PhotosynQ in the news: Malawi

This is a nice story about the potential for collaborative plant research in Malawi, our partners, and the kinds of connections that form in large open research groups.

link: https://prl.natsci.msu.edu/news-and-events/news/photosynq-helping-malawian-farmers-increase-yields/

More Production Delays

Well, it’s July and you still don’t have units.  That’s our fault, we’re learning as we go and you’re the one who is impacted by that process, and we’re sorry.  We have tested several complete working prototype V1.0 devices in the field, thousands of measurements, and they work great (almost better than expected), and I think you’re really going to like them.  So that’s a plus.  But if devices aren’t in your hands when you need them this doesn’t amount to a hill of beans.

Right now, we are still at a minimum a month away, probably more.  We’re doing everything we can to speed up the process – that includes 1) rush ordering circuit boards, 2) working directly with (ie setting up shop at) the manufacturer to try to reduce lag time to troubleshoot questions about the circuit board, 3) and ordering/preparing everything we possibly can before we have final circuit boards are completed.

We’ve been collecting a lot of data here on test plots, and we’ll be sharing what we see so far soon.  I hope this will give you peace of mind – it certainly does for me 🙂

We’re working really hard to get these things out, and we really appreciate your patience and support,

Greg