Hydrographic Measurements with a CTD

from Research Vessels Common Module in Multidisciplinary Offshore

Operations in Marine Science

Dr Martin White (martin.white@nuigalway.ie) and Dr Rachel Cave (rachel.cave@nuigalway.ie)

National University of Ireland, Galway

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This section will introduce to you the basic use of the CTD and rosette system and relevant

sampling considerations to measure the physical and chemical properties of the coastal

environment from a research vessel.

Introduction

To fully understand biological and chemical processes, whether acting in the deep ocean or

coastal waters, a good appreciation of the environmental conditions is a basic requirement.

These physical processes are, for example, turbulence (which mixes temperature, freshwater

and chemical properties), tidal and other currents and wave or wind induced dynamics. These

processes occur on a myriad of time and space scales resulting in a complex dynamical

environment which will control subsequent chemical and biological processes. The physical

time/space scales involved vary from the very small (seconds and sub-mm) up to large basin-

scale processes related to atmosphere-ocean forcing scales covering years and 1000s of

kilometres (Figure 1). There will be an overlap between physical and biological/chemical

process scales related to the biogeochemical response to physical forcing. This necessitates a

detailed understanding of the environmental conditions present to develop an optimal

approach to sampling strategy, particularly when if the research is of a multidisciplinary

nature.

One must keep in mind that ship-based surveys are a one-off ‘snapshot’ of the environment

experiencing a number of dynamical and biological processes (Figure 1). Whilst in the deep

ocean lateral and vertical property changes may be small, in the coastal ocean these may be

very large and occur over relatively short length scales. This is partly due to amplified tidal

influence that will enhance horizontal and vertical mixing but will also advect coastal ocean

features (e.g. river plumes), or the influence of freshwater inputs to the coastal zone creating

fronts or strong haloclines and density stratification (e.g. Figure 2).

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Figure 1. Schematic illustrating the typical length and time scales of (a) relevant physical

processes and (b) selected biological processes within the ocean environment of relevance.

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Figure 2. Examples of small length scale structures in the coastal ocean. Left: Four aerial

photo ‘snapshots’ of the R. Avoca plume outside Arklow taken over a 90 minute period (from

White et al., 2006). Note the sharp frontal structure and the variation in colour due to

dissolved organic matter in the plume (Each photo is 800x800 m). Right: Windrows created

by Langmuir circulation spaced 2-10 m apart and creating small scale vertical motion in the

upper layer of Killary Harbour.

Measurements from a research vessel are Eulerian measurements, i.e. they are a series of

point measurements at a location or grid of stations made over time (i.e. survey duration).

Eulerian measurements measure both a local change in environmental conditions (temporal)

plus what spatial properties changes are being transported past them (i.e. due to horizontal

gradient in the property, e.g. temperature, salinity etc.). This is different to Lagrangian

observations when the measurements are made by a sensor that is following the same piece of

ocean water so measures only the local change the parcel of water experiences as it moves.

This difference in the measurements needs to be appreciated when interpreting results, i.e.

whether changes in a property, e.g. temperature, is a result of local atmospheric driven

heating/cooling, or if it is just the result of a parcel of warmer/cooler water has been advected

past the measurement point by the currents. An appreciation of the relevant length and time

scales of the likely processes and coastal ocean structure present is therefore crucial, both to

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interpret results but also to develop a measurement strategy beforehand that will be able to

resolve these features.

Consider the influence of tides as an example. Tides are a periodic process, typically semi-

diurnal (e.g. the biggest semi-diurnal tide (M2) has a period of 12.421hrs). Tides are a global

ocean process but are amplified in shallow seas, both in terms of the tidal range and in the

currents created by the tidal forcing. Tides in the deep ocean have a range of up to 1 m and

generate currents typically of order 10 cm s-1. The tidal range is very small relative to the

ocean depth (> 200 m). The currents produced may be similar to the currents produced by

forces in the deep ocean, but play a relatively minor role in moving ocean water big distances

relative to the large scale ocean currents produced by the wind or density differences (e.g. see

Figure 1). In coastal waters, especially for depths < 50 m, tidal amplification may cause tides

that have a range up to 5 m and this then becomes a significant proportion of the total water

depth, especially in estuaries where the depth may be 20vm or less. Currents will also be

amplified and often reach up to 50 cm s-1 (1 knot=51.5 cm s-1). These coastal tides with

strong currents will dissipate their energy through turbulence due to frictional forces at the

seabed and hence are the main contributor to the horizontal and vertical mixing length/time

scales shown in Figure 1.

The tidal period provides and immediate timescale of variation of any property in the water

column under study, whether it is being changed directly by the tidal currents (e.g.

turbulence) or advected past the measurement point. But how far will the tide move water

back and forth past a measurement location? This can be estimated through a simple

calculation and assuming a simple sinusoidal variation in the tidal currents.

If the tidal current strength (V) is assumed to vary as a sin wave, i.e. V=Vo*sin(2*π*t/T),

where Vo is the tidal amplitude (maximum current), t=time and T=tidal period (12.421 hrs),

then the resulting displacement (X) of a water parcel over the tidal period will be the integral

of this, i.e.

X= [Vo*T/(2* π)] *cos(2*π*t/T), and will therefore have a magnitude of Xo= Vo*T/(2* π).

For the M2 period of 12.421 hrs and a tidal current magnitude of 50 cm s-1, this displacement

amplitude (or tidal excursion) is ~3558 m or about 3.5 km. Therefore the water will move

about +/- 3.5 km from a central point, or 7 km end to end. This provides a basic length scale

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of variation one might expect for coastal water properties based on tidal movement. There

will be a number of consequences for these different timescales when considering your

sampling strategy. If one desires to look at the tidal variability in a property (e.g. salinity) at a

fixed location, it is likely that a minimum of 5 to 6 observations per period/wavelength of

variability will be required to resolve the tidal changes adequately, say a measurement every

2 hours. One must then also consider how far the tidal currents might move water past the

measuring point in the 2hr interval between measurements. Other measurements should then

be made at locations ‘up and downstream’ of your main station of interest, but a distance that

will also resolve the variability caused by the tidal excursion (as calculated above). Of course,

your sampling time is limited and there may be a number of measurements to be made in a

multi-disciplinary survey. You have to plan very carefully, therefore, your sampling strategy

to get the best trade off between adequate observation points in space/time and the time taken

to complete the survey. Appropriate resolution in the measurement interval and duration,

therefore, is vital to properly ‘sample’ the environment under investigation. One off

(essentially instantaneous) surveys, therefore, can be misleading and not representative of a

long-term steady or quasi-steady state of the ocean. This may lead to over-interpretation of

data.

The Conductivity, Temperature and Depth (CTD) Profiler

The real-time CTD instrument is the workhorse instrument for hydrographic observations

when sampling the ocean from research ships. CTD electronic systems have developed from

the mechanical era instruments of reversing thermometers and water sample bottles, triggered

by weights attached to the winch line (Lawson and Larson, 2001). A basic CTD package

comprises a temperature sensor (fast response thermistor), conductivity cell and pressure

sensor that can be connected to a conducting cable for real time use or as a self recording

instrument (Lawson and Larson, 2001; Williams, 2009). Additional sensors may also be

attached to the sensor recording package, such as those that measure fluorescence (to

determine chlorophyll); optical transmission (turbidity) and oxygen (see Table 1). The basic

sensor measurements (conductivity, temperature, pressure) enable secondary variables to be

calculated (e.g. salinity, depth, density). On a shipboard, vertically profiling CTD with real

time data transmission via conducting cable, the CTD package will have the electronic

sensors located near the bottom of the containing frame. The CTD may also include a rosette

of sampling bottles attached to the frame. These bottles, open at the start of any vertical

profile, may be ‘fired’ from the desk command to close at chosen depths to allow water

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samples to be taken for both calibration of the electronics or to take biological/chemical

measurements on board or back in the laboratory.

Table 1. Basic, derived and supplementary water column properties that are typically

measured by CTDs and additional attached sensors for coastal ocean observations.

Basic

Measurements Method Biological significance

Conductivity (C)

Temperature (T)

Pressure (P)

Inductive resistance

Thermistor

Piezo-electric sensor

General water column structure, water mass

properties

Derived parameters

Depth Use pressure and latitude Location in water column

Salinity (S) Using C,T, P (Practical

Salinity Scale – PSS 78)

Salt content and for calculating density

Density (ρ) Using S, T, P (Eqn. of state) Water column structure and dynamics

Main additional

measurements

Oxygen Optode Oxygen levels, Anoxia, O2 minimum layer.

Fluorescence Fluorescence Chlorophyll levels (plankton abundance)

Turbidity Light transmission Suspended particulate concentrations

Water chemistry &

calibration

Rosette Bottles Water chemistry, plankton, suspended

particulates, salinity, oxygen

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Figure 3. Illustration of the depth profile of a CTD package with time to show typical

deployment methods; (a) The CTD is lowered at constant speed to the seabed or target depth,

before being raised and stopped at target depths for discrete water sampling. In (b) the CTD

is lowered to the target depth and then repeatedly raised/lowered over a smaller depth range

to increase temporal resolution in the target depth range. The firing of rosette bottles on the

CTD descent is shown in (c) and might be used for specific chemical sampling in relatively

shallow water.

For real time vertically profiling CTDs two principal deployments are commonly used. For

general applications, the CTD package is lowered at a constant speed to close to the seabed

and back to the surface. For hydrographic observations, typical lowering speeds of between

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0.5-1 m s-1 (30-60 m per minute, Figure 3a) are used. Slower speeds might be used if strong

vertical gradients in either temperature or salinity are expected. Generally the down profile is

used for the water column structure measurements and the up profile for stopping the CTD to

sample the water column using the rosette to obtain discrete water samples. The 2nd

common way to use the CTD is to ‘yoyo’ the package with repeated descending and

ascending profiles over a target depth range whilst the ship is fixed at a location or slowly

drifting (Figure 3b). This helps to improve the temporal resolution of the water column

structure, for example to resolve tidal variability at a particular location. If bottle sampling for

chemical parameters is the most important aspect of the CTD cast, then bottles may be

programmed to fire as the CTD is descending (Figure 3c). In deep water this may be a

problem as increasing water pressure as the CTD gets deeper may allow water to be forced

into the closed bottle and contaminate the original sample. However if in shallow enough

water that increased pressure is not an issue, closing bottles on the descent will allow a closer

match of the bottle sample to the measurements made by the electronic samples and this may

be important for some chemical oceanographic aspects, particularly oxygen.

Modern CTD systems generally record data many times per second, typically 24 Hz, which

would suggest a possible vertical resolution of 2-4 cm per measurement at typical profiling

speeds of 0.5-1 m s-1, but this is never achieved. This is due to a number of factors including

the response times of the individual sensors to adjust to the surrounding environment and the

fact that the CTD package may be disturbed significantly by surface wave/swell action. With

appropriate data treatment a vertical resolution of measurements O(1 m) for general

hydrography and O(0.1 m) for some fine scale structure may be achieved if the CTD is

profiled slowly. There are a number of errors that are associated with such a complex

instrument and an appreciation of this will help in appropriate data interpretation and

identification of problems that may arise when sampling. Sources of error with CTD data

arise for a number of reasons;

i) It takes time for each of the sensors to adapt to the changing environment and a ‘true’

measurement, and this varies with sensor resulting in two particular characteristics;

(a) water column features will often seem deeper/shallower than in reality for the

down/up portion of the CTD cast respectively. This may be particularly apparent for

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oxygen as typical O2 sensors have long response lags; (b) different lags in the

response of the temperature (T) and conductivity (C) sensors may result in the spiking

in the resultant calculated salinity (S) as essentially the measurements of T and C

come from different parcels of water. This may be important in regions of strong

vertical property gradients (temperature and conductivity).

ii) There are also effects related to the movement of the CTD package through the water

column, such as physical mixing and heating effects – both related to the contact of

the CTD with the water and self heating by the electronics. Also for large CTD

packages, water may be ‘trapped’ within the package and dragged up/down the water

column and may contaminate a water sample. In addition, the sea is restless and both

surface wind/wave actions, as well as the currents within the water column, will

disturb the descent of the CTD.

To reduce these errors, a number of steps can be completed in the processing of the data.

The steps below may be used as a guideline as to a basic strategy for quality control, but

are not hard and fast rules. CTD instruments will have manufacturer software that will

accomplish similar steps.

1) Alignment of temperature and conductivity sensors. This accounts for different lag

of the temperature and conductivity sensors on a real time CTD. Salinity may be

calculated for a number of data samples with the conductivity sample offset by

different measurement lags relative to the temperature to obtain the ‘least spiky’

salinity dataset.

2) Run a median filter through the data. A median filter is used instead of a normal

running mean to remove noise/spikes in the data, as this does not artificially change

or smooth real vertical structure in any of the variables.

3) A temperature calibration is preformed if calibration data is available.

4) Calculate salinity and other secondary variables. Using the filtered temperature,

conductivity and pressure. Use an approved and tested routine for calculation of

salinity, e.g. a UNESCO formula.

5) Filter salinity data. Use a median filter through the salinity data with the same

window size as previously used.

6) Salinity Calibration. Perform a salinity calibration of salinity using bottle data.

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7) Checking for looping in Pressure signal. Data is discarded during the CTD up-cast

or parts of the down-cast when CTD is passing through a depth that has already been

obtained. This is because the sensor package is usually located at the bottom of the

CTD rosette system and therefore it is the downcast that is passing through water that

is relatively undisturbed by the CTD package.

8) Data Averaging. Average the data to required vertical (profiling CTDs) or horizontal

resolution (for towed and self recording instruments).

A typical upper layer profile of T, C, S (Figure 4a-c) and density (Fig. 4.4d) can be used to

illustrate some of the issues raised above. The untreated profiles indicate a surface mixed

layer and seasonal thermocline. Temperature and conductivity profiles are similar and also

show smaller mixed layers (steps in the profile) of a few meters in vertical extent through

depth range of the seasonal thermocline. The salinity profile is spiky, however, in particular at

the top (~35 m) and bottom (~60 m) of the seasonal thermocline when the mismatch in

temperature and conductivity measurements is greatest in the raw data. The treated profiles

smooth out the salinity errors but retain the water column structure, including the unusual

decrease in salinity just below the mixed layer (the profile of density in Figure 4d indicates

this is not an artefact but the water column is stably stratified at that depth). Figure 4e and 5f

show the effect of ‘looping’ of the pressure records (this problem was eliminated in the

profiles in Figure 4a-d for clarity) from the same CTD profile. In the surface layer, surface

wave action and ship movement significantly affects the CTD descent. The apparent

periodicity of 4 cycles in about 800 samples (or ~32s at 24 Hz) indicates a modulation at a

period of 8 s, a typical ocean swell period. Modulation of the descent is apparent at deeper

depths (Fig 4.4f) but is much reduced.

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Figure 4. An example vertical CTD profile showing the upper 120 m of; (a) temperature, (b)

conductivity, (c) salinity and (d) density from deep water in the Rockall Trough, NE Atlantic.

The thin line shows the unaveraged, untreated data and the thick line treated data, offset in

value for clarity. The variation of pressure with sample number for the same downward CTD

profile is shown for portions of the cast in (e) and (f).

BOTTLE SAMPLING

Niskin bottles were developed early in the 20th century and they consist of open ended tubes

(typical capacity 5-10L) equipped with spring loaded cups that can close at required depths at

both ends with the help of a “messenger “(weight that travels down a wire). Niskin-type

bottles are now often mounted on CTD frames (with varying capacity up to 20L per bottle)

and fired electronically. Similar types of bottle include Nansen bottles and NIO bottles. The

rosette bottles on a CTD are a very useful sampling tool, although discrete samples of a finite

number and volume can be taken depending on the size of the CTD frame (and hence bottle

number/size) being employed. It is usual to close these bottles during the up cast of a vertical

profile, as the rosette is typically housed in the upper portion of a CTD frame. It can

sometimes be hard to position the CTD bottles at the exact depth preferred by the scientist,

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and one should be realistic about the accuracy to the vertical location at which samples are

taken, even in shallow water. This is due to inherent characteristics of the CTD, particularly

those involving response times of sensors which result in vertical offset in features for both

up/down profiles (see next section), and not least because of the heaving/rolling of the CTD

tethered to a ship at the surface of a restless ocean!

Since small water volumes are usually required for most chemical and biological analyses

(typically from 100s ml to 1-2 L), therefore water from the same bottle can be used for the

determination of many parameters. Typical parameters that would be routinely collected are

in Table 2.

Table 2. Water sample parameters routinely collected on research vessels. Lab gloves should

ALWAYS been worn when dealing with water samples, both to prevent you contaminating

the sample (e.g. your sweat contains both salt and nitrite, soap residue will contain phosphate,

you skin cells are particles rich in carbon, nail varnish contains trace metals), and to protect

you from reagents used to fix the samples.

Parameter - Water Volume Post-collection Notes

Oxygen

Use plastic tube to

direct flow to bottom

of bottle to prevent

air getting into

sample

250ml plus overflow

Clear or amber glass

oxygen bottle with

plastic stopper and

rubber bands to keep

stopper in place

‘fix’ with two

reagents, store at

room temperature

and under seawater

Water samples for

gas analysis are

collected first to

reduce the uptake of

atmospheric gas as

bottle gets emptied

Dissolved inorganic

carbon (DIC)

Use plastic tube to

direct flow to bottom

of bottle to prevent

air getting into

sample

500ml plus overflow

Schott Duran glass

bottle with glass

stopper, coated with

Apiezon grease.

Rubber bands to keep

stopper in place

‘poison’ with

mercuric chloride,

Store in refrigerator

As above

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Parameter - Water Volume Post-collection Notes

Salinity 150ml

Flat sided glass

bottle, plastic stopper

and screw cap

Store at room temp Next sample taken

after any gas

samples. Used to

confirm accuracy of

CTD salinity

Alkalinity 250ml or 500ml

HDPE. Overflow the

bottle before

capping.

Store in refrigerator Alkalinity can also be

measured on the DIC

samples (see above)

Dissolved Organic

carbon/nitrogen

60ml,

HDPE bottle

Syringe filter through

acid-washed GF/F,

freeze

Dissolved Nutrients

(nitrite, nitrate,

phosphate, ammonia,

silicate)

50ml x 2

Plastic red-top

Falcon tube

Vacuum filter

through 0.4micron

Nucleopore filter

(membrane) and

freeze

Use plastic filtration

unit if silicate

analysis require.

Otherwise can use

glass.

Coloured Dissolved

Organic matter

(CDOM)

Amber glass or

opaque HDPE bottle,

minimum of 100ml to

allow for triplicates

Filter through

0.4micron

Nucleopore filter

(membrane). Keep

dark at room temp,

Analyse on

spectrophotometer

within 24 hours

Can use same filtrate

as for nutrients.

Cannot be stored

beyond ~24 hours as

organic matter will

begin to break down.

Suspended

Particulate Matter

(SPM)

Use 47mm GF/F

filter paper which

has previously been

combusted at high

temp (450C) and

weighed on a high

precision balance

Rinse filter with DI

water to remove salt,

fold, put into labelled

plastic bag or petri

dish and freeze.

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Parameter - Water Volume Post-collection Notes

Chlorophyll-a,

phaeopigments

Use 47mm GF/F

filter paper

Fold filter paper and

store in red-top 15ml

tube, freeze

Particulate Organic

carbon/nitrogen

Use 25mm GF/F

filter paper

Syringe filter known

volume, fold filter

paper and freeze

Material is usually collected onto filters (commonly glass fibre filters but various membrane

filters can be used depending on types of analyses) after gentle vacuum filtration to avoid

particle disintegration or loss through the pore sizes of the filter. However there are issues.

Filtering is often a time consuming process, mostly due to filter clogging, that requires

considerable man-power and effort, particularly when different parameters are measured.

Filter clogging depends on pore size, location and/or water depth, for example it may take

several hours to filter 1L of particle-rich, productive, surficial water onto GF/F (nominal pore

size 0.7 µm) filters; this could lead to severe backlogs, leading to operator fatigue that could

ultimately affect sampling resolution and strategy. In addition the small filter volumes do

pose problems with respect to weighing accuracy, replication and small scale patchiness.

Many other parameters may be sampled for, requiring more specialised handling. Almost

every substance known to man is dissolved to some degree in the oceans, so somebody

somewhere will want to measure them.

SAMPLING ISSUES/STRATEGY

Two very different CTD sampling grids are shown in Figure 5 to illustrate the resolution of

scales discussed earlier. One is a CTD grid used to make observations over a carbonate

mound over a small area and rapidly to ‘sample’ motions within a tidal period. The other is a

transect across the south Pacific - the World Ocean Circulation Experiment (WOCE)

hydrographic transect P06. The yoyo technique of CTD deployment employed for Figure 5a

allowed high temporal resolution measurements of the near seabed approximately every 20

minutes to highlight tidal and short term variability in the benthic boundary layer and

associated suspended particulate material concentrations (see later Figure 6). Conversely the

WOCE P06 section was occupied to measure full depth physical and chemical water column

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parameters (Figure 5b). In total 259 stations were occupied during 70 days at sea occurring over a

period of 3 months and was conducted for the assessment of the long term state of the ocean,

driven by inter-annual or climatic forcing. Such a transect would not resolve either the tidal

motions or even the mesoscale (eddy) variability in the ocean either, which would appear as a

form of small amplitude noise within the large scale oceanic structure.

Figure 5. Examples of CTD station grid for measurements made (a) over a small carbonate

mound, NW Porcupine Bank (NE Atlantic), by ‘yoyo’ CTD from 400 m depth to bottom (the

north-south transect data are shown in Fig 4.5), taking just 4 hours and (b) World Ocean

Circulation Experiment (WOCE) line P06E,C,W occupied between 2-5-1992 and 30-7-1992

and undertaking 259 full depth CTD stations

Conversely the data from the yoyo profiles over the mound show how a CTD can be

manipulated to sample the water column adjacent to the seabed at relatively high temporal

resolution (Figure 6). Data are from a survey of the slope of the Porcupine Bank, NE Atlantic

to assess the dynamics over a carbonate mound (see Mienis et al., 2007). The CTD was

lowered to close to the seabed (depths 700-750 m) from a depth of 400 m. Between each

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up/down profile the ship was edged slowly by a few hundred meters in a transect so a profile

was made every ~20 minutes. The resultant temperature profiles show the variability in the

benthic boundary layer (BBL) height (Figure 6a). Use of a beam transmissometer indicated a

benthic nepheloid layer (BNL) or suspended particulate material associated with the BBL

(Figure 6b). The temperature profiles also indicated the likely presence of an overturning

internal wave in progress, seen as the inversion of temperature in 3 consecutive vertical

profiles between the depths of 650-700 m. If a single profile, perhaps made as part of a

coarser resolution transect across the slope, had shown this temperature inversion, it may

have been interpreted as a temporary mis-function (e.g. blocked sensors) as the associated

inversion in density would not be stable). Here the 3 consecutive profiles made within a time

of 40 min showing a consistent feature is persuasive, given the likely timescale for an

overturn to occur and particularly as the region is know as a region of high internal wave

energy (Dickson and McCave, 1986; Mienis et al., 2007).

Figure 6. Vertical profiles of near seabed (a) temperature and (b) light transmission across a

small carbonate mound on the NW flanks of Porcupine Bank, NE Atlantic (see Fig 4.9a for

local bathymetry and station locations). Values of each property are relative to the value at

the bottom, whose value is indicated by the short thin vertical line, and each profile is offset

relative to the distance across the mound. Data courtesy of Henko de Stigter, Royal NIOZ.