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.

New PhotosynQ Related Publication

Check out the new publication in the journal Front. Plant Sci., using the MultispeQ and PhotosynQ Platform (10.3389/fpls.2018.00767)

Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean (Phaseolus vulgaris L.)

Soltani A, MafiMoghaddam S, Oladzad-Abbasabadi A, Walter K, Kearns PJ, Vasquez-Guzman J, Mamidi S, Lee R, Shade AL, Jacobs JL, Chilivers MI, Lowry DB, McClean P and Osorno JM

Climate change models predict temporal and spatial shifts in precipitation resulting in more frequent incidents of flooding, particularly in regions with poor soil drainage. In these flooding conditions, crop losses are inevitable due to exposure of plants to hypoxia and the spread of root rot diseases. Improving the tolerance of bean cultivars to flooding is crucial to minimize crop losses. In this experiment, we evaluated the phenotypic responses of 277 genotypes from the Andean Diversity Panel to flooding at germination and seedling stages. A randomized complete block design, with a split plot arrangement, was employed for phenotyping germination rate, total weight, shoot weight, root weight, hypocotyl length, SPAD index, adventitious root rate, and survival score. A subset of genotypes (n = 20) were further evaluated under field conditions to assess correlations between field and greenhouse data and to identify the most tolerant genotypes. A genome-wide association study (GWAS) was performed using ~203 K SNP markers to understand the genetic architecture of flooding tolerance in this panel. Survival scores between field and greenhouse data were significantly correlated (r = 0.55, P = 0.01). Subsequently, a subset of the most tolerant and susceptible genotypes were evaluated under pathogenic Pythium spp. pressure. This experiment revealed a potential link between flooding tolerance and Pythium spp. resistance. Several tolerant genotypes were identified that could be used as donor parents in breeding pipelines, especially ADP-429 and ADP-604. Based on the population structure analysis, a subpopulation consisting of 20 genotypes from the Middle American gene pool was detected that also possessed the highest root weight, hypocotyl length, and adventitious root development under flooding conditions. Genomic regions associated with flooding tolerance were identified including a region on Pv08/3.2 Mb, which is associated with germination rate and resides in vicinity of SnRK1.1, a central gene involved in response of plants to hypoxia. Furthermore, a QTL at Pv07/4.7 Mb was detected that controls survival score of seedlings under flooding conditions. The association of these QTL with the survivability traits including germination rate and survival score, indicates that these loci can be used in marker-assisted selection breeding to improve flooding tolerance in the Andean germplasm.


More PhotosynQ related publications are available here

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

New PhotosynQ Related Publication

Check out the new publication in the Biocontrol Science and Technology, using the MultispeQ and PhotosynQ Platform (10.1080/09583157.2017.1376035)

Genotype-specific responses to the effects of commercial Trichoderma formulations in lentil (Lens culinaris ssp. culinaris) in the presence and absence of the oomycete pathogen Aphanomyces euteiches

Pratibha Prashar & Albert Vandenberg

Members of the endophytic fungal genus Trichoderma have been established as plant-beneficial microbes and are most successful commercial biologicals in the form of bio-fertilisers, biocontrol agents, and growth stimulators. We report the variable interactions among different lentil genotypes and Trichoderma strains in both the presence and absence of biotic stress (root-rot pathogen Aphanomyces euteiches). Two commercial Trichoderma formulations, namely RootShield® (RS) and RootShield® Plus (RSP) based on T. harzianum T22 and T. virens G41, respectively, were evaluated for control of Aphanomyces root rot and plant growth promotion in 23 wild and cultivated lentil genotypes. No significant disease control was recorded with either formulation in any lentil genotype. Significant genotype-specific plant growth promotion was observed in terms of root and shoot development and leaf parameters in a genotype-specific manner. Genotypes of Lens culinaris and Lens tomentosus, both in the primary lentil gene pool, demonstrated the maximum response. The overall effect of Trichoderma treatment was markedly higher under biotically stressed conditions in comparison to unstressed conditions. In many cases, negative responses were recorded, particularly in the absence of root-rot disease. L. tomentosus PI 572390 exhibited positive responses for most of the tested parameters. Our findings clearly indicate that, in the case of lentil, plant genotype plays a major role in interactions among the tested Trichoderma strains and the plant. Moreover, the influence of Trichoderma was greater and more favourable under conditions of biotic stress vs. the absence of stress.


More PhotosynQ related publications are available here