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.

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Goodbye Flot, Hello Plotly | Other Website Updates

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 or R. 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.

Contour Plots

Contour plot with additional histograms.
Contour plot with additional histograms.

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.

Histograms

2D histogram using the Jet color gradient
2D histogram using the Jet color gradient

In addition to the already existing histograms, you can now plot two parameters as a 2D histogram.

Box Plots

Box plots with all data points.
Box plots with all data points.

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.

Selecting data points using the lasso tool.
Selecting data points using the lasso tool.

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.

Go to https://photosynq.org/software to find the links to the packages and how to use them.
The tutorial section (https://photosynq.org/tutorials) has some examples for Python and R on how to get your data analysis started.

And There is more to Discover…

  • 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

  1. 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”
  2. 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.

~ Sebastian

MultispeQs on track to ship

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!

– Greg

First batch of 24 finished MultispeQs!

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.

Calibrated, validated devices ready to be boxed

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 🙂

There’s always lots of problems that need to be fixed…

MultispeQ Assembly and how the sausage gets made

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.

Pre-assembled components of the MultispeQ case.

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.

connecting and testing circuit boards.

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.

Some very small parts related to the PAR sensor which is put in during this phase.

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).

undergoing PAR calibration!
PAR calibration setup

5) Pack and ship.  Now the final devices are packed in their boxes and shipped to labs around the world.

The box the MultispeQ is shipped in.

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.

We’ll keep you in the loop as we go.

– Greg

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PhotosynQ | Website Update

As we get ready to release the MultispeQ v1.0 we have been working hard in the background to provide an improved user experience. This includes visible changes, as well as a lot of changes in the background. Over the last couple of months we have updated the website, adding and updating features. Here is a brief summary of the biggest changes to https://photosynq.org.

1. Search

Now you can search not only through Projects, but also through Protocols, Macros, Discussions and Users. The searchable content is scored, so we can hopefully provide more relevant search results at the top of the list for you.
Further you can filter your search results for Projects, Protocols and Macros by their associated category.
Go to https://photosynq.org/search to try it out.

2. Discover

If you are new to PhotosynQ or you don’t know what to search for, take a look at the improved Discover page. Now you can browse Projects, Protocols, Macros and Users, and filter the results by category.
Go to https://photosynq.org/discover and get inspired by the work of others.

3. Help Getting Started

We have added a lot of content that we hope will help users get started with PhotosynQ and collect quality data. This content includes new and updated tutorials, a help center, and frequently asked questions.

A. Tutorials

Over the summer we started to make some new tutorial videos, helping you to get started with the platform and the new MultispeQ v1.0 instrument. We added some advanced tutorials on how to create a measurement Protocol, a Macro and how to do a basic analysis outside the platform, using R. Also, check out the ‘further information’ sidebar for downloadable pdf tutorials.
Go to https://photosynq.org/tutorials to see what we recorded for you.

B. Help Center

Along with providing more detailed tutorials, we have added a new help center that will guide you through: managing your account settings, creating a project, viewing your data, creating and editing protocols and macro’s and much more. We have also moved the blog over to the ‘learn more’ tab of the menu bar and replaced it with a link to the help center.

Changes in the navigation menu

C. Frequently Asked Questions

We often get asked questions directly by email and not through the forum. Because of that, we have started a collection of the most frequent and pressing questions. Over time we will add more questions and answers. Go to https://photosynq.org/faq to check out what we have gathered so far.

4. Data Viewer

We worked on the Data Viewer, improving existing features and adding new ones including adding thresholds and adding custom data in addition to the measurements you have already submitted.

Plotting data in the data viewer

  1. Now you can use create plots with up to four dimensions, adding marker size and marker color. The second y-axis has proven to be less helpful has been removed.
  2. Thresholds allow you to look into a subset of data, after you have filtered your dataset into different series. You can select thresholds for one or multiple parameters.
  3. The parameters are now sorted into Primary Parameters, Project Questions, Custom Parameters (if available) and Advanced Parameters, making it easier to find the parameter you are interested in among the many provided. Furthermore, this order of the parameters applies now to the columns in the spreadsheet view as well.
  4. New range sliders and a calendar are available to allow you to select a specific time and date range more precisely, especially when you have long term projects, or a lot of data over a short period of time.
  5. If you are looking at a single measurement, you can now easily navigate to the next / previous one. The small map indicating the measurement location now shows a bigger section with topography as well as latitude and longitude.
  6. New data types can be used, allowing you to display arrays as sparklines when you are looking at a single measurement. Furthermore, colors can now be defined as hexadecimal, RGB and RGBa, allowing you to use them as coloration in your plots or for your map.

5. Additional Data

Some experiments are going beyond data collection in the field with the MultispeQ or other instruments. Now you can add more information to each measurement after you took them (e.g. yield), as long as you are the project lead. This data is kept separate from the original measurements and can be altered at any time, in case you want to change, remove or add information.

additional data upload

6. User Activity

Previously, your user profile mainly presented a number of stats about your activity on PhotosynQ and the Projects you are involved in, either as a Project Lead or a Collaborator. Now we have an Activity feed, which displays the last 100 important events relevant to you on PhotosynQ. You can see if others contributed to your Project, if somebody posted a comment or question to one of the Projects you are involved in and of course everything you did, so you can more easily navigate to what is important for your workflow.

7. In the Background

One of the biggest changes is the work done in the background. Before the update, the original data for a Project was loaded into the Data Viewer and processed on your computer. Now, we do this step on our server and send you only the results from the calculations. As a result, the amount of data sent to you is reduced to 10–15% of its original size, allowing faster access to Project results.
Updating the calculations for a parameter? No problem, since your data gets re-analyzed when you view it after the changes, so you are always up to date.

Production progress: 250 units

Today we started producing the first 250 of our 500 initial production batch at Saline Lectronics, a contract manufacturing company out of Saline MI.  No major hiccups, though we had one or two LEDs which were switched and a filter which was incorrectly sized, but those are fixable in the next day.  Luckily we found them after the first 30 units, and not after the first 500 🙂

We spent most of today prepping the case itself (as you can see in the picture), and did a dry run of a single unit through the entire process (from assembly to calibration) to ensure we had everything we needed.  Bluetooth continues to be challenging (connecting mostly), and it’s now my least favorite communication standard by far!  But once you get it connected once it gets easier after that.

Expect to see more updates in the next few days as we continue to move forward.  The current estimated ship date is March 3rd.  If there are problems or setbacks I will update you as soon as they happen.

Thanks,

Greg