The advent of X-ray Computed Tomography (CT) as a tool for the soil sciences almost 40 years ago has revolutionised the field. Soil is the fragile, thin layer of material that exists above earth’s geological substrates upon which so much of life on earth depends. However a major limitation to our understanding of how soils behave and function is due to its complex, opaque structure that hinders our ability to assess its porous architecture without disturbance. X-ray imagery has facilitated the ability to truly observe soil as it exists in three dimensions and across contrasting spatial and temporal scales in the field in an undisturbed fashion.
This book gives a comprehensive overview of the “state of the art” in a variety of application areas where this type of imaging is used, including soil water physics and hydrology, agronomic management of soils, and soil-plant-microbe interactions. It provides the necessary details for entry level readers in the crucial areas of sample preparation, scanner optimisation and image processing and analysis.
Drawing on experts across the globe, from both academia and industry, the book covers the necessary “dos and don’ts”, but also offers insights into the future of both technology and science. The wider application of the book is provided by dedicated chapters on how the data from such imagery can be incorporated into models and how the technology can be interfaced with other relevant technical applications.
The book ends with a future outlook from the four editors, each of whom has over 20 years of experience in the application of X-ray CT to soil science.
Author(s): Sacha Jon Mooney, Iain M. Young, Richard J. Heck, Stephan Peth
Publisher: Springer
Year: 2022
Language: English
Pages: 231
City: Cham
Foreword
Acknowledgements
Contents
Chapter 1: 40 Years of X-ray CT in Soil: Historical Context
1.1 Introduction
References
Chapter 2: Practicalities of X-ray CT Scanning for the Soil Sciences
2.1 Introduction
2.2 Manufacturers of μCT Systems
2.3 X-ray Sources
2.4 Detectors
2.5 Obtaining High-Resolution Images
2.6 Image Quality
2.7 Sample Manipulator
2.8 Configurations
2.8.1 Cabinet or Enclosure?
2.8.2 CT Scanning Methods
2.8.3 Software
2.9 Overcoming CT Artefacts
2.10 Evaluating a Potential X-Ray CT System
References
Chapter 3: Soil Sampling and Preparation for X-ray Imaging
3.1 Introduction
3.2 The Main Steps for Successful Sampling
3.2.1 What is the Aim of the Sampling
3.2.2 Where to Sample
3.2.3 Determining Sample Size
3.2.4 How to Orientate the Sample
3.2.5 Number of Samples
3.2.6 When to Sample
3.2.7 How to Sample
3.2.8 How to Document, Transport, and Store Samples
3.3 Representative Elementary Volume
3.4 Geospatial Sampling
3.5 Sample Preparation
3.5.1 Preliminary Laboratory Analysis
3.6 Conclusions
References
Chapter 4: Optimising the Scanning Process: Demystifying the Dark Art of Optimising Microtomography Scan Settings
4.1 Introduction
4.2 Preparing the Sample
4.3 Optimising the Image
4.3.1 Positioning the Sample in the Scanner
4.3.2 X-ray Voltage and Current
4.3.3 Detector Settings
4.4 Acquisition Modes
4.5 Conclusions
References
Chapter 5: X-ray Computed Tomography Image Processing & Segmentation: A Case Study Applying Machine Learning and Deep Learning...
5.1 Image Processing: Cropping and Filtering
5.2 Image Segmentation
5.2.1 Global Segmentation
5.2.2 Local Segmentation
5.2.3 Machine Learning-Based Segmentation as a Solution to New X-ray CT Imaging Challenges
5.3 An X-ray CT Image Segmentation Protocol Based on Machine Learning and Deep Learning Strategies: A Case Study
5.3.1 X-ray CT Image Acquisition and Preparation for the Machine Learning Pipeline
5.3.2 Machine Learning Pipeline
5.3.3 Deep Learning Pipeline
5.4 Conclusions
References
Chapter 6: Quantification of Soil Porous Architecture
6.1 Introduction
6.2 Quantification of Pore Structure
6.2.1 Metrics Based on Binary Image
6.2.2 Metrics Based on Connected Components
6.2.3 Metrics Based on Distance
6.2.4 Metrics Based on Pore Size
6.2.5 Case Study on Tillage-Induced Pore Structure
6.3 Scale Issues in Pore Structure Characterization
6.4 Correlative Imaging
6.4.1 Practical Issues
6.4.2 Software Implementations
6.5 Conclusions
References
Chapter 7: X-ray Computed Tomography for Studying Solute Transport in Soils
7.1 Introduction
7.2 Methods to Study Solute and Water Transport in Soils
7.3 CT Scanning for Estimating Solute and Water Transport
7.4 Limitations of CT Techniques for Estimating Water and Solute Transport through Soil
7.5 Conclusions
References
Chapter 8: X-ray Imaging of Mechanical Processes in Soil
8.1 Introduction
8.2 X-ray CT in Relation to Tillage
8.2.1 Visualisation and Evaluation of Seedling Growing Conditions Produced by Tillage
8.2.2 Macropore Structure and Functioning Affected by Tillage/no-Tillage
8.2.3 Using X-Ray CT to Predict Soil Fragmentation from Tillage
8.3 Soil Compaction Due to Traffic
8.3.1 Identification of the Long-term Effects of Soil Compaction
8.3.2 Segmentation and Compaction
8.3.3 From Soil Displacement to Stress Transmission
8.4 Visualisation of Soil Deformation
8.5 Conclusions
References
Chapter 9: X-ray Imaging of Root-Soil Interactions
9.1 Introduction
9.2 General Overview and Drawbacks
9.3 X-ray Dose
9.4 Opportunity In Situ over Time
9.5 Root Segmentation
9.6 Root System Architecture and Root Traits
9.7 Mutual Interaction of Roots and Soil Structure
9.8 Compacted Soils
9.8.1 Compaction of the Rhizosphere
9.8.2 Root-Soil Contact
9.9 Interaction with (Micro)Organisms
9.10 The Impact of Nutrition on Root Growth
9.11 Image-Based Modelling
9.11.1 Explicit Models
9.11.2 Root System Architecture (RSA) as Input for Models
9.12 Conclusions
References
Chapter 10: X-ray Computed Tomography Imaging & Soil Biology
10.1 Introduction
10.2 Soil Meso-Fauna and X-ray CT
10.3 Soil Microorganisms and X-ray CT
10.4 Indirect Use of CT to Observe the Outcomes of Microbial Activities
10.5 Effect of CT Scanning on Soil Organisms
10.6 CT and Soil Organic Matter Visualization
10.7 Conclusions
References
Chapter 11: Integrating X-ray CT Data into Models
11.1 Introduction
11.2 Direct Integration of X-ray CT Data-Derived Soil Phases into Image-Based Models
11.2.1 Integration of X-ray CT Data of Pore Space Geometry
11.2.2 Integration of X-ray CT Data of Air-Water Distribution
11.2.3 Integration of X-ray CT Data of Solid Organic Matter Distribution
11.2.4 Integration of X-ray CT Data of Roots
11.3 Overview of Image-Based Modelling Works
11.3.1 Modelling of Soil Physical Processes
11.3.1.1 Saturated Water Conditions
11.3.1.2 Unsaturated Water Conditions
11.3.2 Modelling of Biological Processes
11.3.2.1 Modelling of Microbial Activity
11.3.2.2 Modelling of Root Processes
11.4 Conclusions
References
Chapter 12: Future Perspectives
12.1 Introduction
12.2 Conclusions
References
