Recording interesting observations in the field with PhotosynQ

The field data collection season is just getting started here in the USA. I thought this would be a good opportunity to highlight a feature in the app that may be useful when you are out collecting data: adding notes and photo’s to PhotosynQ measurements.

You never know what you are going to encounter in the field, so when you encounter something worth noting, you need a space to do so. For example, maybe you notice disease symptoms or insect damage on a leaf that you want to record. Or maybe you want to note that the plant you measured appears to be dying.

Adding notes and photo’s in the mobile app

There are two ways to add notes and pictures to measurements: 1) add a picture or note question to your project using the project creation tool or 2) add a note or picture to a completed measurement, before uploading the measurement to the website.

The first option requires that you take a picture or add a note for EVERY measurement. If you take a lot of measurements with photo’s attached, you may notice that your data loads slower in the data viewer. You may also notice that all of your photo’s look quite similar, and may not add much value to your project. Who wants to slow down their PhotosynQ project with 500 nearly identical pictures of soybean leaves?

Another option is to only take notes and pictures when there is an interesting observation you want to record, and you want to limit these pictures or notes to JUST interesting observations.

In the mobile app, you can add notes to any completed measurement as long as the measurement is not submitted. Here’s how:

  1. Navigate to the Measurements tab in the app. After you Accept a measurement you are automatically directly to this screen.
  2. Select the measurement that you want to add a note or picture to.
  3. Once you have selected the measurement of interest, a new top menu will provide you with options to add a note, delete the measurement, upload the measurement or take a picture (from left to right, below).
  4. Complete your note or image and select Save note or OK for a picture.
  5. Upload your measurement.

Notes image

Viewing notes and photo’s in the data viewer

You can view your notes from the data viewer in the individual datum view or through the spreadsheet tab. In order to view notes or pictures in the spreadsheet view, click on the More menu at the top of the spreadsheet and check the boxes for what you want to see in your spreadsheet.

view notes post

*You can also add notes and photo’s to the desktop app, see the help article here

PhotosynQ Focus: Isaac Dramadri

Focusing on how the community is using PhotosynQ technologies. This month we are highlighting Isaac Dramadri, who just completed a PhD program in Plant Breeding and Genetics here at Michigan State University.

Isaac Dramadri was another of our early adopters, who started experimenting with PhotosynQ way back in the fall of 2014 (not to be confused with Isaac Osei-Bonsu, who we profiled here).

Not only was Isaac one of our earliest adopters, he has also been one of our most active users. Since he began experimenting with PhotosynQ, he has collected over 38,000 measurements. That accounts for 5% of all measurements on the PhotosynQ platform!

Isaac came to MSU from Uganda in 2013 to pursue his PhD, which he recently completed. Congratulations Dr. Dramadri!

He began in the greenhouse at MSU, attempting to identify drought tolerant lines in a common bean breeding population. In 2016, he took some MultispeQ Beta’s on the road, introducing PhotosynQ to scientists at the Makerere University Regional Centre for Crop Improvement (MaRCCI) and national agricultural research services. In 2016 and 2017, he conducted field trials at multiple sites in Uganda, collecting photosynthesis phenotypes from hundreds of common bean lines.

The PhotosynQ platform generated a lot of interest in Uganda, where inexpensive options for high throughout in-field phenotyping technologies are limited. This eventually led to a broader collaboration between the Kramer Lab and MaRCCI.

The overarching goal of Isaac’s 3 years of MultispeQ use was to link photosynthetic traits to other agronomic traits and drought recovery in common bean. His preliminary results have shown that it is possible to use PhotosynQ parameters to identify quantitative trait loci related to drought tolerance. This is exciting and we can’t wait to see more of his results as he publishes them in the near future.

Isaac has now returned to Uganda as a cowpea breeder, and we are sure we will continue to work with him. Good luck Isaac!

Connecting the PhotosynQ Community

We have built numerous tools to facilitate discussion among the PhotosynQ community. In this post I am going to give a brief rundown of these options. All of these options have been present on the platform for a while. However, we have recently updated some of these features and have not actively promoted other features. So, here is the tour…

Forums

We have recently updated the forums, making two significant changes. First, we changed the forums homepage. Now you can see all of the available forums (left) as well as the most recent activity on the forums (right). Second, we added a new “Measurements, Protocols & Macros” forum. Those of you who posted on the forums may notice that we moved some of your forum posts into this new category.

Have a question? Looking for tips or support from the PhotosynQ community? Please visit our forums!

Forums

Project Discussions

You can have discussions within a PhotosynQ project. This is a great way for all of the project collaborators to communicate with each other. It can also be a good way for people who are interested in your project to reach out to you. Project discussions are accessible from your project page on PhotosynQ.

Discussion

Protocol and Macro discussions

The ability to comment on protocols and macro’s gives you an opportunity to interact with the creator of that protocol or macro. Each protocol and macro on the PhotosynQ platform has its own page where you can comment (below left) or you can post comments from the desktop app (below right).

Protocol discussion

Update for Photosynthesis RIDES users

We have identified an error in the Photosynthesis RIDES macro, which is used to process the data from the Photosynthesis RIDES protocol. If you were using this protocol you may have noticed that your NPQt values were a bit higher than expected, or your PhiNO values were a bit lower than expected. This was due to an error in how we determined Foprime, which is key in calculating these parameters.

The good news is that the PhotosynQ platform is built to allow users to correct issues like this, and apply it to data that you have already collected!

We have now changed the macro to correct the error. So, the next time you go to one of your Photosynthesis RIDES projects, you will see the prompt below asking if you want to recalculate your parameters based on updates to the macro. If you choose yes, the updates will be applied to your data. If you choose no, your data will remain in its present form.project updates

PhotosynQ Website Update and New Features

We’ve updated the PhotosynQ website and added many new features to improve your user experience!

Some of the new features include: expanded plotting, mapping and graphing data options, improving the user page to help users better track their PhotosynQ projects, protocols and macros, and adding more content to the tutorials and help center.

We will be detailing these new features in blog posts over the next two weeks, but let me briefly explain a couple of the updates:

Tutorials

Two area’s where new PhotosynQ users seem to struggle are with creating robust projects and cleaning up their data prior to data analysis.

Project Creation

Since we began shipping the MultispeQ v1.0’s over 9 months ago we have seen a drastic increase in the number of PhotosynQ projects that are being created. Which is really exciting! Occasionally, we’ll check out new projects to figure out how people are doing with the platform and try to come up with ways to improve the PhotosynQ experience. We have noticed that setting up projects has been a problem for many users. The most common problems are choosing the wrong measurement protocol or not asking good project questions, which then makes filtering, analyzing and interpreting data difficult.

So we have added a Project creation tutorial to better guide users through the process.

Data Quality

Recently we published a blog post about how to Flag data to improve data quality. This is an important step in getting the most out of your PhotosynQ project. In our default Leaf Photosynthesis MultispeQ v1.0 and Photosynthesis RIDES protocols we add issue warnings that help identify measurements that may have technical issues, but many people are unfamiliar with what these mean. So we have also added a Data Quality tutorial to explain issue warnings and data flagging.

Help Center

If you have ever visited the help center you may have noticed a little poll at the bottom of each post asking if the article was helpful or not. Well, believe it or not, clicking those buttons actually matters! We have updated a number of help articles to be more helpful and have added numerous articles.

That’s it for today, but stay tuned! More details about new features will be coming soon!

 

Building Strong Research Collaborations

If you have ever visited the PhotosynQ webpage (you’re reading the PhotosynQ blog, so I’ll assume you have), you know that the banner across our homepage reads “Truly Collaborative Plant Research.”

We have always aspired to making PhotosynQ a flexible platform to accommodate many forms of collaboration. For example, we hope the open nature of PhotosynQ data combined with built-in discussion tools will foster communication and collaboration between researchers across the globe.

I recently returned from Uganda, where I conducted some training workshops and (hopefully) established a long-term collaboration between PhotosynQ and the Makerere University Regional Centre for Crop Improvement (MaRCCI). Before my trip, MaRCCI had a few MultispeQ devices, a few students had used PhotosynQ, and they have even published a few papers. However, until now, there has been little direct communication between MaRCCI and PhotosynQ.

After spending 2 days together, learning how to create robust projects and collect, analyze and interpret quality photosynthesis data, we hope to develop a much stronger collaboration.

MaRCCI pic for blog

What does ‘stronger’ collaboration mean?

MaRCCI already has access to PhotosynQ’s low-cost, cutting edge phenotyping technologies and platform for data storage, visualization and management. Building a stronger collaboration means giving MaRCCI students and faculty the opportunity to work directly with the PhotosynQ team to analyze the links between complex photosynthesis phenotypes and crop outcomes (this requires sharing of outcome data such as yield, disease resistance, etc). It also brings MaRCCI into the PhotosynQ development workflow. So, as we continue to work on automating advanced analytical tools like multivariate analysis, prediction and QTL mapping we will work closely with MaRCCI students and faculty to make sure that what we are developing will solve their problems.

On the flip side, collaboration with MaRCCI offers PhotosynQ some great benefits. MaRCCI recently received support from the World Bank as an “African Higher Education Centre of Excellence” in plant breeding and related activities. This means that they are positioned to be a hub of plant breeding training for breeding programs throughout sub-Saharan Africa. They receive Masters and PhD students from 20 different countries, and while I was there I met students from Benin, Burundi and Tanzania, just to name a few. Such a diverse group of students allows us to disseminate PhotosynQ technology over a wide geographical area, and have much greater impact.

The end result, we hope, will be a long-term partnership that improves the education and capacity of young plant breeders across Africa and helps PhotosynQ continue to evolve as an advanced phenotyping platform.

Personally, I look forward to continuing the work with a great institution with enthusiastic students and faculty.

 

 

PhotosynQ measures more than just plants: A history of our forays into measuring soils

Over the past several years there has been quite a bit of interest in measuring soil properties, which makes sense given that most of the plants we care about grow in soil. In response to that interest, we have developed numerous PhotosynQ prototypes, protocols and macros to measure soils over the past two years.

We started by using the MultispeQ to measure soil active C using potassium permanganate. This method used a cuvette to measure a color change in solution. The problem with using colorimetry, however, is that it requires users to do wet chemistry in the field. We would rather avoid that.

Another approach was to measure in situ C mineralization as an indicator of soil health. We have built multiple iterations of in situ soil C chambers (below). In general, the results from these chambers were positive, but there were a few drawbacks. One is that the results were highly dependent on soil moisture content and temperature. Therefore, we would need to collect a lot of data at different moisture and temperature conditions to account for these variations, much like we need to collect photosynthesis data at multiple light intensities to account for the effect of light on Phi2, PhiNPQ and PhiNO. The second problem is that the prototypes were quite clunky, and generated a lot of funny looks around campus when they were half-buried with random wires hanging out. If enough people were interested in using the in situ chambers, we could make a few mechanical changes to make them look less like an IED.

Soil chambers

Going back to the drawing board, we brainstormed different ideas to simply assess soil health without having to take a lot of measurements or have multiple devices. This led us to develop a simple tool for measuring soil C mineralized from a sealed container. Using a “24-hour C mineralization burst” we can control for different temperature and moisture conditions by first air-drying, and then rewetting soil samples in quart jars. Then we use a syringe to sample headspace in the jar and inject it into a pass-through CO2 sensor.

C min

The technology is pretty simple, just a CO2 sensor connected to a microcontroller, loaded with PhotosynQ firmware. To demonstrate our new SoilspeQ, we worked with a professor at MSU and took soil samples from a field where she was testing the effect of cover cropping on soil quality and maize productivity.  We took many samples from different areas including soil that had mixed cover crops, soils without cover crops and some soil from the bare ground bordering the field plots. We also collected the soil from 1-5 cm and 5-10 cm deep, so we could see if there were differences between them. Check out the results here.

Our final approach to measuring soils is still in its early stages, but we are looking forward to see where it goes. We have teamed up with a professor at Colorado State University to develop microfluidics cards. The goal is to use reagent embedded cards to reduce in field wet chemistry and accurately measure key soil properties. We then use the MultispeQ or a version of the CoralspeQ to measure the color change. Our initial test, using Al3+ in solution at different concentrations is shown below.  

Al Fig