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.

One Million Measurements!

 

We are excited to announce that the PhotosynQ Community has collected over one million measurements, since the first one was taken and saved to the cloud in April 2014.

The PhotosynQ community has been busy over the last 4 years, producing not only an amazing amount of projects and measurements, but has also published data in several peer-reviewed journals (find a list here) already.

It all started here at Michigan State University, but we can now truly say, that this project has grown into a global community.

We are so proud of the community, their contributions and we are truly excited about the future!

Your PhotosynQ Team

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.

Caution: Updating from V1.17 to 2.XXX firmware.

We have had reports that some (but not all) devices with old V1.17 firmware have lost their PAR calibrations when updating to V 2.036 or above. We are looking into this issue, and are testing a fix, which we will release as soon as possible. It is pretty clear, though that once the devices are recalibrated there should be no issues, Meanwhile, if you have a device with V1.17, hold off on updating until the fix arrives.

This message is also on the Forum.

Thanks!

New Firmware, Improved Compass Routine

MultispeQ Firmware v2.0038 has a new and improved compass routine, that can more reliably read compass direction when the device is tilted. Once the instrument is updated, you must calibrate the compass to enable it to work.

More information is given in the announcements section of the forum.

Please follow these steps:

1) Connect to the desktop app, and access the console.

2) Enter the command calibrate_magnetometer

3) Rotate the device in ALL directions. Make sure the nose of the instrument draws out a “sphere” in the air. Also, ensure the instrument is rolled in all directions while calibrating (Like a plane does a barrel roll). All movements should be slow and arc-like.

4) After calibrating the magnetometer, find the protocol “compass and tilt only”.

5) Point the MultispeQ towards a cardinal direction, and select “run”. Ensure that the measurement “Compass_direction” shows the direction the device was pointed. Repeat for all cardinal directions.

6) Put the MultispeQ on a level surface and run the protocol again. The measurements “Angle”, “Pitch”, and “Roll” should all be close to 0 or 1. If not, please recalibrate the instrument, taking extra care to rotate the device in all directions.

7) Tilt the instrument on its side. Run the protocol, and make sure “Roll” shows a value of around +/-90.

8) Turn the instrument upside-down. Run the protocol, and ensure the value for “Roll” is close to +/-180.

9) Next, tilt the instrument’s nose upwards at an angle. The value “Pitch” should reflect the angle the MultispeQ is tilted. If the device passes these tests, the magnetometer was calibrated successfully.

After updating, if your device is having trouble taking measurements or is acting slow, calibrate the open and closed positions. To do so, access the console on the desktop app and type in set_open_closed_positions. Open the device’s clamp 2mm~, and enter “+” into the console. Then, open the clamp to 4mm~, and enter “+” into the console.

New Firmware, New MultispeQ, Updated Apps

The PhotosynQ team has been working hard to bring you a new, updated platform! Starting now, and continuing over the next few weeks, we will be releasing new versions of the MultispeQ, firmware (with new associated programming tools), and desktop App.

MultispeQ Version 2.0. Many users are already receiving the new V2.0 device, which has a lot of updated capabilities. Some of these are obvious (like the nice blinking lights that tell you what the instrument is doing. and others. like compatibility with stomatal new conductance measurements, will be rolled out in the coming weeks.

MultispeQ Firmware Version 2.0 for both V1 and V2 devices. This is a major upgrade with lots of new features and improvements. Although the new version is almost completely backwards compatible, it allows much greater flexibility and powerful programming. We will be introducing the new capabilities in installments over the coming weeks.

PhotosynQ Desktop App. We are releasing a new version of the Desktop App which will replace the current one for the Google Chrome Browser (Chrome App). One  reason is that support will be ended for Chrome Apps on Windows and MacOS. Other important reasons for the update are to accommodate new capabilities of Firmware 2.0 and higher, and give you more powerful analytics and visualization tools.

PhotosynQ Android App To make use of the new capabilities of the MultispeQ, the team has been working to update the Android App. You will receive email or popup notifications about how to update your App. (You absolutely need this update to use the new devices, but it will still work with V1.0.).

This blog post is also available on our Forum: https://photosynq.org/forums/announcements/discussions/new-firmware-new-multispeq-updated-apps#comment-1508

PhotosynQ Focus : Osamu Watanabe

Focusing on how the community is using PhotosynQ technologies. This month we are highlighting Osamu Watanabe, a researcher at the Agriculture Facility at Shinshu University studying invasive weed species and their effect on rice.

 

When Osamu Watanabe was first introduced to PhotosynQ by Dr. Kenji.Takizawa, a coworker at his laboratory at Shinshu University in Japan, he thought not only would this platform be great for him, but also his students!  Osamu graduated from and works in the Agricultural Facility at Shinshu University in the Nagano prefecture in central Japan. Nagano was the site of the 1998 Winter Olympics as the surrounding terrain is very mountainous, which is not only great for skiing, but also for high altitude terraced rice farming!

 

Dr. Watanabe’s research focuses on invasive weed species in Japan and how they effect both the natural environment and agriculture. In Japan, rice is the most important food crop grown, and Dr. Watanabe uses his MultispeQ to measure the photosynthesis of both the rice and common weed species such as Ambrosia trifida (Giant Ragweed) and Oryza sativa (Weedy Red Rice). In these cases, Dr. Watanabe will “measure the photosynthesis characteristics of the plants in different density communities using MultispeQ”. This data can help them determine the weed density where the weeds outcompete the crop, causing a drop in crop photosynthesis. Measurements are also made after herbicides have been applied to evaluate how herbicide application rate impacts the photosynthetic rate of both the crop and weed.

 

In addition to research, Dr. Watanabe also teaches multiple classes at the university where he has integrated the PhotosynQ platform into his curriculum. He teaches students in their 3rd year of undergrad, about 50 in the class, all the way up to Master’s students, and they all get out there with MultispeQs, take measurements and learn more about invasive weed species. I was nervous that this might be difficult for his students since Dr. Watanabe says none of them speak English and the platform, app and other aspects are in English. However Dr. Watanabe said that when they pick up devices and create projects they “operate intuitively” and that  as “students teach the other students, [their] skills rise, so I only have to watch” He added that “PhotsynQ’s website is very easy to use, simple analysis of the collected data is also available in the tool, so it is very handy!”

 

It was great to hear the Dr. Watanabe is getting along great with the PhotosynQ platform. He is learning more and more about the weed species he hopes to curtail along with teaching the next generation of plant scientists about PhotosynQ.

 

JapanGroup