Extracting Metrics for Three-dimensional Root Systems: Volume and Surface Analysis from In-soil X-ray Computed...

Area of Science:

• Plant biology
• Soil science
• Imaging technology

Background:

• Plant roots are crucial for soil-microbe interactions, climate regulation, and crop management.
• Quantitative root analysis in situ is vital for understanding plant growth and environmental processes.
• X-ray computed tomography (XCT) is an effective tool for non-invasive root imaging.

Purpose of the Study:

• To develop a costless and efficient tool for approximating root surface area and volume from 3D tomography data.
• To create a method for analyzing root structure regardless of its shape.
• To extract quantitative data from plant root samples.

Main Methods:

• Imaging a Prairie dropseed (Sporobolus heterolepis) root using XCT.
• Reconstructing the root structure and extracting the primary root using licensed and open-source software.
• Generating an isosurface polygonal mesh and analyzing it with the developed imeshJ application in MATLAB.

Main Results:

• Developed imeshJ, a standalone MATLAB application, to calculate root surface area (mm²) and volume (mm³).
• Successfully extracted quantitative size information from 3D root tomography data.
• Demonstrated a powerful combination of XCT and open-source software for non-invasive plant root analysis.

Conclusions:

• The developed methodology provides a costless and efficient way to obtain quantitative root size information.
• The combination of XCT and open-source software enables non-invasive imaging, segmentation, and analysis of plant root samples.
• This 3D data processing approach is potentially applicable to other complex material systems with segmentation challenges.