Sessions, Sharing and Downloads

Sessions, Sharing and Downloads | Website Update

Now you can save and share your analysis as sessions or download your data as a spreadsheet.

The data viewer on PhotosynQ is the tool to analyze your collected data. You can filter the data set and create sub-sets (Series), you can Plot parameters in various ways, view the data on a map based of the geo-location attached to each measurement, do simple statistics, or dive into every value using the spreadsheet. We are introducing a few new functions, we hope you will give you a better experience.

Sessions

Now you can save your results as sessions when analyzing the data. Every session will save your current dashboard, plot, map, filter settings/series and thresholds. They are a great way of saving interesting observations, compare different filters, thresholds, without having to repeat all the steps to get there.

Sharing a Session

When you save a session, you will notice a checkbox labeled shareable, making the session available to others when checked. After you saved your session, just click on the copy button in the list of available sessions, to save the link to your clipboard. Use the link, to share your findings with collaborators, in the forums or for presenting them in the Project results section. You can also un-share the session at any time. The link will still be pointing to the Project’s data, but your session is no longer available. In case you make up your mind, just re-share it and the link works again.

Auto-Save

When you have been been analyzing your data, you might have noticed, that the filters and thresholds you were applying got saved and re-applied the next time you opened the dataset. This was only saved locally, so opening your project on a different computer, would mean you have to start all over again. Now it gets saved to the cloud, so you can continue working where you have left off, even when you are using different computer.


Downloads

We developed the Data Viewer so you can analyze the measurements you have collected for a project, online. But we do understand, that downloading the data and using it in spreadsheets like Excel, Origin or others can be necessary. To this point, we have offered libraries for Python and R to get data from PhotosynQ into an easy to use format to work with. Now we also offer a download* of the data in a spreadsheet (xlsx) or in the JSON format right from the project page.

Yet, we strongly recommend you view your data using the data viewer, since there you can flag measurements that were not taken correctly, you can look at raw traces, etc. That way you can ensure the best data quality, when it comes to your final analysis.

*The downloads are only available for the project lead and project collaborators


Statistics – Summary

The data viewer is offering simple statistic functions as well as a summery for a selected parameter. The histogram in the summary has been extended and is showing now the normal distribution for the sample as well.

Please be aware, that all functions are currently at a beta stadium, so you might experience some issues and the functionality might be different in the final version.

Intelligent Information Technologies in Education and Science – Ukraine

 

On October 18, 2017, the Interdisciplinary Workshop on the dissemination of knowledge on “Intellectual Information Technologies in Education and Science” took place at the Faculty of Chemistry and Biology of the Ternopil National Pedagogical University (TNPU).

The co-organizers of this event were Andriy and Natalia Hertz, employees of the Department of General Biology and Methodology of Natural Sciences Teaching and the Department of Botany and Zoology (Faculty of Chemistry and Biology of TNPU).

According to the program, a demonstration of the possibilities of IT solutions in biological, educational and pedagogical research took place. 

In particular, the on-line PhotosynQ platform was presented as a web tool for an integrated assessment of the physiological state of plants. 

Information was disseminated on how the MultispeQ can measure, collect and analyze photosynthesis data in field and laboratory conditions.

The focus was on the openness and flexibility of the PhotosynQ platform and the development of educational tools through it, and more.

The students and faculty all wished to have the opportunity to work with MultispeQ and PhotosynQ and to evaluate the condition of plants for themselves.

More Info [English] | More Info [Original]

The NPQ(T) Parameter

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!

Read the peer reviewed publication or the story on the Michigan State University’s Plant Research Laboratories Website, Protecting plants from the power of sunlight.

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 complexes Plant. Cell Environ. 40(8), 1243–1255. doi:10.1111/pce.12924

PhotosynQ Focus

Focusing on how the community is using PhotosynQ technologies. This month we are highlighting Matthew Daniel, an Arborist from Australia and one of PhotosynQ’s most active users.

matthew

Matthew is the director of Tree Preservation Australia and CEO of Global Urban Forest Pty Ltd, a company dedicated to the relationship between soil and tree health and the science of urban forestry. He travels to many cities in Australia and abroad collecting data on tree and soil health and prescribing proper health care programs to ensure that cities have happy, healthy trees. These prescriptions include compost tea’s, deep root soil injections, and vascular stem injections of specially formulated microbial plant and soil health inoculants and organic stimulants. However, his job was limited by the lack of affordable tools and the ability to share data and results with others.

How Matthew Connected with PhotosynQ

Matthew Daniel was born and raised in Tasmania, where he first developed his interest in trees and the outdoors in general. We asked him what his first memories with trees were and he told us “When I was 5 years old my uncle found me 40 feet up a tree, freaked my mum out”, no doubt this guy was destined to climb trees for a living! He would eventually receive training and certifications for arboriculture, working near high voltage power lines and in confined spaces, become a partner in Tree Preservation Australia and eventually founded Global Urban Forest Pty Ltd.

From the moment he first heard about PhotosynQ he knew “it was exactly what I needed to understand the tree health response to soil health intervention.” He has now completely integrated the PhotosynQ platform into his workflow saying “I use PhotosynQ before, during and after all the trees I work with.” That is a lot of trees!

He successfully applied to be a PhotosynQ beta tester and created his main project tree health calculator – Beta/Experts Program – 2015-2017, which has over 8,000 data points. Matthew recently received the new MultispeQ v1.0 and is working hard to build collaborations with community groups across Australia.

Now What?

Ultimately, Matthew wants to use PhotosynQ as “an international collaborative platform to be a major part in quantifying and mitigating climate change.” Matthew believes that a global arborist community that shares data on a common, open platform can do more than improve the health of individual urban trees. It can also help to mitigate one of the causative factors of the Urban Heat Island Effect, namely a lack of vegetation in cities. Lack of vegetation in cities decreases levels of both evapotranspiration and carbon dioxide removal. It has been observed over the last century that cities are significantly warmer than the rural areas that surround them. The UHI effect affects many areas of life, such as the weather, health and the environment. It will increase the production of rain clouds and thunder over your city, make you more prone to violence during heat waves, increase your electricity bill, and even kill off fish in lakes and streams just outside your city if mitigation processes are not undertaken. By going around Australian cities and learning about the trees that are present, Matthew and a global arborist community can learn which trees are most effective at mitigating the UHI effect and make your city a more enjoyable environment.

He knows this will not be easy, but it’s the potential that is driving Matthew. The potential to build a global arborist community that can collect data for cities that they can then utilize to manage their urban tree population, the potential to reduce the urban heat island effect, and finally, the potential to mitigate the effects of climate change.

Thank you to Matthew Daniel for allowing us to write about him and taking the time to answer all our questions. Hope to see you back in the US soon!

 

PhotosynQ Focus

Now that the MultispeQ v1.0 instruments are released, we want to share some stories of how the community is using PhotosynQ technolgies. Today we want to focus on Isaac Osei-Bonsu from Ghana, currently a PhD student in the Kramer Lab at Michigan State University.

 

OB_Isaac

Isaac Osei-Bonsu has been a PhotosynQ user since the early beta days in 2015. Over that time, he has collected over 13,000 measurements and created 46 PhotosynQ projects. As we worked towards releasing the new instruments, Isaac was often tasked with testing out new MultispeQ prototypes, and some iterations did not work so well! At the end of the day, Isaac collected over 3,000 measurements with MultispeQ v1.0 prototypes and his feedback helped us to modify and improve the MultispeQ throughout the design and manufacturing process.

Isaac’s background

Isaac hails from the west African nation of Ghana, where he was a research scientist for the Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI). In Isaac’s own words, “The company is a National Agricultural Research institution which focuses on research on different crop species with the aim to improve agriculture in Ghana.” He studied a wide variety of crops including cowpea, peanut, pepper, eggplants, citrus, mangoes, avocado, pear, papaya and watermelon.

Ghana, like many countries in sub-Saharan Africa, is struggling to achieve food security and develop a robust economy. This means that the government wants farmers to produce more high value crops, like cocoa, for international markets. However, this comes at the expense of land for growing food crops, which is why it is so important to improve the productivity and efficiency of important food crops.

What Isaac is doing now

Isaac arrived at MSU with the help of a Legume Scholars Award which he received from the Consultative Group on International Agricultural Research (CGIAR) in 2015. The Legume Scholars Program supports the graduate study of young scientists from developing countries so they can pursue research careers involving grain legumes  (http://legumelab.msu.edu/training/legume_scholars).

Isaac’s is studying the photosynthetic response of  grain legumes to abiotic stress in order to improve grain legume production. His interest with automatic plant phenotyping was piqued “by the simple yet powerful nature of the MultispeQ device, connected to the PhotosynQ platform, and its possible use for rapid phenotyping in the field.” Manual phenotyping can be extremely slow and not entirely accurate. The MultispeQ instrument and the PhotosynQ platform make it easy and quick. He now uses the MultispeQ in most of his experiments. He doesn’t just use PhotosynQ because it is easier, but also because it allows him to develop a deeper understanding of abiotic stress responses in grain legumes.

Thank you to Isaac for taking some time out of your busy days to answer all of our questions. Having Isaac around our lab is a pleasure and his input into the PhotosynQ platform and MultispeQ instruments have been invaluable. We hope our instruments can help him as much as he has helped us and wish him luck in his continued research.

Teachers Workshop at Kellogg Biological Station

I traveled to the MSU K-12 Partnership 2017 Spring Workshop at the Kellogg Biological Station on April 18 with Klara Schnargl. Klara is a Future Academic Scholars in Teaching fellow and she is interested in strengthening the connections between Universities and K-12 education programs. The purpose of the program on this day was to bring graduate students and postdocs from MSU together with middle and high school biology teachers.

Klara and I were going to run a session for teachers who were interested in new, hands on, methods of teaching kids about photosynthesis. We thought that the MultispeQ instrument, combined with the ease of generating simple graphs on the PhotosynQ platform, could be a great way for students to visualize how plants use the light energy they capture and how they respond and regulate photosynthesis in response to their environment.

education blog image

We conducted a really simple experiment with the teachers so they could see PhotosynQ in action. Klara brought along two orchids in small pots and it was a beautiful, sunny spring day. So, we quickly created a project (‘KBS educational module April, 2017’) on www.photosynq.org that asked which session (we had one morning and one afternoon session) was collecting data and whether the plant was inside or outside (2 minutes). Then, after a brief talk about how to connect your phone to the MultispeQ and how to take a quality measurement (4 minutes) the teachers collected some measurements from the orchids in the classroom (5 minutes). Next, we took our orchids out into the sunshine and gave them time to adjust to their new surroundings (2 minutes). After a few more MultispeQ measurements we were heading back into the classroom to check out our data (5 minutes). We logged on to our PhotosynQ project and created a couple of graphs to compare Phi2, PhiNPQ, PhiNO and LEF inside and outside (4 minutes).

In 22 minutes we went from ‘this is MultispeQ’ to ‘look how our orchids regulated incoming light in our experiment.’

The teachers that came to our session were great, with lots of fun ideas on how they could use PhotosynQ in their classrooms and we are looking forward to working with them in the future.

Science Fun – Science faire in Ukraine

A science faire was held on May 22nd in Ternopol – IV at Theater Square.  The goal of the event was to popularize science among young people and excite the next generation of scientists in Ukraine.

There were about a dozen tents where schools and universities demonstrated scientific experiments in chemistry, biology and physics to the public.  Students of the Faculty of Chemical and Biological (http://chem-bio.com.ua), part of Ternopil Volodymyr Hnatyuk National Pedagogical University, http://tnpu.edu.ua)  presented PhotosynQ, created by scientists at Michigan State University.

Schoolchildren, students, and young scientists had the opportunity to personally touch science in the truest sense of the word. With the device MultispeQ, anyone could measure the progress of biophysical processes otherwise invisible to the eye in leaves of Phaseolus vulgaris plants and share data throughout the world via the PhotosynQ platform.

The interest and excitement generated at this event shows that science can be very interesting and exciting thing that unites the world.

by Andriy and Nataliia Herts