Continental Shelf Research 31 (2011) 1236–1247

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Continental Shelf Research

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Research papers

Unsupervised fuzzy classification and object-based image analysis of

multibeam data to map deep water substrates, Cook Strait, New Zealand
Vanessa Lucieer a,n, Geoffroy Lamarche b
a
Tasmanian Aquaculture and Fisheries Institute (TAFI), University of Tasmania, Private Bag 49, Hobart, Tasmania 7001, Australia
b
National Institute of Water and Atmospheric Research (NIWA), Private Bag 14-901, Wellington 6041, New Zealand

a r t i c l e i n f o a b s t r a c t

Article history: A comprehensive 32 kHz multibeam bathymetry and backscatter survey of Cook Strait, New Zealand
Received 10 November 2010 (  8500 km2), is used to generate a regional substrate classification map over a wide range of water
Received in revised form depths, seafloor substrates and geological landforms using an automated mapping method based on the
28 April 2011
textural image analysis of backscatter data. Full processing of the backscatter is required in order to
Accepted 29 April 2011
obtain an image with a strongly attenuated specular reflection. Image segmentation of the merged
Available online 12 May 2011
backscatter and bathymetry layers is constrained using shape, compactness, and texture measures.
Keywords: The number of classes and their spatial distribution are statistically identified by employing an
Segmentation unsupervised fuzzy-c-means (FCM) clustering algorithm to sediment samples, independent of the
Backscatter
backscatter data. Classification is achieved from the overlay of the FCM result onto a segmented image
Bathymetry
and attributing segments with the FCM class. Four classes are identified and uncertainty in class
Habitat mapping
Fuzzy-c-means attribution is quantified by a confusion index layer. Validation of the classification map is done by
comparing the results with the sediment and structural maps. Backscatter (BS) strength angular profiles
are used to show acoustic class separation. The method takes us one step further in combining
multibeam data with physical seabed data in a complementary analysis to seek correlations between
datasets using object-based image analysis and unsupervised classification. Texture within these
identified classes is then examined for correlation with typical backscatter angular responses for mud,
sand and gravel. The results show a first order correlation between each of the classes and both the
sedimentary properties and the geomorphological map.
& 2011 Elsevier Ltd. All rights reserved.

1. Introduction Acoustic backscatter images generated from multibeam echo

Quantifiable methods that map benthic substrates from remotely
sensed data have become a significant focus of the seafloor map-
ping community (e.g., Brown and Blondel, 2009; Le Bas and
Huvenne, 2009; Lucieer and Lucieer, 2009; Wright and Heyman,
2008). Seafloor sediments and geomorphology are valuable proxies
for: (i) substrate composition and sedimentary processes; (ii)
tectonic processes; (iii) benthic habitat (Brown and Blondel, 2009;
Kostylev et al., 2001; Orpin and Kostylev, 2006; Ryan et al., 2007)
and (iv) benthic biodiversity (Schlacher et al., 2009; Thrush et al.,
2006). Moreover, knowledge of the distribution of these proxies
informs species management and the development of marine
protected areas (Anderson et al., 2008, 2007; Jordan et al., 2005;
Kostylev et al., 2003; Lucieer and Pederson, 2008).
n
Corresponding author. Tel.: þ61 3 62277219.
E-mail addresses: vanessa.lucieer@utas.edu.au (V. Lucieer),
g.lamarche@niwa.co.nz (G. Lamarche).
sounder (MBES) data are often complex due to variability in
seafloor roughness and impedance, sediment grain size and
volume heterogeneity, as well as the inherently noisy signal at
nadir and steep grazing angles (Marsh and Brown, 2009). For these
reasons, pixel-based classification schemes are critically limited
when differentiating seabed zones with well-defined boundaries,
resulting in inconsistent classifications that are highly biased by
the specular response at nadir. In contrast, object-based image
analysis techniques overcome these difficulties by first segmenting
the image into meaningful seabed zones of various sizes, based on
their spectral and spatial characteristics (Blaschke, 2010). Such
classification methods, originally developed for remotely sensed
data from satellites, have been successfully applied to multibeam
and sidescan sonar data (Lucieer, 2007, 2008; Preston, 2009).
In this paper we apply an object-based image analysis technique
to segment and classify multibeam backscatter data from Cook Strait,
New Zealand, to generate a first-level quantitative seabed substrate
map. The diverse geological, hydrodynamic and ecological environ-
ments of Cook Strait, together with comprehensive multibeam
bathymetric (Fig. 1) and backscatter coverages (Fig. 2), alongside a

0278-4343/$ - see front matter & 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.csr.2011.04.016
 V. Lucieer, G. Lamarche / Continental Shelf Research 31 (2011) 1236–1247
Fig. 1. Multibeam bathymetry of Cook Strait, New Zealand. The dark colour DTM
corresponds to the Kongsberg EM300 multibeam dataset, whereas the pastel
colours originate from the regional New Zealand bathymetric dataset. Bathymetric
contours are superimposed on the DTM. Insert: the Pacific–Australia plate
boundary in the New Zealand region. The thick teeth line represents the
subduction front. Non-teethed lines are major active faults. Abbreviations on the
map refer to the following locations: NB—Narrows Basin, NC—Nicholson Canyon,
WC—Wairarapa Canyon, Ck—Cook Strait, PB—Palliser Bank, OC—Opouawe
Canyon, OR—Opouawe Ridge, PaB—Pahaua Bank, PaC—Pahaua Canyon (for
interpretation of the references to colour in this figure legend, the reader is
referred to the web version of this article).
Fig. 2. Fully processed (calibrated and statistically compensated) backscatter
imagery of Cook Strait, with strong intensity in white. (A) White dots indicate
locations of geological samples used for the FCM cluster analysis. The thick dash
lines indicate the boundaries of individual datasets. Frames indicate the locations
of enlargements b and v. (B)Enlargement of the backscatter map over the Narrows.
The region is dominated by sediment waves and dunes. (C) Enlargement of the
backscatter map over the Campbell Bank–Cook Strait meander. The fault runs
east–west and separates two regions of contrasting reflectivity.
wealth of geological samples, provide an excellent opportunity to test
and develop automated methods to characterise marine habitats over
large areas using the image analysis approach.
1237
Central to our study is the feasibility and validity of applying
an unsupervised method over a large and geomorphologically
complex area that contains diverse natural environments. This is
achieved through two key steps: (i) unsupervised fuzzy-c-means
(FCM) classification of sediment samples to identify the appro-
priate number of classes and their core spatial areas and (ii) use of
these areas as training samples in an object-based image analysis
of MBES imagery to derive a geomorphological map for the whole
study area. Finally, we present a validation of our results.
In the first stage, we apply a quantitative technique employing
an unsupervised FCM classification that identifies the optimal
number and spatial location of seabed classes, based on seafloor
sediment samples (Lucieer and Lucieer, 2009). The methods
employed here show that FCM can locate potential boundaries
and transition zones between multivariate seabed properties,
which correlate strongly with backscatter, thus providing a
potentially powerful tool to quantify uncertainty associated with
transition zones between the classes. The degree of success of
unsupervised classification is notoriously difficult to quantify
(Canty, 2007; Duda and Canty, 2002) because there is rarely a
reference information to assess the accuracy of the classification
results or there is a lack of independent data to validate the
results. In this paper, we validate the clustering result by
comparing the results with sediment and geomorphological maps
of Cook Strait.
In the second stage, the acoustic backscatter image is segmen-
ted based on texture, and grey scale values and the size and shape
of these segments are differentiated by their depth. An object-
based image analysis framework is employed to classify image
segments into geomorphological classes based on stage one.
Traditionally, benthic habitat classes are assigned based on expert
knowledge of the seafloor or visual discrimination of particular
textures. In this study, we propose a more automated and
objective approach towards seabed classification.
1.1. Geological setting
The diverse and complex geomorphology of Cook Strait is the
result of the dynamic climatic, tectonic and hydrodynamic for-
cings that have impacted on the region since at least the last post-
glacial period (Lewis et al., 1994; Proctor and Carter, 1988). The
20–60-km-wide oceanic Strait separates the North and the South
Islands of New Zealand. Extremely vigorous winds are driven by
the prevailing westerly airflow of the Tasman Sea (Fig. 1) across
mountainous New Zealand, and steered and intensified through
Cook Strait (Harris, 1990). As a result, winds are strong and
distinctly bimodal: prevailing winds are from the south and from
the north to northwest. High winds result in an equally vigorous
wave climate, and when motions are superimposed on the Strait’s
powerful tidal currents, the result is a highly dynamic marine
environment at all water depths. The lunar semi diurnal (M2) tide
is a trapped wave travelling anti clockwise around New Zealand.
High tide on the west coast occurs close to low tide on the east
coast, the Strait effectively short circuiting the phase difference
resulting in rapid tidal currents. These powerful currents coupled
with strong sediment delivery, marked effects of eustatic changes
in sea level, strong meteorological forcing of the circulation, and
active tectonism (Hicks and Shankar, 2003; Lewis et al., 1994)
have produced distinctive patterns of sedimentation, which
include sediment wave fields (Carter, 1992; Lamarche et al.,
2010), coarse gravelly shelf, mud flats, deep-sea canyons
(Mountjoy et al., 2009) and deep turbidite filled channels (Lewis
et al., 1994).
The region lies immediately west of the southern termination
of the active convergent Pacific–Australia plate boundary, which
generates intense seismic activity and associated ground-shaking
1238 V. Lucieer, G. Lamarche / Continental Shelf Research 31 (2011) 1236–1247
in the region (Pondard and Barnes, 2010; Stirling et al., 2000). The
continental shelf and the slope are dissected by active faults and
NE-trending structurally controlled ridges that are the locus
for pronounced slope instability (Barnes and Audru, 1999).
Semi-circular slump scarps are up to 1100 m in height with
evidence of ample debris at their base and in channel axes
(Mountjoy et al., 2009).
The shelf break ranges from  50 m water depth in the Narrows
to  150 m in the eastern Cook Strait. Eastward, beyond the
continental slope, the homogeneously flat-floored Hikurangi
Trough contains a deep turbidite fill (Lewis et al., 1994). During
the Last Glacial Maximum, the continental shelf was emergent as a
coastal plain (Carter, 1992; Lewis et al., 1994), most of which was
subsequently blanketed by a wedge of post-last glacial sediment.
Today, some areas of the shelf remain bare of post-last glacial mud
that the erosional surface outcrops at the seabed (Mountjoy et al.,
2009). Evidence of active and relict fluid flow and seafloor seeps,
usually associated with dense concentrations of distinctive, che-
mosynthetic biota have been reported in the SE approaches of Cook
Strait (Barnes and Audru, 1999; Law et al., 2009).
2. Data
2.1. Backscatter and bathymetry datasets
MBES data were collected during six oceanographic surveys of R.V.
Tangaroa between 2001 and 2005 in Cook Strait by the National
Institute of Water and Atmosphere Research (NIWA) (Lamarche et al.,
2010). The total surveyed area is ca. 8500 km2 at depths 4100 m
(Fig. 1). R.V. Tangaroa has a hull-mounted Kongsberg EM300 (32 kHz)
MBES, that fully compensates the vessel position and motion (heave,
pitch, roll and yaw). Sound velocity was measured at regular intervals
to account for hydrological variability on the acoustic data. A number
of archived sediment cores, seabed grab samples and photographs are
available in the region (Carter, 1992; Lewis et al., 1994; Black, 1986),
thus providing a means to ground-truth the remotely sensed data.
To provide an interpretable acoustic backscatter image, Cook
Strait backscatter data were processed to attenuate effects caused
by recording equipment, seabed topography and water column
acoustics. SonarScopes software (IFREMER, France; Augustin and
Lurton, 2005) was employed for this task, which includes facility
Fig. 3. Simplified geomorphological interpretations of two sub-set regions of the Cook Strait in the Narrows (A) from Lamarche et al. (2010) and the Campbell Bank
and surrounding Cook Strait meander (B) from Barnes et al. (2010) and Mountjoy et al. (2009). WC—Wairarapa Canyon, Ck—Cook Strait. Depth is shown in metres:
(A) every 50 m; (B) 120 m, 250 m then every 250 m.
for signal calibration and statistical compensation as well as
speckle noise filtering (Lamarche et al., 2010). There is a funda-
mental distinction between the Backscattering Strength (BS) and
the Compensated Backscatter Imagery (CBI); the former is used
for quantitative analysis, and in particular for correlation with
sediment grain size (Lamarche et al., 2010) whereas with CBI the
BS is normalised at a conventional reference level. In this study,
the CBI is used for the segmentation and classification.
BS is also related to the sediment grain size, sediment/water
impedance contrast, microscale roughness and volumetric het-
erogeneity (Guillon and Lurton, 2001; Jackson and Briggs, 1992;
Lurton, 2003). BS varies with the signal incidence angle on the
seabed (y) (Fonseca et al., 2009; Le Chenadec et al., 2007), with
strong, sometimes obliterating signal at the nadir (specular
reflection) and rapid decrease with the increasing incidence angle.
This study uses the Generic Seabed Acoustic Backscatter (GSAB)
(Lamarche et al., 2010) model of the BS angular response. BS (y)
is represented as the summation of three components: (i) a
Gaussian law for the specular angles; (ii) a Lambert law for the
grazing angles; and (iii) a Gaussian law for a transitory compo-
nent. The model uses six parameters (A to F) that fully quantify
the angular responses for a given material:
BSðyÞ ¼ 10 log½A expðy2 =2B2 Þ þ C cos Dy þE expðy2 =2F 2 Þ ð1Þ
A is the specular maximum amplitude (dB); it is high (typically
 5 to 0 dB) for smooth sediment interfaces at the scale of the
acoustic wavelength, and for strong water–sediment impedance
contrasts. B is the angular extent of the specular regime (in
degrees); it is given by the average (medium-scale) slope of the
seabed and represents a descriptor of the interface roughness. C is
the average backscatter level at oblique incidence (in dB); it is
associated with the Lambert’s law describing backscattering
strength at intermediate angles for rough interfaces. C includes
the contribution of the volume inhomogeneity backscatter and
increases with the seabed roughness, impedance, and volume
heterogeneity typically ranging from  20 to  30 dB. D is the
angular decrement of the backscatter, controlling the variations at
grazing angles; D is high for soft and smooth sediment interfaces,
and is commonly equal to 2. E is the transitory maximum level (in
dB), and F its angular extent (in deg.) (Lamarche et al., 2010;
Lurton, 2003).
 V. Lucieer, G. Lamarche / Continental Shelf Research 31 (2011) 1236–1247 1239

2.2. Morpho-structural and sediment Analyses classification process is therefore needed to identify cluster attri-
butes and thus label each cluster meaningfully.
We generated simplified morpho-structural maps for two sub- This study applies five data attributes (Fig. 4): (1) multibeam
regions in Cook Strait to provide a basis for discussing the bathymetry, as 3025  2913 cells (gridded at 50 m bin size); (2) the
effectiveness of the object-based segmentation in recognising log of slope and percentage components of (3) gravel, (4) mud and
classes based on landforms. The two regions are the Narrows (5) sand. The sediment data layers were formatted as ENVI (soft-
Basin (Fig. 3A) and the Campbell Bank–Cook Canyon meander ware application currently marketed by ITT Visual Information
(Fig. 3B). These two regions have been intensively studied for Solutions—ITTVIS, 2009) image layers. The attributes values were
other purposes and interpretations of the EM300 multibeam standardised to [0–1] by a linear stretch between the minimum
bathymetry, together with a number of high resolution seismic and the maximum values, thus ensuring that each of the attributes
reflection profiles (see Barnes et al., 2010; Carter, 1992; Carter is equally weighted. The FCM algorithm was implemented in the
and Lewis, 1988; Lamarche et al., 2010; Mountjoy et al., 2009), Interactive Data Language (IDL) (ITTVIS, 2009).
which have enabled us to generate a morphological map of these The FCM approach is valuable when information about the
regions. For the purpose of this study we limited the interpreta- number and definition of substrate classes is lacking. It produces a
tion to the following landforms: dunes and sediment waves, set of optimal, overlapping classes that can also be mapped in data
ridges, top and base of the continental slope, scarps and unde- space and in geographical space (Lucieer and Lucieer, 2009) with-
fined morphological lineaments. Where possible, scarps are iden- out the need of arbitrarily selecting a class number (such as with
tified as being of erosional origin or from seabed displacement k-means analysis). The advantage of using a soft classifier such as
from active faulting. Lineaments are linear features identified on the FCM algorithm is that uncertainty related to class attribution
the bathymetry or backscatter maps without obvious correlation can be visualised and quantified. The amount of overlap between-
with origin. This basic interpretation provides a simple overview class clusters in feature space is user-defined with a fuzziness
of the distribution of morphological feature on the two sub-
regions of the Narrows (Fig. 3A) and the Campbell Bank–Cook
Canyon meander (Fig. 3B), which is later used to correlate with
the classification map. The seismic reflection profiles (not shown
here) provide evidence for the origin of seafloor scarps as fault
generated.
The sediment database consists of 260 seabed samples (Fig. 2)
collected since the late 1950s by the New Zealand Oceanographic
Institute (NZOI) and subsequently by NIWA. Samples were
collected using a gravity corer, piston corer and grab. Sample
information includes textural data determined using a laser
granulometer and classification as a function of the percentage
of mud, gravel and sand. Granulometric statistics such as mean
grain size were obtained using Gradistat (Blott and Pye, 2000).
The next step aims to identify geomorphological classes based
on an unsupervised classification technique. The purpose of
an unsupervised classification is to identify class clusters
objectively.

3. Fuzzy-c-means classification

3.1. FCM methods

The FCM clustering algorithm (also known as the fuzzy-k-

means algorithm) is an unsupervised classification algorithm
designed to identify groups of samples sharing similar character-
istics in a multivariate feature space (Bezdek et al., 1984; Dunn,
1973). Fuzzy clustering provides a means of spatially depicting
classification uncertainty related to transition zones and class
overlap, which is not possible with the non-spatial statistics
derived from other accuracy assessments such as error matrices
(Lucieer and Lucieer, 2009). The main aim of an unsupervised
clustering algorithm is to subdivide a complex, continuous, multi-
variate feature space into a set of clusters. The clusters are optimal
in the sense that the multivariate within-cluster variance is
minimal. Small variance implies that all data points have similar
attributes, which means a high density and small distance between
them in feature space. Large variance is equivalent to low density
and large distances in feature space. An optimal cluster procedure
will identify these dense spots in feature space as class centres,
while the boundaries between classes in feature space should be
Fig. 4. Data input layers for the Fuzzy-c Classification Model (FCM): (A) EM300
located in the lowest density regions. Unsupervised clustering multibeam bathymetry DTM. (B) Log of slope. Interpolation of percentages of
algorithms do not attach meaningful class labels to these (C) gravel, (D) mud and (E) sand provided by sample sediment grain analysis (see
clusters, as opposed to supervised classifiers. A final stage of the text); dots are sample approximate locations.
1240 V. Lucieer, G. Lamarche / Continental Shelf Research 31 (2011) 1236–1247

exponent. In this study the purpose of FCM is two-fold: (i) the

algorithm identifies geomorphological classes in an objective
manner and (ii) it identifies core spatial areas for each class. The
final FCM classification result therefore provides statistically sig-
nificant core areas that can be related to the MBES data. The
advantage of MBES data is that it is a spatially continuous
representation of the seafloor whereas the sediment samples are
spatially discrete. This approach is also referred to as a hybrid
supervised/unsupervised classification (Richards and Jia, 2006).
The key advantage of the hybrid technique is that the unsupervised
classification identifies statistically significant class clusters in an
objective and automated manner rather than a subjective user-
driven selection, which is common to the traditional supervised
approach. Core areas of these class clusters can then be used to
train a supervised classification algorithm based on additional data
layers and feature selection evaluation. We use the backscatter
data as a proxy for the seafloor sediment grain size and hetero-
geneity. The next step is to classify the MBES images based on the
geomorphological classes generated from the FCM analysis.

3.2. FCM results

Application of the FCM algorithm to the five attributes sug-

gests that four clusters provide an optimal partitioning for the
Cook Strait data. Based on this cluster validity outcome we
calculated the FCM results for four classes with the fuzziness
exponent q set to 2.0, which is a value widely used in the
literature (Dunn, 1973; Lucieer and Lucieer, 2009). It took 8 itera-
tions for the FCM algorithm to converge. A final classification
layer was generated based on the maximum membership value
(Fig. 5A). The confusion index layer for the four classes (Fig. 5B–E)
clearly shows high levels of uncertainty (white areas) at class
boundaries. The FCM membership layers were generated for each
cluster where white indicates high membership to the class and
black low membership to the class (Fig. 5B–E). As the FCM
algorithm is an unsupervised classifier, the class labels do not
have any physical meaning. Hence, the final stage in the classi-
fication process is to assign meaningful substrate classes based on
ground-truthed geological data, expert knowledge and the statis-
tical distribution of the attributes in each of the classes.

4. Object-based image analysis

4.1. OBIA methods

Object-based image analysis (OBIA) is a relatively new image

processing technique that classifies objects in an image, based on
a segmentation phase followed by an object-based classification
phase (Benz et al. 2004). A segmentation algorithm was used to
subdivide the combined multibeam backscatter and bathymetric
images into smaller image objects based on an optimisation
procedure, which locally minimises the average heterogeneity of
image objects for a given resolution across the image. Image
segmentation was completed using Definiens Developer& (version
8.0) software (http://earth.definiens.com/). A multi-resolution
segmentation algorithm was chosen for this study, which is a
bottom up, region-growing technique starting with one pixel
objects. Both the multibeam backscatter and bathymetric images
were weighted equally in the segmentation analysis, rather than
analysing the backscatter layer in isolation. Textures that appear
similar at different depths can be separated this way.
The multibeam image was segmented at two scales 50 and
100. The ‘‘scale parameter’’ is a unitless term in the Definiens
Developer& (version 8.0) software; it determines the maximum
Fig. 5. FCM results for four classes membership layers for each cluster. (A) shows
the confusion map, which illustrates the zones of greatest confusion in class
attribution to a cell, or perhaps also a transition zone between classes. The areas of
greatest confusion exist firstly around Class 1 on the Narrows where between each
of the sediment samples there may be a high degree of variance in the sediment
composition and secondly in the areas of the seafloor canyons where the number
of sediment samples may influence a confident result. The degree of membership
for each of the grid cells to one of the four classes is illustrated in (B)–(E). The
bright white areas indicate highest membership whereas black indicates low
membership to a class and white indicates high membership (B: Class 1, C: Class 2,
D: Class 3, E: Class 4).
allowed heterogeneity for the resulting image objects (Benz et al.,
2004). Higher values for the scale parameter result in larger image
objects, smaller values in smaller ones. The object homogeneity to
 V. Lucieer, G. Lamarche / Continental Shelf Research 31 (2011) 1236–1247
which the scale parameter refers is a synonym for minimised
heterogeneity. A certain degree of shape homogeneity, defined by
a compactness criterion, often improves the quality of object
extraction. Object compactness is based on the perimeter to area
ratio. The shape criterion is especially helpful in avoiding highly
fractured image object resulting from strongly textured data (for
example, backscatter data). The 50 and 100 scale parameters
explored in this multi-resolution segmentation were extracted
from a 50 m pixel size dataset of Cook Strait to determine if
different segmentation scales influence the classification result.
4.1.1. Object features
Each image object contains multiple pixels. Objects can be
characterised by hundreds of object features, based on descriptive
statistics of pixel values, object shape, object texture, etc. The
challenge in object-based image analysis is to identify the most
suitable object features for subsequent classification. In this
study, we use the mean, standard deviation, brightness and
maximum difference of the backscatter and bathymetry object
values as object features. The maximum difference is an expres-
sion of the range of values in an object. Brightness is the sum of
values in an object.
Given the textured nature of backscatter imagery, it is helpful
to characterise image objects with a texture measure in addition
to its backscatter and bathymetry values. The Haralick grey level
co-occurrence matrix (GLCM) is a widely used texture model,
which is based on a tabulation of the frequency of the neighbour-
hood combinations of pixel grey levels within an object (Benz
et al., 2004). From this matrix several texture measures, such as
entropy and correlation, can be derived expressing its statistical
structure. GLCM entropy shows high values for highly textured
regions. GLCM correlation measures the linear dependence of
grey levels of neighbouring pixels. Directional invariance of the
GLCM can be calculated in all four directions (01, 451, 901 and
1351). An angle of 01 represents the vertical direction, an angle of
901 the horizontal direction, etc. In this study, GLCM correlation
and entropy measures were calculated for all image objects based
on the bathymetric and backscatter image layers for all directions
individually and all directions combined, resulting in 20 texture
measures per object.
4.1.2. Feature selection
The list of object features described in the previous section
results in an object feature space with a high number of dimen-
sions (i.e. hyperdimensional). In order to reduce the number of
features for object classification, a feature space optimisation
Fig. 6. Segmentation results of multibeam backscatter and bathymetry at levels 50 and 100. The four-class samples (1–4) used for the classification training (coloured)
were selected within the regions delineated by the FCM analysis (Fig. 5) (for interpretation of the references to colour in this figure legend, the reader is referred to the web
version of this article).
1241
technique can be applied. The feature space optimisation in
Definiens Developer& (version 8.0) finds the combination of object
features most suitable for separating the classes of the training
objects, based on the largest average minimum distance between
samples from different classes, i.e. maximising the between-class
difference. The optimisation of object features in feature space is
expressed by the optimal separation distance. This is a dimen-
sionless value showing the class separation distance, where high
values indicate good class separability. This distance measure
therefore only allows relative comparisons. This method also
allows the training objects to be assessed for their ‘quality’ as a
representative sample to that class, i.e. its relative separation
distance from the other samples.
GCLM entropy and GCLM Correlation were shown from the
feature space optimisation method to be the two most useful
variables of texture to separate the image objects. For both
segmentation levels the feature space was separated using the
following variables; GLCM entropy backscatter, GLCM correlation
backscatter (901), GLCM correlation bathymetry (451), GLCM
correlation backscatter (all directions) and the mean of bathy-
metry, mean of backscatter, brightness and the maximum differ-
ence of both backscatter and bathymetry.
4.1.3. Classification
The final stage in object-based image analysis is classification of
image objects based on selected object features. In this study, a
supervised classification is used. In a supervised classification
training samples are used to train the classifier. We selected these
training objects based on the FCM results (Fig. 5). The training
objects are chosen in the core areas of the four classes identified by
the FCM algorithm (Fig. 5B–E). Fig. 6 shows the locations of the
training sample objects. Based on the object features of the training
objects all unclassified image segments can be classified based on
their distance in feature space. The nearest-neighbour classifier
assigns a membership value between 0 and 1, based on the
distance of the object’s feature vector to its nearest training object
(i.e. neighbour) in feature space. The membership value is 1 if the
image object is identical to a training object. This classification step
allows each object to be classified with a discrete class label and
assigned with an associated membership value.
4.2. OBIA results
The majority of the segments display shapes close to an oblong
or square, which suggests that the backscatter specular reflection
(the elongated nadir stripe) has little to no influence on the
1242 V. Lucieer, G. Lamarche / Continental Shelf Research 31 (2011) 1236–1247
segmentation process (Fig. 6). However, in SE Cook Strait the
segments have preferential elongated shape, which are aligned
with the specular reflection attenuation, indicating the segmenta-
tion is not as effective in deep water compared to the shelf-upper
slope environments. The impact of the specular reflection on the
segmentation is considerably stronger at the segmentation 100
(Fig. 6B) scale than in the segmentation 50 (Fig. 6A). This is
because more pixels are analysed per segment in the larger
segmentation, resulting in higher variability in spectral bright-
ness. The segmentation maps at both 50 and 100 scales reflect the
morphological and structural features observed in the bathymetry
map (Fig. 1) as well as the backscatter texture (Fig. 2) across the
region. This is to be expected as the maps are generated from the
combination of the bathymetry and backscatter data.
However, the classes are independent of the water depths.
Large segments are often isotropic or oblong at flat relatively
homogeneous areas of Hikurangi Trough, the shallow continental
shelf in the north, and along the edges in central Cook Strait. This
is also characteristic of flat top ridges and banks, which are on
Fig. 7. Feature space diagram of object backscatter brightness vs. backscatter
maximum difference for the four selected classes. This plot shows the brightness
intensity of the objects by the maximum spectral difference of the objects. The
four classes separate well in the space with a maximum separation of 1.14. The
four classes determined from the independent FCM model show very good
separation in the object-based image analysis. The objects used for training the
classification are indicated by the coloured circles. Classes 1, 2 and 3 have lower
variance, i.e. a tighter cluster than Class 4 (for interpretation of the references to
colour in this figure legend, the reader is referred to the web version of this
article).
Fig. 8. Final classification maps shown at the segmentation levels 50 (A) and 100 (B). Four classes were selected as optimum from the fuzzy-c-mean analysis.
At segmentation 50 class 1 covered 17% of the study area, class 2—13%, class 3—42% and class 4—28%. At segmentation 100, class 1 covered 13% of the study area, class
2—11%, class 3—50% and class 4—26%.
both segmentation maps. The rough morphology of the conti-
nental slope at the mouth of the Cook Strait Canyon is charac-
terised by smaller segments, often with strongly elongated shapes
usually following the bathymetry. The contrast between the
isotropic shapes of the flat areas with the elongated shapes of
the slope emphasise the canyons, ridges and banks. The orienta-
tions of the elongated segments along the slope mostly follow the
bathymetry contour lines. This is distinctively more pronounced
on the segmentation 100 scale than on the 50 scale suggesting a
stronger control of the morphology on the segmentation 100 scale
than on the 50 scale. Flat areas are better depicted with the
segmentation 50 scale than on the 100 scale. Segment shapes on
the 100 scale are noticeably more elongated than on the 50 scale,
even on flat areas, which make the geomorphological recognition
less distinct. This is particularly noticeable on the Wairarapa and
Cloudy Bay shelves (Fig. 6).
5. Classification results and discussion
The feature space optimisation method in Definiens Devel-
oper& (version 8.0) was employed to identify the best combina-
tion of textural and object features most suitable for separating
the classes based on the selected samples from the FCM, in
conjunction with the nearest-neighbour classifier. The best
separation distance that we achieved between the two segmenta-
tions was 1.18 for Segmentation 50 and 1.14 for Segmentation
100, which indicated that the fine-scale segmentation level
provided a slightly better class separation.
After the final classification has been applied to the image
objects, the classified objects in relation to the sample objects can
be compared in a 2D feature space plot. All four classes deter-
mined from the independent FCM model show very good separa-
tion in the object-based image analysis (Fig. 7). Classes 1, 2 and
3 have lower variance than Class 4, i.e. they cluster more tightly.
Subsequently, the classification was applied to all image objects
in both segmentation 50 and 100 scale levels using the nearest-
neighbour algorithm. This produced two final four-class classifi-
cation maps of the wider Cook Strait (Fig. 8A and B). The areas
covered by each of the classes are similar for the two segmenta-
tion levels and range from 11% to 50%. Class 3 covers the largest
area (42% at scale 50; 50% at scale 100), and Class 2 covers the
smallest area (13% at scale 50; 11% at scale 100).
Since the classification is based on the bathymetry and back-
scatter data, the spatial distribution of the classes shows a strong
correlation with bathymetry and geomorphology (compare Figs. 1
and 8). Class 1 dominates over the floor of the Narrows Basin and
 V. Lucieer, G. Lamarche / Continental Shelf Research 31 (2011) 1236–1247
Table 1
Calibrated and statically compensated backscatter values (in dB) for the four
classes identified in this study.
Class 1 Class 2 Class 3
Mean  30.1  25.2  29.3
Std. dev. 7.3 7.4 7.2
Median  30.9  25.4  30.2
Min  62.6  56.2  58.3
Max 11.4 12.1 14.5
ridge and bank tops, Class 2 largely dominates the shallow,
central part of Cook Strait, Class 3 principally covers the con-
tinental slope to the SE but also includes the flanks of the canyons
and parts of the flanks of the Narrows Basin. Class 4 also extends
along the floor of Cook Strait Canyon and part of the Narrows
Basin seafloor but is most extensive in the deep Hikurangi Trough.
The clearer boundaries between the classes at segmentation scale
100 (Fig. 8B) indicate that overall the geomorphological control
on the classification maps is stronger at scale 100 compared to
scale 50.
The correlation between the four-class classification maps and
the backscatter (Figs. 2 and 8) is less apparent. The backscatter
relates to the sediment grain size and volume heterogeneity as well
as the small scale topography (Briggs et al., 2002; Goff et al., 2000;
Jackson and Briggs, 1992) and the areas covered by each class are
extremely large compared to the resolution of the backscatter data.
The class areas capture a large range of backscatter, which results in
relatively small difference between the median intensity values for
the four classes (Table 1). At first order, Class 1 is coincident with
low backscatter intensity (dark grey) with a median intensity of -
30 dB and Class 2 relates to higher intensity with a median value of
25 dB, the 5 dB difference between Classes 1 and 2 median values
being significantly larger than the 1 dB resolution of the EM300
(Lamarche et al., 2010). Class 4 corresponds to intermediate inten-
sity backscatter (median  27 dB). Class 3 corresponds to irregular
backscatter imagery as opposed to the three other classes relating to
more homogeneous imagery.
The unsupervised classification of physical properties, in com-
bination with object-based image segmentation, seeks to find
correlations between physical layers of the FCM result and seafloor
texture and bathymetry. In order to assign a physical meaning to
the four-class labels we compare the classification maps with both
the sediment map of Cook Strait (Fig. 9) and the morpho-structural
maps of the Narrows (Figs. 3A and 10A) and the Campbell
Bank–Cook Canyon meander regions (Figs. 3B and 10B).
5.1. Correlation of the classification map with sediment distribution
We simplified the original 27-classes used for the sediment map
of Cook Strait in a four-class sediment map based on the dominant
percentage of gravel, sand, mud and silt, and compatibility with the
four types of substrates commonly cited as controlling the BS
(Jackson and Briggs, 1992; Lamarche et al., 2010). Furthermore,
the FCM suggests an optimum number of 4 classes based on
backscatter and bathymetry, and similar patterns emerge that
suggest a possible correlation between object-based segmentation
and classification and substrate.
Both the sediment and the classification maps detect the inner
continental shelf in water depths shallower than 120 m, i.e.
shallower than the slope break, as separate classes (Fig. 9). This
is particularly clear around the Wellington Peninsula and along
the SE coast of the North Island, where Class 2 broadly corre-
sponds to sandy seafloor sediments with small to moderate-sized
bedforms. On Campbell Bank, the sandy seafloor also correlates to
1243
Class 4
 27.1
8.8
 29.0
 59.9
17.8
Fig. 9. (A) Simplified sediment map of Cook Strait and (B) classification map at
segmentation scale 100 with sediment class boundaries (thick black lines).
Class 2. The floor of the Narrows Basin and the northern and the
central parts of the Strait correspond essentially to Classes 1 and
2, and to gravelly and sandy substrate. Classes 3 and 4 are
indicative of silty and muddy seafloor. The canyon floors are well
delineated possibly reflecting the bedforms and coarse-grained
sediment observed on canyon floors (Mountjoy et al., 2009). To
the SE, neither the statistical approach developed in this paper
nor the sediment map separate many classes, with Classes 3 and
4 corresponding to muddy seafloor over the continental slope, the
lower part of the canyons and the deep Hikurangi Trough. The
canyon floor changes from classes downslope in a different
fashion for the 50 scale and the 100 scale. We have no suitable
data to validate this observation. The classification maps show
more heterogeneity than the sediment map along the slope and
the canyons, presumably reflecting the complex bathymetry and
backscatter. The low number of classes is somewhat coherent
with the homogeneous seabed of the Hikurangi Trough, but does
not delineate the steep slope of the SE Wairarapa shelf, although
Classes 1 and 3 seem to delineate the slope quite clearly.
5.2. Influence of tectonic structures on the classification map
A comparison of the classification maps generated in this study
with the geomorphological interpretation of the Cook Strait
(Lamarche et al., 2010; Mountjoy et al., 2009) provides another
indirect means to assess the utility of the technique and the
validity of the results, inasmuch as geological structures control
on the morphology and the backscatter of the Cook Strait. Two
areas were selected for the comparison because they cover a wide
range of water depths and geological structures: the Narrows Basin
(Figs. 3 and 10A and B) and Campbell Bank (Fig. 10C and D).
The large sediment wave field of the Narrows Basin is well
differentiated with Class 1 at segmentation scale 50 (Fig. 10A), but
less so with the segmentation scale at 100 where sediment waves
merge with Class 3 (Fig. 10B). Likewise, the landform of Campbell
Bank is well delineated by one single class at both segmentation
scales (Fig. 10C and D). The NE–SW structural trend in the
1244 V. Lucieer, G. Lamarche / Continental Shelf Research 31 (2011) 1236–1247

0 2.5 5 Km 10

Basin
Ridge
Sediment
waves
Dunes
Fault trace
(tick down)
Lineaments
Scarp

classes
2
3
4

km
0 5

Fig. 10. Comparison of the geomorphology maps (Fig. 3) with the four-class classification maps of the Narrows (segmentation level 50 (A) and 100 (B)) and Campbell Bank
(segmentation level 50 (C) and 100 (D)).

northern Narrows is well depicted at the segmentation scales. The
E–W trending fault scarp across Campbell Bank and the Cook
Strait form clear class boundaries at both scales, so do the scarps
demarcating the top of the canyons. The unstable slopes of the
Cook Strait Canyon are also well demarcated by Class 3 at both
scales. At both scales, in several areas the scarps are delineated by
the segmentation and classification routines.
Overall, the classification at scale 50 is patchier than that at
scale 100. The scale 100 map shows classes in larger and better
delineated blocks, particularly in the Narrows Basin and along the
canyon axes and walls, which at regional scales ends up providing
a clearer map. The 50 scale map better defines the sediment wave
field in the Narrows Basin (Fig. 9A and B), but both maps
recognise the conspicuous erosional features observed on Camp-
bell Bank immediately south of the Campbell Bank–Cook Canyon
meander (Fig. 9C and D) .
5.3. Correlation with backscatter angular response
We generated the BS average angular profiles for the four
classes (Fig. 11A) following the method described in Section 3.1
(after Lamarche et al., 2010). The four profiles have distinct
shapes, which relate to the substrate geology (grain size, volume
heterogeneity and seafloor roughness). The four BS profiles,
generated for gravel, sand, mud and mud overlying sediments
(Fig. 11B), can be used as a template for substrate character
(Lamarche et al., 2010). The BS profile for Class 2 is similar to that
of the gravelly seafloor with very short specular amplitude and a
wide high angle lobe, suggesting that Class 2 is gravelly or has
high volume heterogeneity. The BS for Class 4 is also typical and
best fits the profile for mud with underlying sediments, or strong
volume heterogeneity. Class 4 has the highest variance (Fig. 7),
which likely reflects the strong specular reflection of the
backscatter. It is likely that there are more sub-groupings in
Class 4 than the FCM was able to delineate from the low number
of sediment samples in this area. The BS angular response for
Classes 1 and 3 are similar in shape, both close to the BS profile
for sand. Class 3 has higher specular amplitude than Class
1 suggesting stronger interface roughness. This supports the
object-based classification process as a method capable of identi-
fying seafloor areas that are visually as well as acoustically
distinct across a range of water depths.
Although calibration and compensation of the BS data sub-
stantially improved the data quality, the specular reflection is still
pronounced on the backscatter map, and may bias the segmenta-
tion and classification processes. Nonetheless, the segmentation
methodology allows objects of interest, such as scarps, sediment
waves on canyon floors, to be delineated within the backscatter
image throughout the depth zones. These extracted objects form
definitive boundaries around discrete sediment-related features
or physical habitats, which can be geographically recognised for
further exploration, analysis and validation.
 V. Lucieer, G. Lamarche / Continental Shelf Research 31 (2011) 1236–1247 1245

Fig. 11. (A) Backscatter strength (BS) angular profiles for the four classes generated in this study. BS profiles were generated using the Generic Seabed Acoustic Backscatter
model (Lamarche et al., 2010). (B) BS angular profiles for gravel, sand, mud and mud with overlying sediments from Lamarche et al. (2010). These four profiles are used as
references for inferring substrate associated with the four classes. Note that the comparison between (A) and (B) is only relative as no calibration of the EM300 were
undertaken between surveys.

Initial assumptions between sediment attribute classes and
their distribution on the seabed have been shown to be generally
too simplistic given that methods now exist that generate results
that are more efficient and provide total coverage of the seabed.
Zones of rapid change on otherwise homogeneous ones are of
particular interest as they can mark small, distinctive or even
unique habitats. The methods that are employed here show that
FCM can locate potential boundaries and transition zones
between multivariate seabed properties, which correlate with
backscatter. Such methods are required to assess whether image
segments are based on ‘real’ seabed features, such as boundaries
in sediment composition, and not just artefacts in the image that
the segmentation algorithm determines as real. The class data
presented here show much closer correspondence to measured
physical properties than could be attained through traditional
qualitative visual inspection or simplistic statistical correlation.
6. Conclusion
We used an object-based segmentation of the backscatter and
bathymetry data to generate a four-class classification map from
the geomorphologically diverse Cook Strait, New Zealand. This
quantitative first order correlation between the seabed substrate
1246 V. Lucieer, G. Lamarche / Continental Shelf Research 31 (2011) 1236–1247
and the MBES data is a first for Cook Strait at a regional scale. We
use the backscatter data as a proxy for the seafloor sediment grain
size and heterogeneity. The four-class classification map shows
some correlation with the sediment map of the Cook Strait,
whereas comparisons with structural and morphological maps
indicate that the object-based classification may recognise land-
forms such as sediment wave fields and scarps, independently
from the water depth. The correlation with the backscatter
angular response is still in its infancy but has great potential in
enabling the quantitative mapping of the seafloor.
Whereas, traditional image processing and GIS analysis tools
handle data composed of discrete, well-defined objects of known
location, this method takes us one step further toward combining
multibeam data (backscatter and bathymetry) with physical
properties when constructing seabed-feature classes. The method
also acknowledges the application of imprecise and/or uncertain
data through the integration of different approaches: analytical
modelling (fuzzy classification), spectral classification (segmenta-
tion) and spatial analysis (boundaries). The next logical step in
this methodology is to combine physical and biological data
collected across the Cook Strait region to assess the validity of
the classes and distinct habitats. Understanding the relationship
between seabed sediments and substrate diversity in marine
ecosystems will eventually underpin biodiversity assessment
and influence the success of ocean management in describing
the biodiversity of our oceans. The approach has the potential to
be applicable to other seabed types worldwide, and will advance
the research that aims to answer the fundamental questions
relating to the value of the role of high resolution acoustic data
to explain patterns in biodiversity.
Acknowledgments
Anne-Laure Verdier (NIWA) processed the backscatter data
using the Sonarscope software of Ifremer. Arko Lucieer (UTAS)
and Alan Orpin (NIWA) provided very valuable comments on this
manuscript. This project was funded by the Royal Society of New
Zealand, Bilateral Research Action Program of the International
Science and Technology Fund, the New Zealand Foundation for
Research Science and Technology (FRST, programme C01X0702)
and the Commonwealth Environment Research Facilities (CERF)
program, an Australian Government initiative supporting world
class, public good research. The CERF Marine Biodiversity Hub is a
collaborative partnership between the University of Tasmania,
CSIRO Wealth from Oceans Flagship, Geoscience Australia,
Australian Institute of Marine Science and Museum Victoria
(www.marinehub.org).
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