Soil & Tillage Research 226 (2023) 105574

Contents lists available at ScienceDirect

Soil & Tillage Research

journal homepage: www.elsevier.com/locate/still

Applications of Computed Tomography (CT) in environmental soil and

plant sciences
Huan Zhang a, Hailong He a, b, c, *, Yanjun Gao d, Ahmed Mady e, Vilim Filipović f, g, Miles Dyck h,
Jialong Lv a, b, Yang Liu i, **
a
College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, Shaanxi, China
b
Key Laboratory of Plant Nutrition and the Agri-Environment in Northwest China (Ministry of Agriculture), Northwest A&F University, Yangling, Shaanxi 712100,
China
c
The State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, CAS&MWR, Northwest A&F University,
Yangling, China
d
Xi’an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi’an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi’an 710000, Shaanxi,
China
e
Soil Science Department, Faculty of Agriculture, Ain Shams University, 11241 Cairo, Egypt
f
Future Regions Research Centre, Geotechnical and Hydrogeological Engineering Research Group, Federation University, Gippsland, VIC 3841, Australia
g
Department of Soil Amelioration, Division for Agroecology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia
h
Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2H1, Canada
i
Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education) and College of Life Science, Northwest University, Xi’an, Shaanxi
716000, China

A R T I C L E I N F O A B S T R A C T

Keywords: Computed tomography (CT) in combination with advanced image processing can be used to non-invasively and
Plant Science non-destructively visualize complex interiors of living and non-living media in 2 and 3-dimensional space. In
Bibliometrics addition to medical applications, CT has also been widely used in soil and plant science for visual and quanti­
Image analysis
tative descriptions of physical, chemical, and biological properties and processes. The technique has been used
Solute migration
Computed tomography
successfully on numerous applications. However, with a rapidly evolving CT technologies and expanding ap­
Soil Science plications, a renewed review is desirable. Only a few attempts have been made to collate and review examples of
CT applications involving the integrated field of soil and plant research in recent years. Therefore, the objectives
of this work were to: (1) briefly introduce the basic principles of CT and image processing; (2) identify the
research status and hot spots of CT using bibliometric analysis based on Web of Science literature over the past
three decades; (3) provide an overall review of CT applications in soil science for measuring soil properties (e.g.,

Abbreviations: 2D, Two-dimensional; 3D, Three-dimensional; AFCM, Adaptive Fuzzy C-mean Method; AW, Amplitude-wavelength; BTCs, Breakthrough curves;
CAS, Cation adsorption sites; CDE, Convective dispersive equation; CEC, Cation exchange capacity; CO2, Carbon dioxide; CS, Silica-sol; CT, Computed tomography;
DECT, Dual-energy CT; DEM, Digital element method; DLR, Deep-learning reconstruction algorithm; DRP, Digital Rock Physics; ERT, Electrical Resistance To­
mography; EDS, Energy dispersive X-ray spectroscopy; FBP, Filtered back projection; FEGSEM-EDX, Field emission scanning electron microscopy coupled with
microanalysis; FTCs, Freeze-thaw cycles; GAM, Gamma ray attenuation method; GV, Gray value; KDW, Kinematic dispersive wave; Ks, Saturated hydraulic con­
ductivity values; KW, Kinematic wave; LB, Lattice Boltzmann; LSI, Loess structure index; MDLL, The mean diameter of the limiting layer; micro-XRF, Synchrotron
micro-X-ray fluorescence; MOSAIC, Morphological model; MRI, Magnetic resonance imaging; MS, Microspheres; NCT, Neutron computed tomography; NMR, Nuclear
Magnetic Resonance; OsO4, Osmium tetroxide; OTO, Osmium-thiocarbohydrazide-osmium; PT-CT, Photon counting computed tomography; PTFs, Pedotransfer
functions; PSD, Pore size distribution; RSA, Root system architecture; SART-TV, Simultaneous Algebraic Reconstruction Technique-Total Variation; SD, Standard
deviation; SEM, Scanning Electron Microscope; SMAS, Soil Microstructure Analysis System; SIP, Spectral induced polarization; SNR, Signal- noise ratio; SOC, Soil
organic carbon; SOM, Soil organic matter; SWRC, Soil water retention curve; SXRCT, Synchrotron X-ray computed tomography; SRXTM, Synchrotron Radiation X-ray
Tomographic Microscopy; SR-μCT, Synchrotron Micro X-ray CT; TLS, Total link strength; TMM, Truncated multifractal method; TOF, Time-of-flight; Vis-NIR, Visible
and near infrared spectroscopy; WDCs, Wetting and drying cycles; WoSCC, Web of Science Core Collection; XACT, X-ray induced acoustic computed tomography;
XAS, X-ray absorption spectroscopy; X-ray μCT, X-ray microtomography; γ-ray CT, Gamma-ray CT.
* Corresponding author at: College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, Shaanxi, China.
** Corresponding author.
E-mail addresses: [email protected] (H. Zhang), [email protected] (H. He), [email protected] (Y. Gao), [email protected]
(A. Mady), [email protected] (V. Filipović), [email protected] (M. Dyck), [email protected] (J. Lv), [email protected] (Y. Liu).

https://doi.org/10.1016/j.still.2022.105574
Received 25 March 2022; Received in revised form 22 September 2022; Accepted 28 October 2022
Available online 8 November 2022
0167-1987/© 2022 Elsevier B.V. All rights reserved.
H. Zhang et al. Soil & Tillage Research 226 (2023) 105574

porous soil structure, soil components, soil biology, heat transfer, water flow, and solute transport); and (4) give
an overview of applications of CT in plant science to detect morphological structures, plant material properties,
and root-soil interaction. Moreover, the limitations of CT and image processing are discussed and future per­
spectives are given.

1. Introduction characterization of the transport processes of solutes and environmental

tracers in soils or plants (Ziegler-Rivera et al., 2021), based on which we
Sustainable agriculture involves addressing the agricultural and can apply CT to trace and explain contaminant transport, spatial and
environmental issues we are facing in the present. Soils supports about temporal distribution characterization etc. For example, Gattullo et al.
95 % of agricultural production and is a critical resource on which we (2020) evaluated the chromium pollution of agricultural soils using CT
depend for survival (Borrelli et al., 2020). More than about 38 % of the and studied the distribution of chromium at different scales. Combing
world’s arable land has been persecuted by soil degradation since 1945 CT with fluorescence macrophotography, Soto-Gómez et al. (2018)
(Liu et al., 2010), and reports on regional soil degradation in areas such found that the average pore surface is linearly related to the dispersion
as the European-Mediterranean region are clearly state the increasing coefficient of bromide. Their results showed that the dimensionless
degradation (Ferreira et al., 2022a). Soil pollution is another cause of microspheres (MS) transfer coefficient between the matrix and the
degradation of valuable farmland resources, as the harmful elements macropores can well describe the retention percentage of colloidal
may enter the food chain through crops and grains that can even damage fluorescent microspheres. Scotson et al. (2021a) used X-ray CT to trace
human and animal health (Li et al., 2021b). Appropriate techniques are the activity of soluble iodinated contrast agent to simulate solute
required to better understand the properties and processes of soils sub­ migration in soil column. Their results indicated that plant roots are able
jected to degradation or pollution and to provide optimal growing to reduce the depth of solute penetration which was found to be corre­
conditions for plants. There are numerous techniques available to lated with the age of the plants. Kirk et al. (2019) used non-invasive CT
measure soil and plant properties (He et al., 2021a, 2018, 2021b), but scanning to image roots and bubbles in flooded soils and discussed the
very few of them are non-destructive and non-invasive. In recent years, emission pathways of carbon dioxide (CO2) generated from flooded rice
computed tomography (CT), which alleviates the need to disturb soil fields in conjunction with mathematical models. They concluded that
architecture, has become widely used (Baveye et al., 2022). the flux of CO2 through roots is equivalent to one-third of the daily
The non-destructive and non-invasive characteristic allows CT to photosynthetic fixation. These studies all have extraordinary implica­
perform visualization and quantitative analysis of the interior of porous tions for agri-environmental security.
structures (Haubitz et al., 1988). This feature makes CT scanning widely Given the importance and wide application of CT, a detailed
applicable in the field of earth and environmental research (Abdallah description of the principle and application of computerized axial to­
et al., 2021; Heijs et al., 1995; Ketcham and Carlson, 2001). In addition, mography appeared as early as 1999 (Duliu, 1999). Carlson (2006)
CT is suitable for most materials (except for some very dense objects) thoughtfully summarized and explained some professional terms that
and analysis can be performed regardless of the geometry of the object would appear during CT scanning for future generations. Probably
within the required dimensions. In addition, it requires little or no limited by technology before the early years, their focus was mainly on
sample pre-treatment (Pierret et al., 2002), which makes it attractive rocks and soil particles. It is worth noting that while the application of
and explains why it is becoming essential equipment in many disciplines X-ray CT to the study of granular geotechnical materials, coarse sands or
(Baveye et al., 2022). However, it should also be noted that the access to glass beads is intrinsically interesting, the ability of CT to visualize
CT scanner remains relatively limited for many institutions (related to complex soil structure and pore space is what needs to be explored as the
the cost of the device and required expertise) and the accurate analysis soil contain much more than just mineral particles. Therefore, the in­
of the resulting images is challenging and time consuming. The combi­ formation obtained in these idealized systems may deviate from the real
nation of CT scanning and advanced image processing techniques allows soil (Baveye et al., 2018). These past studies had a limited understanding
the sequential generation of a series of two-dimensional (2D) grayscale of the soil. Pires et al. (2010) provided the advancement of CT appli­
slice maps and the reconstruction of a complete three-dimensional (3D) cations in soil physics, but they limit their review to Brazilian related
sample, i.e., a stack of 2D slices (Fang et al., 2019a; Xiong et al., 2020; applications and lack a critical discussion of these applied techniques.
Zhang et al., 2019), allowing the construction of 3D models for nu­ With the rapid development of CT technology, the application areas of
merical simulation that can perform seepage simulation, heat transfer CT are expanding, which brings new challenges to the measurement
simulation, etc. (Li et al., 2021a; Yu et al., 2019). It also means that the process and image processing of CT. This is especially true with the
complex internal structure can be observed using CT in soils or plants, improved equipment and processing techniques for increasingly com­
given that the finite resolution of the CT meets the research objectives. plex and in-depth research questions in the soil or plant research fields.
These abovementioned characteristics (e.g., non-destructive and In addition, although review articles have been published in recent
non-invasive nature, visualization of soil/plant structure, rapidity, years, they have focused on the technical progress in imaging plant roots
combination with other techniques) expand the scope of research in soil and biological processes (Downie et al., 2015; Kumi et al., 2015; Pio­
and plant sciences using CT, making it suitable for studying complex vesan et al., 2021) or the evolution of microstructures (Tang et al.,
pore networks of soils (Xu et al., 2021b; Zhang et al., 2021c), the diverse 2022), with fewer case studies review of CT applications involving the
morphological structures of plants (Zhou et al., 2021), intersecting integrated field of soil and plant research.
rhizosphere soils (Vetterlein et al., 2021), and hydraulic properties In this general context, the objective of this study is to present an
(Schluter et al., 2020). For instance, analyzing and interpreting the updated review on CT applications in soil and plant sciences. The review
pyrolytic behavior of wooden species from a 3D perspective (Murai starts with a brief introduction of the knowledge and background of CT
et al., 2021; Zhou et al., 2021), monitoring the formation and recovery and the basic principles of image processing. The important advances
of embolism of xylem (Secchi et al., 2021), visualizing the voids in plant obtained in CT scanning in recent years are summarized and a series of
reproductive organs (Xiao et al., 2021), and revealing grain traits in targeted process parameters used for CT scanning and image processing
different crop species (Zhou et al., 2021) among others, CT scanning in related directions are collated. The energy types and limitations of CT
provides new insights into these studies that cannot be obtained via the suitable for different directions are also discussed. In addition, biblio­
traditional light or scanning electron microscopy analyses of thin sec­ metrics is used to map the research trend and research hotspots for
tions. Moreover, 3D visualization using CT allows a more detailed applications of CT. The example applications of CT in environmental soil

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H. Zhang et al. Soil & Tillage Research 226 (2023) 105574

and plant science in recent years are systematically reviewed. The re­ acoustic computed tomography (XACT) and photon counting computed
view ends with the existing knowledge gaps and future prospects beeing tomography systems (PT-CT) can be effective in reducing radiation
discussed. damage (Boccalini et al., 2021; Flohr et al., 2020; Kiji et al., 2020;
Maruhashi et al., 2019).
2. Basics of CT and image processing
2.2. Development of CT
2.1. Principles of CT
CT has evolved over multiple generations since its introduction.
The working principle of commonly used CT is based on the fact that Although X-ray CT is very instrumental and widely used for non-
different objects/components have different absorption rates for destructive visualization and evaluation of the interior of porous mate­
permeable rays (Yan et al., 2021). CT can be based on X-ray CT, γ-ray CT, rials, there are still uncertainties in many aspects of the measurements
neutron CT, and X-ray microtomography (X-ray μCT) according to en­ that require further calibration and optimization (Schmitt et al., 2018).
ergy sources and resolution. A highly sensitive detector is used to cap­ The uncertainty in CT dimensional measurements can arise from
ture the intensity of the rays attenuated by the sample, which is used as different measurement parameters and conditions (e.g., detection sys­
an analog signal input to process the data and reconstruct the image, or tem, dimensional resolution, radiation generation, and imaging pro­
to reconstruct the details of a certain area with the help of mathematical cessing) as well as from the material under investigation
algorithms. Different gray color levels are obtained in the reconstructed (Villarraga-Gomez et al., 2020), which requires calibration and opti­
image depending on the material and geometry, enabling real-time mization of parameters. For instance, Lin et al. (2019) calibrated the
observation and processing (Bonnet et al., 2003). Each slice of the CT center-of-rotation parameters by an automatic calibration method based
image is composed of a certain number of pixels with different gray on sinusoidal symmetry. Villarraga-Gómez et al. (2020) described that
levels ranging from black to white. Note that radiation with low atten­ the limitations of CT measurement range are primarily determined by
uation is shown in black, while high attenuation radiation is mostly the penetrating depth of X-rays through the materials. They argued that
assigned as white, with gray shading between black and white. For each CT measurement performance could be improved by effectively setting
pixel, the final display color of the pixel is determined by controlling the CT parameter constraints in terms of resolution and measurement range.
composite ratio of the three primary colors of R (red), G (green), and B Villarraga-Gómez et al. (2021) further utilized ray projection and radon
(blue). Therefore, RGB (0 - 255) images can be converted to grayscale spatial analysis to simulate X-ray traversal paths and to find the optimal
images (Panneton and Brouillard, 2009). These pixels of a slice are ar­ orientation of the estimated sample, i.e., the tilt angle of the rotation axis
ranged in a matrix, whose gray levels provide information on the X-ray in the region of 10 - 35◦ when the measured dimensional deviation is
attenuation of the corresponding sample material at each point in that minimal. The CT scanning method also changed from panning to spiral
slice or the cross-section (Azeredo et al., 2013). scanning (spiral CT scan) (Jacobson et al., 2000).
The scanning time of a CT device depends primarily on the sample In addition, improving the quality of CT images is one of the more
(size and resolution) and rotation (degree of rotation, rotation step, current research efforts to facilitate the applications of CT. Houston et al.
average number of frames in a single rotation). There is a tradeoff be­ (2013b) pointed out that the sharpness of the image is crucial for
tween the sampling time and the quality of the grayscale image. To determining the subsequent spatial segmentation of the pore space,
avoid detector saturation, the acquisition time is recommended to be in which requires a higher resolution at a cost of additional noise. The
the range of 40 % - 60 % of the acquired camera brightness (Vaz et al., intensity of X-rays directly affects the signal-to-noise ratio (SNR) and is
2011). In general, the X-ray spectrum used in conventional CT scanners critical to eliminate the effects of X-ray scattering on the quality of CT
has a polychromatic characteristic. Most reconstruction methods cannot images (Gao et al., 2021a; Zhang et al., 2021b). Although conventional
correctly check the nonlinearity of polychromatic X-rays (Cao et al., image reconstruction methods can obtain high quality images, they are
2018), which causes beam hardening that can lead to artifacts and limited by the reconstruction algorithms (e.g., the filtered back
degrade the quality of the reconstructed image (Yang et al., 2020). projection-FBP algorithm), whose assumptions (e.g., single X-ray photon
Better peak separation is observed with the application of filters. energy and uniform photon propagation direction) are difficult to meet
Research has shown that the efficiency of common aluminum filters was in reality. Deviations from basic assumptions in the acquisition of CT
about 10 % lower than filters made of materials such as copper, brass or images would reduce the accuracy of subsequent segmentation and
iron (Jennings, 1988), but a higher level of experience and skill is identification of image objects (Zhu et al., 2019)). Recently,
required to select the right filter and hardware thickness (Romano et al., deep-learning reconstruction algorithm (DLR) (Franck et al., 2021;
2019). Conventional CT scanners always integrate all signals of detected Higaki et al., 2020; Steuwe et al., 2020; Urikura et al., 2021) was
transmitted X-rays into a single attenuated signal and do not record employed to correct the noise attributes of CT images. A total variable
information about their respective energies (Si-Mohamed et al., 2017). (SART-TV) (Wang et al., 2021b) algorithm-based image reconstruction
Polychromatic CT based on photon-counting detectors works by can better suppress the artifact effect and fixed the problem of sinogram
acquiring several different energy data sets, which allow the energy loss for dual-energy CT (DECT) (Kawahara et al., 2021). Zhang et al.
threshold to be selected according to the application, and allow the (2021d) have alleviated the nuisance caused by the non-ideal focal size
detection of K-edges of a given element for more effective imaging of of the X-ray source for CT imaging and provided high quality images
specific substances (Si-Mohamed et al., 2017). In addition, synchrotron even under non-ideal X-ray source conditions. Alternatively, progres­
X-ray beams are typically mono-chromatic, i.e., have a specific, tunable sively shorter scan times (e.g., high-speed CT scans (Kureta and Iikura,
energy. Both polychromatic CT and synchrotron monochromatic X-ray 2009; Yan et al., 2021) could avoid motion artifacts (Hegazy et al., 2021;
beams can maximize signal-to-noise and have better spatial resolution Hsu et al., 2007). The scanning post hoc image summation method
while reducing the absorbed radiant energy (Melli et al., 2018). For (fused CT) reduces image noise (Kobayashi et al., 2020), while the
energy sources, the commonly used energy sources are ionizing radia­ addition of contrast agents (Aslan et al., 2020; Inose et al., 2021) en­
tion (X or γ rays, neutrons), optical, electronic, and ultrasound etc., all of hances the contrast and image quality of the study area.
which are nondestructive but each with particular advantages (Yan High-resolution chromatographic imaging instruments can be used
et al., 2021). It is worth mentioning that the hyperspectral CT introduces to acquire 3D images of porous materials (e.g., soil samples) and to
spectral reconstruction and identification techniques to achieve a com­ reveal its structure. It should be noted that quality of the CT image
bination of structural and compositional analysis. It includes X-ray should be priority. However, the image itself only is not sufficient for
fluorescence spectroscopy (XFS), X-ray diffraction spectroscopy (XDS), quantitative analysis, and image processing methods are needed to
X-ray absorption spectroscopy (XAS) (Fang et al., 2019b). X-ray induced extract and interpret useful information. It is still challenging for image

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H. Zhang et al. Soil & Tillage Research 226 (2023) 105574

processing methods to specify hole boundaries or analyze errors, dis­ unpredictable compared to reinforcement learning, natural learning,
tortions caused by CT reconstruction (Ojeda-Magaña et al., 2014; Zhao and deep learning. which will significantly improve the efficiency. The
et al., 2019). QCuts-3D that is based on unsupervised segmentation method (i.e.,
spectral clustering) for automatic segmentation makes it an attractive
2.3. Basics of CT image processing candidate for 3D aperture segmentation (Malik et al., 2022). In addition,
little difference is found in X-ray attenuation between water and organic
The main image processing tasks in order of processing include: noise matter and plant roots (Pot et al., 2015), and it is challenging to
reduction, edge enhancement, image segmentation, post-processing, distinguish between components of similar densities if X-imaging is not
and structure analysis (Schlüter et al., 2014). The most difficult and enhanced (Liu et al., 2012; Taina et al., 2008). The use of synergistic
widely studied part of X-ray CT images is commonly based on thresh­ unsupervised and supervised machine learning for image segmentation
olding and segmentation processes. X-ray CT analysis is widely related may be a promising solution for this (Alrfou et al., 2022).
to the thresholding step which is mainly attributed to the calculation Based on the X-ray CT images, Houston et al. (2017) summarized the
accuracy of soil porosity that is linked to the gray value. Gackiewicz currently available software tools and methods for evaluating the pore
et al. (2019) found that the range of the error which is related to the size distribution (PSD). They also evaluated the performance of seven
thresholding step was between 15 % and 40 % at the calculation of commonly used methods (i.e., Avizo, CTAnalyser, BoneJ, Quantim4,
visible total soil porosity and saturated hydraulic conductivity. DTM, DFS-FIJI, and 3DMA) on CT images of different soil types and the
Thresholding of the images must be completed prior to analysis ac­ results showed that PSD as pore volumes per class size derived from the
cording to different histogram shapes, spatial clustering, entropy, object first five methods agreed well with the analytical solution, while the last
attributes, spatial correlation, and local grayscale surface information two methods produced unstable results for complex soil samples. Lucas
(Sezgin and Sankur, 2004). These six categories are used to distinguish et al. (2021) developed a new method of Eulerian number Х joint
between particles and pores and to segment the grayscale map into a Γ-curves to investigate the pore connectivity of pore sizes of more than
binary image to smooth the particle and pore boundaries (Tang et al., three orders in magnitude. Information on pore distribution, fractal
2020). Various statistical and mathematical methods can be applied dimension and pore connectivity could be obtained from images
during this process. through quantitative image analysis tools such as AVIZO, VGStudio­
The widely utilized segmentation process mainly includes local MAX, and Image J, or even plug-ins for semi-automated image pro­
segmentation (Schluter et al., 2014) and global segmentation (Lav­ cessing like SoilJ (Koestel, 2018). However, Zhao et al. (2019) argued
rukhin et al., 2021) that are based on threshold processing. They transfer that many already developed integrated software (e.g., Image-Pro Plus,
images into discrete datasets in order to separate between the solid Photoshop, Image J and ArcView) and self-compiling algorithms (e.g.,
phase and soil porosity for the quantitative description of porous media. adaptive thresholding algorithm and fixed thresholding algorithm) have
The advanced segmentation techniques are mainly based on local seg­ difficulty in identifying irregular pores and fuzzy boundaries, so they
mentation methods, because the global segmentation method shows less recommend a clustering algorithm called Adaptive Fuzzy C-mean
capability dealing with local heterogeneity and is low in global robust­ Method (AFCM) with fuzzy decision making capability. Weller et al.
ness (Iassonov et al., 2009). Houston et al. (2013b) tested four (2021) established an open soil structure database for image analysis
threshold-based segmentation methods (e.g., Thresholding method by and modeling of soil structure, pores and other data. Such work is
Schlüter et al., 2010, Adaptive window Indicator Kriging by Houston far-reaching and substantially helpful to scientific researchers, but un­
et al., 2013a, Fully Automated Extension method based on Otsu by fortunately it requires users to upload images that have been segmented.
Hapca et al., 2013 and Global segmentation method by Otsu, 1979) Here, we also provide practitioners with a reference for imaging pro­
commonly used in soil research. The performance of the first three cesses and the selection of segmentation processing methods.
methods are stable in the image process but with different noise levels, An example of the imaging workflow to demonstrate the procedure
the first two methods tend to eliminate small holes and smoothen the for spatial detection and quantification of major pores, solids and
surface of larger holes (Houston et al., 2013a). Wang et al. (2021a) gravels in 2D CT soil images, as well as 3D reconstruction of binary
proposed that the pore structure of soil samples usually cannot be images is shown in Fig. 1. Table 1 collated some of the commonly used
reconstructed using a single threshold, and it is important to select the CT instruments and associated processing methods for soil and plant
appropriate thresholds for each CT image in order to ensure segmenta­ related analysis.
tion accuracy. Other commonly used alternatives of segmentation
methods include region growing (Gerke and Karsanina, 2021), water­ 3. Bibliometric analysis
shed algorithms (Sun et al., 2019), unsupervised learning and super­
vised learning (Chauhan et al., 2016) based on clustering, etc. The Web of Science Core Collection (WoSCC) Science Index Exten­
Supervised machine learning (e.g., Neural network, Random forest, sion (SCI-EXPANDED) contains high-quality publications for research
Support vector machine, Linear and logistics regression, and Classifi­ access since 1992. The literature dataset from January 1992 to
cation trees) that are trained the with well labelled data to better predict December 2020 was downloaded from the WoSCC on May 21, 2021 for
outcomes of new data/images are widely adopted (Lai and Chen, 2019; scientometric analysis. Two query sets were used to for mapping the CT
Sidorenko et al., 2021; Wang et al., 2022). However, it requires time, applications in environmental soil and plant related studies (query sets
efforts, and a team of data scientists with expertise and experience in 1) and in all disciplines (query sets 2), respectively. Only articles, notes,
specific subject to build, scale, and deploy accurate supervised machine letters, books/book chapters, data papers, database reviews, and re­
learning model (Hashemzadeh and Adlpour Azar, 2019; Piccoli et al., views written in English were retained. The results of the query sets 1
2019). Such requirements are especially challenging for image seg­ were imported into Endnote for manual filtering following the criteria
mentation of naturally heterogeneous materials such as soils and plants. presented in Fig. S-1. The search resulted in a total of 4,182 publications
In contrast, unsupervised learning techniques (e.g., Cluster algorithms, and only 1,770 relevant studies were included for analysis after
Hierarchical clustering, and K-means) based segmentation allow the screening.
model to work independently to discover information of unknown Bibliometric software tools (e.g., VOSviewer, CiteSpace, Histcite,
pattern or useful features for categorization without manual interven­ Gephi, Leximancer, etc.) allow the analysis of large amounts of literature
tion, more importantly they can perform more complex processing tasks data by means of both performance analysis and science mapping. They
and provide results for users in real time (Hapca et al., 2013; enable the presentation of the research state and emerging trends of a
Jafari-Marandi, 2021; Schlüter et al., 2010; Zhang et al., 2008), specific research topic or field (Feng et al., 2021; He et al., 2020; Zhang
although the unsupervised machine learning methods could be more et al., 2021a). In this study, VOSviewer (v1.6.15 (Van Eck and Waltman,

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H. Zhang et al. Soil & Tillage Research 226 (2023) 105574

Fig. 1. A case of an imaging workflow: spatial detection and quantification procedures and 3D reconstruction of major pores, solids and gravels in 2D CT soil images,
after (Ojeda-Magana et al., 2020). In this case, image segmentation was performed using standard clustering algorithms (k-Means, Fuzzy c-Means) and multilevel
thresholding methods (Otsu method), and the quality of image segmentation was evaluated based on NU values (a measure of regional nonuniformity based on
unsupervised methods). The closer the NU value is to 0, the better the segmentation is.
Reprinted from APPLIED MATHEMATICAL MODELLING, with permission from Elsevier.

2010), from Leiden University, the Netherlands) was used to carry out 3.2. Co-occurrence analysis of keywords
cluster analysis on keywords in literature. Algorithm of VOSviewer is
based on association strength and is preferable to other bibliometric A total of 652 keywords (filtered by keyword frequency ≥5 times)
software tools (Lan et al., 2022). It can effectively avoid label overlap were selected for research related to CT in soil and plant science, with
and directly reflect the weight of the analyzed data and the relationship the most frequent keywords being "computed-tomography", "agricul­
between the analyzed data (Fu Jian, 2019). ture", "engineering", "materials science", "geology", "plant sciences",
"soil", "environmental sciences & ecology", "quantification", "forestry".
3.1. Annual publication trend Fig. 3 shows a total of nine clusters of different colors, each one repre­
senting a corresponding research theme. The larger clusters are yellow,
The results of query sets 2 (252,825 studies) show almost the same blue, green, and pink, which represent the different directions of CT
trend as the query sets 1, but with a 100-fold magnitude (Fig. 2). This applications in soil and plant science, respectively. For instance, the
means that the application of CT has been in a booming state. yellow cluster focuses on agricultural soils and ecological issues, and
The results of Query sets 1 were divided into four groups that are includes "soil structure", "solute transport", "organic-matter", "water re­
closely related to plant or soil. The green and brown colors indicate sources and water-flow". The pink cluster concentrates on research on
studies directly applying CT visualization techniques in plant and soil geotechnical engineering. The green and blue clusters are both about
science only, respectively (Fig. 2). The number of publications of related plant science, but the green focuses more on forestry and material
studies was small until 2005, with less than 10-article each year. The properties of wood, while the blue focuses more on using CT tools to
number of publications started to increase since 2005 with fluctuations, show plant growth and root systems, as well as water use.
indicating that the application of CT in plant and soil sciences has
become increasingly popular. The blue bars started from 2002 refer to
publications using CT in geotechnical applications. The purple bars refer 3.3. Burst of keywords
to the CT related research work on interactions between plant roots and
soil, which started to grew slowly since its occurrence in 2006. A keyword with strong emergence can reflect a new perspective with
a high impact in a certain period of time, thus showing a phase of aca­
demic frontier. The word frequency exploration was performed in
CiteSpace, and the top 15 keywords related to CT scans in soil and plant
scientific research from 2010 to 2020 were used (Fig. 4). From

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Table 1
Selected computed tomography (CT) instruments and processing, modeling methods for soil and plant analysis.
Author CT model/parameters Resolution Image segmentation Other information
processing

Zuniga et al. Phoenix Nanotom X-ray μCT; Resolution of pores > Select two thresholds by Global segmentation technique, is a robust method when applied
(2019) 65–82 kV, 167–370 μA 60 µm (2 voxels) in applying Otsu algorithm to the image with low complexity
diameter twice
Budhathoki et al. Medical X-ray CT; 140 kV, Voxel size of 0.35 * Adaptive local threshold Used for processing low contrast images; can solve the problem of
(2022) 140 Ma 0.35 * 0.625 mm3 method uneven staining
Pot et al. (2020) HMX CT; 225 kV Spatial resolution is 24 Otsu’s global method Thresholding method based on clustering; the small pores are
µm and 54 µm segmented into continuous holes at high initial resolution; not
sensitive to noise reduction level
Hapca’s method Segmentation results are the most robust; porosity is less at the
point of minimum contraction; when the voxel strength is close to
the solid phase of liquid or oil phase, the performance is poor
Schlüter’s method Small pores are divided into independent clusters at high initial
resolution; penetration holes may break at high noise reduction
levels
Adaptive-window Indicator Small pores are divided into independent clusters at high initial
Kriging method of Houston resolution; when the solid phase dominates, porosity may be
masked
Martín-Sotoca Metris X-Tek X-ray micro-CT Resolutions of 30 µm The maximum entropy Thresholding method based on entropy information of gray
et al. (2018) system; 160 kV, 201 μA (voxel length size) method distribution; doesn’t particularly rely on bimodal histograms;
underestimated the true total number of pores
Singularity-CV segmentation High sensitivity; some small pores may be misidentified;
method underestimated the true total number of pores
Cheng and Wang The BL13W beam line of the – Improved region growing The interface of the lowest (P1) and highest (P3) phases is
(2020) Shanghai Synchrotron segmentation method effectively avoided to be misidentified as the P2 phase; more
Radiation Facility time-consuming; cannot be used for objects with more than three
phases
Lavrukhin et al. SkyScan-1172 XCT desktop Resolutions of Convolutional neural Independent, automatic, high throughput; prediction quality
(2021) scanner 15.85–15.88 µm network + local depends on the completeness of the real sample used for training
segmentation
Malik et al. (2022) – – Unsupervised QCuttS-3D Unsupervised, automatic, class-independent significant object
spectral clustering detection method; area boundaries can be better preserved;
segmentation method identification of changes in particle geometry is more robust
Sun et al. (2019) EinScan-SP 3D laser scanner Scanning accuracy is Improved watershed Suitable for separating particles in contact; overcome the
0.05 mm algorithm oversegmentation: not available for complex soils
Chirol et al. Nikon Metrology XT H 225 The voxel grid is 62.5 Hysteresis thresholding Can distinguish living roots from dead tissue; live roots attached
(2021) X-ray µCT; 205 kV, 46 µA µm method + Frangi filter outside the core are mistaken for necrosis; parameters need to be
manually selected in advance
Maenhout et al. ’HECTOR’ X-ray μCT 2000x 2000 voxels New division protocol Based on the protocol proposed by Pfeifer et al. (2015); root
(2019) scanner; 150 kV, 50 W; 0.5 volume segmentation was less affected by soil type; can be
mm Cu filter applied to complex root systems; time-consuming and requires
proactive intervention
RooTrak Free software packages; not suitable for large sample systems
such as mature plant roots
Region growing algorithm Calculate the tolerance value based on gray level; the scope of
for VGSTUDIO MAX 3.2 application is limited to small and uniform soil cores; tolerance
values need to be chosen carefully

2010–2015, research perspectives were mostly focused on the three- dissolution, solute transport, gas exchange, rheological properties, root
dimensional quantification of soil or plant health indicators by X-ray development, and biological activity of soils while preserving the
CT, including the aggregate structure of the soil and the spatial het­ integrity of the sample.
erogeneity of the voids around the structural units, water flow and
biology of the soil, and plant growth. From 2015–2020, a large number 4.1. Soil physicochemical properties quantification using CT
of qualitative and quantitative research cases on saturated hydraulic
conductivity and preferential water flow emerged, indicating that the 4.1.1. Soil pore space and pore network structure quantification
research area is more refined in terms of the hydraulic properties of soil. In terms of pores, soil structure can be defined as "the combination of
Particular attention is paid to the interconnection and comparison of different types of pores and aggregates" (Pagliai and Vignozzi, 2002).
values obtained from X-ray CT measurements with model parameters, Qualitative and quantitative soil pore structure is crucial for soil
which contributes to the accurate estimation of hydrodynamic behavior research, because the spatial arrangement and pore connectivity of soil
of soil. pores control the soil-plant-atmosphere interface (Dexter, 1988). The
difference in X-ray attenuation between soil pores and soil solid com­
4. CT applications in soil science ponents is significant and contrasting (Young and Crawford, 2004),
which make it relatively easy to distinguish pores in the CT recon­
Improvements in technology and equipment, as well as cost re­ structed images. Therefore, X-ray CT is widely used to describe the
ductions, have made CT available in soil science (Torre et al., 2020). shape, size, connectivity, arrangement, volume, distribution, geometry,
Petrovic et al. (1982) pioneered the application of CT in soil science and and orientation of pores to calculate soil porosity (Hu et al., 2020;
demonstrated a linear relationship between soil capacity and X-ray Peyton et al., 1992), as well as to scan the three-dimensional micro­
attenuation, opening up a grand opportunity to use CT in soil science. CT structure of soil aggregates (Alskaf et al., 2021; Pagenkemper et al.,
provides useful information to better understand and describe the 2015). The porosity of the soil (e.g., total porosity, microporosity,
porous media structure, hydraulic properties, heat transfer, carbonate macroporosity) can also be obtained from the gamma ray attenuation

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H. Zhang et al. Soil & Tillage Research 226 (2023) 105574

et al., 2020).
Soil pore network is complex and pore size distribution generally can
only be indirectly estimated through soil water retention curve (SWRC)
(Singh et al., 2021a). X-ray CT on the other hand provide precise and
effective characterization of the number, shape, size, orientation, con­
nectivity, curvature, and spatial distribution of pores, enabling the
acquisition of a complete 3D structure. However, the pore size volume
estimated by SWRC is usually larger than that calculated by X-ray CT
(Shein et al., 2016). In addition, only a small soil sample can be scanned
with the high-resolution X-ray CT (Singh et al., 2021b) which still pre­
sent a method limitation.
CT can be also employed to characterize the soil disturbance state
and damage. The mean density (MD) and standard deviation (SD) of X-
ray CT images are used to define the soil disturbance perturbation state
intensity, where the SD value is considered to be more appropriate (Li
et al., 2019). The CT scanning combined with 3D image reconstruction
technique could also be used to build soil morphology, which verified
Fig. 2. Annual analysis of publications on application and research of computer freeze-thaw cycles (FTCs) induced damage to soil microstructure (Fan
tomography (CT) technology in soil and plants science with query sets 1 (pillar, et al., 2021; Gao et al., 2021b; Liu et al., 2021b; Ma et al., 2021) and the
with a total of 1,770 publications) and all applications and research related to small pore expansion changes eventually formed cracks (Xu et al.,
computed tomography techniques with query sets 2 (line, with a total of 2021a). Xu et al. (2019) analyzed the crack morphology, shear strength
252,825 publications) based on the SCI-EXPANDED, SSCI, CCR-EXPANDED and under salt erosion and FTCs. Their results showed that the fractal
IC databases of the Web of Science Core Collection (WoSCC) between 1992 and
dimension implied structural damage and the spiral CT mean value
2020. The query sets 1 used for the literature search are: TS= ("gamma-ray CT"
behaved similarly to the variation of shear strength. Multiple FTCs leads
OR "X-ray CT" OR "computed tomography" OR "micro-CT") AND TS= ("soil" OR
"ped*" OR "ground" OR "plant" OR "wood" OR "flora" OR "botany" OR "vegeta*"
to increase total porosity, pore connectivity, total available water, and
OR "grain" OR "food" OR "timber" OR "root") NOT TS= ("medicine" OR "acro­ hydraulic connectivity (Liu et al., 2021a). If the soil was treated with
megalic" OR "patient" OR "operation" OR "human" OR "disease" OR "cancer" OR lime, structural damage could be reduced and the resistance of soil to
"coronavirus" OR "radiologists" OR "cardiac" OR "COVID" OR "surgery" OR freeze-thaw damages was improved (Nguyen et al., 2019). Mady and
"hepetic" OR "skele*" OR "dentine" OR "teeth" OR "canine" OR "pediatric" OR Shein (2020) used X-ray CT to monitor the changes in pore space during
"cervical" OR "intestines" OR "bubble" OR "bone" OR "chest" OR "pancreas" OR the wetting and drying cycles (WDCs). They found that the pore struc­
"mandibular" OR "dairy" OR "subgrade" OR "blood vessels"). Query sets 2: TS= ture differed under the two WDCs curves at the same soil water poten­
("gamma-ray CT" OR "X-ray CT" OR "computed tomography" OR "micro-CT"). tial, which could potentially explain the reasons of hysteresis in the
SWRC. Continuous WDCs increased soil porosity and improved pore
method (GAM), where the bulk density is the only parameter required to connectivity (Pires et al., 2020), and the magnitude of change in mac­
evaluate these pores (Pires, 2018). However, it should be noted that roporosity was greatest in clay-rich soils (Diel et al., 2019). Xu et al.
even though the advanced X-ray CT techniques have multiple advan­ (2020) found that the change of fracture rate in loess is synchronous
tages, only a relatively small fraction of pore scape (visible porosity) can with CT average value after WDCs. Yu et al. (2020b) suggested that the
be characterized in real soils, as a fraction of the pore space below the coefficient of variation associated with X-ray CT slices can reliably
scan resolution remains unidentified. evaluate soil heterogeneity.
Tillage directly affects porous media structure (Schluter et al., 2020; The conceptual model in conjunction with laboratory measurements
Zhou et al., 2013), which can be measured by the CT. The X-ray CT is needed to correctly describe and verify the complex soil pore structure
results showed that conventional tillage generally increases macro­ and properties (Lamande et al., 2021; Li et al., 2018). The loess soil
porosities (>500 µm) as well as anisotropy and fractal dimension of structure index (LSI) could be expressed as a nonlinear function related
pores, but interrupts vertically well-connected bio-pores, shrinkage to CT image parameters (Tang et al., 2021). Complex quantification of
cracks, and decreases biota (Guo et al., 2020; Hellner et al., 2018). While soil pore networks can also be achieved by multifractal model analysis,
no-tillage leads to increasing microporosity (100–500 µm) as well as the the gray value (GV) synthetic maps created with the truncated multi­
connectivity of pores (Guo et al., 2020). Bio-tillage is believed to fractal method (TMM) are able to resemble real CT soil images (Torre
improve soil structure (Elkins, 1985) and more intuitive evidence can be et al., 2020). The multifractal parameter is significantly correlated to the
achieved by CT to determine the effect of the resulting bio-pores on the macropore number and was the main variable controlling the expression
growth of plant roots (Zhang and Peng, 2021). The double logarithmic of the total porosity in the model (Ju et al., 2021). While Perrier et al.
stress-macroporosity diagrams (σPMP) based on X-ray CT studies indi­ (2021) discussed from several perspectives of mathematical modeling,
cated that a critical mechanical precompressive stress value appears to physical modeling, computer modeling, and statistical modeling, they
exist around 100 Kpa for strip tillage, cover tillage, and no-till, where the concluded that multifractal modeling for spatial distribution of soil pore
macroporosity and connectivity reach the irreducible minimum with and solid mass is not applicable. Tang et al. (2020) developed
considerable increases in anisotropy (Pöhlitz et al., 2018). In addition, MATLAB-program based soil microstructure analysis system (SMAS),
examination of soil from a 23-years experimental plots showed which can effectively identify soil microstructures and extract infor­
long-term manure can change the microstructure of the soil (Yu et al., mation accurately.
2020a), i.e., increasing the soil bulk density and decreasing soil porosity The accuracy of the description of the soil microstructure largely
(Zhou et al., 2013). Application of inorganic and organic compound depends on the resolution of the CT instrument. However, Baveye et al.
fertilizers tends to decrease soil bulk density and increase connectivity (2018) stressed that a portion of the soil pore space was still difficult to
(Fang et al., 2021; Lan et al., 2020). Moreover, rotation diversification identify even CT resolution could be increased to a fraction of a micron
was also believed to increase soil organic carbon (SOC) and improve soil (i.e., sub-resolution pores smaller than the resolution of the CT image).
pore characteristics (Singh et al., 2020a). Furthermore, An innovative solution for this issue is to concurrently scan soil samples
biochar-remediated soils would lead to significant pore network with three distinct X-ray energies and specific stains (Baveye et al.,
reconfiguration (Yu and Lu, 2019), while the distribution of soil pores 2017), which was then tested by Fonseca et al. (2019) who applied
was optimized in calcium lignosulfonate-modified swelling soils (Wu X-rays and γ-rays CTs to scan the same sample with a double ratio

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H. Zhang et al. Soil & Tillage Research 226 (2023) 105574

Fig. 3. Keywords co-occurrence network visualization is generated by VOSviewer. Each color represents a topic cluster, where the font size and density (background
color) of the keyword indicate total link strength (TLS). A greater font indicates greater TLS, and the closer the distance between keywords, the higher the relevance
of these studied topics.

soil samples over a wider range, from nm to mm, but at a cost of time
compared to X-ray CT scanning (Jaeger et al., 2009; Pohlmeier et al.,
2018). It is time consuming and laborious for the focused ion beam plus
scanning electron microscopy (FIB-SEM) that characterize the structure
of soils at the nanoscale level (Gerke et al., 2021).

4.1.2. Soil water and air quantification

Soil water and air movement are usually related to the pore size
distribution, as well as the connectivity and tortuous degree of pores
(Osozawa, 1998). In general, a large diameter and well-connected pore
network usually facilitates water penetration and gas aeration (Rabot
et al., 2018). As early as 1992, CT imaging was used to measure soil
water distribution (Hopmans et al., 1992) and indirectly infer soil hy­
draulic functions. Kido and Higo (2020) studied the connectivity be­
tween water and pores using X-ray μCT and related image processing.
They evaluated the morphology of soil pore full of water, liquid bridges,
and water-gas interfaces, the hydraulic conductivity is related to the
uniformity of porosity, pore size distribution, and pore connectivity
(Wang et al., 2021a). Mady et al. (2021) demonstrated that a greater
influence of mesoporosity than macroporosity on saturated hydraulic
conductivity values (Ks) of undisturbed soil core samples from four
Fig. 4. Information about keywords with the strongest citation bursts from depths (i.e., 5–10, 15–20, 25–30, and 40–45 cm) using X-ray CT. More
2010 to 2020 by CiteSpace. mesoporosity results in greater Ks, while more closed pores and poorer
poor connectivity lead to smaller Ks. The pedotransfer functions (PTFs)
method to evaluate the ray energy levels and mass attenuation. The used to predict Ks proposed by Koestel et al. (2018) is based on three
results indicated a maximum error of only 1.5 % compared to the parameters (i.e., the pore geometry factor, the critical pore diameter,
NISTXCOM database, which is promising for high-precision character­ and the effective porosity), the last two of parameters determining
ization of soil structure. The alternative is the use of 1H Nuclear Mag­ variation in Ks were calculated from X-ray CT measurements. Smet et al.
netic Resonance (NMR) relaxation to assess the pore size distribution in (2018) reported that the usage of pore size distribution estimated by

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H. Zhang et al. Soil & Tillage Research 226 (2023) 105574

X-ray CT images increased accurate estimation of SWRC and hydrody­ osmium-thiocarbohydrazide-osmium (OTO) was also used as alternative
namic behavior. In fact, the transport of water and air is limited by the for staining to reduce the risk OsO4 (Arai et al., 2019). In addition, liquid
soil layer with the smallest macroporosity (Katuwal et al., 2015b). In the and gaseous iodine (I2) and heavy elements (e.g., Ag, Cu, Co, Fe, Mn, Mo
case of low water potential, Zhang et al. (2019) stated that the estima­ and Zn) are often used for staining, with Ag performed best among the
tion of Ks and air permeability are more correlated with the mean heavy elements as other heavy elements are naturally present in the soil.
diameter of the limiting layer (MDLL, the layer with the lowest value of Under K-edge SR-μCT scanning, gaseous I2 was treated more effectively
macroporosity) than other pore characteristics (e.g., total porosity, than Ag (Lammel et al., 2019).
connectivity, etc.) derived from X-ray CT. Schluter et al. (2020) In addition, samples for CT scan are usually prepared with resin
restructured pore structures with CT images for Stokes-Brinkmann embedding techniques that immobilize the sample and better preserve
solvers to model saturated and near-saturated water flows under the sample microstructure. However, all resins contain carbon that in­
different tillage treatments. The resulted Ks was greater than estimated fluence mapping organic carbon concentration distributions (Koestel
Ks with Hood Infiltrometer and Tension Disc Infiltrometer and best et al., 2022). Moreover, organics with more double bonds lead to
correlated was established with pore space attributes. stronger signals, which requires to systematically study the correlation
The sensitivity of magnetic resonance imaging (MRI) to 1H makes it of osmium signal strength with the organic type (Peth et al., 2014). It is
ideal for studying aqueous liquids (Carlson, 2006), but it can cause also not possible to stain the fraction of SOM that cannot be represented
distortions in the generated MRI images if the porous medium has an by unsaturated carbon as well as the fraction of SOM that OsO4 cannot
inherent relaxation time (Sadeghi et al., 2017). Another commonly used diffuse (gas phase) and permeate into soil matrix. For SOMs with sizes
non-invasive technique, Electrical Resistance Tomography (ERT), uses below the effective resolution of CT, it is difficult to detect the absorbed
the electrical conductivity of water to distinguish between the effects of stain in order to provide sufficient contrast for SEM/EDS and μCT ana­
capillary barriers, water movement, and steam intrusion in complex lyses (Arai et al., 2019). SR-μCT has the best resolution of μCT to detect
geological environments (Daily et al., 1992; Ramirez et al., 1993). SOM (Lammel et al., 2019), but its high expense limited its broader
Cimpoiasu et al. (2020) compared ERT and X-ray CT and developed a application. Overall, stains have the potential to identify discrete SOMs
new relationship for the data conversion between them, which could be in soil, while staining make it more difficult to segment CT images.
conducive to our further exploration of soil hydraulic function. How­ Alternatively, it is also possible to quantify SOM without staining.
ever, it is noteworthy that CT is still not flexible enough to realize on-site Neutron CT and X-ray CT imaging have received attention due to their
delayed monitoring (especially for the movement of water vapor in complementary attenuation properties. Koestel et al. (2022) introduced
pores) (Liu et al., 2022). In addition, CT is not suitable for soils where time-of-flight (TOF) neutron imaging into soil research, and combined it
most of the pores are finer than the CT resolution, because CT images of with X-ray CT imaging to map soil SOM concentration and minerals.
such soils do not reveal any of the underlying architecture, pore ge­ However, their findings argue that this combination is not suitable for
ometry, or pore connectivity. distinguishing SOM and clay minerals at the voxel scale, because it was
Entrapped air in near-saturated and saturated soils, mainly in the impossible to differ SOM from clay minerals, especially when these
form of single pore bubbles, clusters or ganglia, may clog the pores and components were mixed together. In addition, the low SNR of current
thus affect water transport (Faybishenko, 1995). CT scanning combined TOF neutron imaging poses a challenge for image analysis.
with the priming and infiltration tests were used to obtain information
on the spatial distribution of bubbles, together with image processing to 4.1.4. Other soil properties quantification
obtain the morphological information on the size, shape and thickness of CT can also be used to better understand soil heat transfer, which is
bubbles (Muller et al., 2019a; Princ et al., 2020). If the morphology and largely determined by soil water content, bulk density, soil mineralogy,
transformation of pore air and pore water in the two phases of drying and porosity etc (He et al., 2018; Liu et al., 2021c; Zhao et al., 2022).
and wetting were specified by scanning at different water retention During the drying process, X-ray CT estimated total porosity (and mes­
states, this would be useful to elucidate the reasons for the lag in the soil opore content) were negatively correlated with the soil thermal diffu­
water characteristic profile exhibited after drying or wetting (Kido et al., sivity and conductivity as well as volumetric heat capacity (Mady et al.,
2020). However, it should be noted that X-ray CT analysis is often based 2020). In addition, Mady et al. (2020) reported that the influence of
on local tomography, multiresolution analyses are required to obtain a visible total porosity is larger than pore size distribution (mesopores
global view of the whole sample. content) on the values of soil thermal diffusivity and other soil thermal
parameters (soil thermal conductivity and volumetric heat capacity).
4.1.3. Soil organic matter quantification In addition, CT images have been used to determine the effective
Combination of CT with other methods (staining or labeling) can be cation exchange capacity (CEC) of soil cores (Keck et al., 2017) and soil
used to facilitate visualization of soil organic matter (SOM). Because the colloids (Scotson et al., 2019). Because of the high adsorption affinity
X-ray attenuation coefficient of SOM lies between the pore space and the between Br2+ and cation adsorption sites (CAS), Keck et al. (2017) used
soil matrix, and the SOM is closely related to the mineral surface, it is Br2+ as a contrast agent to visualize CAS bound by Br2+ in 3D images
difficult to separate it in the image using CT detection alone (De Gryze reconstructed by X-ray CT by differential imaging technique, which was
et al., 2006). For example, CT can be combined with staining technology used as an indicator to measure CEC. However, this method also suffers
to identify SOM (Chenu and Plante, 2006). Osmium tetroxide (OsO4) from estimation errors in some cases, for example, the CEC of organic
vapor can react with unsaturated carbon bonds in organic compounds matter-rich samples is overestimated and the CEC of clay-rich samples is
with a clear absorption edge at a specific photon energy. OsO4 was used underestimated. Leue et al. (2020) combined the image data measured
as a dye to locate the distribution of SOM in soil aggregates by Peth et al. by X-ray CT with OC content and CEC values for specific types of coat­
(2014). It is noted that OsO4 cannot dye all types of organic materials ings on the surface of soil core macropores for the purpose of quanti­
evenly (Zheng et al., 2020) and volatilized OsO4 is also toxic to human tative estimation. They found that OC content and CEC accounted for
beings. Maenhout et al. (2021) tested four alternative chemical stains, i. about one-third of all macroporous surfaces, and biopores dominated
e., lead nitrate (Pb(NO3)2), lead acetate (PbAc), phosphomolybdenic the storage of OC. They also noted that larger cores were more repre­
acid (PMA) and silver nitrate (AgNO3), to enhance the contrast of images sentative, but the resolution of the X-ray CT spatial measurements
in soils containing specific minerals. Their results indicated that only limited the size of the samples, and a regrettable drawback in their study
PMA was comparable in staining ability to OsO4, the other three stains was that the thickness of the macropore surface layer was not very clear
can only perform well in sandy soils. However, PMA infiltrated soils and was difficult to distinguish from the soil matrix. The use of other
suffered from only a small increase in X-ray attenuation when SOM was techniques (e.g., diffuse reflectance infrared Fourier transform (DRIFT)
subjected to polychromatic X-ray beams. Liquid-phase spectroscopy to obtain valid CEC information (Leue et al., 2019)), can

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yield more accurate information in smaller soil slices. To better describe 4.3. Using CT to quantify fluid migration in soil
soil processes, the spatial information from these 2D mappings can be
interpolated into a 3D image of the soil column. This versatile combi­ CT has also been used to monitor fluid transport in soils. In general, it
nation allows correction of geometric distortions in the 3D image caused provides the detection of the spatial distribution of chemicals after their
by the sample during the cutting process and also uses the CT image to application to the soil.
help map other soil chemical parameters, pointing to a future connec­
tion between the 3D visualization of not only the physical aspects of soils 4.3.1. Preferential water flow
but also their chemical characteristics (Hapca et al., 2011, 2015; Preferential water flow in soils is a widespread phenomenon, clas­
Schlüter et al., 2019). Interestingly, researches showed that combined sified as finger, funnel, and macropores (Lissy et al., 2020). Current
TOF neutron imaging and X-ray CT imaging is useful for the identifi­ research on preferential flow focuses on two extreme scales (pore scale
cation and characterization of substances such as plastic beads that are and larger management scales such as fields and watersheds) and the
larger than the pixel size of the detector (Koestel et al., 2022), and the continuum between them (Jarvis et al., 2016). The dye tracer technique
microplastics in the millimeter size range (Tötzke et al., 2021). is usually used as an effective and commonly used method to evaluate
preferential flow in soil due to its low toxicity, high visibility, high
4.2. Soil biology quantification mobility, and no accumulation in soil plants and animals (Sander and
Gerke, 2007; Yi et al., 2020), but it may be adsorbed to the macropores
Soil microbes (Juyal et al., 2019; Kravchenko et al., 2019; Portell walls and result in inaccurate and time-consuming estimates (Jarvis
et al., 2018) and macrofauna (e.g., ants, termites and earthworms (Cheik et al., 2016). In contrast, X-ray CT can accurately quantify soil pore
et al., 2019) as well as their activity dynamics (Ray et al., 2019) and space above the resolution and it’s possible to do dynamic experiments
burrow distribution (Schomburg et al., 2019; Zhang et al., 2018) are with smaller samples in a synchrotron that have been recognized
required to understand soil biochemical processes, but the complex worldwide. The combination of staining and CT imaging can monitor
heterogeneity and opacity of the soil environment makes such study the flow paths and preferential flows in soil porous systems (Sammartino
difficult to be conducted. Compared to the 2D methods, 3D techniques et al., 2015; Zhang et al., 2016), providing us with the possibility of
(e.g., X-ray CT) can describe the natural soil pore space-natural habitat in-depth understanding and analysis of flow mechanisms associated
more accurately (Balseiro-Romero et al., 2020). The behavior of earth­ with soil structure, from pore to pedon scales. However, the field of view
worms in the soil can be demonstrated by particle tracer in combination and image resolution are paradoxes (Jarvis et al., 2016) and there are
with X-ray CT (Capowiez et al., 2021). For example, Guo et al. (2021) changes in matrix conductivity between samples, which make it difficult
has shown that the earthworm activity increases soil anisotropy and to account for variability in tracer migration and mobility at low reso­
reduces pore connectivity, possibly because some earthworm species (e. lution (Katuwal et al., 2015a).
g. Lumbricus terrestris (Jegou et al., 1999) prefer to use burrows as per­ The combination of CT with numerical simulation has seen growing
manent structures. For microorganisms, soil aggregates affect significant trend in soil science. However, the success of numerical model simula­
soil microbial activity and distribution (Liang et al., 2019). Harvey et al. tions depends mainly on the values of its parameters. Can the structural
(2020b) suggested that microbial communities may be able to be pro­ data obtained from CT images replace the parameters of the water flow
tected by the complex porous structure of aggregated soils from specific model? Lissy et al. (2020) pointed out that the kinematic wave (KW)
environmental disturbances (e.g., heat stress). Ruiz et al. (2020) studied model overestimated the preferential flow in large pores, because the
the effects of soil nitrogen transport and concentration distribution on parameters of the dual porosity model need to be further related to the
microorganisms based on the obtained image model and the respiration actual sample structural properties. In general, the parameters of these
experiment of microorganisms. The use of CT to monitor microorgan­ models are obtained by inverse calculation and deduction of funda­
isms in soil habitats was described in detail by Harvey et al. (2020a). mental properties, but the operability of experiments and the complexity
Unfortunately, the examples given by Harvey et al. (2020a) only used CT of reasoning limit their applications. They coupled the improved kine­
to examine the habitat structure of microorganisms, and the inspection matic dispersive wave model (KDW) (Di Pietro et al., 2003) with the
of microorganisms often combined with methods such as microbial matrix flow equation to compare the two versions (classical: parameters
respiration and abundance, and DNA extraction. Limited by CT resolu­ obtained by inversion from calibration data; advanced: parameters
tion, there is currently no way to directly visualize bacteria and archaea evaluated from CT images) by experimental observations. In their ex­
in soil only by CT. Although in situ CT detection of fungi is hampered in periments, the inverse parameters provided a better simulation. In
some ways (e.g., high electron density of soils, and the same attenuation contrast, the advanced version overestimated the water exchange, but
of X-ray absorption between fungi and water (Falconer et al., 2012)), had the advantage of reducing the number of parameters that need to be
synchrotron X-ray computed tomography (SXRCT) revealed significant optimized. Li et al. (2020a) combined X-ray μCT and the Brooks-Corey
differences in hyphal morphology (Keyes et al., 2022). However, the model (Brooks and Corey, 1965) to predict the effect of capillary suc­
findings could not represent the hyphal population of the entire soil, as tion during water transport, they found that capillary suction is deter­
their method could only extract hyphal morphologies in soil pore space. mined by pore size and phase morphology simultaneously, and μCT has
Visualization techniques like Fluorescence staining stated in Section satisfactory results in obtaining parameters of air entry pressure and
4.1.3 to strengthen the contrast of target objects with background (Juyal pore size distribution index. For modeling of preferential flow, in
et al., 2021), and the integration of multiple techniques, as Schlüter et al. addition to providing commonly used pore parameters and permeability
(2019) discussed, may open up new avenues for research. parameters, CT also supports the construction of a pore topology
It is worth noting, however, that ionising radiation can be harmful to network model, which can be used to analyze flow characteristics. After
organisms and in severe cases can lead to damage to imaging features determining the ease of fluid flow in all voids, an algorithm is further
(Odstrcil et al., 2019). Therefore, it is necessary to consider the problem used to compare the road resistances of different paths in the topology,
of radiation dose without affecting imaging (Harvey et al., 2020a). In and the preferential path of fluid flow can be determined. For the se­
general, as mentioned by Vogel et al. (2022), interdisciplinary research lection of the preferential path, Ant Colony Algorithm, Genetic Algo­
combining soil structure and soil ecology is a possible way in the future, rithm, and Dijkstra Algorithm are the commonly used choices (Meng
which will help to understand the spatial development of soil organisms et al., 2020).
and realize the soil functions better, such as carbon sequestration and In general, modeling of soil preferential flow still needs to be further
turnover, the degradation of pollutants. investigated, especially in terms of correctly modeling water exchange
between the pore space and the soil matrix (Lissy et al., 2020) and
quantifying water fluxes, rainfall or groundwater recharge. It is expected

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H. Zhang et al. Soil & Tillage Research 226 (2023) 105574

that novel CT imaging techniques and processing tools can improve our 2019). The key to most flow studies involving neutron tomography is to
understanding of preferential and nonlinear transport processes in soils run them from dry conditions (Deinert et al., 2004; Tengattini et al.,
(Tan and Dong, 2022). 2021). In addition, the scattering effect of neutrons should be consid­
ered, otherwise the water content may be underestimated (Tengattini
4.3.2. Solute transport et al., 2021).
The two-dimensional velocity distribution of water and solutes in soil
cores can be determined by measuring breakthrough curves (BTCs), 5. CT applications in plant science
which further allows the development of functions for calculating the
pore water velocity distribution as a function of soil cores position Nowadays CT is mainly applied in anatomy and analysis of plant
(Anderson et al., 1992). Nondestructive in situ sampling techniques morphology and structure (McCoy et al., 2021), plant material charac­
(micro suction cups (Göttlein et al., 1996) and microdialysis method terization (Jaskowska-Lemanska and Przesmycka, 2021), detection and
(Hammarlund-Udenaes, 2017)) are usually required to establish the transport of solutes or components, and root structure and development
BTCs of soil solute concentration (Petroselli et al., 2021). Another in soil.
method to build BTCs is to collect leachate from soil columns (Hochman
et al., 2021), which can be combined with convective dispersive equa­ 5.1. Plant anatomy and analysis of morphological structures
tion (CDE) to simulate the spatio-temporal change of solute concentra­
tion (Zhen et al., 2017). In addition, the use of X-ray CT to observe soil CT has shown significant advantages for anatomical and analytical
solute transport processes usually requires the addition of tracers (e.g., studies of plant morphology and structure because of its non-invasive
contrast agents, adulterants, and heavy elements). Scotson et al. (2021a) detection properties. X-ray CT allows the reconstruction of the 3D ge­
employed soluble iodinated contrast agents to simulate field-applied ometry of flowers and the visualization of voids in the reproductive
solutes (e.g., soluble fertilizers or pesticides) and X-ray CT was used in organs of plants (Reich et al., 2020), which have been used to gain
combination with modeling to demonstrate the solute leaching process insight into the anatomy and internal organization of plant fossils,
in the field. Guber et al. (2021) showed a new segmentation method including the "monkey hair tree" in German lignite (McCoy et al., 2021)
based on the combination of mass calculation of dopant mass attenua­ and the fossilized fruits of the American genus Mauve (Manchester et al.,
tion coefficients in CT image voxels and mass conservation equations for 2021). Regarding the anatomical structure of Eucalyptus dry wood,
dopants in soil, which can more realistically describe the spatial distri­ quantitative and qualitative data on pits, thin-walled tissue, and others,
bution of soil liquids, but this can only be applied with dual-energy can be obtained in X-ray CT images (Ramos et al., 2020). Murai et al.
monochromatic X-ray beams. The use of single-exposure or (2021) focused on the internal structural changes of wood samples
dual-energy X-ray CT to identify heavy elements in soils was considered during pyrolysis and observed interstices within the wood. Similarly, CT
to be flawed, because ambiguities in the reconstructed images of the has been used to nondestructively study the tissue structure of plant,
former leads to errors and the latter appearing less reliable at atomic such as stem nodes and tree rings (Torres-Silva et al., 2020), extending
numbers greater than 40 (Nakashima, 2021). To solve this issue, the the study of plant pest damage (Schmidt et al., 2020). Vaz et al. (2020)
triple-exposure CT method that can identify different material compo­ used MRI, X-ray CT, and μCT to investigate symptoms of grapevine trunk
nents with the same or very similar attenuation coefficients is intro­ defects due to fungal infections. They showed that high resolution CT is
duced to identify heavy elements (Niu et al., 2020). Nakashima (2021) more advantageous in nondestructive identification. However, it has
used a triple-exposure X-ray CT method to nondestructively characterize also been argued that CT is not suitable for in situ testing of live trees
Pb concentrations in simulated contaminated soils. It is also possible to (Taskhiri et al., 2020b), because it takes time to capture from multiple
obtain distribution and migration information of elements or contrast directions. The reconstruction of the image is challenging if the sample
agents by superimposing fluorescent displays (Muller et al., 2019b) onto under test changs as it is difficult for CT to capture motion images.
the CT-obtained 3D pore network (Soto-Gomez et al., 2019). Gattullo Automatic detection techniques for wood defects are key to opti­
et al. (2020) investigated the microscopic and large-scale distribution mizing the value of forest products in manufacturing processes (Beau­
and morphology of soil chromium (Cr) contamination combining μCT, lieu and Dutilleul, 2019). Typically, the options to detect internal defects
Micro X-ray fluorescence (μXRF), and field emission scanning electron in trees include ultrasound techniques (Taskhiri et al., 2020b),
microscopy coupled with microanalysis (FEGSEM-EDX). Nevertheless, it three-dimensional stress wave imaging method (Du et al., 2018) and
is noted that tracer addition may make image processing more difficult synchrotron X-ray CT (Murai et al., 2021; Singh et al., 2020b). However,
sometime. The 4D description of 3D-CT image analysis based on time Saeidi et al. (2020) considered that acoustic waves cannot propagate
series will be very beneficial to the estimation of motion (Heyndrickx along a straight line in heterogeneous materials (e.g., oil palm trunks),
et al., 2018), which requires speeding up the establishment and appli­ making it harder for ultrasound to locate cavities in the xylem.
cation of 4D-CT models. High-resolution CT is limited by problems of size and distance, γ-ray CT
Neutron tomography is a commonly used method to measure the is too bulky for the equipment. They recommended microwave tomog­
flow and distribution of water (solute) in porous media (Zarebanadkouki raphy as it works by identifying the dielectric properties of the material
et al., 2015). Unlike X-ray CT, which is a function of atomic number and and is usually more suitable for identifying cavities. Given that plants
density, the principle of neutron tomography is based on the interaction are tissues with complex multicellular structures, Zhang et al. (2020)
of neutrons with nuclei, resulting in a strong reaction between neutrons developed a program for cell identification and quantification, suitable
and hydrogen. Therefore, the advantages of neutron CT lie more in the for analyzing the global nature of cells.
high sensitivity to light elements (e.g., water containing hydrogen, hy­ In addition, CT has great potential in the field of grain and fruit
drocarbons) and isotopes, the high penetration of metals (e.g., science. A detailed spatial description of the structural damage of seeds
aluminum, titanium, lead), and the much lower radiation damage than at different fertility stages could be provided with X-ray μCT visualiza­
X-rays (Tengattini et al., 2021). Some experiments have demonstrated tion tools (Zhou et al., 2020). Su and Xiao (2020) provided a solution for
that it can be used to quantify the advance of fluid fronts (Jailin et al., the identification and screening of chalky phenotypes in living rice seeds
2018; Tudisco et al., 2019). Although the motion of the fluid caused with High Resolution μCT. Van De Looverbosch et al. (2020) proposed
distortion of the reconstructed volume, the distortion problem might be an automatic identification and quality grading method for fruits using
partially overcome if the advancing velocity was measured at fronts with translational X-ray CT, which can later be applied for rapid sorting of
the same rotational direction (i.e., all fronts had the same type of fruits. Texture analysis of X-ray μCT images has also been shown to
distortion), or if the data were analyzed as a sequence of projected times distinguish rice grains from rice blast infestation (Srivastava et al.,
rather than as a reconstructed tomographic volume (Tudisco et al., 2020), and Synchrotron micro-X-ray fluorescence (micro-XRF)

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H. Zhang et al. Soil & Tillage Research 226 (2023) 105574

technique has been used to detect trace elements (iron and zinc) in root, techniques in root studies.
shoot, and grain sections in situ (Guo et al., 2022), which has However, CT sampling may underestimate root length (Perret et al.,
far-reaching implications for grain development and quality control. 2007), because fine roots below instrumental resolution and therefore
large number of small roots near the main root cannot be distinguished
5.2. Plant material properties quantification from the soil substrate (Fang et al., 2019a; Heeraman et al., 1997). It is
tricky for scientists to distinguish soil components (e.g., pore water and
Because the intensity of CT data or image property highly correlates organic matter) from plant roots (Karunakaran et al., 2015; Yang et al.,
with the density of the tissue material (Helgason et al., 2008), re­ 2017) as it shows similar signal as that of organic matter, although the
searchers have been inspired to apply CT scanning to quantify the significance of plant roots is widely acknowledged (Zhao et al., 2020).
properties of plant tissues (Kurei et al., 2021; Tao et al., 2020). For There are also researchers following the medical treatment using
example, synchrotron μCT was used to quantify the nanoscale defor­ contrast agents (Keyes et al., 2017), but it is complicated to estimate the
mation of individual wood cells (Sanabria et al., 2020) and to determine time and dose of contrast agents reaching the root system through the
the impact resistance of materials in the loading direction by segmenting plant. There are potential hazards of contrast agents for living plant
different types of cells by tracking their microscopic geometric changes bodies (excessive toxicity) that limit its applications (Scotson et al.,
during mechanical loading (e.g., tensile or compressive) (Matsushita 2021b).
et al., 2020). 3D imaging of X-ray μCT scanning has been used to reflect Another issue is that different root systems show similar grayscale
the true structure (Liu et al., 2020) and variation in the stem internodes values in CT images because of similar attenuation coefficients due to
of rice in order to identify important influences on collapse resistance in density, making them difficult to be identified separately. Mairhofer
rice. Stubbs et al. (2020) developed a method to determine the X-ray CT et al. (2015) used root cross-sections in combination with X-ray μCT data
strength versus material transverse elastic modulus to assess the spatial to describe the three-dimensional framework of multiple interacting
distribution of material properties of corn stover materials. The struc­ roots in the soil. Although their method was able to isolate the roots of
tural changes inside the test sample recorded by CT together with image different plants, the explanation for multi-root competition has yet to be
analysis and model building (Li et al., 2020b) enable the analysis of broken through. Chirol et al. (2021) developed a hybrid segmentation
stress characteristics, elasticity (Stubbs et al., 2020), and shear modulus method to visualize and quantify the spatial analysis of wetland roots
and viscoelasticity under the microstructure of real materials, which is and enhanced tubular structures with a "Frangi" filter to distinguish
less possible for regular methods such as bio-electron microscopy (Wang living roots from necrotic tissue, but the segmentation method has yet to
et al., 2020a). gain widespread acceptance. The root segmentation algorithm "Rootine"
(Gao et al., 2019b) and the subsequent version "Rootine V.2" (Phalempin
5.3. Presence and transport of substances in plants et al., 2021) was developed with higher detection accuracy, but seg­
mentation of root-stubble-soil complexes is still a big challenge. Zhao
Researchers have used CT image values to estimate the water content et al. (2020) performed 3D modeling of maize root stubble by seg­
of wood (Yasushi, 1992) and to determine the density of wood (Couceiro menting roots and stubble by means of variational level sets, but their
et al., 2020; Wang et al., 2020b). Ossler et al. (2021) visualized the method was not very effective in extracting multiple interacting lateral
spatial distribution of elements H\C\O in wood of different tree species roots. The scan-reconstruction-segmentation process takes a long time
and their biochar formation using both ex-situ neutron computed to­ because there are a lot of interactive parameter interpretation and
mography (NCT) and X-ray CT, but its resolution is still not desirable. optimization (Pfeifer et al., 2015), while manual segmentation is
The development of near-field X-ray holographic nano-tomography time-consuming and error-prone, requiring the development of an effi­
(XNH) (Schudel et al., 2021) can scan at very high resolution to visu­ cient and automated process (Gerth et al., 2021; Teramoto et al., 2020).
alize tiny structures (e.g., depressed membranes, cell wall surface
structures). McElrone et al. (2021) used this method to demonstrate that 5.4.2. Rhizosphere application
water flows primarily in discrete xylem along the axis of the tree trunk. The interaction between the soil and the root system plays a key role
The pathway of the modifier into the modified wood can also be ob­ in agro-environment. Compared to destructive methods such as digging
tained from X-ray μCT analysis (Softje et al., 2020), but the results may profiles and rinsing roots, CT provides insight into this interaction. On
be resolution dependent. As with soil, the addition of tracers is a routine the one hand, both the physical structure and chemical composition, e.
method for visualizing flow. Wascher et al. (2020) added an iodine g., nutrients (Gao et al., 2019a), of the soil influence root growth. In the
contrast agent to visualize the distribution and flow path of melamine X-ray μCT images, there was a strong positive correlation between root
resin in beech veneer. Bubba et al. (2020) treated time as the third volume and the surface/volume ratio of solids, which means that roots
dimension and proposed a method for reconstructing images of moving grew better in porous soil and the volume and surface of root decreased
objects from sparse dynamic data, which is responsive for capturing the in sites with high land use intensity (Kuka et al., 2013). Root diameter
motion transport process of perfused fluids such as contrast agents. In increased under soil compaction conditions, accompanied by swelling of
addition, CT was also used to detect and analyze the activity (Choi et al., the root tip (Tracy et al., 2012). Later, Tracy et al. (2013) explored the
2017; Himmi et al., 2016; Keszthelyi et al., 2016) and distribution effects of bulk density and texture on crop root development. Their re­
(Robin et al., 2018; Teixeira-Costa and Ceccantini, 2016) of animals or sults stressed that it is important to consider specific time points,
microorganisms (Lewinska et al., 2016) within plants. because the greater effect of bulk density on root system was manifested
at day 3, while the main factor became texture at day 10. In addition,
5.4. Study of root-soil integration Blaser et al. (2020) used micro suction cups and X-ray μCT to monitor
the dynamics of soil nutrients and the response of in situ root
5.4.1. Root system visualization morphology. Their results indicated that high NO-3 inhibited the growth
Understanding the root system structure and root growth state is of transverse roots and high NH+ 4 stimulated the formation of primary
essential for plant productivity. In the studies of plant root system ar­ lateral roots. In turn, root development can have an impact on the soil
chitecture (RSA) and root growth processes in soil, the opacity of the soil (Galdos et al., 2020). In some cases plant roots can make the soil denser
body affects direct visualization of root (Mooney et al., 2012). However, (Helliwell et al., 2019), which significantly reduces the water retention
conventional methods such as excavation and profiling are destructive capacity of the inter-rooted soil (Daly et al., 2015). In contrast, Hu et al.
and labor-intensive and CT becomes a powerful analytical tool (Metzner (2019) reported that the developed root system under shrub encroach­
et al., 2015; Rogers et al., 2016; Tumlinson et al., 2008). Anderson et al. ment resulted in increased soil macroporosity and connectivity. Floriana
(1994) pioneered the use of X-ray CT non-destructive detection et al. (2021) showed that the soil response to plant root growth is related

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to the initial soil capacity, such that this response shows swelling "single-mode" approach, and is likely to be the most popular
characteristics in denser soils and shows a slight shrinkage in looser imaging method in the future as it can identify features that
soils. In addition, the root system also leads to chemical changes in the cannot be distinguished in a single dimension (Lucas et al., 2020;
inter-root soil. For instance, the roots emit a variety of organic com­ Mitchell et al., 2021).
pounds that significantly increase microbial activity and dissolve iron (3) For the study of soil health, it is necessary to strengthen the
and sulfur elements near the root system (Veelen et al., 2020). application of CT to promote the understanding of soil health
Roots can actively detect pore spaces in the soil (Pfeifer et al., 2014). process from the micro scale. This would give insights into the
The root-soil interface is unique and critical, but it is not easy to role of microorganisms in soil carbon turnover and sequestration,
determine the soil-root contact. Schmidt et al. (2012) demonstrated that the formation of soil health and the characterization of the spatio-
X-ray μCT can determine the root-soil contact area in situ with an ac­ temporal evolution of biological communities, the efficient uti­
curacy of ± 3 %. Keyes et al. (2013) used Synchrotron Radiation X-ray lization of soil nutrients, and the environmental remediation of
Tomographic Microscopy (SRXTM) to show live root hairs of wheat and contaminated soil.
to assess root hair uptake of phosphorus. Daly et al. (2016) modeled (4) In an added bonus, a long-standing dilemma in CT scanning is the
nutrient uptake by root hairs based on structural X-ray CT images of relationship between resolution and sample size and scan size.
inter-root soil. It is also noted an increasing volume of studies on And limited by the resolution obtained by imaging tools, a large
inter-root bacterial microbial life activities (Ganther et al., 2020) and proportion of the sub-resolution pore space in soils are tentatively
inter-root soil solution organic matter (Lohse et al., 2020; Mawodza unidentifiable, where are important habitats for bacteria,
et al., 2020). archaea, and viruses in soils (Pot et al., 2022a). Therefore, ac­
Although CT scanning is considered a nondestructive detection curate imaging analysis of sub-resolution pore Spaces may pro­
technique that has little effect on soil and water properties with pre­ vide new insights into soil microhabitats and microbial activity,
scribed radiation dose, it has negative effects on plants (e.g., plant but this does not sound like something that we shall be able to
mutations in breeding) and organisms in the soil, especially at high achieve any time soon. More realistically, we should ensure that
doses of X-ray or γ-ray exposure (Magdy et al., 2020; Pérez-Jiménez the resolution of the CT images is as fine as needs to be. Efforts to
et al., 2020). But these radiation applied doses have not been measured develop a new generation of synchrotron quality X-ray sources
in most studies, but rather estimated by a RadPro calculator (v3.26). may allow us to look forward to the future use of relatively
Lippold et al. (2021) used actual measurements from plant growth ex­ inexpensive monochromatic X-ray beams, which will be of great
periments to test the estimates from the calculator and concluded that benefit in future research. For image reconstruction and pro­
the calculator was only suitable for assessing attenuation in air. In cessing analysis, there are different interpretations at different
addition, the use of appropriate radiation doses in plant growth exper­ resolutions, and it is difficult to compare between different means
iments was requested, and they suggested that the critical dose for plant of use, so we suggest that this needs a global map network to
growth barriers in a typical single pot scan was 1.2 Gy. distinguish and compare image processing tools and algorithms
used by scientists worldwide when applying CT in soil or plant
6. Conclusions and perspectives science research, to summarize commonalities and advantages, to
accelerate the establishment of standards, and that this map
The use of CT analysis techniques as a non-invasive analytical tool in needs to be kept up to date. For modeling, a new generation of
soil and plant science has been reported extensively. The basics of CT mathematical models should be developed to better derive in­
and image processing are briefly presented. A bibliometric analysis was formation from CT images, For instance, the introduction of dy­
performed to demonstrate the increasing trend on CT publications and namic soil structure in micro-scale modeling for soil
identify the research hotspots. CT applications in plant and soil science microorganisms (Pot et al., 2022b), more in-depth modeling and
were reviewed and discussed. The knowledge gaps and perspectives for analysis of soil fluid movement and root competition effects.
future study are: (5) For equipment, we summarized the different CT types and
different energy sources used in several popular application
(1) We must be aware that CT analysis is mainly used as a means to areas, and compared their limitations (Table 2). In general, CT
assess the structural characteristics of soils and plants, and that it scanning based on X-ray radiation is still the mainstream. Due to
has some shortcomings, such as the dynamics of solute transport, the complementary attenuation characteristics of neutron and X-
where the combination of complementary techniques (fluores­ ray, it is expected that their combined method will be applied in a
cence tracing, nuclear magnetic resonance, etc.) with other large number of fields. The future may belong to more accurate
techniques has become a trend. In future research, it is possible to tabletop multicolor CT or dedicated synchrotron monochrome X-
accelerate the construction and application of 4D-CT technology ray beam CT, owing to the call for high resolution and dedicated
in soil and plant science research, which will be very friendly for detection of specific substances. Dealing with the artifacts caused
the study of integrated disciplinary problems such as root-soil by beam hardening is an urgent problem to be solved in most
interaction and interfacial exchange, as well as the dynamic desktop X-ray CT devices, and more parameters may bring more
measurement of solute transport in soil and plants (e.g., transport subjective choices. The benefits of synchrotron are well estab­
and distribution of heavy metals in super-enriched plants), but lished. X-ray produced by synchrotron has the characteristics of
new 4D image analysis procedures needs to be developed (Fer­ high intensity, high collimation and tunability, which can effec­
reira et al., 2022b). Moreover, for studies related to plants and tively avoid the noise problem caused by scattered photons and
organisms, the use of radiation doses needs to be more careful. the beam hardening effect related to multicolor beams (Lav­
(2) CT instruments cannot distinguish liquid water, ice, and freezing rukhin et al., 2021). If routine access to synchrotrons can be
front in frozen soil, which limits the application of CT technology achieved in the future as technology advances, then dedicated
in frozen soils related studies. However, its combination with synchrotron monochrome X-ray beam CT may be more welcome,
MRI or NMR technology that can detect change in unfrozen water especially for specific substances or elements (Aidene et al., 2021;
content is promising to study freezing and thawing processes. Guo et al., 2022).
Methods like this combination of different technologies require
multiple modality imaging that can combine 2D and 3D data from Finally, it is expected that CT scanning would have great opportunity
multiple acquisition modes. It offers new perspectives across for future development in the directions of soil health and soil man­
scales/dimensions/technologies compared to the traditional agement, dynamic study of solute transport and visual presentation of

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Table 2 Table 2 (continued )

Methods and energy types used in different applications in recent years. Application Category Energy Advantages/
Application Category Energy Advantages/ Limitations
Limitations
ERT(Chaali et al., Conductance Monitor fluid flow;
Structure/ X-ray CT (Schluter X-ray Ubiquitous; device 2022) large-scale; two-
pore et al., 2020) access is relatively dimensional
easy; limited measurements;
resolution; artifacts cannot be used in the
caused by multicolor presence of
beams conductive materials
Dual-resolution X- X-ray Limited by sample (e.g. clay); surface
ray CT (Zeng size conductivity is often
et al., 2022) neglected
X-ray micro- X-ray Resolution is higher Spectral induced Conductance Coarse elements
computed than ordinary X-ray polarization (SIP) (with very low
tomography (Yu CT; micron level; tomography ( relaxation
et al., 2021) small sample size Revil et al., 2021) frequencies) were
SR-μCT (Ma et al., X-ray High resolution; high excluded; the quality
2021) collimation; of the forecasts needs
monochrome; micron to be further
level; global device evaluated
access is difficult Spectral X-ray (absorption High resolution; can
Dual energy X-ray and γ-ray Improve the computed spectra) identify minerals and
procedure (X, γ) effectiveness of X-ray tomography ( specific elements
rays CT (Fonseca CT; high precision Sittner et al., (such as heavy
et al., 2019) representation; γ-ray 2021) elements) in
CT requires a good materials; artifact
collimated narrow problem caused by
beam; time multi-color light
consuming needs to be solved
Organic Dual-energy X-ray X-ray Limited by sample Micro X-ray Fluorescent Problem of
matter/ μCT (staining size; limited by fluorescence ( radiation excited fluorescence
organism assisted) (Zheng dyeing effect; pay Gattullo et al., by an X-ray beam attenuation needs to
et al., 2020) attention to the 2020) be avoided
toxicity Plants/roots Microwave Electromagnetic Safe; low cost; easy to
SR-μCT (Lammel X-ray Same as above; can tomography ( wave use; limited
et al., 2019) reveal local mycelial Saeidi et al., resolution
morphology 2020)
Joint X-ray and X-ray and neutron Taking advantage of ultrasonic Ultrasonic No radiation damage;
time-of-flight the complementary tomography ( limited resolution
(TOF) neutron attenuation Taskhiri et al.,
imaging (Koestel characteristics of 2020a)
et al., 2022) neutrons and X-rays; ERT ( Conductance Same as above
inability to Giambastiani
distinguish SOM from et al., 2022)
clay minerals (at X-ray (μ) CT (Hou X-ray Subject to sample
voxel scale) et al., 2022) size; difficult to
X-ray CT (Cheik X-ray Same as above distinguish root and
et al., 2019) soil organic matter
μX-ray Fluorescent Problem of SR-μCT (Hou X-ray Same as above
fluorescence radiation excited fluorescence et al., 2022)
microscopy ( by an X-ray beam attenuation needs to Positron emission Electronic, X-ray Suitable for larger
Védère et al., be avoided tomography samples; fewer cases
2022) (PET)/CT ( in recent years
Water, gas, (Dual energy) X- X-ray Relatively common; Garbout et al.,
solutes ray CT (contrast increases the 2012)
(heavy medium) (Guber difficulty of Neutron Neutron Same as above; can
metal et al., 2021) segmentation; tomography ( visualize the roots in
elements) difficult to identify Mawodza et al., soils with high
heavy elements with 2020) organic matter
atomic numbers content; complexity
much higher than of segmentation
about 40
Triple-Exposure X-ray Heavy elements in
X-ray CT ( clay minerals can be freezing and thawing processes in frozen soils, which is expected to
Nakashima, 2021) identified; provide a reference for the promotion of CT technology in agriculture
complicated
and environment research.
operation
Neutron Neutron High sensitivity to
tomography ( light elements; high CRediT authorship contribution statement
Jailin et al., 2018) penetration; little
radiation damage; Conceptualization, H.H. and L.Y.; Methodology, H.Z.; Software, H.
high cost; high time
consuming; weak
Z.; Validation, J.L.; Formal analysis, H.Z.; Investigation, H.Z.; re­
neutron source; small sources, H.F.; Data curation, H.Z.; Writing – original draft preparation,
number of available H.Z. and H.H.; Writing – review & editing, H.H., A.M., M.D., and V.F.;
instruments Visualization, H.Z. and Y.G.; Supervision, H.H. and L.Y.; Project
administration, H.H.; Funding acquisition, H.H.; All authors have read

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and agreed to the published version of the manuscript. Azeredo, F., de Menezes, L.M., Enciso, R., Weissheimer, A., de Oliveira, R.B., 2013.
Computed gray levels in multislice and cone-beam computed tomography. Am. J.
Orthod. Dentofac. Orthop. 144, 147–155. https://doi.org/10.1016/j.
Declaration of Competing Interest ajodo.2013.03.013.
Balseiro-Romero, M., Mazurier, A., Monoshyn, D., Baveye, P.C., Clause, J., 2020. Using
X-ray microtomography to characterize the burrowing behaviour of earthworms in
The authors declare that they have no known competing financial heterogeneously polluted soils. Pedobiologia 83, 150671. https://doi.org/10.1016/j.
interests or personal relationships that could have appeared to influence pedobi.2020.150671.
the work reported in this paper. Baveye, P.C., Pot, V., Garnier, P., 2017. Accounting for sub-resolution pores in models of
water and solute transport in soils based on computed tomography images: are we
there yet. J. Hydrol. 555, 253–256. https://doi.org/10.1016/j.jhydrol.2017.10.021.
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