Li et al. (2026) A comprehensive China topsoil dataset of high-resolution microstructure, topographical characteristics and physical properties

Identification

• Journal: Scientific Data
• Year: 2026
• Date: 2026-03-30
• Authors: Xueying Li, Huanyu Duan, Xiaofan Yang
• DOI: 10.1038/s41597-026-07049-x

Research Groups

• Guangdong Provincial Observation and Research Station for Coupled Human and Natural Systems in Land–Ocean Interaction Zone, Beijing Normal University at Zhuhai, China
• State Key Laboratory of Earth Surface Processes and Disaster Risk Reduction, Faculty of Geographical Science, Beijing Normal University, China

Short Summary

This study presents CHARM3D, a novel high-resolution 3D topsoil microstructure dataset for China, integrating X-ray computed tomography imaging with comprehensive measurements of topological and physical properties to quantitatively characterize soil morphological parameters across diverse ecosystems. The dataset provides crucial parameters for reactive transport modeling and calibrating soil hydraulic models, addressing the scarcity of such detailed soil microstructural data.

Objective

• To present a novel 3D soil microstructure dataset (CHARM3D) for China, integrating high-resolution imaging data with comprehensive measurements of topological and physical properties to quantitatively characterize soil morphological parameters.

Study Configuration

• Spatial Scale: 120 topsoil samples collected from 30 sites across six major Chinese ecosystems.
• Temporal Scale: Static snapshot of soil microstructure properties.

Methodology and Data

• Models used: Avizo 4.1, VG Studio Max 3.4, ImageJ/FIJI, MorpholibJ, COMSOL Multiphysics 6.3, Netfabb, JHNY-DPM V3, ilastik 1.4.0 for XCT data processing, reconstruction, image processing, morphological parameter calculation, pore-scale modeling, mesh generation, and permeability calculation.
• Data sources: High-resolution X-ray computed tomography (XCT) reconstructions of soil samples.

Main Results

• A novel 3D soil microstructure dataset for China, CHARM3D, was developed, comprising high-resolution XCT reconstructions of 120 topsoil samples from 30 sites across six major Chinese ecosystems.
• The dataset includes derived morphological, topological, and physical parameters such as pore connectivity, permeability, and porosity distribution.
• A case study demonstrated the dataset's utility in providing key parameters for reactive transport modeling.
• The dataset offers benchmark values of soil topological and physical properties for different soil types across various ecosystems, supporting the calibration of soil hydraulic models.
• The CHARM3D dataset is publicly available, providing 3D topsoil microstructures in TIFF format and a dataset of soil topological and physical properties.

Contributions

• Provides the first comprehensive, high-resolution 3D soil microstructure dataset for China, addressing a significant gap in existing literature due to the scarcity of such data.
• Integrates advanced XCT imaging with comprehensive measurements of topological and physical properties, offering a quantitative characterization of soil morphological parameters.
• Delivers a valuable resource for reactive transport modeling and the calibration of soil hydraulic models by providing key microstructural parameters.
• Establishes a general framework for characterizing porous media structure, with potential applicability beyond topsoil to other porous materials.

Funding

• Guangdong Provincial Observation and Research Station for Coupled Human and Natural Systems in Land–Ocean Interaction Zone (Grant No. 2024B1212040003)
• National Natural Science Foundation of China (Grant No. 42477214)
• National Natural Science Foundation of China (NSFC) Youth Student Basic Research Project (Grant No. 424B2019)
• Joint research project from the Comprehensive Survey Command Center for Natural Resources, China Geological Survey

Citation

@article{Li2026comprehensive,
  author = {Li, Xueying and Duan, Huanyu and Yang, Xiaofan},
  title = {A comprehensive China topsoil dataset of high-resolution microstructure, topographical characteristics and physical properties},
  journal = {Scientific Data},
  year = {2026},
  doi = {10.1038/s41597-026-07049-x},
  url = {https://doi.org/10.1038/s41597-026-07049-x}
}