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Proceedings ArticleDOI

A frequency spectrum-based processing framework for the assessment of tree root systems

08 Nov 2020-Vol. 11525, pp 310-316
TL;DR: This research aims to investigate the changes occurring in the frequency spectrum of the GPR signal during root system surveys, which will lead to the development of a new approach for investigating root systems using GPR.
Abstract: The monitoring and conservation of natural assets are nowadays increasingly important, as the emergence of unknown pathogens endangers tree survival. In this respect, root systems are affected by fungal infections that cause root rot and ultimately contribute to the death of trees. Such diseases can quickly spread to surrounding trees and affect wider areas. Since these decays do not usually show visible symptoms, early identification is key to the protection of trees. Within this framework, non-destructive testing (NDT) methods are becoming increasingly popular, as they are faster and more flexible than destructive methods. Specifically, ground penetrating radar (GPR) is emerging as an accurate geophysical tool for tree roots mapping. Recent research has focused on the implementation of automated algorithms for root mapping in a 3D environment and the investigation of root mass density. This research aims to investigate the changes occurring in the frequency spectrum of the GPR signal during root system surveys. To this extent, advanced signal processing techniques (both in time and frequency domain) are applied, to eliminate noise-related information and the disturbance induced by the presence of other features (i.e. pavement layers or underground utilities). The proposed processing framework can be applied for expeditious analyses or on trees difficult to access, where more comprehensive survey methods are not applicable. The results of the application of this methodology to a real-case scenario showed the potential of the applied procedure and will lead to the development of a new approach for investigating root systems using GPR.

Summary (2 min read)

1. INTRODUCTION

  • Trees and forests are invaluable components of humanity and wildlife.
  • In fact, they anchor the tree to the soil and provide support 7, absorb soil minerals and water, store nutrients and synthesise hormones 1. Different techniques were proposed to effectively map a given tree's root structure, which can be classified into destructive and non-destructive testing (NDT) methods.
  • The main aim of this research is to investigate the feasibility of a novel tree root assessment approach, based on the analysis of GPR data both in time and frequency domain.
  • The suggested processing system may be implemented for expeditious analyses or on trees difficult to reach, such as in some urban environments, where more comprehensive survey methods are not applicable.

2.1 Test Site and Equipment

  • The survey was carried out as part of a major research campaign in Walpole Park, Ealing, London (United Kingdom) .
  • A number of 24 circular scans were performed around the investigated tree, starting 0.50 m from the bark and spaced 0.30 m from one another, therefore surveying an overall area of 175.67 m2 around the tree.
  • The survey was carried out using the Opera Duo ground-coupled GPR system, manufactured by IDS GeoRadar (Part of Hexagon).
  • The system is equipped with 700 MHz and 250 MHz central frequency antennas.
  • Data were collected using a time window of 80 ns, discretised across 512 samples.

2.2 Data Processing

  • This stage aims primarily at reducing information on noise from the GPR data and at obtaining quantifiable information and easily interpretable images for the analysis and interpretation of data.
  • The raw data were hence analysed in both time and frequency domains, following a multi-stage processing procedure 28, 29: Zero-offset removal Time-zero correction Singular value decomposition (SVD) filter Band-pass filtering Subsequently, data were processed using a short-time Fourier transform (STFT) 30.

3.1 Target Identification and Application Windows

  • Figure 2 shows the radargram of the selected scan after the application of the signal processing techniques.
  • Inside, a smaller area was chosen on which to apply the STFT function.
  • Such area was chosen as it includes two relatively isolated hyperbolas of comparable shape, positioned one above the other at a distance of approximately 5 ns from each other.
  • The two hyperbolas are likely due to the top and bottom reflections of a structural root, with a diameter of about 0.15 m.
  • The selected area was then divided into 5 application windows, as shown in Figure 3.

3.2 Application of the STFT Function

  • Within each of the above-identified windows, the average value of the signal was calculated, which was subsequently used for the application of the STFT function.
  • Figure 4 shows the time-frequency analysis carried out using the STFT approach.
  • It is worth noting that the centroids of both areas are found in a frequency range between 500 and 700 MHz.
  • For all cases, the areas mentioned above are centred in a frequency range between 600 and 700 MHz.
  • Unlike window 0, in all other cases, the energy is attenuated less rapidly.

3.3 Error Maps

  • To analyse in more detail the differences in the behaviour of the STFT spectra between the two cases (i.e. root or horizontal layer), error maps have been created, given by the difference between the elements in the examined map and those of the reference map.
  • The presence of an area of positive energy is recurrent, centred around the 1000 MHz frequency, at an arrival time between 6 and 8 ns.
  • In order to observe the trend of these characteristics, compared with the response of the time-frequency analysis in the presence of a root, the spectra of the energy in the error maps were evaluated.
  • To this extent, a time window was selected, of width and depth equal to those of the reference hyperbola (i.e. between 4.5 ns and 5.5 ns), as shown in Figure 6.
  • The average spectra trend of the error maps within the selected time window is shown in Figure 7.

4. CONCLUSIONS AND FUTURE DEVELOPMENTS

  • This study presents the preliminary outputs of novel research within the context of the applications of ground penetrating radar (GPR) in detecting and assessing tree roots systems.
  • The primary aim of this research is to explore the feasibility of a new approach for tree root assessment, based on the time and frequency domain analysis of GPR data.
  • To this extent, a data processing framework was established, where advanced signal processing techniques were applied to eliminate noiserelated information and the disturbance generated by the presence of other features.
  • Besides, the latter allowed the detection of recurring patterns in the data analysis, proving this method to be worthy for further development and implementation in tree root systems’ assessment.
  • The preliminary results have shown the potential of this methodology which, if further investigated and automated, could be successfully used in urban areas, where some trees are difficult to access and to be thoroughly investigated.

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A frequency spectrum-based processing framework for the assessment
of tree root systems
Livia Lantini*
a
, Fabio Tosti
a
, Luca Bianchini Ciampoli
b
, Amir M. Alani
a
a
School of Computing and Engineering, University of West London (UWL), St Mary’s Road,
Ealing, London W5 5RF, UK;
b
Department of Engineering, Roma Tre University, Via Vito Volterra
62, 00146 Roma, Italy
ABSTRACT
The monitoring and conservation of natural assets are nowadays increasingly important, as the emergence of unknown
pathogens endangers tree survival. In this respect, root systems are affected by fungal infections that cause root rot and
ultimately contribute to the death of trees. Such diseases can quickly spread to surrounding trees and affect wider areas.
Since these decays do not usually show visible symptoms, early identification is key to the protection of trees.
Within this framework, non-destructive testing (NDT) methods are becoming increasingly popular, as they are faster and
more flexible than destructive methods. Specifically, ground penetrating radar (GPR) is emerging as an accurate
geophysical tool for tree roots mapping. Recent research has focused on the implementation of automated algorithms for
root mapping in a 3D environment and the investigation of root mass density.
This research aims to investigate the changes occurring in the frequency spectrum of the GPR signal during root system
surveys. To this extent, advanced signal processing techniques (both in time and frequency domain) are applied, to
eliminate noise-related information and the disturbance induced by the presence of other features (i.e. pavement layers or
underground utilities). The proposed processing framework can be applied for expeditious analyses or on trees difficult to
access, where more comprehensive survey methods are not applicable. The results of the application of this methodology
to a real-case scenario showed the potential of the applied procedure and will lead to the development of a new approach
for investigating root systems using GPR.
Keywords: Ground Penetrating Radar (GPR), short-time Fourier transform (STFT), tree root mapping, urban trees
1. INTRODUCTION
Trees and forests are invaluable components of humanity and wildlife. Oxygen provision, carbon storage, soil stabilisation,
food supply and wildlife habitats are only some of the natural heritage’s key benefits
1
. Besides, the impact that trees have
on human health and behaviour
2, 3
is a scientifically recorded evidence, as they contribute to noise and pollution mitigation
4, 5
and create an enjoyable environment for socialisation
6
.
Of all the tree organs, roots play a vital role in the health of plants and trees. In fact, they anchor the tree to the soil and
provide support
7
, absorb soil minerals and water, store nutrients and synthesise hormones
1
. Tree roots adopt stochastic
patterns that differ considerably from one tree species to another
8, 9
. Besides, tree patterns often relate to the tree's health
status and therefore have been extensively used in arboriculture applications as a diagnostic tool
10
.
Different techniques were proposed to effectively map a given tree's root structure, which can be classified into destructive
and non-destructive testing (NDT) methods. Excavation, uprooting and profile wall technique fall into the destructive
methods category
11
. Such approaches can also inflict permanent damage to the surrounding rhizosphere, apart from being
inefficient and not suitable for large-scale forestry applications
11-13
, and hence are not favoured by foresters and tree
agents. In comparison, NDT methods can map root patterns efficiently, without interfering with the host material and
irreversibly harming the tree. Several NDT methods have been employed for root-mapping, including X-ray tomography,
nuclear methods and magnetic resonance
14-16
, acoustic methods and electrical resistivity tomography
17
. Ground-
penetrating radar is an NDT method which covers a wide range of applications, such as civil and environmental engineering
applications
18
, landmine detection
19
and archaeology
20
. Due to its ease of use, versatility and high resolution, GPR is an
extremely attractive option for forestry applications. As such, GPR is becoming increasingly common amongst foresters
and tree officers as an efficient method to non-destructive estimate of root patterns
21-23
. Recent research concentrated on
automated root mapping algorithms within 3D environments
24
. In more depth, these studies focused on evaluating root

interconnections with nearby trees' root systems
25
, estimating the mass density of tree root systems and improving root
detection through advanced GPR signal processing technology
26
. Also, recent studies proved that GPR is an effective tool
for mapping the root system’s architecture of street trees
27
.
The present study reports the preliminary results of an experimental campaign conducted on a test site located in an urban
park in London, United Kingdom. The main aim of this research is to investigate the feasibility of a novel tree root
assessment approach, based on the analysis of GPR data both in time and frequency domain. The suggested processing
system may be implemented for expeditious analyses or on trees difficult to reach, such as in some urban environments,
where more comprehensive survey methods are not applicable. The specific objectives of this research can be outlined as
follows: i) understanding the influence of different features (i.e. roots, layers, etc.) on the time-frequency analysis of GPR
data; ii) identifying recurring patterns in the data analysis, in order to establish a repeatable data processing methodology.
2. METHODOLOGY
2.1 Test Site and Equipment
The survey was carried out as part of a major research campaign in Walpole Park, Ealing, London (United Kingdom)
(Figure 1). A number of 24 circular scans were performed around the investigated tree, starting 0.50 m from the bark and
spaced 0.30 m from one another, therefore surveying an overall area of 175.67 m
2
around the tree. Among the scans
mentioned above, the one located at 2.60 m from the outer surface of the trunk was selected for analysis purposes.
Figure 1. The investigated area
The survey was carried out using the Opera Duo ground-coupled GPR system, manufactured by IDS GeoRadar (Part of
Hexagon). The system is equipped with 700 MHz and 250 MHz central frequency antennas. Data were collected using a
time window of 80 ns, discretised across 512 samples. The horizontal resolution was set to 3.06 × 10
-2
m. In order to
achieve the optimal effective resolution, only data collected using the 700 MHz antenna were analysed. This choice was
due to the need to achieve a depth of investigation such as to analyse the whole tree root system, without excessively
affecting the signal resolution.
2.2 Data Processing
This stage aims primarily at reducing information on noise from the GPR data and at obtaining quantifiable information
and easily interpretable images for the analysis and interpretation of data. The raw data were hence analysed in both time
and frequency domains, following a multi-stage processing procedure
28, 29
:
Zero-offset removal
Time-zero correction
Singular value decomposition (SVD) filter
Band-pass filtering

Subsequently, data were processed using a short-time Fourier transform (STFT)
30
. This approach allows data to be
analysed in both time and frequency domain, by evaluating how the frequency spectrum changes with time, as follows:

󰇛
󰇜
󰇟
󰇛
󰇜
󰇛
󰇜
󰇠


(1)
where STFT is the frequency energy at time t and frequency ω, x is the reflected amplitude and w is the window function.
3. RESULTS AND DISCUSSION
3.1 Target Identification and Application Windows
Figure 2 shows the radargram of the selected scan after the application of the signal processing techniques. Inside, a smaller
area was chosen on which to apply the STFT function. Such area was chosen as it includes two relatively isolated
hyperbolas of comparable shape, positioned one above the other at a distance of approximately 5 ns from each other. The
two hyperbolas are likely due to the top and bottom reflections of a structural root, with a diameter of about 0.15 m. The
root interjects a semi-horizontal layer (presumably a geosynthetic layer), which is visible on both sides of the top hyperbola.
Figure 2. Radargram of the analysed scan. The red square identifies the selected application area.
The selected area was then divided into 5 application windows, as shown in Figure 3. Such windows, tailored to be as wide
as the reference hyperbolas, consist of 19 tracks (i.e. A-scan) each, with a width of about 0.55 m per window, for a total
width of 2.75 m.
Figure 3. Subdivision of the selected area into application windows.

3.2 Application of the STFT Function
Within each of the above-identified windows, the average value of the signal was calculated, which was subsequently used
for the application of the STFT function. Figure 4 shows the time-frequency analysis carried out using the STFT approach.
Figure 4. STFT spectra for the selected application windows
From the analysis of the STFT spectrum of the window 0, it can be seen how the energy is concentrated in two peaks, the
first centred at an arrival time of about 5 ns and the second at an arrival time of about 10 ns. This is then followed by an
energy drop between 11 and 14 ns. It is worth noting that the centroids of both areas are found in a frequency range between
500 and 700 MHz. Conversely, in the other windows, the energy is concentrated in a single peak, of greater intensity in
windows -2 and -1 than in windows 1 and 2. Consistently with the semi-horizontal trend of the layer, as highlighted in the
B-scan, the centroids of the areas of greatest energy are located respectively at 5 ns for the -2 window, at 6 ns for the -1
window, at 7 ns for window 1 and 4 ns for window 2. For all cases, the areas mentioned above are centred in a frequency
range between 600 and 700 MHz. Unlike window 0, in all other cases, the energy is attenuated less rapidly.
3.3 Error Maps
To analyse in more detail the differences in the behaviour of the STFT spectra between the two cases (i.e. root or horizontal
layer), error maps have been created, given by the difference between the elements in the examined map and those of the
reference map. Figure 5 shows the error maps created for the selected application windows, with reference to the window
0 STFT spectra.

Figure 5. Error maps for the STFT spectra, with reference to the window 0 STFT spectra.
It can be noted how some characteristics occur in all the error maps. For example, the presence of an area of positive
energy is recurrent, centred around the 1000 MHz frequency, at an arrival time between 6 and 8 ns. In the same way, it is
possible to notice in all the error maps a negative peak, also centred around the 1000 MHz frequency, at an arrival time
between 4 and 5 ns. In order to observe the trend of these characteristics, compared with the response of the time-frequency
analysis in the presence of a root, the spectra of the energy in the error maps were evaluated. To this extent, a time window
was selected, of width and depth equal to those of the reference hyperbola (i.e. between 4.5 ns and 5.5 ns), as shown in
Figure 6. The average spectra trend of the error maps within the selected time window is shown in Figure 7. It is worth
noting that the error maps' average spectra all have the same trend, with an energy peak around 250 MHz and a negative
peak between 600 and 800 MHz.
Figure 6. Selection of the time window for the analysis of the error maps spectra trend

Citations
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11 Dec 2020-Energies
TL;DR: A massively parallel simulation framework (PFLOTRAN-SIP) was built to couple SIP data to fluid flow and solute transport processes and was demonstrated through a synthetic tracer-transport model simulating tracer concentration and electrical impedances for four frequencies.
Abstract: Spectral induced polarization (SIP) is a non-intrusive geophysical method that collects chargeability information (the ability of a material to retain charge) in the time domain or its phase shift in the frequency domain. Although SIP is a temporal method, it cannot measure the dynamics of flow and solute/species transport in the subsurface over long times (i.e., 10–100 s of years). Data collected with the SIP technique need to be coupled with fluid flow and reactive-transport models in order to capture long-term dynamics. To address this challenge, PFLOTRAN-SIP was built to couple SIP data to fluid flow and solute transport processes. Specifically, this framework couples the subsurface flow and transport simulator PFLOTRAN and geoelectrical simulator E4D without sacrificing computational performance. PFLOTRAN solves the coupled flow and solute-transport process models in order to estimate solute concentrations, which were used in Archie’s model to compute bulk electrical conductivities at near-zero frequency. These bulk electrical conductivities were modified while using the Cole–Cole model to account for frequency dependence. Using the estimated frequency-dependent bulk conductivities, E4D simulated the real and complex electrical potential signals for selected frequencies for SIP. These frequency-dependent bulk conductivities contain information that is relevant to geochemical changes in the system. This study demonstrated that the PFLOTRAN-SIP framework is able to detect the presence of a tracer in the subsurface. SIP offers a significant benefit over ERT in the form of greater information content. It provided multiple datasets at different frequencies that better constrained the tracer distribution in the subsurface. Consequently, this framework allows for practitioners of environmental hydrogeophysics and biogeophysics to monitor the subsurface with improved resolution.

5 citations

30 Mar 2020
TL;DR: Ground Penetrating Radar has proven the viability of the proposed method for root detection and mapping under road pavements and proven the potential of GPR in identifying safety-related occurrences from the interaction between the root system and the existing pavement structure.
Abstract: The importance of street trees in the urban environment is widely recognised. Nevertheless, the absence of proper urban planning, combined with lack of resources and methodologies for road maintenance, have made the interaction between trees and the urban environment as a priority task to pursue. The uncontrolled development of tree roots can cause extensive damage, such as the cracking and uplifting of pavement and curbs, that could seriously endanger safety of pedestrians, cyclists and drivers. Within this framework, Ground Penetrating Radar (GPR) has already proven its effectiveness for the non-destructive evaluation and monitoring of road pavements. This research aims to demonstrate the potential of GPR in mapping the root system architecture of street trees. To this purpose, a GPR system equipped with a 700 MHz central frequency antenna was used to survey the area around a street tree (natural soil and flexible pavement structure). A multi-stage data processing methodology is proposed to map the tree root system architecture. Moreover, information on the mass density of roots at different depths is also provided. Results have proven the viability of the proposed method for root detection and mapping under road pavements. Analyses of results have also proven the potential of GPR in identifying safety-related occurrences from the interaction between the root system and the existing pavement structure.

4 citations

Posted Content
TL;DR: In this paper, a massively parallel simulation framework (PFLOTRAN-SIP) was built to couple SIP data to fluid flow and solute transport processes, without sacrificing computational performance.
Abstract: Spectral induced polarization (SIP) is a non-intrusive geophysical method that is widely used to detect sulfide minerals, clay minerals, metallic objects, municipal wastes, hydrocarbons, and salinity intrusion. However, SIP is a static method that cannot measure the dynamics of flow and solute/species transport in the subsurface. To capture these dynamics, the data collected with the SIP technique needs to be coupled with fluid flow and reactive-transport models. To our knowledge, currently, there is no simulator in the open-source literature that couples fluid flow, solute transport, and SIP process models to analyze geoelectrical signatures in a large-scale system. A massively parallel simulation framework (PFLOTRAN-SIP) was built to couple SIP data to fluid flow and solute transport processes. This framework built on the PFLOTRAN-E4D simulator that couples PFLOTRAN and E4D, without sacrificing computational performance. PFLOTRAN solves the coupled flow and solute transport process models to estimate solute concentrations, which were used in Archie's model to compute bulk electrical conductivities at near-zero frequency. These bulk electrical conductivities were modified using the Cole-Cole model to account for frequency dependence. Using the estimated frequency-dependent bulk conductivities, E4D simulated the real and complex electrical potential signals for selected frequencies for SIP. The PFLOTRAN-SIP framework was demonstrated through a synthetic tracer-transport model simulating tracer concentration and electrical impedances for four frequencies. Later, SIP inversion estimated bulk electrical conductivities by matching electrical impedances for each specified frequency. The estimated bulk electrical conductivities were consistent with the simulated tracer concentrations from the PFLOTRAN-SIP forward model.

2 citations

Proceedings ArticleDOI
06 Apr 2022
TL;DR: In this article , a joint time frequency analysis (JTFA) method called short-time Fourier transform (STFT) was proposed to reduce noise and enhance tree root detection.
Abstract: Accurate monitoring of tree roots using ground penetrating radar (GPR) is very useful in assessing the trees' health. In high moisture tropical areas such as Singapore, tree fall due to root rot can cause loss of lives and properties. The tropical complex soil characteristics due to the high moisture content tends to affect penetration depth of the signal. This limits the depth range of the GPR. Typically, a wide band signal is used to increase the penetration depth and to improve the resolution of the GPR. However, this broad band frequency tends to be noisy and selective frequency filtering is required for noise reduction. Therefore, in this paper, we adapt the stepped frequency continuous wave (SFCW) GPR and propose the use of a Joint time frequency analysis (JTFA) method called short-time Fourier transform (STFT), to reduce noise and enhance tree root detection. The proposed methodology is illustrated and tested with controlled experiments and real tree roots testing. The results show promising prospects of the method for tree roots detection in tropical areas.
Proceedings ArticleDOI
17 Jul 2022
TL;DR: In this article , a joint time frequency analysis (JTFA) method called short-time Fourier transform (STFT) was proposed to reduce noise and enhance tree root detection.
Abstract: Accurate monitoring of tree roots using ground penetrating radar (GPR) is very useful in assessing the trees' health. In high moisture tropical areas such as Singapore, tree fall due to root rot can cause loss of lives and properties. The tropical complex soil characteristics due to the high moisture content tends to affect penetration depth of the signal. This limits the depth range of the GPR. Typically, a wide band signal is used to increase the penetration depth and to improve the resolution of the GPR. However, this broad band frequency tends to be noisy and selective frequency filtering is required for noise reduction. Therefore, in this paper, we adapt the stepped frequency continuous wave (SFCW) GPR and propose the use of a Joint time frequency analysis (JTFA) method called short-time Fourier transform (STFT), to reduce noise and enhance tree root detection. The proposed methodology is illustrated and tested with controlled experiments and real tree roots testing. The results show promising prospects of the method for tree roots detection in tropical areas.
References
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TL;DR: In this paper, the authors explain how physiological processes (such as photosynthesis, respiration, transpiration, carbohydrate, nitrogen and mineral relations) are involved in the growth of woody plants and how they are affected by the environment.
Abstract: Plant physiology is the scientific study of how plants grow and respond to environmental factors and cultural treatments in terms of their physiological processes and conditions. This book aims to explain how physiological processes (such as photosynthesis, respiration, transpiration, carbohydrate, nitrogen and mineral relations) are involved in the growth of woody plants and how they are affected by the environment, in addition to explaining the mechanisms of the processes themselves.

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"A frequency spectrum-based processi..." refers methods in this paper

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    [...]

Journal ArticleDOI
TL;DR: Empirically and intuitively, architectural features seem to determine the effect of root systems on erosion phenomena and an effort is made here to link both aspects.
Abstract: The contribution of plant root systems to slope stability and soil erosion control has received a lot of attention in recent years. The plant root system is an intricate and adaptive object, and understanding the details of soil–root interaction is a difficult task. Although the morphology of a root system greatly influences its soil-fixing efficiency, limited architectural work has been done in the context of slope stabilization and erosion control, and hence it remains unknown exactly which characteristics are important. Many of the published research methods are tedious and time-consuming. This review deals with the underlying mechanisms of shallow slope stabilization and erosion control by roots, especially as determined by their architectural characteristics. The effect of soil properties as well as the relative importance of different root sizes and of woody versus non-woody species are briefly discussed. Empirically and intuitively, architectural features seem to determine the effect of root systems on erosion phenomena and an effort is therefore made here to link both aspects. Still, the research to underpin this relationship is poorly developed. A variety of methods are available for detailed root system architectural measurement and analysis. Although, generally time-consuming, a full 3D architectural description followed by analysis in software such as AMAPmod offers the possibility to extract relevant information on almost any root system architectural characteristic. Combining several methods of measurement and analysis in a complementary way may be a useful option, especially in a context of modelling.

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Frequently Asked Questions (1)
Q1. What are the contributions in "A frequency spectrum-based processing framework for the assessment of tree root systems" ?

Within this framework, non-destructive testing ( NDT ) methods are becoming increasingly popular, as they are faster and more flexible than destructive methods. This research aims to investigate the changes occurring in the frequency spectrum of the GPR signal during root system surveys. The results of the application of this methodology to a real-case scenario showed the potential of the applied procedure and will lead to the development of a new approach for investigating root systems using GPR.