Marine Scotland Science Report 1/11

THE POTENTIAL OF DIGITAL PHOTOGRAMMETRY FOR

CHARACTERISING STREAMBED GRAIN-SIZE
DISTRIBUTIONS IN FISH HABITAT STUDIES: A
FEASIBILITY AND LIMITATIONS REPORT

Millidine, K. J., Malcolm, I. A. and Gibbins, C. N.

© Crown copyright 2011

This report represents the views of the authors and has not been subject to
a full peer review process

Marine Scotland Science Report 01/11

The Potential of Digital Photogrammetry for Characterising

Streambed Grain-Size Distributions in Fish Habitat Studies:
A Feasibility and Limitations Report

Millidine, K.J., Malcolm, I.A. and Gibbins, C.N.

Published by Marine Scotland – Science

 The Potential of Digital Photogrammetry for Characterising Streambed
Grain-Size Distributions in Fish Habitat Studies: A Feasibility and
Limitations Report

Millidine, K. J.1* Malcolm, I. A.1 and Gibbins, C. N.2

1
Marine Scotland Science Freshwater Laboratory
Faskally, Pitlochry, Perthshire, PH16 5LB

*
k.millidine@marlab.ac.uk

2
Northern Rivers Institute, School of Geosciences
University of Aberdeen, Aberdeen, AB24 3UF

Executive Summary

• The characterisation of streambed substrate is important to most fish habitat models

and studies of habitat suitability. There is increasing interest in the use of digital
grain-size characterisation in such studies, owing to recent technological advances
which make collection and analysis of digital data straightforward. However, such
techniques are cost prohibitive and there is consequently a need to explore
additional methods which are cheaper and capable of working in streams where
overhanging banks or vegetation prevents clear line of sight.

• This study investigated the viability of using in-stream close range digital
photographs and an automated image analysis program (Sedimetrics photographic
package ‘Digital Gravelometer’). The report is divided into 4 sections: (1) obtaining
digital images of streambed substrate; (2) sediment characterisation using image
processing applications; (3) comparison of results using quadrat and digital analysis
methods; and (4) discussion of the limitations and opportunities for the use of digital
image analysis in fish habitat studies.

• There were significant challenges obtaining realistic sediment distributions using the
sedimetrics software. However, providing a lot of care and time were taken during
the image processing procedure, the digital analysis method provided good results
and was comparable with standard visual assessments.

1
Introduction

The composition of streambed sediments is an important control on the distribution and

abundance of fish populations and can be particularly important in streams supporting
salmonids (Whitman et al. 2003). The grain-size distribution affects the availability and
spatial distribution of spawning habitat (Moir et al., 2002; Moir et al., 2009) and under
certain circumstances can also influence spawning success (Jensen et al., 2009).
Streambed substrate also provides important refuges for salmonid fry (Chapman &
Bjornn 1969; Hillman et al. 1987) and parr (Valdimarsson & Metcalfe 1998; Johnson &
Douglass 2009) and has been shown to be influential in controlling the distribution and
abundance of a range of fish species (Berkman & Rabeni 1987; Jowett & Richardson
1995; Glova et al. 1998; Jowett & Boustead 2001).

Instream habitat modelling is potentially useful for assessing the physical processes
influencing the distribution of different fish species and age classes (Lamouroux et al.,
1999; Guay et al., 2000; Kennard et al., 2006; Buisson et al., 2008). Typically fish habitat
models require the characterisation of habitat that is used (utilised) and present
(available) but not used by fish. In the context of riverine fish, habitat utilisation describes
the use of locations by individuals and, requires characterisation of depth, velocity,
substrate and cover. The techniques used to characterise the streambed grain-size
composition vary greatly in both accuracy and effort (Whitman et al. 2003). One
traditional method of rapidly assessing and quantifying particle size is by using a quadrat
and estimating, by eye, the percentage cover of the dominant and sub-dominant
substrate (Mäki-Petäys et al., 1997). However, results from these traditional methods
can vary substantially between observers, introducing significant bias where use of the
same observer is not always possible. Moreover, the results are usually reported in the
form of ‘dominant’ and ‘subdominant’ size-classes or as percentages of classes. These
metrics are rather coarse and are not necessarily the most biologically relevant metric
for describing substrate characteristics. Consequently these approaches may be of
potentially limited value in the development of habitat models for fish.

Another frequently used method for quantifying coarse particle size composition is the
Wolman pebble count (Wolman 1954). This involves walking along a transect and
selecting random clasts at the toe point, which are then measured along the
intermediate axis (b-axis). A large sample can be acquired rapidly and used to generate
a size-frequency distribution. However, Wolman is a reach- or morphological unit-scale
method which is not appropriate for patch-scale analysis of microhabitat use by fish.
Also, it underestimates the proportion of fine material (<8mm); this is a significant issue,
given the importance of fines in determining the quality of salmonid habitat (Greig et al.
2005; Levasseur et al. 2006). Bulk samples of material from patches of bed can be
collected and taken back to the laboratory for sieving and accurate determination of

2
grain size distributions (GSDs). However, bulk sampling is destructive (i.e. it disturbs the
bed) and this affects the availability and, potentially, subsequent use of bed locations by
fish. Other limitations relate to the fact that large volumes of material are needed for
accurate characterisation (particularly where the bed is coarse) and so bulk sampling
becomes impractical in some circumstances.

Given the limitations of the various approaches discussed above, sediment

characterisation using digital imagery potentially offers major advantages in terms of the
overall characterisation and provides the opportunity to derive a range of potentially
informative metrics which can then be tested for biological significance. In addition, this
approach can provide a permanent record of the observed sites for future reference and
remove the problem of observer bias that can occur in the field. Recent developments in
digital image processing methods have already allowed for close range terrestrial remote
sensing to determine particle sizes automatically (Butler et al. 2001). Further progress
using high-resolution airborne imagery (LiDAR) showed that automated grain size
measurements of exposed reaches of a gravel bed river are possible (Carbonneau et al.
2004). However obtaining quantitative grain size distributions in shallow wetted areas of
the channel requires specialised processing algorithms and, although has had limited
success in coarse fluvial environments (Carbonneau et al. 2005), often has other
associated problems such as glary reflections on the water surface which require
manual manipulation and potential error associated with the presence of algae. The
most obvious optical constraint is that the stream must be visible from above since
remote sensing of streams cannot be done where trees, bridges, woods or other
obstacles overhang the stream (Marcus & Fonstad 2007).

Given this context, a series of methods were field trialled in order to develop a protocol
for streambed sediment size characterisation that could be used for habitat
characterisation and modelling. The objectives of this study were to (1) obtain high
quality digital images of streambed substrate, (2) characterise grain-size composition
using image processing applications and (3) identify limitations and opportunities for
using digital image analysis in fish habitat studies. Field trials were carried out in the
Newmills Burn, Donside, as part of a broader research project on the use of habitat by
fish in agricultural streams (SFO273). However, the limitations and benefits of the
approach identified in this report are generic and consequently will be applicable to other
sites and locations.

3
1. Obtaining Digital Images of Streambed Substrate

Most habitat modelling studies attempt to locate fish and characterise habitat use at
similar spatial scales. Various methods are available for determining the location of fish,
including snorkelling, PIT tag detection antennae and electrofishing. Each of these
methods has its benefits and limitations. However, for the purposes of this assessment
we assumed the use of a modified electrofishing method with an estimated locational
accuracy of ca. 0.5 m2.

In order to use digital photogrammetry software, it is necessary to obtain high quality

digital photographs of the streambed. Historically this approach has been used to
characterise exposed gravel features (Graham et al. 2005a, b). Where areas of interest
are underwater, the necessary assumption has been that adjacent exposed areas that
can be photographed have similar GSDs. Of course, this assumption may be not always
hold.

In order to use the same technology in studies of fish habitat it is necessary to obtain
photographs from below the water surface. This is problematic due to constraints
associated with reflection and lighting. Initial efforts to overcome these issues focussed
on the use of standard digital SLR cameras fitted with polarising filters, together with
perspex-bottomed basins to see into the stream (Plate 1). Both of these approaches
proved unable to provide photographs of adequate quality, owing to the following
problems:

1. A flash was required to illuminate the bed sufficiently. However this resulted in
reflection back from the perspex and made the photographs unusable.

2. Without the flash it was necessary to use an extremely high ISO speed and low
shutter speed (to allow for poor light conditions). This combination resulted in
grainy / noisy images (due to high ISO) and a lack of sharp focus on the images
due to camera shake (resulting from the slow shutter speed). These images were
too poor in quality to use in digital analysis.

4
Plate 1
Perspex-bottomed box used in initial trials

Subsequently a series of under water compact cameras were trialled. While these were
able to obtain good quality photographs of the sediment (Plate 2), it was necessary for
the camera lens to be fully submerged. Therefore the area of streambed that could be
photographed largely depended on water depth. This limits the use of underwater
cameras to deeper areas; for example, to obtain a 0.5 m2 image using a 6.4 – 19.2 mm
camera, the minimum distance away from the substrate is 90 cm.

Plate 2
Digital images of bed substrate using a compact underwater camera.

Therefore, to obtain representative grain-size distributions in shallow areas, it would be

necessary to stitch together several photographs of smaller areas. However, this would
be problematic as (a) taking photographs of contiguous patches of streambed, in the
field, is extremely difficult; (b) matching photographs to avoid overlapping is also difficult
and time consuming, and (c) differences in exposure between photographs would
complicate the derivation of optimal settings in the grain size analysis software.

5
In order to overcome these problems a perspex bottomed box was constructed within a
frame that allowed height adjustment (Figure 1). With the bottom of the box in contact
with the water surface, it was then possible to fill the box with water to a desired height
and obtain photographs of the streambed using compact under water cameras below the
water surface (Plate 3). This equipment enabled good quality photographs of the
streambed at the required scale even in very shallow waters.

Figure 1
Schematic of substrate-viewing box

0.7m

0.7m

0.7m

External frame
The moveable Perspex box within the external
frame enables height adjustment, allowing for
variable substrate size.

6
Plate 3
Apparatus for obtaining photographs of the streambed

2. Sediment Characterisation using Image Processing Applications

Once the photographs had been obtained it was necessary to process the photographs
within the analysis software in order to produce a grain size distribution.

2.1 Sedimetrics – Digital Gravelometer Software

Digital Gravelometer (www.sedimetrics.com) is a commercial software application for

Windows that enables estimation of the composition of unconsolidated gravel rapidly
from digital photographs, and the construction of a complete grain-size distribution for
the sample (Graham et al., 2005a, b). The software has an easy-to-use graphical
interface and is able to analyse photographs individually, providing information about the
grain-size distribution in each, or aggregate the information obtained from a group of
images. In addition to basic size-distribution parameters, Digital Gravelometer produces
customisable reports containing a wide selection of commonly used statistical
parameters along with graphical grain-size distribution curves and histograms. Once the
reports have been customised to suit particular requirements, the settings can be saved
as a template, allowing for rapid analysis of subsequent samples.

7
2.2 The Grain Measurement Procedure

The identification and measurement of grains by Digital Gravelometer is an eight-stage

process. The individual steps are as follows:

Stage 1: Convert to greyscale

The colour image is first converted into a greyscale (intensity) image.

Stage 2: Apply correction for radial lens distortion

If specified that the radial lens distortion should be corrected, the greyscale image is
modified to incorporate this correction.

Stage 3: Apply a projective transformation

A projective transformation is applied to the image to correct for the axis of the camera
not being held perfectly vertically above the centre of the sample patch.

Stage 4: Identify the grains in the image

This stage converts the greyscale image into a binary (black and white) image in which
the grains are represented by white and the interstices by black.

Stage 5: Separate touching grains

It is common for those regions that represent grains in the resulting binary image to be
connected. Therefore, in a further attempt to separate touching grains, the binary image
is segmented by the application of a watershed transformation.

Stage 6: Select the grains to measure

Those grains that lie within the sampling area defined by the control points are now
selected for measurement.

Stage 7: Measure the grains

The selected grains are now measured. Information is recorded about grain size,
orientation, shape and area. At this stage, the grain sizes are specified in pixels.

8
Stage 8: Convert grain sizes to millimetres
The final stage is to convert the measured grain sizes into millimetres using the known
scale of the image.

To illustrate the full range of image processing stages, Plate 4 shows the series of
images produced using the default settings within the software (Stages 1, 3, 4, 5 and 6).

Plate 4
Digital image of bed substrate processed for particle size analysis

River beds present a particularly complex problem because grains are highly variable in
shape and may be partially hidden or inclined relative to the plane of the image. In
addition there may be significant heterogeneity in colour and grain-surface texture
between and within individual grains, and the surface has elevation variations which may
result in uneven lighting and shading across individual grains and across the image
(Graham et al. 2005b). Also, algae and macrophytes can obscure sediment and make it
difficult for the software to correctly discriminate between adjacent clasts.

9
Differences in Grain-surface texture between and within individual grains were evident in
the digital photographs taken from the Newmills Burn and this prevented the software
adequately identifying each individual substrate particle using the default settings
(Plate 5). To rectify this problem, the image analysing parameters used within the grain-
identification procedure were modified in an attempt to capture an improved
representation of the digital sample. Plate 6 shows the effects of modifying the default
parameters within the Digital Gravelometer software package, which shows a
reasonable discrimination between the stones and would be more suitable for further
analysis, although it can be seen that erroneous identification of individual clasts
remains.

Plate 5
Converted greyscale image (left) and the same image processed for particle size
analysis using default parameter settings (right)

Plate 6
Converted greyscale image (left) and the same image processed for particle size
analysis using modified parameter settings (right)

10
Digital Gravelometer offers the user considerable flexibility in producing, viewing and
exporting the sediment report. In addition to the basic / default size-distribution
parameters, it enables customisable reports containing a number of statistical
parameters along with graphical grain-size distribution curves and histograms. These
reports include:

• User defined or default percentile estimates (in mm, phi and psi)

• Standard grain-size distribution statistics (mean, sorting, skewness, kurtosis)

based on moment or graphical methods using logarithmic, geometric and
arithmetic methods

• Proportion of grains in Wentworth size classes, standard sieve size classes or

user-defined classes

• Fully customisable graphical representation of the grain-size distribution as a

histogram and cumulative curve

• Information about the project (client, operator etc.) and each individual image
(filename, sample ID, collection date etc.)

This customisation is enabled by a series of user-friendly checkboxes, and also allows

the user to export the report as a comma-separated variable (*.csv) file that is readable
by most data analysis packages. Figure 2 shows a combined grain-size histogram and
cumulative curve produced within the report.

Figure 2
Example of a grain-size distribution obtained from Digital Gravelometer software

25 Wentworth size class Percent in class

100
Boulder (>256 mm) 0.00
Cobble (64 mm - 256 mm) 0.00
20 Pebble (4 mm - 64 mm) 21.46 80
Granule (2 mm - 4 mm) 32.95
Sand (<2 mm) 45.59 % in class
Cumulative %

15 Cumulative % 60
% in class

40
10

20
5

0
4 2 0 -2 -4 -6

Phi

11
3. A Comparison of the Results Obtained from the Quadrat and Digital
Analysis Methods

Basic output from the sedimetrics application (dominant and sub-dominant substrate
size) should be comparable with conventional characterisation techniques (i.e. using a
quadrat and estimating the percentage dominant and sub-dominant substrate
composition) if the software is capable of adequately identifying the grains within the
image. Using a quadrat, the substrate particles in the Newmills Burn were classified
using an index developed by Brusven (1977) with the modifications of Bovee (1982)
(Table 1).

Table 1
The Brusven substrate code (as modified by Bovee 1982) used for substrate
classification

Code Substrate description

1 Fines (< 4 mm)
2 Small gravel (4 – 25 mm)
3 Medium gravel (25 – 50 mm)
4 Large gravel (50 – 75 mm)
5 Small cobble (75 – 150 mm)
6 Medium cobble (150 – 225 mm)
7 Large cobble (225 – 300 mm)
8 Small boulder (300 – 600 mm)
9 Large boulder (> 600 mm)

In order to assess the comparability of the digital analysis method to the more
conventional quadrat method, a small number of photographs with dominant and sub-
dominant information were analysed using both the default and modified parameter
settings (Table 2). The output settings of the Digital Gravelometer were customised in
order to obtain the proportion of grains as defined in Table 1. The largest and second
largest proportions of grains were respectively classed as dominant and sub-dominant
substrate.

12
Table 2
A comparison of digital analysis and quadrat substrate sampling methods (The numbers
represent the code from Table 1)

Size-class
Size-class using
Size-class using using
Sample Category modified image
quadrat default image
settings
settings
Dominant 1 1 1
1
Sub-dominant 2 2 2
Dominant 2 1 2
2
Sub-dominant 1 2 1
Dominant 3 2 2
3
Sub-dominant 2 4 3
Dominant 4 2 4
4
Sub-dominant 2 1 2
Dominant 2 2 3
5
Sub-dominant 3 1 2
Dominant 2 2 2
6
Sub-dominant 1 1 1

The individual clasts were poorly defined in all samples using the standard setting
(similar to Plate 5) (Table 2). The software was particularly poor at identifying larger
substrate sizes (size-class 3 or more) due to the grain-surface texture which tended to
break up the image into smaller particles. After parameter modification to enhance
substrate discrimination, the results were generally closer to those obtained using the
quadrat method. There was a slight disagreement in a two samples (samples 3 and 5),
but it is uncertain whether this was due to observer or analysis error owing to the fact
that the percentage composition of both the dominant and sub-dominant were very
similar.

4. Limitations and Opportunities for the use of Digital Image Analysis in

Fish Habitat Studies

4.1 Obtaining Digital Images of Streambed Sediments using the Perspex Box

The time taken to obtain the initial photographs can be substantial for shallow water
areas due to the size and weight of the apparatus involved (shown in Plate 3). In order to
obtain images of the necessary substrate area, the perspex box was large (see
section 1). Furthermore, because a considerable volume of water was needed to fill the

13
apparatus, heavy Perspex sheeting was needed to withstand the forces involved.
Consequently the overall weight of the apparatus was substantial, requiring at least two
people to move and position it; this made deployment in areas surrounded by steep-
sided banking difficult. In addition, there were further difficulties with its deployment at
some locations; for example it was not possible to deploy it near to the banks, especially
if highly vegetated or undercut due to the physical size of the apparatus.

The practicality of using the box may also be limited by the size of substrate to be
photographed, since its elevated height was restricted to 0.5 m (elevation height was
limited to 0.5 m to minimise overall weight of apparatus). Other considerations include
circumstances where substrate mobility reduces the quality of the photographs, or where
coarse irregular emergent substrate prevents deployment.

In addition to the logistical constraints associated with physical deployment, further

difficulties were encountered during the trial. For example, bubbles formed underneath
the box (where it came in contact with the stream water) which limited the quality of
resulting images. Furthermore, layers of sand and silt were found to settle on the bottom
of the box which affected the auto-focus on the camera. It was possible to overcome this
problem by initially positioning the camera close to the substrate within the box and then
slowly moving the camera away until the acquired substrate area was within view and in
focus. Furthermore it was possible to raise the water level slowly within the apparatus
through the two holes inserted into the base allowing for filling and draining of water
within the box, so that the streambed remained relatively undisturbed.

The use of the perspex box in wider yet shallow streams would be easier, particularly
when access in and out of the water is not impeded by steep, highly vegetated banks.

4.2 Image Processing

Although digital image analysis is novel and potentially offers major advantages in terms
of the detail of information provided, in practice it proved to be extremely time consuming
given that the default settings did not adequately represent the grain sizes within the
digital image. The main reason for this appeared to be due to the surface-grain texture of
the substrate which caused the image processing software to break-up larger clasts into
smaller ones. In this circumstance, the user has to manually manipulate the settings for
each of the images. This manipulation can be considerable – e.g. it took approximately
one hour to adequately process each of the samples in table 1. The manual
manipulation of the measurement process also results in observer bias, given that how
effectively the substrate is defined is dependant on the person using the software.
Despite these problems the Digital Gravelometer software was able to identify the
dominant and sub-dominant substrate type present within the images. However,

14
comparisons with other more detailed sediment analysis methods have not been carried
out and we are unsure how they would compare.

This method may work better where sediments are more uniform in colour or where you
need more detailed grain size information e.g. spawning studies or spawning habitat
assessment.

5. Summary and Conclusions

The use of digital image analysis (Digital Gravelometer) has advantages for the
characterisation of exposed gravel surfaces. However, it has many limitations when
used for characterising areas inundated with water, most of which have been identified
in the trial summarised in this report. The full benefits of using this sampling approach
are only likely to be realised in streams that contain substrate with less variable surface-
grain texture, where access in and out of the water is not impeded by steep banking or
where water depths are sufficient for direct use of underwater photography. The
potential to acquire a range of sediment size metrics which can then be tested for
biological value is itself a clear benefit of using digital photogrammetry; however these
benefits would have to outweigh the substantial constraints and limitations identified in
this report. The value of this approach in understanding fish-habitat relationships, where
fish sample sizes are very small, may be very limited and costs too excessive. However,
its value may be greater in other studies, such as spawning habitat use or assessment.

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© Crown Copyright 2011

Marine Scotland – Science

Freshwater Laboratory
Faskally
Pitlochry
PH16 5LB

Copies of this report are available from the Marine Scotland website at
www.scotland.gov.uk/marinescotland