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.

CoralspeQ Beta, The next generation — a short update

CoralspeQ new boards
New boards!

We have just received the brand new boards!  We have been working on this since last year.  It took longer than we anticipated, because both Dave and I kept adding the features (“we want a laser,” “more LEDs,” “we need longer wavelengths,” “I found this cool LED. Can you use it?” & etc.).  I truly appreciate the patience of Robert and Chris.  We surfed through the wave of holidays, and finally, the initial trial electronics boards are here.

The new board is largely modified from the MultispeQ V.1 board, and the idea is that it will be used not only for the CoralspeQ, but also for other instruments currently under development. GrainspeQ is one of them.

It will still take time to build a complete CoralspeQ Beta. I hope I could update again soon.

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.

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!

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/

PhotosynQ Workshop details + videos

We had our first PhotosynQ day-long workshop on April 22nd at Michigan State. We had over 90 attendees, 9 breakout sessions ranging from education to data analysis, and posters from 12 beta testers.  You can see almost all of the main and breakout sessions on our YouTube Channel.

We discussed everything from abiotic stress, what photosynthesis parameters mean (there’s a nice overview by Professor David Kramer in there which I’d suggest), the new features coming in the MultispeQ V1.0, alternative uses of the platform for microbial detection and measuring coral bleaching, use of the MultispeQ in Africa, and lots lots more.  Definitely check it out!

CoralspeQ Prototype 2.0 update

After the field test in Hawai’i  (updates on g+), we have been working hard to modify both the hardware and software of CoralspeQ. Now five new instruments, PT 2.0, have completed, and distributed. Chris Zatzke has re-joined us after graduated from MSU, and working on every aspect of the instrument construction – electronics, machining, programing and testing.


IMG_0977IMG_0970FullSizeRender (9)

 

 

 

 

Since we are still using the same ready-made case, it looks same as you can see in the photo, but the quality is improved. Chris made a holder for the electronics board that fits snuggly inside of the case, and reorganized the magnetic reed switch and batteries. Therefore, no component would move around inside by the impact of transportation. The light guide is shorter and the distribution of light is more even, thanks to the suggestion by Jeremy Brodersen. Production of light guide was well established now by Geoff Rhodes and Chris Zatzke. Now when the CoralspeQ is turned on and connected through Bluetooth, you can see the LED lighting up through the window. It is more user-friendly.

It took some time to improve the signal quality with light sensor using the light intensity at the sample level. This involved the modification of both protocols and firmware. This part was hugely contributed by Dave Kramer and Greg Austic. Also light calibration was repeatedly done by Chris Zatzke with helps from Dan TerAvest and Robert Zegarac.

As this batch of CoralspeQ is out, we have already started making the next set. We are introducing the inductive charging system, and it will be no longer necessary to open the device for charging the batteries.

Sebastian Kuhlgert informed me that they are implementing the images as a part of the questionnaire when you take a measurement. Even if you do not know the name of the coral you are measuring, you could select and tap the image, and it will be recorded along with the signals. Operating a phone under water is not an easy thing to do, even if you know the name of the coral. Tapping on an image, and pushing one button to start measuring is our goal in the near future.
As I write this blog, one more major improvement is going on. We are trying to add the analysis tool to the PhotosynQ web site. Dave has been compiling the analysis program, and now with his suggestions/guidance, Sebastian and Greg are working to add it so that we could see the Phi2 value and the colors of the coral besides the raw data. This process includes not only the coding, but also yet another firmware change, while we need to re-distribute the memory usage for the device. But we are almost there!

By the way, Global Center for Food Systems Innovation at Michigan State University posted a story about PhotosynQ/CoralspeQ project. That’s right! That’s why there is a picture of Godzilla in this page. Please find our story at their website here.  We also had the first PhotosynQ Workshop on April 22. I am sure Greg will post the story soon.

— Atsuko

Updates, and MultispeQ orders now public!

We had a slew of activity this last week I want to share, so here it is –>

Now anyone can get a MultispeQ

The MultispeQ is now publicly available at www.photosynq.org/buy-multispeq!  So if you’ve been itching to tell people about it but you’ve been holding back, feel free to forward that link along 🙂 .

Solder, test, repeat

Robert soldering a MultispeQ v1.0 board
Robert soldering a MultispeQ v1.0 board

We are testing the new MultispeQ circuit boards right now.  Our hardware team (Robert, Jon, and myself) hope to have a working version ready in the next week or two.  The new board is very similar to the beta in some ways, but has many added components and upgrades – we went from 180 components in the beta to about 275 in the V1.0!  The firmware (written in c++) is also similar but not exactly the same, so we have our work cut out for us in the next month to get everything ready

As soon as we have some outputs from the new board you will receive updates.

PhotosynQ at the Organic Seed Conference

If any group was collaboration-inclined, it’s the community of breeders, both professional and  hobbiest, in the organic seed community.  There are a number of really great projects which I wanted to point out as sources of inspiration for what we feel is coming in the next 10 years both to plant breeding, but also to extension and farmer outreach.  These guys share a vision with our project in terms of expanding involvement in and access to the creation and collection of information in agriculture.

Last year, Nate from Experimental Farm Network organized 300 people to take part in a range of research projects.  EFN acts as a matchmaker, helping to connect individuals who are capable of taking part in research efforts (growing plants, following directions, collecting data, and returning seed) with those who have research.  You can join as a collector or as someone with a research project here – http://experimentalfarmnetwork.org/

 

http://labs.russell.wisc.edu/organic-seed-potato/

I also talked with Dr. Ruth Genger, who runs the Organic Potato Project in Madison Wisconsin.  She’s working with ~25 farmers to both collaboratively select for traits, and build seed stock for, new organic potato varieties.  This is one of the best examples of participatory breeding, a phrase I didn’t know but heard a lot at the conference.  For their blog and more info – http://labs.russell.wisc.edu/organic-seed-potato/

 

I was really impressed by the Culinary Breeding Network, out of Oregon State.  They integrated the opinions of chefs and the public into the breeding program in a way that I’d never seen but which made so much sense.  They brought chef’s to the field, and had tasting parties in Portland, basically anything to better connect consumer to breeder.  This kind of thing should be integrated into any breeding program of crops which are bought and consumed directly by human beings (like not cow corn, but maybe sweet corn 🙂

 

IMG_20160204_165335The folks in the Barley Breeding Program at OSU are passionate about barley in a way I’ve never seen (http://barleyworld.org/) .  They have their own malting machine, and they also have tastings and get lots of public feedback.  I came out pretty convinced that barley is the grain of the future!

 

Overall, I think other land grant universities (*cough* M *cough* S *cough* U *cough*) should follow the lead of these kinds of highly collaborative, integrated breeding programs.

more next time!