The automatic recognition and measurement of soil pore types by image analysis and computer programs

A system, ANOPOR, has been developed which uses the Quantimet 720 image analyser to recognize and measure the different types of pores in impregnated soil blocks. The system is concerned with three types of pores: channels, planar voids (cracks and fissures) and vughs but is not suitable for highly interconnected pore patterns. Each of the three types has a different origin and function and presents a different two-dimensional (2-D) shape when sectioned. A learning set consisting of these three pore classes was used to teach the system how to recognize statistically soil pores in images using measurements made by Quantimet. To describe the pore outlines in 2-D, shape factors giving the best class separation of the learning set in the pattern space were derived. Bayes equation was used to give the probability of a pore belonging to a particular class by comparing its position in the pattern space with the learning set. Class boundaries were determined which ANOPOR uses to allocate each pore in any image to the most likely class. The system measures the proportion of the pore space attributable to each class and the perimeter and intercept density for each. The system is used to measure the pore patterns in three soil horizons.     

Soil macroporosity evaluated by a fast image‐analysis technique in differently managed soils

Abstract

Porosity, pore size distribution and a pore shape factor were measured from resin impregnated soils by means of a fast technique of image analysis. Images are directly captured by a video camera from polished impregnated blocks. Micromorphology was also used to assist in the comprehension of soil porosity changes in three differently managed soils: dry‐farming plus tillage, irrigated plus grass‐covered, steppe natural soil. Under study, alluvial soils from a semi‐arid region in NE Spain.

Even if there are no significative differences in total macro‐porosity between the differently managed soils, pore size distributions are significatively different Both natural and irrigated permanently‐covered soils have a larger amount of pores bigger than 1 mm in diameter, most of them of biological origin, greatly favouring aeration. Tillage contributes significantly to change the relative distribution of pore shape: the amount of rounded pores (vughs) decreases and elongated pores as well as fissures appear.     

THE MEASUREMENT AND CHARACTERISATION OF VOIDS IN SOIL THIN SECTIONS BY IMAGE ANALYSIS. PART II. APPLICATIONS

Image analysis was used to measure and characterise the voids in two sets of soil samples; (i) a surface water gley soil of the Deighton series and (ii) soils from a compaction experiment. The results show that the Deighton soil contains two impervious horizons separated by a much more porous horizon. In all the horizons most of the pore space is due to pores >180μm diam. In the case of the soils from the compaction experiment compaction was shown to change the shape, orientation and size distribution of the pores considerably. The range of measurements demonstrates that image analysis is applicable to several areas of soil research.     

基于数字图像技术的土壤孔隙结构定量研究进展

土壤孔隙结构是土壤孔隙的形态大小、数量搭配和空间分布状况的综合反映，其结构的复杂性和异质性决定着土壤水分迁移、气体扩散和生物活动等过程。近年来数字图像技术的发展虽然实现了土壤孔隙结构的直接可视化和定量化，但孔隙提取的精度仍然受采样方法、设备分辨率和分割技术的限制。本文基于现有土壤孔隙研究方法的发展历程，以图像获取、图像分割和量化分析为主线，综述了当前常用土壤孔隙研究方法(间接法和直接法)的基本原理、主要步骤和优缺点，剖析了从图像中提取孔隙结构的分割技术，概括了孔隙结构的常用量化指标，最后针对现有研究方法存在的问题和不足，对未来研究方法的发展方向进行了展望。     

A comparative study of three methods of water removal prior to resin impregnation of two soils

The water in replicate samples from sub-surface horizons of a clayey and a fine-silty soil was removed either by oven-drying, freeze-drying or by acetone-replacement prior to resin impregnation. Pore space photograms (pores >60 μm diam.) from thin sections were analysed on a Quantimet 720 image analysing computer following each drying technique. During oven- and freeze-drying the clayey soil contracted considerably and subsequently satisfactory impregnation of these samples was either difficult or impossible. This macro-shrinkage caused a decrease in number and lengths of most planar pores and a decrease in size and number of all intra-aggregate pores. The loss in pore space and continuity obviously affected resin impregnation. The clayey samples in which water was replaced by acetone, and all samples of the silty soil, however pretreated, showed no measurable macro-shrinkage and all impregnated well. Oven-drying the silty soil appears to increase the porosity, causing an increase in size of all pores. A mechanism for this apparent enlargement is proposed. It is evident that acetone-replacement of the soil water prior to resin impregnation is the best of the three methods used here and should be seriously considered when image analysis is to be carried out on resin-impregnated blocks from soils of similar or related textures.     

Morphological determination of pore connectivity as a function of pore size using serial sections

The geometry of pore space in soil is considered to be the key in understanding transport of water, gas and solute. However, a quantitative and explicit characterization, by means of a physical interpretation, is difficult because of the geometric complexity of soil structure. Pores larger than 40 μm within two soil horizons have been analysed morphologically on 3-dimensional digital representations of the pore space obtained by serial sections through impregnated specimens. The Euler-Poincaré characteristic has been determined as an index of connectivity in three dimensions. The pore connectivity is quantified as a function of the minimum pore diameter considered leading to a connectivity function of the pore space. Different pore size classes were distinguished using 3-dimensional erosion and dilation. The connectivity function turned out to differentiate between two soil materials. The pore space in an upper Ah horizon is intensely connected through pores between 40 and 100 μm, in contrast to the pore space in the AhBv beneath it. The morphological pore-size distributions were compared to the pore-size distribution obtained by water retention measurements. The discrepancy between these different methods corresponds to the expectation due to pore connectivity.     

免耕制度下耕作土壤结构演化的数字图像分析

利用数字图像方法 ,研究了室内模拟和自然田间免耕下的土壤结构演化状况。图像定性表明随免耕时间的推移土壤中团聚体由小变大 ,土体逐渐趋于紧实。图像定量分析结果表明随着免耕时间的推移 ,小团聚体和小孔隙减少而大团聚体和大孔隙增加。田间土样的结果表明了自然的阶段性降雨对土壤结构可能具有一定的调节作用 ,但从图像与团聚体粒径分布和孔隙孔径分布的变化来看 ,免耕是否有利于土壤性质和农业生产尚很难确定     

Three-dimensional analysis of a loamy-clay soil using pore and solid chord distributions

Examples of pore and solid chord distributions obtained for ideal porous media are presented, and the distributions of the porous and solid phases of a soil have been studied by pore and solid chord distributions. Serial sections, 100 μm apart, were cut in a soil core, impregnated with resin, and images were obtained of them. The 2D images from 160 sections were used to build a 3D reconstruction of the core. The initial 2D images, the 3D reconstructed medium and 2D computed images from the latter were studied. We found that the solid matrix of the particular soil is homogeneous and isotropic at the scale studied, and it could be characterized with a single 2D image. For pores ranging from 500 μm to 2 mm we also found similar pore chord distributions for the 2D images in the three orthogonal directions and the 3D medium. A single 2D image can be used to study these pores. For larger pores more than one 2D image is required, and we showed that eight 2D images are sufficient to describe these pores.     

基于全卷积网络的土壤断层扫描图像中孔隙分割

针对土壤断层扫描图像中存在部分容积效应及因孔隙成分复杂、结构不规则等引起的分割精度低的问题,该文提出一种全卷积网络(fully convolutional network,FCN)土壤孔隙分割方法,为土壤科学研究提供技术支持。该文以黑土土壤断层扫描图像为研究对象,通过卷积和池化运算输出不同尺度的孔隙特征图;将孔隙的深层特征和浅层特征相融合,采用上采样算子对融合特征进行插值操作,从而输出孔隙的二值图。与大津法、分水岭法、区域生长法和模糊C均值聚类法(Fuzzy C-means,FCM)4种常用孔隙分割方法的对比结果表明,FCN法在低,中,高3种孔隙密度的土壤图像中优于其他4种方法。FCN法的平均分割正确率为98.1%,比4种常用方法分别高25.6%,48.3%,55.7%和9.5%;FCN法的平均过分割率和欠分割率分别为2.2%和1.3%,仅为次优方法(FCM法)的33.8%和23.6%。通过融合土壤孔隙结构的多重特征,FCN法能够实现土壤孔隙整体和局部信息的精准判断,为土壤学的研究提供了一种更加智能化的技术手段。     

The anisotropy of the structure and the microspatial pattern of the pores at the aggregate level of texturally differentiated soils

The anisotropy of the soil pores in texturally differentiated soils is an important soil-genetic index. The morphological study of thin soil sections with vertical and horizontal orientation showed that the pore space of a texturally differentiated light gray forest soil at the aggregate level of organization has isotropic, anisotropic, and partially anisotropic structures in the different horizons. In the horizons with a platy structure, the anisotropy of the pore space is largely determined by the anisometry of the structural units. In the horizons with a massive structure not separated into aggregates, the anisotropic indices can be related to the structural features of the recent and relic biogenic pores. To reveal the total anisotropy of the soil pore space, the most informative and genetically determined indices should be studied: the shape, area, and orientation of the pores. In the soil studied, the variation of the pore sizes in the vertical thin sections was higher than in the horizontal thin sections, which agreed with the concept of the anisotropy of the entire soil profile. The fixed vertical and horizontal orientation of the soil thin sections allowed the obtained results to be integrated into the full-profile anisotropy of the soil properties. The vertical thin sections were found to be of greater information value for the profile-genetic analysis of the structure and variability of the soil pore space than their horizontal analogues.     

Morphometric profiles of pore space in loamy soils of the forest and steppe zones of European Russia

A computer-based image analysis of vertically oriented thin sections was applied to study changes in the shape and orientation of fine soil macropores (d = 0.2−2.0 mm) in the profiles of soddy-podzolic soils and typical (migrational-mycelial) chernozems. Generalization of the obtained morphometric data was based on the theory of mereology, a scientific discipline studying the structure (part-whole relationships) of classified objects. As a first approximation, generalized data characterized archetypes of morphometric porespace profiles of the studied soils. The archetype of the pore-space profile of the soddy-podzolic soil consists of four components (meronyms) corresponding to the humus-accumulative, eluvial, textural (clay-illuvial), and transitional to the parent material (BC) horizons. Sharp boundaries between the upper horizons specify sharp changes in the studied meronomic indices of the shape and orientation of soil pores. The pore-space profile of the migrational-mycelial chernozem consists of two major components: specific pores in the granular dark-humus (AU) horizon and complex pore space of the BCA and BCca horizons that are poorly differentiated with respect to the shape and orientation of their fine macropores despite clear genetic differences between these horizons. Pore-space patterns in the lower (transitional to the parent material) horizons of the studied soils are characterized by the high degree of similarity (>75%). Pore-space patterns in the upper horizons of the studied soils are different; the level of their similarity does not exceed 24–41.5%. The results obtained in this study hold promise in the use of morphometric characteristics of the pore space in separate genetic soil horizons as meronyms composing archetypes of the pore-space profiles of different soils. Such archetypes may be used for diagnostic purposes as reference pore-space profiles of the particular types of soils.     

SW—Soil and Water: Transport of Particulate and Colloid-sorbed Contaminants through Soil, Part 2: Trapping Processes and Soil Pore Geometry

It was established in Part 1 that potential impediments to movement of colloids through soil can be subdivided into straining and filtration, depending on whether a particle has a dimension similar to pores (leading to physical trapping) or much smaller. Information about size distributions of particles was also presented in Part 1. Owing to the dependence of colloid or particle capture processes on the relative size distributions of the particles and pores, information about pore sizes distributions has been derived here (Part 2) from hydrological equations. Various approaches to extending this mathematical treatment to indicate when particles would be trapped by necks or irregularities in the pore are also presented. Results suggest that protozoan microorganisms (such as Cryptosporidium and Giardia) are the only colloidal contaminants with sufficiently large diameter to have their movement restricted by physical straining in the soil pores when water drains from the soil under gravity, but if the soil is very wet (near to saturation) even these will move without restriction.     

使用自由软件和便携式光学显微镜研究土壤孔隙特征

Total porosity (TP), determined by image analysis, pore type and pore size distribution were evaluated on impregnated soil blocks from an undisturbed Brazilian sandy loam soil using a digital portable optical microscope. The free software Image J (version 1.40g) was used for image analysis. Procedures for soil image collection and analysis were presented. The image analysis allowed the evaluation of pore sizes with diameters ranging from 20 to >1 000 μm. The following types of pores were also obtained: rounded, elongated and intermediate. The results allowed the characterization of the soil as moderately porous (TP=21.6%). Rounded, intermediate and elongated pores were responsible for 11.6%, 31.7% and 56.7% of TP. In relation to pore size 51.1% of TP was in the 100-500 μm size class and a third of TP came from the pores larger than 500 μm.     

MEASUREMENT OF PORE SIZES IN FINE-TEXTURED SOILS: A REVIEW OF EXISTING TECHNIQUES

Pore size distributions obtained from the relationship between moisture content and suction are not dependable in fine-textured soils because of shrinkage. To overcome this problem, methods such as nitrogen sorption, mercury intrusion porosimetry, non-polar liquid desorption and thin sectioning have been used. In order to pre-dry samples without changes in the pore system, freeze-drying, organic liquid replacement of soil water, and critical point drying techniques have been employed. These methods of soil drying and pore size measurement are described and compared, and the validity of their use in soil studies is examined. The measurement of pore sizes by water desorption is also discussed.     

利用计算机断层扫描技术研究土壤改良措施下土壤孔隙

为探明不同土壤结构改良措施（秸秆覆盖、免耕、有机肥、保水剂）对土壤孔隙特征及分布的影响,采用计算机断层（computed tomography,CT）扫描法定量分析了土壤孔隙的数目、孔隙度及孔隙在土壤剖面上的分布特征。结果表明：不同措施均提高了土壤总孔隙数、大孔隙数及0.13～1.0 mm孔隙数,且其孔隙度也相应提高。同时孔隙成圆率也得到了改善。各处理中以有机肥和免耕处理效果较佳,其次为保水剂和秸秆覆盖,对照最低。此外,不同措施显著提高了土壤的田间持水量和＞0.25 mm 水稳性团聚体含量,降低了土壤容重,且各处理中,仍以有机肥和免耕处理效果最佳,其田间持水量分别较对照提高了15.9%和16.4%,而土壤容重较对照降低了6.8%和8.8%。相关分析表明：田间持水量、容重和＞0.25 mm水稳性团聚体含量与土壤总孔隙度和大孔隙度呈显著或极显著正相关;而土壤容重对于总孔隙度和大孔隙度及孔隙成圆率呈显著负相关。     

Consequences of slotting on the pore characteristics of a sandy soil in northeast Thailand

In the sandy soils of northeast Thailand, root development is generally limited to the topsoil (0–20 cm depth) but a simple slotting intervention (20–40 cm) significantly increased the root frequency in the slotted material (E_slot) compared with the undisturbed subsoil (E horizon). The aim of this study was to investigate the consequences of slotting on the soil structure by analysing at different scales the pore characteristics of the original soil profile and of the soil material inside the slot. These characteristics were studied using bulk density measurements, image analysis of thin sections and mercury porosimetry. Our results showed that the total porosity of the E horizon and E_slot material was similar when measured in 100 cm³ cylinders, but that the pore size distribution had been changed by slotting. The unaltered E horizon contained mainly small pores characterized by a narrow distribution related to close packing of the sand grains, associated with some biological macropores probably with poor continuity as they did not contain roots despite their size. On average, pores were larger in the E_slot material, with a broader distribution resulting from looser packing of the sand grains but with fewer biological macropores. Although slotting reduced the number of biological pores, the looser packing appeared to be more favourable to root development than the presence of macropores in the E horizon. Finally, the comparison of the porosity in the different horizons with the porosity of the E_slot material, indicated the significance of the closeness of the sand packing on root development.     

Microtomographic analysis of pore space in a virgin soddy-podzolic soil

The method of X-ray microtomography was applied to study pore space of a virgin soddy-podzolic soil at the natural soil water content. The morphometric parameters of the pores of more than 100 μm in diameter were determined in the vertically oriented undisturbed soil monoliths (d = 3 cm, h = 3–4 cm) from the genetic horizons of the most differentiated part of the soil profile (the AY, AEL, EL, BEL, BT1, and BТ2 horizons). A tendency for the horizontal orientation of these pores was found in all the horizons, except for the humus (AY) horizon. Isolated vesicular pores of different sizes were abundant in the eluvial part of the profile. Numerous recent and relict phytogenic channels were found in the intraped mass of the BT2 horizon. Differently directed interfaces of structural units in the soil horizons were visualized. Cluster analysis was applied to estimate differences between the genetic horizons with respect to their textures, aggregate sizes, and shapes of pores as seen in vertical two-dimensional X-ray images.     

基于CT分析露天煤矿复垦年限对土壤有效孔隙数量和孔隙度的影响

露天煤矿排土场由于排土过程中大型机械压实等作用会对土壤的孔隙结构产生影响,重构适合于植被生长的土壤孔隙结构是排土场土地复垦的重要工作。为对排土场重构土壤孔隙结构进行定量分析,该文采用高精度无损计算机断层扫描技术(CT)对山西平朔矿区安太堡露天煤矿排土场平台全黄土母质覆盖的不同复垦年限(0、20、23 a)以及原地貌的土壤进行分层扫描成像,并利用Photoshop和Arcgis软件对扫描图像进行处理和统计分析,探讨了排土和复垦对土壤孔隙数量和孔隙度的影响,分析了排土场重构土壤大、中和小孔隙的变化。结果表明:原地貌土壤孔隙数量和孔隙度最大,其次是复垦23和20 a的土壤,排土后未复垦土壤孔隙数量和孔隙度最小。采矿和排土等活动由于大型机械压实作用降低了土壤孔隙数量和孔隙度,尤其是大孔隙数量和大孔隙度;土地复垦对增加土壤孔隙数量和孔隙度有一定的作用,但是过程比较缓慢。采矿和排土等活动对表层土壤孔隙数量和孔隙度的影响要高于底层土壤。该研究可为黄土区大型露天煤矿排土场重构土壤结构的优化与土地复垦措施选择提供依据。     

Structural differences between bulk and rhizosphere soil

The physical characteristics of the soil at the root–soil interface are crucial because they determine both physical aspects of root function such as water and nutrient uptake and the microbial activity that is most relevant to root growth. Because of this we have studied how root activity modifies the structure and water retention characteristic of soil adjacent to the root for maize, wheat and barley. These plants were grown in pots for a 6‐week growth period, then the soil adjacent to the root (rhizosphere soil) and bulk soil aggregates were harvested. These soil aggregates were then saturated and equilibrated at matric potentials between ?600 kPa and saturation, and the water retention characteristics were measured. From subsamples of these aggregates, thin sections were made and the porosity and pore‐size distributions were studied with image analysis. Both image analysis and estimates of aggregated density showed that the rhizosphere soil and bulk soil had similar porosities. Growing different plants had a small but significant effect on the porosity of the soil aggregates. Image analysis showed that for all the plant species the structure of the rhizosphere soil was different to that of the bulk soil. The rhizosphere soil contained more larger pores. For maize and barley, water retention characteristics indicated that the rhizosphere soil tended to be drier at a given matric potential than bulk soil. This effect was particularly marked at greater matric potentials. The difference between the water retention characteristics of the bulk and rhizosphere soil for wheat was small. We compare the water retention characteristics with the data on pore‐size distribution from image analysis. We suggest that differences in wetting angle and pore connectivity might partly explain the differences in water retention characteristic that we observed. The impact of differences between the water retention properties of the rhizosphere and bulk soil is discussed in terms of the likely impact on root growth.