A comprehensive China topsoil dataset of high-resolution microstructure, topographical characteristics and physical properties

Soil microstructure regulates the transport and reaction of air, water, and nutrients within terrestrial ecosystems. However, high-resolution soil microstructural data remain scarce due to the inherent heterogeneity and opacity of soils as well as the technical and financial limitations of advanced imaging. In this study, we present a novel 3D soil microstructure dataset that integrates high-resolution imaging data of soils across China (CHARM3D) with comprehensive measurements of topological and physical properties to quantitatively characterize soil morphological parameters. The dataset comprises high-resolution X-ray computed tomography (XCT) reconstructions of 120 soil samples from 30 sites across six major Chinese ecosystems, with morphological, topological, and physical parameters derived through advanced image processing and pore-scale modeling. A case study analyzing representative samples from six ecosystems illustrates the dataset's ability to provide key parameters for reactive transport modeling, including pore connectivity, permeability, and porosity distribution. The dataset provides a general framework for characterizing porous media structure and supporting the calibration of soil hydraulic models, with potential applicability to other porous materials such as deeper soil horizons and rock samples.