Developing a Root Imagery Tool to Analyze Cover Crop Roots

Summer Research Experience
Olivia Wallace, undergraduate at the University of Guelph

This summer I have been working in Dr. Claudia Wagner-Riddle’s agricultural meteorology lab at the University of Guelph. Much of my summer has centered on constructing and testing a minirhizotron system to image cover crop roots for an upcoming field experiment at the Elora Research Station. One of the objectives of this experiment will be to characterize relationships between root traits, microbial communities, and greenhouse gas emissions.

Most commercial minirhizotrons on the market are extremely expensive – the CI-600 by CID bioscience costs just shy of 20,000 dollars! This limits the number of minirhizotrons that can be used for an experiment and increases the amount of time needed for image taking in the field. Following a similar design approach to Marie Arnaud’s ‘Enroot’ minirhizotron (EnRoot: a minirhizotron for imaging fine root production), I set out to design an affordable and easy-to-construct imagery tool to analyze fine roots.

What I have enjoyed most about my project is how many skills I have had the opportunity to learn while completing it. I have been exposed to so many different softwares and tools in the past 4 months! Some of my favorites include:

Autodesk Fusion 360

This is a computer program that allows you to design 3D-printed pieces. I created 4 pieces using this software – a mirror holder, camera support, rotator, and end cap. The mirror holder and rotator are very similar to pieces used in the Enroot system, but the camera support is an entirely new piece designed to support a design change in our version. This software and I have spent a lot of time together this summer as I’ve had to adjust and readjust pieces to make sure they turn out just right!

Figure 1: Camera support piece designed on Autodesk Fusion 360

3D Printer

If you happened to walk into the lab this summer, chances are you heard the 3D printer working away in our research technician’s office. The 3D printer brought to life the pieces I designed on Autodesk Fusion 360… and sometimes it did not. I have learned that using a 3D printer is not as easy as pushing the start button! It requires levelling, proper adhesion, temperature control, etc. All in all, it’s a super cool piece of equipment that I hope to keep creating with after this summer is over.

Figure 2: Creality Ender-3 Pro 3D printer with a freshly printed drilling jig

Georeferencer Tool on QGIS

This was by far the most challenging software to figure out, but the most satisfying when it finally worked. I would like to thank Jonny Huck from the University of Manchester for being so kind and helping me out with this! Since the tubes we were using created some distortion in the images taken with the minirhizotron, an image processing step was required to fix this. Using the Georeferencer tool on a program called QGIS, I was able to tell the horizontal and vertical lines where they were supposed to be to get a more accurate image.

Figure 3: Left is the image before transformation and right is the image after transformation.

Although the summer is almost over, this won’t be the end for me and the minirhizotron. Come fall, I will continue to help in Dr. Wagner-Riddle’s lab, testing at the Elora Research Station and building duplicates to deploy in Elora and Ridgetown.

References

Arnaud, M., Baird, A.J., Morris, P.J. et al. EnRoot: a narrow-diameter, inexpensive and partially 3D-printable minirhizotron for imaging fine root production. Plant Methods 15, 101 (2019). https://doi.org/10.1186/s13007-019-0489-6