TopoRoot+ presents a complete, automatic, and high through-put phenotyping system based on TopoRoot using a single 3D X-ray CT scan of excavated maize root crowns. We build our computational methods for whorls and soil planes upon TopoRoot’s pipeline and its hierarchical skeletons.
TopoRoot: A method for computing hierarchy and fine-grained traits of maize roots from X-ray CT images
https://www.biorxiv.org/content/10.1101/2021.08.24.457522v1
First, please follow this github page to download the vanilla version of TopoRoot: https://github.com/danzeng8/TopoRoot
Please download the .exe file and put it at the same directory with the TopoRoot.exe
TopoRoot+ can be run as follows. The first three arguments are required, while the rest are optional:
TopoRoot_v2.exe --in [input_file] --out [output_file] --S [shape] --K [kernel] --N [neighborhood] --d [downsampling rate] --maxLevel [level]
Mandatory Parameters:
--input: Path to image slices (for instance, D:/samples/image_slices/) or a .raw file. If you're using a .raw file, you must also provide a .dat file using --data [data_file.dat].
--output: Determines the path and filenames for the results. For an argument value like folder/output_filename, the outputs would be:
folder/output_filename.ply (structural skeleton) folder/output_filename_notes.txt (notes file) folder/output_filename_metrics.csv (measurement hierarchies) folder/output_filename.visual.off (Mesh visualization) --S: Iso-value for shape. This is utilized to generate an initial iso-surface. For more details, refer to the "Selecting shape, kernel, and region" subsection.
Optional Parameters:
--K (suggested, particularly for non-Maize CT purposes): Iso-value for kernel. Refer to the "Selecting shape, kernel, and region" subsection for more information.
--N (suggested, especially for non-Maize CT uses): Iso-value for neighborhood/region.
--d: Rate of downsampling: it balances between execution speed and accuracy. Ideally, pick a rate that yields a 400^3 volume dimension, which usually takes about 5-10 minutes to process. As an example, for a 1600^3 initial image size, a rate of 4 might be suitable.
--maxLevel: Highest level in the hierarchy to calculate characteristics. If this exceeds the root system's present highest hierarchy, it adjusts to that level.
--lowerRadius: Defines the slimmest section's width threshold. Only points above this threshold might be higher (default = 0.15 of the widest point). Adjust this if certain stem sections aren't appearing.
--upperRadius: Sets the threshold for the widest stem section. The identification process for stems starts from points exceeding this value (default is 0.95 for single-stem mode, 0.35 for multi-stem). Adjust this if certain stems aren't detected in multi-stem mode.
Note that this tool only supports maize roots. The accuracy of whorls and soil planes are only verified on maize root samples. It does not support multiple tillers / stems.
The data used for ground truth validation in our manuscript can be found here: There are three datasets available:
NAM2022: https://wustl.app.box.com/folder/214518933853
PlantHaven2021: https://wustl.app.box.com/folder/214380610514
PlantHaven2020 can be found in TopoRoot: https://wustl.app.box.com/s/yklsinv5v86est2vxk20bwt8e6inq7l0
The graphical user interface can be found at this link: https://github.com/Jurwen/RootGUI
Our workflow generates a trait file in .csv format, which compiles statistics for all analyzed samples. Additionally, there are visual representation files that illustrate the skeletal hierarchy, which come in .ply, .off, and .txt formats.
Details of the Trait File
For each analyzed sample, we offer the subsequent traits:
For every hierarchy tier within the plant's structure (typically tiers 1-3; refer to settings), combined lateral roots (tiers >= 2), and a collective analysis of all roots (across all tiers), we provide:
Count of roots (for the entire root/for each whorl/for above or below the plane)
Mean root span (for the entire root/for each whorl/for above or below the plane)
Cumulative root span (for the entire root/for each whorl/for above or below the plane)
Mean root width (for the entire root/for each whorl/for above or below the plane)
Mean root twist or deviation (for the entire root/for each whorl/for above or below the plane)
Root tip inclination (for the entire root/for each whorl/for above or below the plane)
Root emergence inclination (for the entire root/for each whorl/for above or below the plane)
Central point inclination (for the entire root/for each whorl/for above or below the plane)
Child root count (for the entire root/for each whorl/for above or below the plane)
Length of the stem (for the entire root/for above or below the plane)
Diameter of the stem (for the entire root/for above or below the plane)
Count of whorls (for the entire root/for above or below the plane)
Internode distance between whorls
Root Length Density: the total length of nodal roots and lateral roots per unit soil volume for each centimeter depth under the soil line, considering all roots in a “virtual” soil core - a cylinder whose axis is aligned with the root stem and whose radius covers 95% of all roots in our data set.
If images boast a resolution exceeding approximately 500^3, it's advised to reduce their resolution before utilizing the tool. Various software options like ImageJ are available for this purpose.