Data from: A new approach for rapid measurement of directional root responses to neighbors using the root centroid
Data files
Mar 09, 2026 version files 52.54 KB
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Hymenocarpos_circinnatus_data.xlsx
26.83 KB
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Pisum_sativum_data.xlsx
20.82 KB
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README.md
4.90 KB
Mar 16, 2026 version files 250.58 KB
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centroid_calculation_example_img_one_neighbor.csv
927 B
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centroid_calculation_example_img_one_neighbor.jpg
153.57 KB
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centroid_root.ipynb
29.61 KB
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Hymenocarpos_circinnatus_data.xlsx
26.83 KB
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Pisum_sativum_data.xlsx
20.82 KB
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README_for_centroid_root.md
13.82 KB
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README.md
5 KB
Abstract
Measuring directional root placement is critical for understanding plant responses to their belowground environment, and particularly their competing neighbors. Directional root placement is commonly measured using image analysis of roots growing in transparent pots (rhizoboxes), where the length of the root system of the target plants is tracked. However, tracking roots with a soil background can be highly challenging, particularly in competition studies, where two or more root systems are intertwined within the same experimental setup. In this study, we propose a new approach for measuring directional root placement in competitive setups, with two methods that calculate the centroid of the root system without measuring overall root length. In the first method, the centroid is calculated by marking all the intersection points of the target plant roots along a fixed number of equally spaced horizontal lines superimposed on the image. In the second method, the centroid is calculated from a contour line (polygon) created by marking only the peripheral intersection points. We developed an open-access, interactive Python algorithm that automates and standardizes the centroid calculation for both methods. We validated these methods by comparing them to the centroid calculated from the traditional root length measurements using results from two rhizobox competition experiments, with either uniform or patchy soil nutrient distribution. While the two methods offer a more rapid and standardized calculation of the root system centroid, they differ in their investment time vs. accuracy levels, particularly when root density is heterogeneous. By focusing solely on a few sample points from the root system or its contour line rather than tracking the entire root system, this approach offers a potentially faster way for measuring directional root placement. The centroid approach could therefore facilitate the study of plant responses to belowground competition, enabling more efficient tracking over time and across multiple samples.
Dataset DOI: 10.5061/dryad.xd2547dx3
This project contains two distinct file sets:
1. Centroid root code
2. Raw data
The file names and descriptions included in each fileset are detailed below:
1. Centroid root code files
* centroid_root.ipynb: The code for the three centroid methods of polygon centroid, sample centroid, and total length.
* README_for_centroid_root.md: Instructions and guidance for the centroid root code. In the code manuscript, this file is named README.md.
* centroid_calculation_example_img_one_neighbor.jpg: An image for demonstrating the code sample.
* centroid_calculation_example_img_one_neighbor.csv: The results of the three centroid calculations using the image example.
2. Raw data files
Hymenocarpos_circinnatus_data.xlsx: Raw data of Hymenocarpos circinnatus measurements.
- Plant ID: ID number of the rhizobox and target plant Hymenocarpos circinnatus.
- Neighbor density: a fixed factor with three treatments (0, 1, or 2 neighboring plants).
- Site: a random factor with the names of the native populations' locations in Israel.
- Block: a letter that indicated the block, according to which the plants were arranged on the experimental benches (12 treatment combinations per block).
- Relative root length: a response variable estimated per Hymenocarpos circinnatus plant, the directional root placement as the relative change in root length measured between two sections of the rhizobox.
- X value of total root centroid: a response variable estimated per Hymenocarpos circinnatus plant, the horizontal directional root placement by the total root centroid method. (cm)
- Y value of total root centroid: a response variable estimated per Hymenocarpos circinnatus plant, the vertical directional root placement by the total root centroid method (cm)
- X value of sample centroid: a response variable estimated per Hymenocarpos circinnatus plant, the horizontal directional root placement by the sample root centroid method. (cm)
- Y value of sample centroid: a response variable estimated per Hymenocarpos circinnatus plant, the vertical directional root placement by the sample centroid method (cm)
- X value of polygon centroid: a response variable estimated per Hymenocarpos circinnatus plant, the horizontal directional root placement by the polygon centroid method (cm)
- Y value of polygon centroid: a response variable estimated per Hymenocarpos circinnatus plant, the vertical directional root placement by the polygon centroid method (cm)
- Total root length: a response variable estimated per Hymenocarpos circinnatus plant, the total investment in roots by root length (cm)
- Polygon area: A response variable estimated per Hymenocarpos circinnatus plant, the extension of the root system(cm2)
- Empty cells represent unavailable data.
Pisum_sativum_data.xlsx: Raw data of Pisum sativum measurements.
- Rhizobox ID: ID number of the rhizobox and target Pisum sativum plant.
- Block number: number of the block, according to which the plants were arranged on the experimental benches (four treatment combinations per block).
- Neighbor size and density: a fixed factor with four treatments (Single Big vs. Single Small and Double Big vs. Double Small Festuca glauca neighbors).
- Directional root placement: a response variable estimated per Pisum sativum plant as the relative change in root length measured between two sections of the rhizobox.
- X value of total root centroid: a response variable estimated per Pisum sativum plant, the horizontal directional root placement by the total root centroid method (cm)
- Y value of total root centroid: a response variable estimated per Pisum sativum plant, the vertical directional root placement by the total root centroid method(cm)
- X value of sample centroid: a response variable estimated per Pisum sativum plant, the horizontal directional root placement by the sample root centroid method (cm)
- Y value of sample centroid: a response variable estimated per Pisum sativum plant, the vertical directional root placement by the sample centroid method(cm)
- X value of polygon centroid: a response variable estimated per Pisum sativum plant, the horizontal directional root placement by the polygon centroid method (cm)
- Y value of polygon centroid: a response variable estimated per Pisum sativum plant, the vertical directional root placement by the polygon centroid method (cm)
- Total root length: a response variable estimated per Pisum sativum plant, the total investment in roots by root length (cm)
- Polygon area: A response variable estimated per Pisum sativum plant, the extension of the root system (cm2)
- Empty cells represent unavailable data.
Sharing/Access information
If you need further information, please contact the corresponding author.
Changes after Mar 9, 2026:
Additional files were added to the repository.