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

User Page | PhotosynQ Website

User Page | Website Update

We are working on making your user page the central hub for all the information regarding your work with PhotosynQ.

We have found that one of the most useful features for any PhotosynQ project is the Dashboard, which allows you to quickly view important project results on one page.

We are currently using the same approach to allow users to have a personal dashboard that makes all of their PhotosynQ information (e.g. projects, protocols, macro’s etc) available in one place.

If you haven’t visited your user page recently, you should try it now, we think you’ll be pleasantly surprised! To get there, click on your name in the top right hand corner of the PhotosynQ webpage, this leads to your user page.

Over the past couple of months we have made a number of changes to this page that should really help you navigate through your PhotosynQ projects and collaborations.

user page image

Recent Activity

This change has been around for a while, but if you haven’t been checking in you may have missed it. We have now added your most recent projects, collaborations and comments to your user homepage. This should help you navigate quickly to your most active projects, instead of always going through the PhotosynQ search bar.

Side Menu

The side menu now contains a link to the instrument page (see below), your invitations, and the last two updates posted on PhotosynQ.

About – Contributions

We replaced the bar chart showing your contributions over the past year and doughnut chart with a calendar histogram. This view will provide more details about when and how many contributions you made over the last year.

Contributions over the last 12 months, shown as a calendar heat map.
Contributions over the last 12 months, shown as a calendar heat map.

Protocols & Macros

Do you make any of your own protocols and macros? If you do, now you can see all of your protocols and macros, sorted alphabetically and by their category, right from your user page.

Instruments

Now you can see all the instruments you have used in the past. It will show some basic information, based on the last measurement, including the firmware version, the total number of contributions (you and others, if you borrowed/lent the instrument) and the last time the instrument was seen (based on the latest submitted measurement).

Basic information panel for an instrument
Basic information panel for an instrument

If you have questions or need support, please check our forum or send us an email to support@photosynq.org.

New Data Selection & Plotting | Website Update

Data Selection & Plotting | Website Update

This is just a small update to the data viewing tool on https://photosynq.org, but we think, it will be very helpful for your data analysis.

Data Selection

Plots

With switching the plotting library to Plotly we introduced selecting a series by using the lasso tool or box selection tool to generate a new series, instead of using the filters (Goodbye Flot, Hello Plotly | Other Website Updates). Now you can also use the inverse of a selection as a new series or generate both at the same time. Just check the appropriate box in the dialog before you create a new series or download selection.

The new selection dialog allows you to not only select a range of markers as a new series, but also the inverse of your selection or even both as new series.
The new selection dialog allows you to not only select a range of markers as a new series, but also the inverse of your selection or even both as new series.

Map

Now you can also generate a new series by drawing a rectangle or a polygon around markers on the map. When viewing graphs you can use the selection tools to create new series of data selected, or the inverse.

Select a group of markers by dragging a rectangle or polygon to create a new series (buttons in the center top). Similar to the plot, the map as well allows you to use the selection, the inverse selection or both as new series.
Select a group of markers by dragging a rectangle or polygon to create a new series (buttons in the center top). Similar to the plot, the map allows you to use the selection, the inverse selection or both as new series.

Dashboard

A new panel is available, which lists all the Data Quality Issues, which were found in your project, listing each issue with a count of affected measurements. You can now generate a series containing these measurements for an easier screening and potential flagging.

Plotting

What’s in my selection?

When you are working with a scatter plot and you are using a color gradient as a third dimension, it might be hard to tell, if for example, a certain crop variety is enriched in your selection. Now you can use the Enrichment feature to plot fractions of a category for each series.

Just select the bar-graph tab, check Enrichment and choose a category. The bar-graph will display the fractions as to the following selections:

  • category / series Will show the fraction of category appearances in each series compared to the total appearances in each series.
  • category / total Will show the fraction of category appearances in each series compared to the total appearances.

2D Heat-Map

The 2D Heat-Map will now adjust based on the selected series and not only show the map for all all series combined.


Spreadsheet

If you save photos along with your measurements, no matter if it is a project question or if you take them as notes, inside the spreadsheet you see a small image icon. When you hover over the icon, you will see the picture instead on top of your list of series. The same is true for long arrays of numbers. Instead of those, you now see a chart icon and hovering over it, will bring up a line graph.

Copying the data still works the same. You will get all the data or the link to the picture.

The “ID” and “Series” columns are now sticky and will stay visible when scrolling vertically in the table.

Statistics: Chi Square Test

We added another statistical test, the Chi Square test. This allows you to compare categorical data.

Dashboard

The functionality of the dashboard got extended a little bit. The graphs you save to the dashboard are now images, so you can simply save them to you hard-drive.

Hiding Advanced Parameters

As I am sure you’ve noticed by now, we at PhotosynQ like to provide you with a lot of data. Not just the primary parameters (e.g. Phi2, PhiNPQ, Light Intensity (PAR), time, etc) that you are interested in, but also many other parameters that may go into calculating those parameters. However, viewing all of this data in the plotting tool or spreadsheet view may be a bit much for some users.

We have now added a feature that allows users to decide whether or not they want to view the primary parameters and Project questions together with the Advanced parameters (e.g. absorbance_420, FvP_over_FmP, etc) or if they would prefer to hide the advanced parameters. The new default setting is to hide the advance parameters. If you want to view these parameters, select the settings icon near the Add Series and click the Show Advanced Parameters checkbox. Now all of the parameters output by the MultispeQ will be available in the Plot Data, Spreadsheet, Map and Statistics tabs.

Advanced data

If you have questions or need support, please check our forum or send us an email to support@photosynq.org.

 

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!