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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

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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.