PhotosynQ Workshop Recap

On Tuesday April, 30th 2019 the first annual PhotosynQ workshop was held in East Lansing, MI. We would like to thank all the attendees for joining us, for their feedback, participation and making this day a success! It helped us tremendously, understanding what the needs of our community are and how we can support them. Thank you for your support!

After a short welcome, Prabode Weebadde presented how PhotosynQ has developed over the years and announced new products. The PhotosynQ Academic Subscription for the PhotosynQ platform, allowing Projects to be private, as well as CaliQ, a device to calibrate the MultispeQ’s PAR (Photosynthetically Active Radiation) sensor. Both will be available in Q3 this year. He also presented PhotosynQ Enterprise, a separate cloud instance of the PhotosynQ platform, helping enterprises to keep their data private.

Prabode announcing new products coming in Q3
Prabode announcing new products coming in Q3

 

Following the introduction, David Kramer presented an overview of possible use cases and how to use the PhotosynQ platform. Further, he gave an introduction into photosynthesis and the most important photosynthetic parameters that can be measured using the MultispeQ v2.0. Another important part of his presentation was on how to avoid bias when planning and collecting field data.

Dave presenting on comparing experimental approaches
Dave presenting on comparing experimental approaches

 

After that, Sebastian Kuhlgert gave an overview on how to set up a Project using the PhotosynQ platform. The focus was on how to use the MultispeQ in combination with the mobile application to collect measurements successfully together with meta data that can be used to analyze the subsequent dataset more efficiently. He also presented on some of the experiences reported from users who have already collected large amounts of data in the field.

Next, David Kramer started a hands on Project, that allowed all attendees to collect data comparing cowpea plants (Vigna unguiculata) grown in low or bright light. After the data was collected in groups, the analysis tools were presented, doing a “live” data analysis of the data that had just been collected.

Hands on, taking measurements with the MultispeQ for a test Project and subsequent analysis
“Hands on”, taking measurements with the MultispeQ for a test Project and subsequent analysis

 

In the afternoon, the attendees were able to gain a more detailed look into how to create protocols and macros to take measurements, analyzing collected data and on how MultispeQs are calibrated.

Sebastian explaining on how to create protocols for the MultispeQ and build a macro to analyze the data coming from the instrument
Sebastian explaining how to create protocols for the MultispeQ and build a macro to analyze the data coming from the instrument

 

During the last session, Isaac Osei-Bonsu, who collected more than 40,000 measurements at this point, was presenting datasets he had collected using the MultispeQ in combination with the PhotosynQ platform and a new method to account for collection bias he is developing to analyze his massive dataset.

We hope we were able to give insights into how the PhotosynQ platform can accelerate your research and how versatile and flexible it is, when it comes to data collection and analysis. The workshop was intended to be as interactive as possible and we would like to thank all the attendees for their questions and participation!

Feedback from the Workshop

When planning the workshop we wanted to offer a very broad program, that would touch topics that are relevant to experienced as well as inexperienced users and we hope we were able to accomplish that. We would like to thank everyone for giving us such positive feedback as well as providing ideas and requests when it comes to improving the workshop. The most frequent ones are listed below. Please feel free to contact us, if you have more ideas and suggestions.

  1. More insights into how to data analysis, statistical analysis and removing bias from data collection
  2. More details on the theory behind measurements, how to read them and how the instrument works
  3. More training on taking measurements and using the instrument, more time in general

Impressions from the Workshop


All Photos by Annie Barker

Register Today! PhotosynQ Presents the First Annual MultispeQ Hands-On Workshop

Register Today! (limited seating)

Lead by Prof. David Kramer the MultispeQ Hands-On Workshop will improve your knowledge regarding all aspects of the MultispeQ instrument, data collection and interpreting results.

Tue, April 30, 2019
8:00 AM – 5:30 PM EDT

Register Today! (limited seating)

Location
PhotosynQ HQ
325 East Grand River Avenue
Room 300
East Lansing, MI 48823

New Help Center

New Help Center

We have updated the Documentation and redesigned the Help Center. Please visit help.photosynq.org to see what has changed.

We are trying to make the Help Center for PhotosynQ more accessible and provide detailed information on how to use the platform and instruments. This is an ongoing process, as we are trying to document updates to the platform, the mobile and desktop applications as well as including questions you are sending us on various topics. For that reason we have moved the documentation to a new location that will allow faster release cycles.

We are still testing, but soon we will link the documentation everywhere on PhotosynQ. Please go ahead, take a look and let us know what you think.

With this new release we would also like to remind you, that it is possible to make contributions to the documentation and help us improve it as well as help others.

New PhotosynQ Related Publication

Check out the new publication in the journal Crop Science, using the MultispeQ and PhotosynQ Platform (10.2135/cropsci2018.04.0275)

Screening for Heat Tolerance in Phaseolus spp. Using Multiple Methods.

Jesse Traub, Timothy Porch, Muhammad Naeem, Carlos A. Urrea, Greg Austic, James D. Kelly and Wayne Loescher

Common bean (Phaseolus vulgaris L.) is a nutritious crop grown around the world, a staple that provides high levels of protein and iron in the diets of Central and South Americans and East Africans. Heat stress negatively affects common bean seed yields and prevents cultivation in certain areas. Furthermore, under field conditions, heat stress often coincides with and exacerbates drought stress effects. Breeding more heat-tolerant cultivars would stabilize seed yield and open new regions to field production. To support these efforts, we examined a variety of methods for screening large numbers of bean germplasm exposed to heat stress at the vegetative growth stage as opposed to the reproductive stage, which would prolong the screening process. Tepary bean (P. acutifolius A. Gray), a closely related species to common bean, was used as a heat-stress-tolerant check. Plants exposed to day/night temperatures of 45/36°C for 2 d showed measurable signs of heat stress, but tepary bean outperformed the common beans on all stress tolerance measures. Gas exchange, chlorophyll fluorescence, and oxidative stress were only affected by this high temperature and not by temperatures below 45/36°C. Heat stress measurements also correlated well with visual signs of leaf tissue damage. Gradually raising temperatures was useful for screening large number of entries for heat tolerance, but this heat tolerance was only partially related to drought tolerance in the field. Plant breeders can use some of these methods to supplement field data and to further characterize the stress tolerance of bean lines.


More PhotosynQ related publications are available here

New PhotosynQ Related Publication

Check out the new publication in the journal Planta, using the MultispeQ and PhotosynQ Platform (10.1007/s00425-018-3014-7)

DOTAP, a lipidic transfection reagent, triggers Arabidopsis plant defense responses

Carolina Grandellis, Betiana S. Garavaglia, Natalia Gottig, Caroline Lonez, Jean-Marie Ruysschaert, Jorgelina Ottado

DOTAP is a cationic lipid widely used as a liposomal transfection reagent and it has recently been identified as a strong activator of the innate immune system in animal cells. Plants are sessile organisms and unlike mammals, that have innate and acquired immunity, plants possess only innate immunity. A key feature of plant immunity is the ability to sense potentially dangerous signals, as it is the case for microbe-associated, pathogen-associated or damage-associated molecular patterns and by doing so, trigger an active defense response to cope with the perturbing stimulus. Here, we evaluated the effect of DOTAP in plant basal innate immunity. An initial plant defense response was induced by the cationic lipid DOTAP in the model plant Arabidopsis thaliana, assessed by callose deposition, reactive oxygen species production, and plant cell death. In addition, a proteomic analysis revealed that these responses are mirrored by changes in the plant proteome, such as up-regulation of proteins related to defense responses, including proteins involved in photorespiration, cysteine and oxylipin synthesis, and oxidative stress response; and down-regulation of enzymes related to photosynthesis. Furthermore, DOTAP was able to prime the defense response for later pathogenic challenges as in the case of the virulent bacterial pathogen Pseudomonas syringae pv. tomato. Disease outcome was diminished in DOTAP-pre-treated leaves and bacterial growth was reduced 100 times compared to mock leaves. Therefore, DOTAP may be considered a good candidate as an elicitor for the study of plant immunity.


More PhotosynQ related publications are available here

New Desktop App

A New Desktop App Is Coming

We are releasing a new version of the Desktop App which will replace the current one for the Google Chrome Browser (Chrome App). The reason is a discontinued support for Chrome Apps on Windows and MacOS (see below). So please go to https://photosynq.org/software to check out the new Desktop App. If you have any issues, please let us know and write to support@photosynq.org.

What’s New

First and foremost we tried to make the new app work in the same way as the old one, so you can immediately feel comfortable using it. Further, we have fixed issues, improved the workflow, added compatibility and better support with the latest Firmware and added some new features.

The new Desktop App on Windows and MacOS
The new Desktop App on Windows (right) and MacOS (left)

General

  • QR codes and barcodes can now be scanned with a webcam to answer questions
  • More and better keyboard shortcut support
  • Drag ‘n drop for images
  • Images can be previewed inside the app
  • More native look and feel depending on the OS you are using
  • Faster search inside the app
  • Instrument Settings available through the app
  • The instrument console has been moved to a separate window
  • Instead of tags, measurements in the notebook are now sorted by name and experiment

Protocol Editor

  • Ctrl/Cmd+Space will bring up Commands and Hardware configurations in the Protocol Editor (advanced view)
  • Code folding and code can be displayed more compact
  • Hover over commands to get a description of their function
  • Search and replace, search hits are highlighted along the scrollbar

Macro Editor

  • The Macro Editor supports protocol sets introduced with the last firmware update (1.23 or later)
  • Code folding
  • Non linear fit for exponential decay
  • New functions to access parameters in protocol sets
  • Search and replace, search hits are highlighted along the scrollbar

Installation & Updates

  • An executable one click installer for Windows
  • Drag ‘n drop installation from a disk image on MacOS
  • Updates will be automatically downloaded and installed

What will Change

There are only minor changes for you as a user. Instead of the Chrome Store, now you have to download the new Desktop App from our website (https://photosynq.org/software). Updates are downloaded automatically and you only have to confirm installing the update.

Making the Transition

The transition to the new app will be easy. After you installed the app, just sign in with your PhotosynQ account and all your Projects, Protocols and Macros will be synchronized. No need to do anything else. In case you have measurements saved in your Notebook, you can transfer them following these steps:

  1. Open your old app and select the Notebook from the side bar.
  2. Select all the measurements you want to keep and select Export from the Action menu.
  3. Open the new app and select File->Import Notebook… from the menu.
  4. Select the file you just exported and click on open to import all measurements.
  5. And… you are done!

Windows, Mac and Linux Support

Windows

If you are using Windows, you just download the app and execute the installer. It will automatically install the app and add a shortcut to your desktop. Updates will be automatically downloaded and installed. If you are using Windows 7 or 8, you have to download and run the Windows serial installer to connect an instrument, if you haven’t already done it.

Mac

If you are using a Mac, just download the app, open the disk image and drag ‘n drop the app into your applications folder. Updates will be automatically downloaded and installed.

Linux

The Linux version is currently at an early developing stage. If you are interested in helping us by testing the app, please drop us a line (support@photosynq.org). Due to the framework we are only providing installers for Debian based distributions like Ubuntu.

TL;DR

The great features of Chrome Apps were amongst others, their small size (about 3mb), the easy way of installing them, the sandbox they were running in and the automatic updates and push notifications.

So, why exactly do we abandon the existing app?

A while ago, Google announced, that Chrome Apps in their current form will be discontinued by mid 2018 for Windows, MacOS and Linux and will only kept for ChromeOS. Nevertheless, Chrome extensions will remain available. Those are pretty similar to apps, yet they have one big issue, they don’t have all the APIs available that we need and as a consequence don’t allow communication with serial devices. This means, that we will no longer be able to use Google Chrome apps / extensions to take measurements with PhotosynQ instruments like the MultispeQ.
As a consequence, we started to build a new app that is not depending on the Google Chrome Browser infrastructure any more. We are using the popular Electron Framework that is used by apps like Atom, Slack, WordPress, Skype or Visual Studio Code and allows to build cross platform applications using HTML and JavaScript as well as Node.js packages.

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

In memory of Prof. Ruth Gates

Prof. Ruth Gates, one of the prominent coral scientists in the world, the director of Hawai’i Institute of Marine Biology, and the president of the International Society for Reef Studies (ISRS), passed away on October 25 after a battle with cancer (In Memory of Ruth Gates – The Atlantic).

Her recent works include breeding heat tolerant corals or “super corals”, for the effort to save the coral reefs from severe bleaching, and holding the public forums to make the communities aware the benefit of saving the reefs and what kind of actions the normal citizens can take. She was one of the PhotosynQ/CoralspeQ collaborators. You could find her detailed scientific works, news articles and contributions elsewhere. Here, I would like to write about brief but memorable interactions with her.

It started in summer of 2015. Prof. Peter Ralph at University of Technology, Sydney, visited us in Michigan, telling us about the upcoming monstrous El Nino… officially called Godzilla El Nino. Peter, our long time collaborator and early adopter of PhotosynQ, proposed us if we could make a field deployable instrument like MultispeQ (it was Beta type back then) to monitor corals. It was a challenge, because it has to work under water. Thus, CoralspeQ was born. Peter strongly suggested Ruth Gates as a collaborator, because not only she was a respected coral expert, but also she constantly touted the importance of collaboration and data sharing. We had also contacted several other scientists who are marine biologists and spectroscopists, and received a positive response.

When we finally built a prototype in November when the damages from El Nino had already started, we needed a field test instead of the lab test. It was Ruth who emailed me directly and said, “What can I do for you?” I flew to her Institute in Coconut Island with 2 instruments in December, 2015 (CoralspeQ Prototype 1.5 Update – Ready to go for the field test!), and took measurements with captive corals with a help from Jennifer Davidson, and in the reef with a help from Elizabeth Lenz. This field test was crucial to see what we could tell about the coral conditions in the real environment.

In the following summer, at the 13th International Coral Reef Symposium in Honolulu, I finally had an opportunity to talk to her in person (CoralspeQ Debut at International Coral Reef Symposium). Being the president of the ISRS and one of the Symposium organizers, she had people lined up to have a brief private conversation. I was fortunate to have an interaction, and was totally flattered by her saying “Thank you for doing this!” She meant that making inexpensive instrument and sharing the data through the cloud-connected scientific platform would benefit everybody. Her closing plenary talk was about the need of scientists and communities working together and coming up with the solutions to save the reef ecosystem. I think she had been inspiring many people with her optimistic open-minded attitude. Now she has passed a baton to the next generation. CoralspeQ is a difficult long-term project, but equipped with Ruth’s optimism, we will get there.