Last step to generate habitat map

Hey guys. Now we know about habitat mapping techniques, and today I am going to talk about using our data and making the final habitat map. OK. Let’s get to the point.

Habitat maps are the final result of integrating continuous coverage of physical properties of seafloor with the observation of communities present at discrete sections. It is worth mentioning that the final product is a prediction of the distribution of habitats the best habitat mapping approach is the one which integrates the remote-sensing data providing a full coverage of seabed and ground-truthing data that validate the sensed data. For remote sensing data, the best technique is acoustic remote sensing. However, with this technique, we cannot directly define the habitat. They provide the physical attribution of the seafloor, using the backscatter strength images; except for the regions that the seafloor is formed by biotas such as biogenic reefs or mussel/oyster beds (MESH).

Figure 1.generating benthic habitat maps procedure (C.J Brown et al., 2011)

The final map is a prediction of the distribution of seabed habitats, with the complete coverage environmental data acting as a proxy for the habitat data.

  1. Environmental data layer

Seafloor geology along with morphological characteristics and overlying water column attribute has a huge impact on benthic biology. This environmental data layer mainly provides spatial information of these parameters which are collected using different methods. Each method has its benefits and drawbacks. The new approach, using MBES; records information related to bathymetry and backscatter strength and other valuable seafloor information can be extracted from both bathymetry (slop, aspect, terrain variability) and backscatter (hardness, roughness, acoustic class) and the resolution of these system varies from ten centimeters to ten meters.

Another important factor that has a dominant influence on biological characteristics of the seafloor are oceanography parameters.  Spatial oceanographic data are multi-sourced. They can be gathered at continuous coverage from satellite (SST or chlorophyll content that can be used as an indication of productivity) or interpolated from point sample measurements (Temperature, salinity, oxygen) or continuous coverage by models and in comparison to acoustic data(MBES), they have the resolution of tens of meters to tens of kilometers which in turn introduce a limit on the scale of habitat mapping and the habitat maps which use oceanography parameter tend to be conducted at border scales.

   2. Utilization of environmental data sets (High-resolution acoustic data)

Environmental data should be mange in a way that can be integrated with in-situ data efficiently. Although habitat patterns can be continuous or discrete sections, however, in the majority of cases high-resolution acoustic data sets are divided into “spatial unites” before integration of habitat information. These units are called segment (C.J Brown et al., 2011).

  • Backscatter analysis approaches

The most widely used from MBES data in habitat mapping is acoustic backscatter data which identify different region from acoustic backscatter strength and these acoustic classes are then linked to the specific seafloor habitat attributes from the ground-truthing dataset. MBES system covers a wide range of area with high resolution in comparison to SBES that suffers from discrete data between survey lines, however, segmenting the backscatter from SBEC are much easier than MBES. In the field of habitat mapping MBES are becoming the first choice due to being capable of gathering both bathymetry and backscatter data simultaneously and using motion reference system to adjust the vessel pitch, heave and roll when positioning the data relative to the seafloor. Different image-based approach methods in the segmentation of MBES backscatter have been used such as neural network technique, Bayesian decision rules, textural analysis based on grey level co-occurrence matrices but there is no widely accepted approach to segment the backscatter data. Another approach to extract quantitative information from MBES backscatter data is a signal-based method. In this method, the variation of backscatter strength with the angle of incident (which is an intrinsic property of seafloor) can be used for acoustic seafloor characterization by extracting several parameters from successive sonar pins. Then to link the acoustic backscatter observation to the seafloor properties, the average angular response is compared to mathematical models. This approach shows the best approach in the field of habitat mapping however it should be tested over a range of benthic marine ecosystems.

Figure 2.The distribution of Backscatter strength. Light-toned areas show the high backscatter
energy and  dark-toned areas show low backscatter energy (J.Shaw et al., 2012)
  • Bathymetric analysis approaches

Bathymetry can be used to segment an area in which identify distinctive biological characteristic because benthic species show a tendency to stay in certain depth and topographic conditions. We can use other features of bathymetry such as slope, orientation, and curvature to segment the seafloor (C.J Brown et al., 2011).

    3. Utilization of environmental data sets: oceanographic data

We can predict the distribution of biological characteristic using the properties and conditions of underlying water column which are important in supplying food, nutrient, and gametes. According to the low resolution of oceanographic data (from ten meters to ten kilometers), there is a disparity between the resolution of acoustic data and oceanographic data to provide habitat maps.


Figure 3.Oceanography parameter layer (C.J Brown et al., 2011).


   4. Ground-truthing (adding the benthic biological information)

To measure the biological feature of the seafloor the best approach is in situ ground-truthing which can be linked to environmental layer and the type of in situ method depend on many factors (the purpose of the survey, survey platform and etc.) and it has a profound effect on the final product. Some methods are grab sampling, trawls, underwater photographs or video, each of which can be applied to a specific region or for comprehensive data collection, applied two of them together(C.J Brown et al., 2011). There should be some sample video recording for training site as ground-truthing and some other sites to validate the final result (A.Micallef et al., 2011).Two strategies are used to identify the distribution of a species. The first method is fully quantitative which is based on the abundance, the number of individuals of each species or the biomass (the total weight) of each species and is widely used in the grab and trawl sampling. In the second method, semi-quantitative; they score the abundance of each species according to their amount using a predefined table like SACFOR.


SACFOR scale
Figure 4 Figure 3. ‘SACFOR’ scale. Mesh 2008


Figure 5.Backscatter image and seabed photography for ground-truthing (A.Michallef et al., 2011)


   5. Correlate biological and physical patterns

A number of methods are available to examine the correlation between biological and physical patterns. Two commonly used computer packages with a variety of multivariate methods are PRIMER and CANOCO. These are based on a multivariate statistical analysis which calculates the correlation between the parameters.

Figure 6. Combination different environmental variables with PRIMER (%gravel, %silt, and depth)Mesh 2008.


   6. Final product

The lack of high-resolution spatial environmental data has led to finding some difficulties in benthic habitat mapping. Therefore, most of the marine habitat mapping studies use simple statistical models to determine associations between ground-truthing and environmental data sets.


  • abiotic surrogates (unsupervised classification – limited or no ground validation)

It is mostly used in broad scale such as continental shelf region but there are studies used this strategy for smaller scales, however, output maps in this scale are not a good reference for prediction of species patterns and useful for management objectives.

  • Assemble first, predict later (unsupervised classification)

This is the most common strategy used for producing single species maps, community maps, or maps of generalized habitat classes based on observed geological/biological seafloor characteristics. This strategy uses a top-down approach and includes combining organized data of environment and biology/geology. In the case of single species habitat mapping, presence/absence of an important species is modeled considering environmental situations which are usually a simple statistical assessment of the correlation between the data sets. In community mapping ground-truthing data are organized into classes then the data sets are modeled.

  • Predict first, assemble later (supervised classification)

The third strategy takes a bottom-up approach which uses biological/geological ground-truthing data to organize environmental data. In the case of single species mapping the presence of an important species is modeled as a function of the environmental predictors. Theoretically, we can combine single species habitat maps to produce a community distribution map. However, commonly for producing community maps, data are organized into classes then use to perform some form of supervised classification on the environmental data sets to segment the continuous coverage variables.



Figure 7. Habitat map of the seafloor offshore north-east Malta (Micallef et al., 2012).


Over the past decade, there has been much attention in the field of benthic habitat mapping and rapid improvement in our ability to map seafloor habitat. With the advancement in acoustic survey tools and using three aforementioned strategies, we can provide valuable benthic habitat maps and insight for decision makers to achieve a sustainable marine environment.



A.Micallef, T.P.L.Bas, V.A.I.Huvenne, P.Blondel, V.Huhnerbach, A.Deidun. (2012). A multi-method approach for benthic habitat mapping of shallow coastal areas with high -resolution multibeam data. Continental Shelf Research, 14-26.

C.J.Brown, S.J.Smith, P.Lawton, J.T.Anderson. (2011). Benthic Habitat Mapping: A review of progress towards an improved understanding of the spatial ecology of the seafloor using acoustic techniques. estuarine, Coastal and Shelf Science, 205-520., B.J.Todd, M.Z. Li. (2012). Seascapes Of Bay of Fundy. Nova Scotia/New Brunswick: Geological Survey of Canada.

Mapping European Seabed Habitat (MESH).





Acoustic Ground Discrimination System technique(AGDS)

Following the previous posts about the importance of benthic habitat mapping, some ongoing projects in the world, and briefly about the airborne techniques in habitat mapping, now it is the time to go to some details about the techniques.

   Benthic habitat mapping process consists of three steps:

  • Habitat characterization (description of physical and biological observation): using bathymetric survey, acoustic backscatter, seabed sampling and towed video camera to provide a comprehensive characterization of the habitat.
  • Habitat classification (provide a set of habitat type base on above description): define the types of the seabed (sand, mud, etc.) and seabed animal and plants.
  • Habitat mapping (spatial distribution of classified habitat): generating a classified map for the different habitat in the region

At first, we explain the techniques for the habitat characterization which are consisted of two main categories:

  1. Broad-scale acoustic seafloor characterization
  • Acoustic ground discrimination system (AGDS)
  • Multi-beam and swath sounders
  • Side Scan Sonar
  • Seismic and sub-bottom reflection
  1. Airborne electro-optical near shore characterization
  • Aerial Photography
  • Hydrographic LADS and LIDAR
  • Airborne Hyperspectral Imaging
  • Satellite Multispectral

Let’s start with Broad-scale acoustic technique.

Acoustic ground discrimination system (AGDS):

Where the water is deep or turbid for optical techniques, the most appropriate techniques in the water for these regions are acoustic tools. There are different types of acoustic system that can be used to generate habitat maps, each with varying cost and benefit. According to the objectives of the project, water depth, time and size of the area we should choose the best set of systems to cover all these parameters. For any remote sensing technology, we need adequate ground-truth information which will describe later.

The strength of an echo from an echo sounder and its characteristic which is decaying in the water over time produce a signal that is largely dependent on the proprieties of the seafloor. Two instruments are used in this method together:

  1. Single Beam
  2. Bottom classifier

The theory behind Single Beam

Single-beam is configured with a transducer and receiver which are mounted to the hull, or side- mounted to the ship. It measures the water depth directly beneath the research vessel. They are simple to use and cheaper than other tools. They send the sound signal and measure the properties of returning echo from the seafloor. Echo sounder measures water depth on the basis of the time which the sound signal is transmitted and received by the transducer. The type of single beam that we chose depends on the objectives of the project, resolution, water depth and temperature. The typical frequency ranges from 10 to 300 kHz.

Echo sounder creates an electric signal pulse for the transducer which is mounted under the boat. The transducer converts the electric signal to mechanical signal. The signal passes through the water column and the objects on its way to the seabed. After hitting the seafloor, a fraction of signal penetrates to subsurface sediment and the refraction happens and some of them reflect the transducer which again converts this echo to an electric signal to the surface unit. The time which the signal is sent and received named Two-Way Travel Time and is a function of depth.

Frequency is one of the most important parameters in the transmitted signal. It influences on the penetration level of sound energy in the seabed, it means lower frequency penetrate more distance in the seabed than the higher one. We use a lower frequency (e.g., 30 kHz) for the deeper area, due to the fact that the attenuation in water for lower frequency is less than the higher one; and higher frequency (e.g., 300 kHz) for shallow water.

Seafloor plays a dominant role in the properties of returning echo to the transducer. The signal in the center of cone arrive sooner than other ones to seabed and depending on the roughness of seafloor, the echo energy will change; softer seabed absorb more sound energy and the echo will be weaker, in contrast, a harder seabed (rocks and compact sediment) reflect a stronger echo and by use of this decaying pattern in echo the seabed can be identified. Subsurface features (the hard surface beneath the soft sediment) of the seabed affect the decaying echo and this trend is more applicable in lower frequencies where they have greater penetration into seabed than higher ones. One method of determining differences in seabed composition which is related to roughness is measuring energy at the edge of the first echo, after the peak of the signal has passed. There is a possibility that when echo is rebounded from the seabed to sea surface back to the seafloor and finally to the transducer. It is called the second echo (E2) which is used in some ADGS.

The steps of AGDS method

-Bottom classifier

Two types of common instrument which have been used for surveying in recent years:

1-      RoxAnn

This device uses analog signal processing hardware to measure two features of the echo sound signal. The first one is the signal strength over time of decaying for the first echo, E1, which is a measure of seabed roughness. The second feature which is a function of seabed hardness is a measure of the whole of the first multiple echo or E2. In the logging software, E1 and E2 variables are plotted in XY coordinate showing rectangular area with a different color

And after ground-truthing, they can be identified by the actual seabed types.

2-      QTC view (Quester Tangent Corporation)

It operates in a different method to RoxAnn, while the later use the second echo, E2, Qtc does not. Analysis and classification are based on the whole of the first echo. The signal is converted from analog to digital form then subjected to a number of algorithms creating Full Feature Vectors which will be processed by the software package; “QTC Impact”, to generate the three eigenvalues Q1, Q2 and Q3 that explain 95 % of the total variability. Finally, the user creates the 3-D cluster plot with the following grand-truthing step.

In the configuration of AGDS, we use single beam technology which means that the interpolation methods are necessary if continuous coverage maps are required. This definitely led to poor discrimination features for the following reasons:

  • The values between the un-surveyed tracks are estimated base on the adjacent track lines
  • There are some sorts of averaging across the echo sounder footprint which leads to poor discrimination on the diverse seabed.
  • It is difficult to decide what the proper frequency is in the regions of large depth range.

Well, I will explain other techniques in the following post.


  1. J D Penrose, P J W Siwabessy, A Gavrilov, I Parnum, L J Hamilton, A Bickers, B Brooke, D A Ryan, P Kennedy. (2005). Acoustic Techniques for Seabed Classification. Coastal Zone Estuary @ Waterway Management.
  2. J.Brown, C. (2007). Seafloor Imagery, Remote Sensing, and bathymetry: Acoustic Ground discrimination System(AGDS). Geological Association of Canada, 3-10.
  3. The OzCoasts (Australian Online Coastal information)

Soundwaves versus Electromagnetic waves in benthic habitat mapping

In this post, I will briefly talk about airborne techniques in habitat mapping and their limitations.

Have you ever thought why sound wave is more common than electromagnetic waves in measurements the ocean?

Let go into some details about it. There are two types of waves:

  1. Mechanical waves: they need the medium to propagate throughout. It includes sound waves, ocean wave etc.
  2. Electromagnetic waves: they do not need the medium to travel. They can propagate in space.

Sound as a mechanical wave travel at higher speed in the seawater than in the air and attenuate according to the physical parameter of seawater, however, it can reach the deepest part of the oceans. In contrast, only 1 percent of light (or the electromagnetic wave) can reach to 100 meters and rarely any significant light beyond 200 meters is detectable.

Why is it so?

The electromagnetic field, as it is clear from its name; consists of electric field and magnetic field perpendicular to each other. As they pass through a medium, ocean, in this case, the electric field pushes the ions away. This process reduces the electric field energy which attenuates the electromagnetic wave.

There are two basic techniques in this field:

  • Broad-scale acoustic seafloor characterization technique
  • Airborne electro-optical near shore characterization technique

The first method which can be called acoustic remote sensing includes different systems such as single beam echo sounder, acoustic sediment classification, multi-beam and swath sounders, side scan sonar, seismic and sub-bottom reflection. Choosing one of these methods depends on various parameters such as the depth of water, available sources for the project, area size, time and so one. The basis of an acoustic method is finding differences in speed and energy between acoustic waves sending to the medium and their reflection due to the interaction of waves and sea-bed (reflection, scattering, and penetration). Generally, this technique is preferred when we are working on areas with muddy or deep water which optical methods do not work properly.

However, when we are working on the wider areas with lower accuracy at a lower cost, optical methods are recommended. The Different system such as aerial photography (depending on water clarity, sun angle and sea state) and satellite multispectral images are used to provide general information from shallow clear waters in this method. Hydrographic LADS/LIDAR (highly dependent on water clarity and for depth <40) and airborne hyperspectral imaging are other systems can be used in this method. In this technique which is an image processing method, it is necessary to compare multiple images of the area got by different sensors or images taken by the same sensor at different times. Remember using high-resolution imaging sensors improve your ability to get more information of the images.

Aerial photography
Cloud shadows on the water can be confused in aerial photography make interpretation impossible( Clouds and shadows over St. Lucie River,

Finally, I have to mention that for mapping purposes, after using proper techniques we need to accomplish the results of underwater surveys carried out by visual or photo/video transects and sampling.

I will explain about one of the aerial technique in more details later.


  1. Eugenio, J. Marcello, J. Martin. (2014). High-Resolution Maps of Bathymetry and Benthic Habitat in Shallow-Water Environment Using Multispectral Remote Sensing Imagery. IEEE TRANSACTIONS ON GEOSCIENCE AND REMOTE SENSING.
  2. C. Huff (2008). Acoustic Remote Sensing as a Tool for Habitat Mapping in Alaska Waters. Unversity of Alaska Fairbanks.
  3. Finkbeiner, B. Stevenson, R.Seaman. (2001). Guidance for Benthic Habitat Mapping: An Aerial Photographic Approach. NOAA.
  4. D. Ventura, M. Bergin. (2016, 02). Passive and Active: Remote survey solution for the nearshore. Coastal Zone Canada Conference.



Some Projects about Benthic habitat mapping

Hey guys. I am here again and I hope you have enjoyed my posts so far. Today I am talking about some habitat mapping projects all over the world. (There are some abbreviations that you can find their complete terms at the end of the post)

  • Benthic Habitat Mapping of Main Hawaiian Islands done by NCCOS

The project began in January 2002 and was completed in December 2007. The goal was improving local managers’ actions and researchers in reef fish management, monitoring, and sampling design to improve strategies for restoration of coral reefs. They mapped seafloor habitats using the visual interpretation of satellite imagery. To accomplish the project, the accuracy of maps was assessed by a group of independent scientists and maps were reviewed and edited by local experts. If you are interested to know more you can google their website.

Benthic Habitat Mapping of Main Hawaiian Islands
  • The Mesh Atlantic project

The aim of the project is producing marine habitat maps of Atlantic Area by collecting old habitat mapping information of the countries in the area including Ireland, France, Spain, and Portugal besides gathering new information of these countries. You can access their data and interactive map in this link.

Biological community and the supporting physical structure around it

It is an international association established in 2001 and has held conferences about benthic habitat. They gather scientist and an agency engaged in benthic habitat mapping to share their experience with each other. They study the geological and oceanographic signs of benthic habitat and ecosystem to determine the biological community and species diversity. The main objectives of this group are to provide awareness of development in this field and survey standards, how oceanography, biology, and geology are contributing to benthic habitat mapping, support MPAs, apply and evaluate the habitat classification.

  • Well, the last one is not a project but a useful link for a group work on different marine issues including habitat mapping. ICES WGMHM is a group which reviews habitat classification and mapping activities in the ICES area and works on improving standards of and techniques. The group meets annually to collate new information for seabed and habitat mapping in the area that you can find their reports on their website.

Of course, there are more projects than what I mentioned. If you are interested maybe it is better to check these sites too:

NOAA: National Oceanic and Atmospheric Administration, Department of Commerce
ASMIWG: Atlantic Seabed Mapping International Working Group
NCCOS: National centers for coastal ocean science
MESH: Mapping European Seabed Habitats
ICES: The International Council for the Exploration of the Sea
WGMHM: Working Group on Marine Habitat Mapping


Introduction to Habitat Mapping

Let´s start with a simple question. What is the main source of our vital element (oxygen)?

Whatever the answer is, it has a tremendous responsibility to deal with such important task. Yes, Oceans. We know that 2∕3 of planet earth is covered by water, however, 95 percent of the oceans are still unexplored and our knowledge of the other 1∕3 is much more. Well, maybe you say “so what; we live on Earth. That is what really matters”. So you should know that:

Our marine ecosystems such as seas, lakes, rivers, and oceans

  • include 80% of life on the planet earth
  • produce the most part of earth oxygen
  • are important to have a moderate climate
  • are a huge source of nutrient storage and its cycling
  • Reduce climate change impact by CO2 absorption

If you need more I can name financial, recreational or medical issues. Finally, I have a better reason: Do you like seafood? Do you think gaining more information about ocean ecosystems is not such a big deal yet?

In my opinion, all of these facts show the importance of marine ecosystem and the necessity for protecting them. It means we should let them remain as natural as they are while exploitation them. To protect this vital environment we have to know about them more and more. A good solution for this purpose is habitat mapping which I want to talk about on my blog.

Let’s start with some basic definitions:

  • Habitat is the natural environment of a living organism and it includes all the places that it lives in, finds food, reproduces and so on
  • Habitat mapping means exploration (in our case, underwater exploration) to provide a map showing the probable geological distribution of different habitats in a particular area. In a simple word, finding out what the physical properties of a region are to be chosen by a certain living  species as its habitat and generalizing the possibility for other parts of the ocean

Human activities such as mining, fishing, and pollution have a significant impact on the ecology of the marine environment. The final goal of habitat mapping is to provide a better perspective of seafloor spatial geology for decision-makers to take into account the marine ecosystem not to reduce the benthic diversity.

The next question can be how is it done? Well, we need some academic terms here, but do not panic; we will talk about all of them later. It is just my first post. Let’s get back to the point. Habitat mapping can be done by different methods and technologies such as multi-beam echo-sounding, side-scan sonar, single beam acoustic ground discrimination systems, Light Detection and Ranging-LiDAR and Aerial photography. These remote sensing techniques combined with ground-truthing techniques such as sediment grabs, camera tows, and dredging can be used to validate data and create detailed habitat maps.

Ok. I think that is enough for today. I am going to explain more about habitat mapping and its methods later. Please let me know if you have any question about my post.


Useful links:

  1. Why we protect our oceans?
  2. Habitat mapping
  3. Benthic Habitat Mapping
  4. Marine Geological and Biological Habitat Mapping
  5. Seabed Habitats Interactive Map
  6. Rebecca Allee, Megan Dethier, Dail Brown, Linda Deegan, R. Glenn Ford, Thomas F. Hourigan, Jim Maragos, Carl Schoch, Kathleen Sealey, Robert Twilley, Michael P. Weinstein, Mary Yoklavich.(2000). Marine and Estuarine Ecosystem and Habitat Classification. NOAA Technical Memorandum NMFS-F/SPO-43.
  7. Brian J Todd; H G Green; Geological Association of Canada; Brian Jeremy Todd. (2007). Mapping the Seafloor for Habitat Characterization. St. John’s N.L.: Geological Association of Canada.
  8. Aaron Micallef; Timothy P. Le Bas; Veerle A.I. Huvenne; Philippe Blondel; Veit Huhnerbach; Alan Deidun. (2012).A multi-method approach for benthic habitat mapping of shallow coastal areas with high-resolution multibeam data. Continental Shelf Research.
  9. Blondel, P. (2009). The handbook of sidescan sonar. Berlin: Springer.
  10. Mark Finkbeiner, Bill Stevenson, Renee Seaman.(2001). Guidance for benthic habitat mapping. U.S. NOAA Coastal Services Center.


Brian J Todd; H G Green; Geological Association of Canada; Brian Jeremy Todd. (2007). Mapping the Seafloor for Habitat Characterization. St. John ‘s N.L. : Geological Association of Canada.

Craig J. Brown, Stephan J. Smith, Peter Lawton, John T. Anderson. (2011). Benthic habitat mapping: A review of progress towards an improved understanding of the spatial ecology of the seafloor using acoustic techniques. Estuarine, Coastal and Shelf Science, 502-520.