Measuring non-photochemical quenching in a few seconds without an initial long dark acclimation.
Over the past 3 years, many MultispeQ users have noticed that the NPQ(T) parameter (and ΦNPQ) can be a powerful predictor of plant stress, either biotic or abiotic. The NPQ(T) parameter has also correlated with crop yields in some PhotosynQ projects, like this project from Malawi.
Indeed, one of the big breakthroughs with the MultispeQ is the ability to estimate NPQ (Non-Photochemical Quenching) without a long dark acclimation period, which allows us to develop robust protocols that take less than 20 seconds. So how is the NPQ(T) parameter derived and how does it compare to the established NPQ parameter?
Tietz et al. out of the Kramer Lab have just published a paper in Plant, Cell and Environment describing the parameter and its derivation. Congratulations!
Tietz, S., Hall, C. C., Cruz, J. A., Kramer, D. M. (2017) NPQ(T): a chlorophyll fluorescence parameter for rapid estimation and imaging of non-photochemical quenching of excitons in photosystem-II-associated antenna complexesPlant. Cell Environ. 40(8), 1243–1255. doi:10.1111/pce.12924
The first version of the MultispeQ, the MultispeQ beta has been a great instrument, workhorse and proof of concept for the PhotosynQ platform and its utility in phenotyping plants outside the lab in large sample sizes. There are still MultispeQ beta instruments out there which are in use. We have decided with a heavy heart to stop the active development for them, since they have already exceeded their anticipated lifespan and focus our limited resources on the new MultispeQ v1.0.
So, what does it mean?
You will still be able to use the instruments and use the existing protocols, as well as create your own new ones. If there will be a change that breaks the compatibility with the Platform, we will give you enough of a heads up, so you can finish your experiments before we release the update. Since all the informations about the instrument is open, we hope that fixes or improvements might be made by the community to extend the instrument’s lifetime.
We are no longer supporting hardware fixes, mainly, because we don’t have parts in stock any more. Pieces like the light guides were custom made and can’t be ordered. Electronic parts can be ordered and we are more than happy to point you to where to source the needed parts. Just let us know and write to email@example.com. Otherwise, we advice you to get the new MultispeQ v1.0 for your future data collection.
There are no more measurement protocols developed for the old MultispeQ beta. The structure and some of the commands have changed when we introduced the new MultispeQ v1.0 and some of the new features would need a complete re-write of the instruments software (firmware).
We are no longer updating the firmware since we want to focus our limited resources on the current instruments and make sure they receive updates and improvements on a regular bases. As long as the communication protocol doesn’t change, the instruments can be used with the apps and submit data to the PhotosynQ platform.
We would like to say thank you again to all the beta testers not only for testing the MultipseQ beta, but the PhotosynQ platform as a whole. We learned a lot and the new MultispeQ v 1.0 has benefitted from those experiences a lot.
The PhotosynQ project started in David Kramers lab at Michigan State University, but it is by far not the only project, that is devoted to gain a deeper understanding into how plants do photosynthesis and how it is regulated. See what else is developed in this lab to study plant photosynthesis, all with the ultimate […]
Our most recent website update probably got lost in the excitement about the news that we had started shipping the new MultispeQ v1.0. We have continued to work on the tutorials and data analysis and are happy to announce another update to https://photosynq.org. There are several libraries out there to graph data in the browser and when we started the platform, we decided to use Flot, a great, performance library, which is unfortunately no longer actively developed. Implementing new methods of plotting would have required us to build certain features from scratch. Instead we are now using Plot.ly which opened up its libraries to the public. It not only provides the library, but also its own platform to create and manipulate plots, as well as libraries for popular languages like Python orR. We would like to give you a quick update on what has changed and improved.
New and Improved Tutorials
While some people really like using YouTube videos to learn new technologies, others don’t find them very helpful. So, we updated the tutorials (available in the learn more menu from the top of the page) to include text pages that include step by step directions, pictures and screen caps to get you started with PhotosynQ. Also, you can now download a Getting Started manual in pdf form if you need to refer to the tutorials while working offline! We kept the the video’s for those you like them, you can find them in their own videos tab on the tutorials page.
New Plot Options
Scatter plots are a great way of looking at data down to individual measurements. At the same time it can be hard to see trends in a big cloud of points. We hope these new plotting options will help analyzing your data.
The 2D contour plot allows you to do exactly that. With additional histograms they are a great way to visualize populations within a big data set.
In addition to the already existing histograms, you can now plot two parameters as a 2D histogram.
Box plots are available now. Like the bar charts, you can use a category as well.
New Parameter – Time of Day
We added the parameter Time of Day, showing the time, when the measurement was recorded as a number (e.g. 1:30 pm = 13.5). This will be helpful to plot time dependent trends, which could not be visualized using a regular timescale, which could be the case when measurements were recorded over multiple days.
New Data Selection and Plot Capturing
With the new ways to plot data comes the ability to select a set of data points in a scatter plot using the box or lasso selection. It can be used to generate a selection based Series, or the data can be saved with the measurement identifiers as well as the meta data including time and the project questions and answers. The little camera icon enables you to save the current graph as an image (png or jpeg), including the graphs’ legend.
Using Python and R
Analyzing big datasets using the data viewer inside the browser might be difficult. Or you might want to do your own statistical analysis or plot the data in a way that is not available. For this reason we made packages for Python and R to help you get the most out of your data.
On your user page, you can now see your Network. Your Network includes people who collaborate with you and have joined one or more of your Projects, as well as all Project Leads of projects you have joined.
Tags and Project Categories are now displayed on your user page.
Tags are now links and can be searched. Just click on a tab or type your tag into the search field (e.g. #beans).
What’s No Longer Available
Plots – We said goodbye to a few features, because there was no good way of adding it to the new plotting library or the available options didn’t turn out to be all that useful.
The options of plotting spline lines and area charts.
“Time (normalized)” is no longer available. It got replaced by the parameter “Time of Day”
Dashboard – To make the dashboard a little easier we decided to remove the following options.
The Panel with a pie chart of total submitted and flagged. The totals are added to the other data quality panels.
We hope that these new features will help you to analyze your collected data.
Hi everyone – we’ve had 3 days of production with a pace of 24 finished, boxed, ready to ship units per day! We should be able to fill the first 200 units over the course of the next 2 – 3 weeks. With a few exceptions, we will be shipping MultispeQs in the order they were received.
Thank you all for your immense patience as we have worked through this long process.
On a personal note, this is my last week as part of the PhotosynQ project. My hope is that the project continues to strive for the values of open software, hardware, and data in science, and to create tools which are broadly useful to the both the scientific and non-scientific communities. I know that these ideals are sometimes hard to hit, but if not us then who, and if not now then when?
Thanks to everyone that I’ve interacted with over the years for your patience, enthusiasm, support, and collaboration. In the future I’ll be on google plus +GregAustic and twitter @GregAustic. Hope to see you in my next project!
Hi everyone – it’s been about 3 weeks working here at Saline Lectronics to get the initial build of 250 MultispeQs underway. There have been lots of ups and downs, but we finally got the motor running.
We can now make about 24 units per day, which means we can fulfill the initial 250 in about 11 working days. Here are some pictures of the first 24, ready to be put in a box.
Thank you so much Jared, Paul, Jan, Cathy and everyone else at Lectronics for pushing through and getting 250 units through completion… it would probably surprise people how much we had to touch every single one of these devices to get them out into the world. Hopefully the next 250 are easier than the first 250 🙂
For the manufacturing uninitiated, a manufacturing facility can be pretty impressive. Robots, half-million dollar pick-and-place machines and assembly lines with people diligently working on making stuff produce a lot of ‘ooohs’ and ‘aaahs’.
But, automation is only part of the story. There is a lot of decision-making and little details to make things actually work. Our first week in manufacturing has had some setbacks with a few misplaced parts and similar issues, but our manufacturing partner has beefed up their support and Sean, Dan and I have working side by side with them. We’re refining our production process and ironing out errors. In all, we are still making decent time.
All production processes look different, but here’s a peek at ours:
1) Pre-assemble case. Many parts are more efficiently pre-assembled in bulk – placing the small light-blocking o-rings in the main case, for example, or installing the battery. These pre-assembly steps are largely done for all 500 units, so once circuit boards are ready the device will snap together pretty quickly.
2) Assemble + test circuit boards. The 2 circuit boards are connected, bluetooth and DACs are configured, EEPROM (memory) is zeroed out and lights are tested.
3) Place boards in case. Circuit boards are installed in the case. The PAR sensor, which contains several very small parts which fit precisely around the TCS light sensor, is assembled at this time as well.
4) Calibrate + validate. We have 7 individual calibration steps, as well as a final validation on 3 different plants of varying leaf colors and thicknesses. All of this data is saved to the website and you (the user) can follow up on your devices factory calibration (if you want).
5) Pack and ship. Now the final devices are packed in their boxes and shipped to labs around the world.
As of today (Thursday), we have almost all of the pre-assembly work done, and are in phases (2) and (3) above. Most of next week will be spent calibrating devices and boxing them up to ship.