Report of the 

National Marine Fisheries Service 

Workshop on Underwater Video Analysis 

August 4-6, 2004 

D. A. Somerton and C. T. Glendhill (editors) 

U.S. Department of Commerce

National Oceanic and Atmospheric Administration 

National Marine Fisheries Service 

NOAA Technical Memorandum NMFS-F/SPO-68 

May 2005 

Report of the 

National Marine Fisheries Service 

Workshop on Underwater Video Analysis 

August 4-6, 2004 

D. A. Somerton and C. T. Glendhill (editors) 

NOAA Technical Memorandum NMFS-F/SPO-68 

May 2005 

U.S. Department of Commerce

Carlos M. Gutierrez, Secretary

National Oceanic and Atmospheric Administration

Vice Admiral Conrad C. Lautenbacher, Jr., USN (Ret.)

Under Secretary for Oceans and Atmosphere

National Marine Fisheries Service

William T. Hogarth, Assistant Administrator for Fisheries
Suggested citation: 

Somerton, D. A. and C. T. Glendhill (editors). 2005. Report of the National Marine Fisheries 

Service Workshop on Underwater Video Analysis. U.S. Dep. Commerce, NOAA Tech. Memo. 

NMFS-F/SPO-68, 69 p. 

A copy of this report may be obtained from: 

Alaska Fisheries Science Center 

7600 Sand Point Way NE 

Seattle, WA 98115 

Or online at: 

http://spo.nmfs.noaa.gov/tm/ 
CONTENTS 

Introduction.........................................................................................................1


Alaska Fisheries Science Center 

Using Video to Map Distribution of Habitat and Fish in Alaska 

C. Rooper, and M. Zimmerman...................................................................................2


Underwater Video Observations Made 

with a Towed Video Camera Sled Near Seguam Pass, Alaska 

H. H. Zenger, Jr..........................................................................................................4


Use of Video and Sector Scanning Sonar 

for Studying Tanner Crab Aggregations 

B. G. Stevens.............................................................................................................6


Use of Video at the AFSC’s Newport Laboratory 

A. Stoner....................................................................................................................8


Aerial Video of Beluga Whales in Cook Inlet, Alaska: 

Transitioning From Manual to Computerized Analysis 

C. Sims, R. Hobbs, and D. Rugh................................................................................9


Underwater Video Systems Designed and 

Built at the Alaska Fisheries Science Center 

S. McEntire..............................................................................................................10


Tracking Fish in Trawls With the 

DIDSON Acoustic Camera 

C. Rose....................................................................................................................11


Reproductive Ecology of Atka Mackerel 

in the Aleutian Archipelago 

R. Lauth, and S. McEntire..........................................................................................12


Use of Underwater Video at the Auke Bay Laboratory 

R. Stone, and E. Brown.............................................................................................14


Northwest Fisheries Science Center 

Estimating the Density of Thornyheads, Sebastolobus spp., 

Using a Towed Video Camera Sled 

R. Lauth, W. Wakefield, and K. Smith......................................................................16


iii 
Optical Imaging and Analysis at the 

Northwest Fisheries Science Center 

W. Wakefield.........................................................................................................................................18


Southwest Fisheries Science Center 

Using Video Observations From Submersibles and Laser Line 

Scanners to Survey Benthic Fishes, Macro-invertebrates 

and Habitat Types in Deepwater off California 

M. Yoklavich..........................................................................................................................................19


Fish Surveys and Habitat Investigations of Cowcod and Bocaccio 

J. Butler.................................................................................................................................................24


Pacific Islands Fisheries Science Center 

Video Surveys of Fish Assemblages in the Pacifi c Islands Region 

F. Parrish...............................................................................................................................................26


Towed-diver Surveys, a Method for Mesoscale Spatial 

Assessment of Benthic Reef Habitat: a Case Study at Midway Atoll 

in the Hawaiian Archipelago 

J. Kenyon, R. Brainard, R. Hoeke, F. Parrish, and C. Wilkinson.............................................................27


The Use of Digital Video Recorded During Towed Diver Surveys 

to Estimate Reef Fish Assemblages Over a Large Spatial Scale 

B. Zgliczynski........................................................................................................................................36


Botcam – Bottom Fish Camera Bait Station 

D. Merritt...............................................................................................................................................37


Southeast Fisheries Science Center 

SEAMAP Reef Fish Survey of Offshore Banks 

C. Gledhill, K. Rademacher, and P. Felts..............................................................................................38


Northeast Fisheries Science Center 

Underwater Video Research at the Northeast Fisheries Science Center 

W. Michaels..........................................................................................................................................40


iv 
Other State and Government Research Programs 

Video Scallop Stock Assessment in Alaska 

G. Rosenkranz......................................................................................................................................41

Use of Video for Inshore Rockfish Stock Assessment 

C. Grandin............................................................................................................................................42

Invited Experts 

Use of Stereo-video Photography in Remote Camera 

and Diver Transect Assessments of Fish Populations 

E. Harvey, and J. Seager......................................................................................................................44

Video Mosaics 

Y. Rzhanov............................................................................................................................................49

Resolution Underwater Imaging and Image Processing 

for Identifying Essential Fish Habitat 

S. Gallager, H. Singh, S. Tiwari, J. Howland,P. Rago, and W. Overholtz 

and 

R. Taylor and N. Vine.............................................................................................................................50

Archiving, Annotating and Accessing Video as Data 

J. Connor..............................................................................................................................................54

Remote Sensing using Laser Projection 

Photogrammetry for Underwater Surveys 

T. Jagielo...............................................................................................................................................56

Development of a Diver-held Stereo Video Camera 

C. Boynton, and K. Voss.......................................................................................................................58

A Review of the Use of Underwater Video in Australia 

E. Harvey, and M. Cappo......................................................................................................................60 

Recommendations.......................................................................................................................64 

List of Participants.......................................................................................................................66

v 

Introduction

David Somerton

Alaska Fisheries Science Center

7600 Sand Point Way NE

Seattle, WA 98115

Email: David.Somerton@noaa.gov

Christopher Gledhill

Southeast Fisheries Science Center

Pascagoula Laboratory

3209 Frederic St.

Pascagoula, MS 39567

Email: Christopher.T.Glendhill@noaa.gov

Underwater video photography has been an 

important tool used in research applications by 

the National Marine Fisheries Service (NMFS) 

for many years. Recent and rapid development 

of digital video camera equipment with improved image resolution and low-light sensitivity, as well equally impressive advances in video 

analysis software, has given underwater video 

photography new emphasis as an important tool 

for providing quantitative data useful for assessment of fish stocks and evaluation of essential 

fish habitat. 

To showcase and explore this emerging technology and to provide a forum to allow NMFS 

researchers from its various programs that use 

underwater video to meet each other, exchange 

ideas, and possibly form partnerships, the 

NMFS’ Advanced Sampling Technology Working Group sponsored a workshop on August 4-6, 

2004 at the Alaska Fisheries Science Center to 

bring together university, industry, and government researchers. 

Within NMFS alone, 20 separate programs 

use underwater video either to assess fish or 

invertebrate stocks or to classify essential fish 

habitat (EFH) and its use. Researchers from 16 

of these programs attended the workshop and 

presented the objectives of their programs, the 

role played by underwater video and the technologies used for the collection and processing of 

video data. Although these projects differ widely 

in the technologies used to collect video data -

including towed, dropped or diver-held cameras, 

minisubs and remotely operated vehicles – nearly all of the projects conduct research in areas 

with irregular, hard bottoms that are unsuitable 

for sampling with trawls or other tools traditionally used in fisheries research. 

In addition to NMFS scientists, scientists 

from two non-federal governmental research 

projects that use underwater video attended, as 

did a variety of university and non-governmental 

researchers specializing in such diverse topics as 

optical pattern recognition for automatic counting of object, video mosaics for determining 

larger scale orientation of objects, stereo video 

for estimating fish length and sampled area, and 

video databases for allowing the retrieval of 

video data according to other variables such at 

time, depth and species. 

1

Using Video to Map Distribution 

of Habitat and Fish in Alaska 

Chris Rooper and Mark Zimmermann 

Resource Assessment and 

Conservation Engineering Division 

Alaska Fisheries Science Center 

7600 Sand Point Way NE 

Seattle, Washington 98115 

Email:Chris.Rooper@noaa.gov 

The objectives of the habitat research team 

within the Alaska Fisheries Science Center’s 

Resource Assessment and Conservation Engineering (RACE) Division are to 1) map fish 

habitat, 2) determine the characteristics that 

make some habitats important for fish, and 3) 

assess the impacts of commercial fishing on fish 

habitat. Within this framework, underwater video 

is being used to groundtruth sidescan sonar maps 

to determine the importance of sponge and coral 

habitat to juvenile rockfish in five study areas in 

the Aleutian Islands. Video is also being used to 

assess the distribution and microhabitat use of 

fishes and benthic invertebrates. Combining the 

video assessment of habitat with rockfish abundance and fish condition will provide an assessment of the relative value of habitats to their 

inhabitants, as well as providing insight into the 

mechanisms controlling fish-habitat relationships. 

To date, we have collected video using a 

drop camera system and a towed video camera 

sled. The drop camera system consisted of an 

aluminum frame with two attached lights and an 

underwater housing containing one black and 

white video camera with a recording unit (Fig. 

1). Two tail chains and two floats were utilized 

to orient the drop camera system. The camera 

unit was a modified Waytech CCD camera, and 

both the lights and camera were powered by a 

13.2 volt nickel-metal hydride battery. The 

entire unit was self-contained, with the battery 

and camera housed in a metal tube mounted on 

the frame. This system is easily used off any 

Figure 1. Drop camera system used in the Aleutian Islands in the 

summer of 2003. 

research platform, since you simply lower it over 

the side of the vessel using any type of line 

available. The video collected was adequate to 

provide gross classification of habitat types. For 

example, at one site we observed a sand bottom 

with brittlestars punctuated by boulders covered 

with coral and sponges (Fig. 2), while at another 

site we saw hard bottom completely covered 

with sponges and coral (Fig. 3). The major 

disadvantage of this system is the lack of realtime video. Additionally, black and white video 

Figure 2. Still frame from the drop camera system collected in 

habitat consisting of intermittent sand and boulders with coral and 

sponge covering. 

2

was not ideal for identification of fish, coral and 

sponges, and the unit cannot be towed, limiting 

its utility for line-transect work. 

In summer 2004, video was collected with a 

towed, automatically compensating observation 

system (TACOS); description and sample video 

can be found at http://www.afsc.noaa.gov/race/ 

groundfish/habitat/tacos_seguampass.htm). This 

camera sled was equipped with four underwater 

lights that were powered from the research 

vessel. The TACOS unit also utilized a downweight 20 m in front of the camera sled to 

stabilize the sled motion. The down-weight had 

an altimeter mounted on it for navigational 

purposes. The TACOS video system was 

equipped with analog (Tritech Osprey color 

CCD) and digital (JVC-HD1) video cameras and 

a three-laser visual measuring system (Fig. 4). 

The video was geo-referenced to sidescan sonar 

mosaics using a calibrated Trackpoint II ultra 

short baseline system. The video from the analog 

camera was fed to the research vessel in real 

time to allow navigation of the camera sled. The 

digital video camera (high definition) was 

mounted in a self-contained housing and is not 

viewed in real time. 

Four TACOS transects, each 1,000 m in 

length, were video taped in three study areas. 

Data analysis has yet to be completed, but we 

Figure 4. The TACOS video system used in the summer 2004 field 

research. 

will use an event-logging program to count the 

rockfish observed in both of the videos. Habitat 

changes and the percent cover of coral, sponge 

and other benthic invertebrates will be recorded 

from the high definition video along each 

transect. This data will then be imported into a 

Microsoft® Access database containing other 

data collected during the project, such as catch 

data from trawl hauls. Each entry will be georeferenced and time stamped. 

In future projects, we hope to enhance our 

video collections by using higher resolution 

digital CCD cameras linked to the research 

vessel via fiber-optic cable and IEEE1394 

connections, giving us more options in terms of 

data storage, time and location stamps on the 

video, etc. without loss of picture quality. Moving to a fiber optic system will allow us to store 

the video directly to a computer hard drive, and 

monitor the high definition video in real time. 

We also hope to build and demonstrate our own 

stereo video system to accurately describe fish 

length and size of coral and sponge on the 

seafloor. 

Figure 3. Still from from the drop camera system collected in 

habitat consisting entirely of hard bottom with a covering of coral 

and sponge. 

3

Underwater Video Observations 

Made with a Towed Video Camera 

Sled Near Seguam Pass, Alaska

Harold H. Zenger, Jr.

Resource Assessment and 

Conservation Engineering Division

Alaska Fisheries Science Center

7600 Sand Point Way NE

Seattle, Washington 98115

Email: Harold.Zenger@noaa.gov

The area near Seguam Pass in the Aleutian 

Islands has been fished for decades, and at one 

point the North Pacific Fishery Management 

Council cited it as possibly having experienced 

significant trawl damage, especially to gorgonian corals. In 1999 the Alaska Fisheries Science Center’s (AFSC) Resource Assessment 

and Conservation Engineering (RACE) Division 

conducted a study to observe the status of that 

demersal environment. A robust, maneuverable 

observation platform was required because the 

region is notorious for swift currents and irregular terrain. RACE scientists adapted the 

design for a towed automatically compensating observation system (TACOS), developed 

at the Commonwealth Scientific and Industrial 

Research Organization (CSIRO) laboratory in 

Hobart, Tasmania. In August 1999, we conducted 

a short cruise to videotape images of that demersal habitat. The objectives of this study were to 

1) examine whether the corals in heavily trawled 

areas are more damaged and less abundant than 

in nearby, less-trawled areas, and 2) attempt to 

verify the extent to which fish and invertebrates 

use coral for shelter. 

The camera sled is a cylindrical frame constructed of aluminum with three, 12-inch trawl 

floats secured to the upper frame. A 2 m drag 

chain that controls height above bottom at about 

1-2 m counterbalances flotation. The frame is a 

protective cage and furnishes mounting points 

for a color video camera, four flood lights, laser 

measuring array, electrical junction box, and a 

bathythermograph (Fig. 1). A four-point bridle 

is attached at the upper and lower extremes of 

the outer rings. The bridle is secured to the bottom of an electrical tow cable above a depressor 

weight. The cable is deployed from a remotely 

controlled hydraulic winch. Live-feed video output allows the operator to control cable length, 

thus responding to changes in the bottom terrain. 

Videos were recorded at 25 sites. Subsequent 

review showed that the demersal topography is 

extremely varied, ranging from very irregular, 

rocky substrate covered with dense “gardens” 

of benthic invertebrates to large, almost barren 

sand dunes. On several occasions what appeared 

to be Atka mackerel (Pleurogrammus monopterygius) spawning activity was recorded from 

large, offshore rock piles and pinnacles. Rockfish (Sebastes spp.) were frequently observed in 

close association with sponges, hydrocorals, and 

fan corals (Fig. 2). The only area with apparent 

trawl damage was on the known fishing grounds 

between Amlia and Seguam Islands where widespread broken hydrocorals were found. 

Five primary habitat types were observed: 1) 

relatively shallow (80-87 m), rocky, heavily 

overgrown “gardens” of sessile invertebrates 

composed mainly of sponges, hydroids, bryozoFigure 1. Towed automatically compensating observation 

system(TACOS) camera sled.

4
ans, and hard corals (hydrocorals) occupied by 

schools of roaming Atka mackerel and scattered 

Pacific cod (Gadus macrocephalus), prowfish 

(Zaprora silenus), skates (Bathyraja spp), and 

sculpin (Cottidae); 2) deeper (152-165 m) areas 

with large rocks and boulders on black volcanic sand with relatively heavy growth of large 

sponges and fan corals occupied primarily by 

rockfish with scattered Atka mackerel; 3) still 

deeper adjacent areas (165-185 m) where large 

rocks gave way to sand dunes and large sand 

waves occupied by scattered Pacific cod, skates, 

and Pacific halibut (Hippoglossus stenolepis); 4) 

large offshore rock piles and cliffs (87-112 m) 

with relatively heavy growth of stalked sponges, 

fan corals, hard corals, hydroids, and bryozoans 

occupied by scattered Pacific cod and very large 

numbers of Atka mackerel, females lying hard 

on bottom and males in spawning color — possibly evidence of Atka mackerel spawning activity; and 5) relatively flat or rolling deep bottom 

(150-163 m) area within the historical fishing 

grounds for Pacific cod and Atka mackerel (now 

closed to trawling), with bottom type ranging 

from stones to cobbles to large rocks with sparse 

growth of small sponges, small fan corals and 

soft corals with scattered small groups of on-bottom Atka mackerel, mostly associated with larger 

rocks, scattered Pacific cod, rockfish, and skates. 

This latter area has extensive broken hard corals 

(apparently Stylaster sp. and Errinopora sp.) and 

very few standing specimens. The broken hard 

corals probably resulted from extensive exposure 

to fishing. The lack of standing specimens is 

probably the result of those species’ slow growth 

rate. Much of the substrate appears to be too 

small to support the growth of large fan corals 

and large sponges, given the severe currents they 

would have to withstand. 

Figure 2. Rockfish in open sponge and fan coral habitat.

5
Use of Video and Sector Scanning 

Sonar for Studying Tanner Crab 

Aggregations

Bradley G. Stevens

Kodiak Fishery Research Center

Alaska Fisheries Science Center

310 Research Court

Kodiak, Alaska 99615

Email: Bradley.Stevens@noaa.gov

For roughly 10 months of the year, female 

Tanner crabs (Chionoecetes bairdi) remain buried in the sediment in low-density aggregations 

of 1-3 crabs per m2. These aggregations span 

areas of about 1 km2

, and may be separated by 

tens of kilometers. During a 2-month period surrounding mating and larval release, crabs emerge 

from the sediment and form mounds of 100-

5,000 crabs (Stevens et al. 1994). Mounds can be 

up to 5 m long and 2 m high. Meta-aggregations 

may include 100,000 crabs, in up to 200 mounds. 

Since 1991, submersibles, video camera 

sleds, and remotely operated vehicles (ROVs) 

have been used to observe crab mounds in 

Chiniak Bay, Kodiak Island, Alaska, at depths 

from 125 to 200 m (Stevens et al. 2000a). They 

allow excellent close-up observation of small 

areas (several square meters), but the density 

of crabs is so great that abundance cannot be 

estimated adequately. The center of crab density 

moves only a few hundred meters from year to 

year. A moored current meter was installed in 

March 1999, and replaced annually, in order to 

record bottom temperatures, salinity, and current 

patterns near the aggregation site. The peak of 

aggregation occurs almost exactly with the highest spring tide in late April, and coincides with 

larval hatching by crabs held in the laboratory 

(Stevens 2003). A major obstacle to studying 

Tanner crab density and aggregation is that it 

has not been possible to quantify the extent and 

density of crab aggregations using video technology. During periods of peak aggregation, crabs 

are too concentrated to be counted accurately 

with video sleds. A video sled can only be used 

when crabs are at low densities; once they begin 

to aggregate, the sled causes too much disturbance, and mounds are so large they obscure the 

camera. The area viewed by ROVs is also too 

small. In addition, making daily observations of 

crab abundance with ROVs or video sleds from a 

surface ship is expensive, and such efforts cannot 

be conducted over long periods of time. We have 

also investigated the use of laser line scan (Tracey et al. 1998) and sidescan sonar (Stevens et al. 

2000b) which helped us locate 200 derelict crab 

pots but no crab mounds; neither technique is 

cost-effective for use over long periods of time. 

As a result, we have considered the feasibility of 

using high frequency (325 MHz) sector scanning 

sonar for estimation of crab density by capturing 

images from the sonar and analyzing optical density with Image-Pro Plus® (Fig. 1). Sonar equipment could be modified to operate in time-lapse 

mode at pre-determined intervals and record the 

data to a computer hard drive. Interpretation of 

the sonar images should allow users to create a 

quantitative density index that would allow assessment of crab abundance during aggregation 

events. We would like to further develop such a 

system. The first goal will be to capture image 

frames, and analyze them with existing software. 

Figure 1. Sonar image of crab aggregation on 5 May1999. Radius 

is 10 m. White splotches are crab aggregations (except at center 

point).

6
The second step would be to build a self contained system for underwater use that would turn 

on a scanning sonar unit, make several sweeps of 

the area, record the data to a hard drive, then turn 

off again. Using a chartered boat and a remotely 

operated vehicle, the system would be placed 

at an optimum location during crab aggregation 

and operated for several weeks. Comparative 

data would be collected at a non-aggregation 

site, where few crabs are present, and density 

estimates would be made (as well as possible) by 

video techniques for comparison. Hatching and 

spawning of Tanner crabs is synchronized with 

spring tide cycles. In Chiniak Bay, Tanner crabs 

have used “traditional” spawning grounds in the 

same area for 11 years. Traditional trawl survey 

technology works well for low densities of crabs, 

but large catches create problems with statistical 

analysis. Because such large catches occur at low 

frequencies, they have traditionally been viewed 

as “outlier data”, and sometimes eliminated. 

However, our research shows that probably 90% 

of all female crabs occur in meta-aggregations 

during a 2-month period surrounding larval release, and thus are not susceptible to assessment 

using traditional trawl survey methodology. In 

addition, males are in very low abundance at aggregation sites, so interpretation of sex ratio data 

is rendered unreliable. Despite repeated searches, 

we have not found any concentrations of female 

Tanner crabs at any other sites around Kodiak. 

They probably exist, but at a spatial scale that 

has not yet been determined. These results make 

it more apparent that the aggregation site in 

Chiniak Bay is a rare find, and an important site 

to continue monitoring in the future. Sonar is 

a standard tool for assessment of midwater fish 

stocks, but it has not been used to assess benthic 

fishery resources. Sidescan sonar has been used 

to study the impacts of trawling on the seafloor 

(Krost et al.1989), and more recently, to estimate the extent of crab pot loss and ghost fishing 

(Stevens et al. 2000b). Sonar tools can be used to 

provide more accurate estimates of crab abundance than can be achieved with traditional trawl 

survey technology. This would be a great addition to our arsenal of assessment tools. 

Citations

Krost, P., M. Brenhard, F. Werner, and W. 

Hukriede. 

1989. Otter trawl tracks in Kiel Bay (Western 

Baltic) mapped by side-scan sonar. 

Meeresforschung 32:344-353. 

Stevens, B.G. 

2003. Timing of aggregation and larval 

release by Tanner crabs, Chionoecetes bairdi, 

in relation to tidal current patterns. Fish. Res. 

65:201-216. 

Stevens, B.G., J. A. Haaga, and W. E. Donaldson. 

1994. Aggregative mating of Tanner crabs 

Chionoecetes bairdi. Can. J. Fish. Aquat. Sci. 

51:1273-1280. 

Stevens, B. G., J. A. Haaga, and W. E. Donaldson. 

2000a. Mound formation by Tanner crabs, 

Chionoecetes bairdi: Tidal phasing of larval 

launch pads?, p. 445-453. In J. C. V. V. Klein and 

F. R. Schram (eds.), Crustacean Issues 12: The 

biodiversity crisis and crustacea. Proceedings of 

the Fourth International Crustacean Congress, 

Amsterdam, The Netherlands, July 20-24, 1998. 

Vol. 2. A. A. Balkema, Rotterdam, Rotterdam. 

Stevens, B. G., I. Vining, S. Byersdorfer, and W. 

E. Donaldson. 

2000b. Ghost fishing by Tanner crab 

(Chionoecetes bairdi) pots off Kodiak, Alaska: 

Pot density and catch per trap as determined 

from sidescan sonar and pot recovery data. Fish. 

Bull. 98:389-399. 

Tracey, G. A., E. Saade, B. Stevens, P. Selvitelli, 

and J. Scott. 

1998. Laser line scan survey of crab habitats 

in Alaskan waters. J. Shellfish Res. 17:1483-

1486. 

7
Use of Video at the 

AFSC’s Newport Laboratory

Al Stoner

Fisheries Behavioral Ecology Program

Alaska Fisheries Science Center

2030 S. Marine Science Drive 

Newport, Oregon 97365

Email: Al.Stoner@noaa.gov

Research conducted by the Fisheries Behavioral Ecology Program is directed toward 

providing critical information needed to improve 

survey techniques and to improve predictions of 

population distribution, abundance and survival 

for economically significant marine resource 

species. 

The Program focuses on behavioral mechanisms associated with the performance of fishing 

gear, predator-prey dynamics, habitat requirements, and responses by fishes to environmental 

variables. Almost all of the research is conducted 

with live animals and video tools including 

stationary cameras, towed video sleds, infra-red 

lighting, and high-frequency imaging sonar are 

used on a daily basis. Field operations using 

video techniques are focused on estimating densities of juvenile fishes and characterizing their 

habitat associations, observing behavior of fishes 

around towed and fixed fishing gear, and in situ 

observations of movement and activity patterns 

related to environmental variables (Fig. 1). 

Figure 2. Large video room at the Newport Laboratory.

Video tools are used extensively to monitor 

the behavior of fishes in laboratory experiments 

designed to examine feeding, predator-prey 

interactions, habitat choices, swimming performance, vision and olfactory capabilities, activity 

rhythms, and interactions with fishing gear (Fig. 

2). New tools are currently being developed for 

motion analysis and three-dimensional tracking 

of fishes and groups of fishes in our laboratory 

experiments using stereo videography. 

Figure 1. Small camera sled used in the field at Kodiak Island, 

Alaska.

8
Aerial Video of Beluga Whales 

In Cook Inlet, Alaska:

Transitioning from Manual to 

Computerized Analysis

Christy Sims, Rod Hobbs, and Dave Rugh

National Marine Mammal Laboratory

Alaska Fisheries Science Center

7600 Sand Point Way NE

Seattle, Washington 98115

Email: Christy. Sims@noaa.gov

Since 1994, the AFSC’s National Marine 

Mammal Laboratory (NMML) annual aerial 

surveys of beluga whales in Cook Inlet Alaska 

have made video recordings of observed beluga 

groups (Fig. 1). This video data is then used to 

estimate group size and other population parameters. Counts from videotapes are very precise 

and repeatable when compared to real time 

counts by aerial observers. The video can also 

be used to collect other data such as the time a 

whale spends at the surface, whale image size, 

and coloration. 

Our standard video analysis is very labor 

intensive, requiring around 100 hours of viewing per hour of recorded tape. With the advancements in digital video, we have begun 

looking for a way to transition from traditional 

manual counting of video to a computer-assisted 

method. Several different software options were 

researched from pattern recognition to video animation software. Finally, video analysis software 

called VideoScript appeared to have the potential 

to answer our need to decrease analysis time 

with computer assisted analysis at an affordable 

price. VideoScript is available as a free download as well as a licensed professional version 

for both Macintosh and Windows operating systems, however the Mac software has more capabilities than the PC version. Currently, a custom 

script has been written to allow us to analyze 

our data in VideoScript maintaining all of the 

video clips and documentation overlays on the 

computer. This approach duplicates our manual 

analysis which uses plastic sheet overlays, but 

with improvements in efficiency, consistency and 

documentation. 

This is our first step at computer-assisted 

analysis and we plan to further automate the 

process. Our next step will be to utilize several 

tools in VideoScript that can track and measure 

beluga images, further improving the efficiency 

of our analysis. Our final goal would be image recognition of the beluga, allowing a fully 

automated analysis. However, this may require a 

more sophisticated, custom software package. 

Figure 1. An aerial view of a group of belugas and an enlargement of the area enclosed within the yellow box. The beluga “dots” can be 

seen against the grey glacial waters of Cook Inlet and counted as they surface.

9
Underwater Video Systems 

Designed and Built at the 

Alaska Fisheries Science Center 

Scott McEntire 

Resource Assessment 

and Conservation Engineering Division 

Alaska Fisheries Science Center 

7600 Sand Point Way NE 

Seattle, Washington 98115 

Email: Scott.McEntire@noaa.gov 

A variety of underwater video cameras are in 

use at the Alaska fisheries Science Center, many 

of which have been developed in-house. These 

can be roughly categorized into four types. First, 

self-contained video systems consisting of a 

pressure housing for batteries, video recorder 

and control electronics connected to external 

camera and lighting. Cameras are low light 

charge-coupled device (CCD) and intensified 

charge-coupled device (ICCD) with infrared or 

red light-emitting diodes (LEDs) or low voltage 

high intensity discharge (HID) lighting. These 

are used to monitor fish behavior and gear 

performance of trawl and pot gear at depths up to 

2,000 m. 

Second, self-contained drop video systems 

consisting of a progressive scan camcorder with 

battery and synched high rate strobe that is 

totally automatic and designed to be deployed 

from vessels of opportunity with minimally 

trained personnel (1,500 m depth rating). Third, 

time lapse video systems consisting of low 

electrolysis housings for camcorders with Sony 

LANC control for long-term deployment 

(3 months). Fourth, live feed towed and drop 

video systems consisting of small winch camera 

systems that are suitable for use from inflatables 

13 feet and up are in use to scout dive sites and 

collect video images to over 200 m. These 

consist of small battery powered winches with 

small diameter armored cable, and high bright 

monitors with video overlays of GPS and depth. 

Future developments include: 1) recording 

directly to digital, without a compression Codec 

using PC104 single-board, embedded computers; 

2) reduce costs and size of IR camera systems; 3) 

improve lighting efficiency by moving from 

halogen to LED arrays and low power HID 

lights; 4) simplify integration of serial sensor 

data with video; and 5) develop a remote stereo 

system for deployment on trawl gear to depths 

greater than 1,000 m. 

10

Tracking Fish in Trawls with the 

DIDSON Acoustic Camera 

Craig Rose 

Resource Assessment and 

Conservation Engineering Division 

Alaska Fisheries Science Center 

7600 Sand Point Way NE 

Seattle, Washington 98115 

Email: Craig.Rose@noaa.gov 

Both mechanically scanned sonars and 

underwater cameras have significant limitations 

for observing the behavior of fish in waters with 

limited ambient light. Cameras require artificial 

visible illumination, which may affect behavior, 

or infrared illumination, which greatly limits 

range. Sonars have much greater range, but lack 

the spatial and temporal resolution to confidently 

track and identify individuals. 

A new tool, the Dual-frequency 

IDentification SONar (DIDSON), developed at 

the University of Washington’s Applied Physics 

Laboratory, makes a significant breach in the 

barrier to direct behavioral observations. This 

high frequency (1.0 and 1.8 MHz) scanning 

sonar provides images with sufficient resolution 

to clearly distinguish the shapes of individual 

fish at an update rate (4 - 21 frames per second) 

that allows tracking between images. It images a 

sector 29 degrees wide and 12 degrees deep out 

to a maximum range of 30 m. The sonar has a 

small enough size (30.7 × 20.6 × 17.1 cm) to be 

deployed flexibly and effectively protected (Fig. 

1). It can be operated in real time with a cable or 

with a battery pack and recorder, remotely 

deployed. The DIDSON was used in the aft end 

of a pelagic trawl to track walleye pollock and 

Pacific salmon, with the goal of identifying 

behavioral differences, which could be exploited 

to reduce salmon bycatch. 

While the DIDSON programming has a 

number of counting, measuring and tracking 

algorithms, included automated methods, 

DIDSON imagery collected on the pelagic 

trawls required manual tracking of targets. This 

was facilitated by a routine that tracked and 

recorded the position of the computer cursor 

over the imagery and annotated it with the time 

of recording. Using this routine, salmon and 

pollock were tracked, revealing that salmon 

dropped back into the net much more slowly 

than pollock and frequently made short forays 

forward. Pollock uniformly dropped back into 

the net at nearly the towing speed. Several trawl 

modifications have been designed around this 

difference and are being tested. 

Figure 1. A DIDSON acoustic camera within its protective housing. 

11 
Reproductive Ecology 

of Atka Mackerel in the 

Aleutian Archipelago* 

Bob Lauth and Scott McEntire 

Resource Assessment and 

Conservation Engineering Division 

Alaska Fisheries Science Center 

7600 Sand Point Way NE 

Seattle, Washington 98115 

Email: Robert.Lauth @noaa.gov 

Rocky substrate is vital to Atka mackerel for 

successful breeding and propagation. Except for a 

few studies in Kamchatkan waters (Gorbunova 

1962, Zolotov 1993), very little is known about 

the bathymetric range, spatial extent, and habitat 

characteristics of Atka mackerel spawning and 

nesting habitat. Such scientific studies are totally 

lacking from Alaskan waters. The long-term 

sustainability of this commercial fish species 

depends on knowing the location and characteristics of this habitat. Nesting and spawning sites in 

Kamchatka are in nearshore areas to a maximum 

depth of 32 m. Bottom type, temperature, and 

moderate tidal current are other important factors 

for these nesting sites. Spawning begins in late 

June and ends in the early fall. Females are batch 

spawners that lay their adhesive eggs in rock 

crevices and among stones. Males fertilize the 

eggs and remain to guard the incubating clutches 

until they hatch. Nest guarding is important to 

protect incubating eggs from cannibalism and 

predation from other fish and invertebrates. 

The specific objective for our study is to 

locate and characterize nesting and spawning 

habitat in Alaskan waters including its spatial 

extent, bathymetric range, temperature, and other 

physical and biological features (Figure 1). The 

study area will focus on the Aleutian Archipelago 

from Stalemate Bank to the Shumagin Islands. A 

portable video drop camera will be used to locate 

nesting sites. Cameras drops will be made during 

the time of year when Atka mackerel spawn and 

nest. Nesting sites are identified by the presence 

Figure 1. A male Atka mackerel in habitat typically used for nesting in the Aleutian Islands. 

*Not presented at workshop 

12 
of aggregations of sexually dichromatic males 

exhibiting nesting behavior. 

The drop camera and winch system is fabricated for use on any size research vessel ranging 

from a 5 m inflatable to a large ship (Fig. 2). A 

small inflatable is used to investigate nearshore 

areas and larger vessels are used for investigating 

offshore areas and inside island passes. The drop 

camera frame holds the video camera, 12 V 

NiMH battery pack, 12 V MR12 halogen and 

LED lights, and a depth and temperature data 

logger. Both a low light black-and-white or color 

camera can be used and lights are interchangeable between a red light-emitting diode (LED) 

array, or 20 W halogen or high intensity discharge (HID) light. The combination of a lowlight camera and red LED array is preferred 

because it works at all depths and light levels 

and fish appear unaffected by the red light. The 

video camera frame is deployed using a portable 

24V winch with 300 m of 3/16” armored and 

shielded 4-conductor cable. The small diameter 

cable and weighted camera frame (15 kg of lead) 

produce very little drag so the drop camera can 

get to the bottom in strong currents or surface 

winds. The 24 V winch has a speed controller for 

adjusting the height of the camera frame above 

bottom. Real-time video feed and winch controls 

are used to navigate the camera over rocky 

bottom with high relief while the vessel and 

camera drift. The NTSC video signal from the 

camera is monitored and recorded topside and 

overlaid with time and geodetic position. 

The presence of nesting male aggregations 

will be analyzed in relation to bottom depth, 

water temperature, and the physical and biological habitat. Videotapes provide a record of the 

Atka mackerels’ spatial distribution and behavior, as well as information about the physical and 

biological habitat. Data reduction from videotapes will involve recording events and characterizing habitat. Events will include presence of a 

nester (i.e., guardian male), a female or school of 

Figure 2.The drop camera used for the Atka mackerel nesting 

habitat studies. 

females, or other noteworthy activities relating to 

Atka mackerel reproductive ecology. Habitat will 

be characterized by describing the biological and 

physical attributes. Marine plants and animals 

will be identified to the extent possible using the 

recorded video images and the percent of invertebrate coverage. 

In addition to depth, temperature and location, and the bottom structure of nesting habitat 

will be described based on substrate type and the 

degree of vertical rocky relief. The relation of the 

nesting sites to other major geographic and 

bathymetric features of the Aleutian archipelago 

will also be investigated using Geographic 

Information Systems (GIS) mapping software. 

13

Use of Underwater Video 

at the Auke Bay Laboratory*

Robert Stone and Eloise Brown

Auke Bay Laboratory

Alaska Fisheries Science Center

11305 Glacier Highway

Juneau, Alaska 99801

Email: Robert.Stone@noaa.gov

The AFSC’s Auke Bay Laboratory (ABL) 

has been using underwater techniques to study 

marine fisheries for over 25 years. Scientists 

have employed scuba, remotely operated vehicles (ROVs), and manned submersibles (HOVs) 

to collect underwater photos and video footage 

of the seafloor and marine life. Scientists first 

used the HOV Nekton Gamma in 1978 to study 

rockfish and coral distribution in Southeast 

Alaska. Similar studies with the Nekton Gamma 

followed in the early 1980s, and for the most 

part, were limited to non-quantitative studies. 

Beginning in 1988, scientists began a 17-year 

unofficial partnership with Delta Oceanographics 

and have used their submersible Delta each year 

since to study living marine resources. Much of 

the research has been quantitative in nature and 

has included 1) assessment of groundfish stocks, 

2) behavioral studies on fish and crabs, 3) assessment of fish habitat, 4) gear behavior studies, 5) 

effects of fishing gear on seafloor habitat, and 

6) site reconnaissance. Many of these studies 

have employed distance-sampling techniques to 

estimate abundance of biological populations. 

The ABL is currently using the Delta and 

the ROV Jason II to study coral and sponge 

habitat in the Aleutian Islands. The vehicles 

are deployed at different depths but both are 

used to collect continuous video footage of the 

seafloor along predetermined transects. Corals, 

sponges, and commercially important fish and 

invertebrates are enumerated using strip transect 

methodology thus providing a census for these 

organisms. Transect width is determined using 

Figure 1. A view of the video event logging software used by the Auke Bay Laboratory to analyze video data collected on ROV 

and HOV dives on deepwater coral and sponge habitat.

*Not presented at workshop. 14
semi-conductor lasers fixed at a known distance. 

Transect length is determined using ultra-short 

baseline tracking and differential global positioning (Delta) or long baseline underwater acoustic 

and dynamic positioning systems (Jason II). 

Video footage is collected on a High-8 videotape 

format (Delta) or digital video format with a 1-

chip color camera (Jason II). 

In the laboratory, video footage is encoded to 

an MPEG-2 format at a bit rate of 30 frames per 

second and copied to DVDs. Video post-processing is completed using VideoRuler 7 Software 

whereby each event (coral, sponge, or commercially important fish and invertebrate) is recorded with an assigned keystroke. Habitat variables 

including substrate type, mega- and meso-habitat 

type, and seafloor rugosity have been defined 

and are also measured on each transect. 

Great advances have been made in event-logging software technology in just the past 

2 years. Auke Bay Laboratory scientists have 

customized the VideoRuler 7 software for use 

with the current research program and the system 

works well. Underwater video analysis is a labor 

and time-consuming process. Sub-sampling 

methodology can be developed for many habitats 

which will save time, so, the past limitations of 

post-processing software is no longer a barrier to 

underwater video analysis. One major problem is 

the inability or unwillingness of the entire deepdiving vehicle community to upgrade to fully 

digital camera systems. Post-processing of High8 video footage is difficult due to lost resolution 

at slow playback speeds. Resolution is critical to 

accurate identifications. 

Event recognition software is currently being developed and may show some promise for 

counting large, conspicuous taxa like the sea 

whips (Halipteris willemoesi). Our current task 

is to enumerate and identify many complex taxa 

such as gorgonian corals, hydrocorals, bryozoans, hydroids, and sponges (Fig. 1). Unfortunately, software designed to discriminate such 

complex taxa is unlikely. 

15
Estimating the Density of 

Thornyheads, Sebastolobus spp.,

Using a Towed Video Camera Sled

Robert Lauth1, Waldo Wakefield2, and Keith Smith1

1 Resource Assessment and 

Conservation Engineering Division

Alaska Fisheries Science Center

7600 Sand Point Way NE

Seattle, Washington 98115

Email: Robert.Lauth @noaa.gov

2 Fishery Resource Analysis and Monitoring Division

Northwest Fisheries Science Center

Newport Research Station

2030 S. Marine Science Drive

Newport, Oregon 97365

Email: Waldo.Wakefield@noaa.gov

A video camera sled was used to obtain an 

independent estimate of the density of Sebastolobus spp. (thornyheads) at three different 

depths (450 m, 750 m, and 1,150 m) within a 

given space and time (Lauth et al. 2004a, b). 

Camera sled video footage was processed using 

an oblique grid plane and line transect methods. 

Thornyheads were randomly distributed across 

the seafloor within the sampling area, and variation in the dispersion over increasing spatial 

scales (10 m to 1,280 m) and depths was not 

significant. Thornyhead density estimates were 

derived using the program DISTANCE. Densities ranged from 344 to 1005 thornyheads per 

square kilometer with coefficients of variation 

from 10% to 18%. 

The camera sled (Fig. 1) was constructed 

of hot-dipped galvanized schedule-40 50.8-mm 

steel pipe measuring 366 cm long by 213 cm 

wide by 152 cm high, and weighing about 500 

kg. The same basic design was tested and used 

by Wakefield (1990), Wakefield and Smith 1990, 

and Lauerman et al. (1996). A rigid bail was attached to a pivot point 61 cm from the front of 

the sled. The bail allowed for vertical change in 

the sled’s towing point and its attachment point 

Figure 1. Video camera sled outfitted with Deepsea Power and 

Light (DSPL) Autonomous Video Camcorder System (AVCS; upper 

left), perspective grid (and field of view) used to determine size 

of objects and location on the seafloor (upper right), probability of 

detection function used in line transect methods for thornyheads 

(lower left) and a typical view from the sled mounted video cameras (lower right).

was positioned at the approximate center of 

gravity when suspended. The video camera sled 

was connected to the starboard trawl wire using 

a 70-m bridle made from 19 mm Spectra 7 line. 

The color video camera system was based on a 

high-resolution Sony CCD Hi-8 camcorder (400-

line resolution) integrated as part of a Deepsea 

Power and Light (DSPL) Autonomous Video 

Camcorder System (6,000 m depth rating), lit 

with two 150 W halogen DSPL Deep Multi 

SeaLites powered by two 24 V/38 amp hour 

DSPL SeaBatteries, and controlled by a Pisces 

Design delay and timing circuit. Batteries were 

placed one atop each sled runner to lower the 

center of gravity and balance the sled. A small 

trawl net was strung between the two skids behind the camera sled to dampen the movement of 

the sled when being dragged along the seafloor. 

The sled was towed along the seafloor at speeds 

between 0.75 and 1.0 m/s for 2 to 3 hours. In 

order to prevent the tow cable from impacting 

the seafloor, the bridle and trawl wire altitude in 

front of the camera was monitored on a precision depth recorder (PDR) using a 12 kHz pinger 

16
attached near the end of the trawl wire. Slight 

adjustments to the ship’s speed or the amount of 

trawl wire out were used to maintain the height 

of the trawl wire 25 to 35 m above the seafloor. 

Citations

Lauerman, L. M. L, R. S. Kaufmann, and 

K. L. Smith, Jr. 

1996. Distribution and abundance of epibenthic megafauna at a long time-series station 

in the abyssal Northeast Pacific. Deep-Sea Res. 

(Part I) 43(7):1075-1103. 

Lauth, R. R., W. W. Wakefield, and K. Smith. 

2004a. Estimating the true density of thornyheads, Sebastobolus spp., using a towed video 

camera sled. Fish. Res. 70:39-48. 

Lauth, R. R., W. W. Wakefield, and K. Smith. 

2004b. Estimating the size selectivity and 

catching efficiency of a survey bottom trawl for 

thornyheads, Sebastolobus spp., using a 

towed video camera sled. Fish. Res. 70:27-37. 

Wakefield, W. W. 

1990. Demersal fishes of the upper continental slope off central California. Scripps Instit. 

Oceanogr. Ph.D. Thesis. 281 p. 

Wakefield, W. W., and K. L. Smith, Jr. 

1990. Ontogenetic vertical migration in Sebastolobus altivelis as a mechanism for transport 

of particulate organic matter at continental slope 

depths. Limnol. Oceanog. 35:1314-1328. 

17
Optical Imaging and Analysis at the 

Northwest Fisheries Science Center 

W. Waldo Wakefield 

Northwest Fisheries Science Center 

Fishery Resource Analysis and Monitoring Division 

Newport Research Station - Bldg. 955 

2032 S. E. OSU Drive 

Newport, OR 97365-5275 

Email: waldo.wakefield@noaa.gov 

The Northwest Fisheries Science Center’s 

Fishery (NWFSC) Resource Analysis and Monitoring Division (FRAM) Division currently uses 

the latest optical imaging technologies to map 

the seafloor and for making direct observations 

with in situ video as part of ongoing 

habitat-based groundfish research. For example, 

the NWFSC is currently involved in an interdisciplinary study off Heceta Bank, Oregon, to 

determine habitat-specific biomass estimates for 

selected groundfish species (Fig. 1a). The 

project utilizes the advanced imaging and sampling tools on both the ROPOS ROV and Delta 

(a) 

submersibles (Fig 1b). The NWFSC is also 

using the tools aboard the ROPOS ROV to 

explore and map poorly known marine ecosystems such as Astoria Canyon off Oregon. 

The Northwest Fisheries Science Center’s 

FRAM Division collaborates with a number of 

regional research programs along the U.S. West 

Coast to maintain a coast-wide network of sites 

where seafloor mapping and direct observation 

(with optical imaging systems) support ongoing 

habitat-based groundfish research. Through these 

coordinated studies and collaborations, a systematic approach is emerging for the classification of 

marine habitats in both shallow and deep water 

with increasing attention being given to the 

inclusion of megafaunal invertebrates as significant biological components of continental shelf 

and slope ecosystems. 

(b) 

Figure 1a - A side-scan mosaic of the Heceta Bank area off Oregon and the tracklines of ROPOS dives; b. The 

Canadian ROV ROPOS being launched from the NOAA ship Ronald Brown. 

18

Using Video Observations From 

Submersibles and Laser Line 

Scanners to Survey Benthic Fishes, 

Macro-Invertebrates and Habitat 

Types in Deepwater off California 

Mary Yoklavich 

Santa Cruz Laboratory 

Southwest Fisheries Science Center 

110 Shaffer Road 

Santa Cruz, CA 95060 

Email: mary.yoklavich@noaa.gov 

The Southwest Fisheries Science Center’s 

(SWFSC) Santa Cruz Laboratory has developed 

a research program to effectively respond to the 

Magnuson-Stevens Fishery Conservation and 

Management Act (MSFCMA) mandates with 

respect to West Coast groundfishes. Several West 

Coast groundfish species have been designated as 

overfished; it is especially important to characterize and protect essential fish habitat (EFH) of 

these species and to improve our assessments of 

these stocks. From past research, we know that 

adults of many species of rockfishes, in particular, are difficult (or impossible) to accurately 

appraise with traditional survey methodologies 

such as surface-based fishing and acoustic gear. 

This is due to the close association between many 

of these species and their rugged, rocky heterogeneous habitats. Additionally, classification of 

habitat attributes on scales pertinent to animal 

distributions and ecological problems in 

deepwater marine environments is difficult 

because of the restricted access to this system. 

Consequently, we have been developing new 

tools, technologies, and partnerships to characterize deepwater fishes and habitats since 1992. 

We are using direct observation and video 

transects from occupied submersibles, together 

with geophysical seafloor mapping techniques, to 

improve assessments and track the recovery for 

some groundfish species and their associated 

habitats. We have applied this approach to 

de facto marine reserves, in and adjacent to 

marine protected areas, submarine canyon heads, 

and rocky areas elsewhere along California. 

Several funding opportunities for marine groundfish habitat research both within Fisheries and 

from other NOAA offices (Sea Grant, Undersea 

Research Program (NURP), Ocean Exploration, 

NOS), USGS, state agencies, and private foundations have been successfully pursued in implementing our program. Our general research goals 

are to describe and conserve EFH, identify areas 

in need of additional protection, and improve 

assessments of groundfish populations. Our 

approach is especially critical when focusing on 

benthic habitats of extreme heterogeneity and 

biological assemblages of high diversity. 

Current Projects 

Cowcod Conservation Areas Surveys 

In collaboration with Milton Love (University 

of California Santa Barbara) and researchers 

from Moss Landing Marine Labs and the California Department of Fish and Game, and with 

funding from NMFS’ Offices of Protected Resources and Habitat Conservation, NURP, 

NOAA Center For Marine Protected Areas 

(MPA) Science, and the David and Lucile 

Packard Foundation, we have initiated a monitoring protocol for fish, macroinvertebrates, habitats, and incidence of fishing gear disturbance on 

offshore banks in and around the Cowcod Conservation Areas (CCA) off southern California. 

Underwater surveys of groundfish populations 

and their habitats were conducted off southern 

California using non-extractive video-transect 

methodologies and direct observations from an 

occupied research submersible (Delta; Figs. 1,2). 

19

We asked two fundamental questions of our 

research: (1) are the CCAs meeting their objective to protect and rebuild the cowcod population? and (2) can we effectively survey cowcod 

(and, by extension, other benthic fishes) by direct 

observation rather than by conventional techniques such as hook and line or bottom trawl? 

Digital geo-referenced maps of the seafloor 

acquired from available side-scan sonar, 

multibeam bathymetry, seismic reflection, and 

other past geophysical surveys were used to 

identify and select sites of appropriate bottom 

type and depth. Past and recent groundfish catch 

and effort records were also used to assist in 

locating appropriate survey sites. We tracked the 

submersible in real-time in relationship to depth 

and seafloor habitats. We used line transect 

methodology to estimate densities (and associated CVs) of cowcods on the rocky banks within 

the CCAs. Absolute abundance of cowcods 

(juvenile and adults separately) was estimated by 

expanding the density estimates by the total area 

represented by the habitats surveyed on each 

bank. 

We also used video transects from this survey 

to quantify structure-forming invertebrates as 

components of benthic habitat in the CCAs. 

There is increasing interest by science and conservation communities in the potential impacts 

that fishing activities have on megafaunal benthic 

invertebrates, such as sponges and corals, occurring in continental shelf and slope ecosystems, 

and the role these large invertebrates have in 

enhancing the diversity and structural component 

of fish habitat. We are collaborating with Brian 

Tissot (Washington State University, Invertebrate 

Ecologist) to describe patterns in the density, 

distribution, and size of structure-forming 

megafaunal invertebrates on the deep rocky 

banks and outcrops in the CCAs. Our specific 

objectives are to identify structure-forming 

invertebrates, quantify their density and size 

distributions specific to depth and substratum 

types, and quantify associations between 

Figure 1.The Delta research submersible accommodates one 

scientific observer and one pilot, has a maximum operating depth of 

about 350 m, and a cruise speed of 1.5 knots. We equipped the 

submersible with three video cameras: a low-light, wide-angle blackand- white CCD camera positioned externally on the bow; a High-8 

color video camera and associated lights externally positioned on 

the starboard side and flanked by paired lasers at a distance of 20 

cm apart; and a hand-held digital video camera positioned inside the 

submersible in the lower port on the starboard side. (photo credit: M. 

Yoklavich) 

large, structure-forming invertebrates and other 

organisms, particularly fishes. About 520,000 

megafaunal invertebrates of 15 taxa were observed in the video footage. Deep-sea 

corals and sponges were the largest structureforming invertebrates but were relatively 

uncommon. The corals were patchy in distribution and were found in low-relief mixed cobbleboulder- sand habitats at 100-225 m depths. Few 

large invertebrates and almost no fishes appeared 

to be associated with these animals. Our comprehensive survey and analysis of the distribution, 

abundance, and species composition of large 

invertebrates in the Southern California Bight is 

unique and contributes new and significant 

information to our understanding of biodiversity, 

indicators of environmental conditions, and 

components of essential fish habitats. 

We will use these established baselines of 

groundfish species, megafaunal invertebrates, and 

associated habitats to monitor changes within the 

CCAs by conducting direct observation surveys 

of abundance, size structure, and diversity on a 

routine basis. 

20

Intercalibration of Direct Observation and 

Extractive Survey Methods 

We are using direct observation methods and 

video transects from an occupied submersible to 

survey fishes and habitats in 100 m water depth 

at the location of longline surveys conducted off 

central California. Our objective is to compare 

occupied submersible quantitative transect 

methods with bottom longline methods for 

determining abundance, size and species composition, catchability coefficients and selectivity, and 

appropriate conversion factors for relative and 

absolute abundance. Quantitative transect methods, collection of accurate visual observation and 

navigation data, database management and 

analysis follow protocols based on our past 

experience with in situ methods. This study 

includes participation by a commercial longline 

fisherman in the submersible operations. Our 

results should contribute to improved assessments of groundfish stocks in untrawlable habitat 

off California. 

Fish and Habitats at Varying Spatial Scales 

Many species of groundfishes are strongly 

associated with specific substratum types. 

A predictable relationship between organism and 

habitat presents the possibility of using habitat as 

a proxy for distribution and abundance of fish 

species over large areas. The ability to extrapolate up to large scales relies on the capability to 

map the seafloor, over areas of interest and 

calculate the availability of benthic habitats. 

Acoustic systems such as sidescan and multibeam 

sonars collect wide swaths of seafloor data and 

thus can map large regions quickly. The interpretation of acoustic data into seafloor classifications however is complex, and requires reliable 

and accurate groundtruthing to transform the 

acoustic signal into biologically meaningful 

information. 

In a collaborative effort between USGS, 

National Marine Fisheries Service, and NOAA’s 

National Marine Sanctuaries Program off California (Cordell Bank, Channel Islands, and 

Figure 2. A vermilion rockfish (Sebastes miniatus) viewed from the porthole of the Delta. (photo credit: M. Nishimoto). 

21 
Monterey Bay), Tara Anderson (a post-doctoral 

fellow) is testing a novel application of a video 

camera sled to groundtruth seafloor habitat maps 

in real time. To characterize abiotic and biotic 

aspects of the seafloor, a series of multidirectional transects are conducted using a mini video 

camera sled. Video observations are annotated in 

real time every 30 seconds using an electronic 

programmable keypad integrated with navigational software. These seafloor characterizations 

adequately describe substratum types, bedform, 

relief, and presence of benthic macro-organisms. 

These data are used to groundtruth acoustic 

mosaics of the seafloor within hours of its collection, providing an initial description of seafloor 

habitats and some aspects of their communities. 

This approach is ideal for those projects that 

require rapid feedback. 

Laser Line Scan Development 

One of our challenges is to efficiently relate 

small-scale observations and assessments of 

animal-habitat associations to the large geographic scales on which benthic fisheries operate. 

Laser line scan (LLS) systems potentially can 

serve as a bridge between fine resolution, low 

coverage video survey tools (e.g., remotelyoperated vehicle (ROV), occupied submersible, 

towed sled) and coarse resolution, high coverage 

acoustic technologies (e.g., multibeam and 

sidescan sonar). In an evaluation of LLS for 

fishery habitat assessments, the Habitat Ecology 

Team conducted a survey off the central coast of 

California using a Northrop-Grumman SM2000 LLS. A video survey also was conducted 

using an ROV across parts of the study area to 

groundtruth the LLS data and to compare observations made from a forwardlooking video 

camera with those from LLS reflectance imagery. 

The LLS was successful in generating high 

resolution (1-2 cm across-track) imagery of rock 

outcrops, sand waves and ripples, drift kelp, 

patches of large anemones, groups of fishes off 

and on the seafloor, starfish, sea pens, and salp 

chains. As expected, the LLS system provided 

imagery of higher areal coverage but with a 

lower degree of taxonomic identification than the 

ROV video. 

Developing the capability to process and 

mosaic imagery and produce seafloor maps is 

a significant step in advancing the efficient 

application of LLS technology. To assess the 

mapping capabilities of the system, we generated 

a tiled-image mosaic of georeferenced LLS data 

with 2-cm pixel resolution across the survey area. 

The data acquisition hardware down-sampled or 

did not log all sensor data, which made an accurate expression of the LLS configuration (i.e., 

instrument settings) difficult to achieve. As a 

result, a large degree of detail and object recognition observed in the original LLS imagery was 

lost upon geometric translation. However, 

combined with information obtained from reviewing the original imagery, the mosaic representation did demonstrate spatial configuration 

and context of organisms and geologic features at 

varying spatial scales. This system has been 

newly revised based on results from our field 

studies and is now ready for further evaluation as 

an advanced imaging technology for EFH and 

improved stock assessments. 

For Further Reading 

Yoklavich, M. and Love, M. 

(In Review) A fishery independent assessment 

of cowcod in the Cowcod Conservation Areas 

using direct observations from an occupied 

submersible. 

Tissot B., M. Yoklavich, M. Love, K.York, and 

M. Amend.

(In Review) Structure-forming invertebrates 

as components of benthic habitat on deep banks 

off southern California. 

Amend M., M. Yoklavich, Y. Rzanhov, C. 

Grimes, and W. Wakefield. 

(In Review). Mosaics of benthic habitats 

using laser line scan technology: It’s in the 

details. Proceedings of GeoHab 2002. 

22

Anderson, T., M. Yoklavich, and S. Eittreim. 

In Press. Linking fine-scale groundfish 

distributions with large-scale seafloor maps: 

issues and challenges of combining biological and 

geological data. In In P. Barnes and J. Thomas 

(eds), Benthic habitats and the effects of fishing. 

AFS Symposium 41, Bethesda, Maryland. 

Love, M. and M. Yoklavich. 

In Press. Fishes on deep rock habitats. In L. 

Allen, M. Horn, and D. Pondella (eds.), Ecology 

of California marine fishes. University of 

California Press. 

Brock, R., J. Bohnsack, M. Fogarty, S. 

Murawski, M. Yoklavich, and M. Love. 

2003. Marine fisheries of the USA: moving 

from single-species management to a more 

holistic ecosystem-based approach, p. 521-531. 

In J. Beumer, A. Grant, and D. Smith (eds.), 

Aquatic protected areas: what works best and 

how do we know?, University of Queensland 

Printery, St. Lucia, Queensland, Australia. 

Yoklavich, M., C. Grimes, and W. Wakefield. 

2003. Using laser line scan imaging technology to assess deepwater seafloor habitats in the 

Monterey Bay National Marine Sanctuary. Mar. 

Tech. Soc. J. 37(1):18-26. 

Love, M., M. Yoklavich, and L. Thorsteinson. 

2002. The rockfishes of the Northeast Pacific. 

University of California Press, Berkeley, California. 405 p. 

Yoklavich, M., G. Cailliet, R. Lea, H. G. Greene, 

R. Starr, J. de Marignac, and J. Field. 

2002. Deepwater habitat and fish resources 

associated with the Big Creek Ecological Reserve. CalCOFI Rep. 43:120-140. 

Yoklavich, M., H. G. Greene, G. Cailliet, D. 

Sullivan, R. Lea, and M. Love. 

2000. Habitat associations of deep-water 

rockfishes in a submarine canyon: an example of 

a natural refuge. Fish. Bull., U.S. 98:625-641. 

Greene, H.G., M.M. Yoklavich, R.M. Starr, V.M.


O’Connell, W.W. Wakefield, D.E.


Sullivan, J.E. McRea, Jr., and G.M. Cailliet.


1999. A classification scheme for deep 

seafloor habitats. Oceanol. Acta 22(6):663-678. 

Yoklavich, M.M. 

1997. Applications of side-scan sonar and in 

situ submersible survey techniques to marine 

fisheries habitat research, p.140-141. In Boehlert, 

G.W. and J.D. Schumacher (eds.), Changing

oceans and fisheries: environmental data for 

fisheries research and management. U.S. Dep. 

Commer., NOAA Tech. Memo. NOAA-TMNMFS-SWFSC-239. 

Yoklavich, M.M., G.M. Cailliet, and G. Moreno. 

1993. Rocks and fishes: submersible observations in a submarine canyon, p. 173-181. In 

Proceedings of the American Academy of Underwater Sciences: 13th Annual Scientific Diving 

Symposium. 

23

Fish Surveys and 

Habitat Investigations 

of Cowcod and Bocaccio* 

John L. Butler 

Southwest Fisheries Science Center 

8604 La Jolla Shores Drive 

La Jolla, California 92037-1508 

Email:john.butler@noaa.gov 

Our goal was to establish a quantitative 

process of assessing rockfish stocks in the 

California Bight using new technology. Rockfish 

schools over local banks were mapped quantitatively with split-beam echo-sounders and habitat 

was mapped using multi-beam sounders (Fig. 

1). Remotely operated vehicle transects were 

conducted to identify species composition of 

fish schools and to “ground truth” bottom type. 

First, a multi-beam sonar was used to map 

rockfish habitat and thereby minimize the area 

to be more comprehensively surveyed. For 

habitat classification, we combined a 200 kHz 

multi-beam sonar, state-of-the-art positioning 

instrumentation, and mature algorithms to 

produce digital terrain maps of the seafloor 

Figure 2. Three dimensional image of Forthy-Three Fathom Bank. 

(Fig. 2). Additionally, we exploited the frequency- and angular-dependencies of the acoustic 

backscatter from the echo sounders and the 

sonar, respectively; that is, backscatter from 

different seafloor types is dependent on the 

acoustic wavelength relative to the particulate 

size, density, and sound speed, and it is a function 

of the acoustic incidence angle. Therefore, much 

more information about essential bocaccio habitat 

can be remotely sensed and classified by combining the data from these instruments and exploiting the fundamentals of scattering physics. High 

resolution underwater video and still-camera 

Figure 1. Fish schools above Forty-Three Fathom Bank. 

*Not presented at workshop. 24 
images were obtained with an ROV to validate 

the acoustic seabed classifications. 

Next, volume backscattering strengths at four 

frequencies were used to remotely identify 

scatterer taxa (i.e., large fish, small fish, and 

zooplankton) and to observed their diel behavioral characteristics. The acoustic backscatter 

data was identified as rockfish via an empirical 

four-frequency acoustical signature and the ROV 

video. Again, the backscatter from different fish 

species is dependent on the acoustic wavelength 

relative to the particulate size, density, and sound 

speed, and it is a function of the acoustic incidence angle. One square mile grids were established over key rockfish habitat. These grids were 

mapped at 0.2 nautical mile (nmi) intervals using 

split-beam echo sounders (four frequencies). 

Because the four different frequencies allow 

us to distinguish the size of individual fish, 

schools of small rockfish can be distinguished 

from larger fish (Fig. 3). 

Figure 3. A cow cod (Sebastes levis). 

25 
Video Surveys of 

Fish Assemblages in the 

Pacific Islands Region 

Frank Parrish 

Pacific Islands Fisheries Science Center 

2570 Dole Street 

Honolulu, HI 96822-2396 

Email: Frank.Parrish@noaa.gov 

The Pacific Islands Fisheries Science Center 

employs video to survey fish assemblages using a 

variety of techniques. For some, the data is 

derived exclusively from the video images and in 

others the video is used to augment visual observations made by scientists conducting surveys on 

scuba or in submersibles. In all methods, the fish 

data are manually scored from the video and 

entered into a data base. Automating the transition of information from video images to a digital 

data base presents a challenge given the diversity 

of species, the small size of many fish, and the 

varied habitats of the Pacific Islands. Methodologies currently used in the Pacific can be 

a 

divided into mobile transects (e.g. scuba, ROV, 

tow sleds, submersibles - Fig. 1a), stationary 

archival cameras (baited and un-baited video) and 

dynamic systems (animal mounted systems such 

as CRITTERCAM – Fig. 1b). Surveys conducted 

from submersibles generally rely on the audio 

portion of the video record to document fish 

assemblages. It is possible voice recognition 

software could be employed in this situation to 

expedite transfer to digital format. In contrast, 

archival video and video from CRITTERCAM is 

entirely dependant on the video images. Given 

the stationary nature of the archival video it may 

be well suited for image recognition software. 

The dynamic movements of animals on which 

CRITTERCAMs are fitted will likely limit automated 

analysis of these video images. However in all 

cases improved meta data and event logging 

software would expedited the transfer of video to 

a relational data base. 

b 

Figure 1. a) Launching the Pisces V submersible to conduct surveys (Photo: Hawaii Undersea Research Laboratory). b) A Hawaiian monk 

seal fitted with National Geographic Television’s CRITTERCAM. 

26

Towed-diver Surveys -- A Method 

for Mesoscale Spatial Assessment 

of Benthic Reef Habitat: A Case 

Study at Midway Atoll in the 

Hawaiian Archipelago 

Jean C. Kenyon1

 · R.E. Brainard2 · R.K. Hoeke1 · F.A. 

Parrish2 · C.B. Wilkinson1 

1 Joint Institute for Marine and Atmospheric Research 

University of Hawaii 

1125B Ala Moana Boulevard 

Honolulu, Hawaii 96814, USA 

E-mail: Jean.Kenyon@noaa.gov 

2 Pacific Islands Fisheries Science Center, National 

Marine Fisheries Service, NOAA 

2570 Dole Street 

Honolulu, Hawaii 96822, USA 

ABSTRACT 

An integrated method for reef benthic habitat 

assessment to the depth limits of conventional 

SCUBA is described, in which divers maneuver 

boards equipped with digital video, temperature, 

and depth recorders while being towed behind a 

small boat. The tow path is concurrently recorded 

by a Global Positioning System (GPS) receiver 

onboard the tow boat, to which a layback model is 

applied to more accurately map the position of the 

recorded imagery. Percent cover of salient benthic 

categories is quantified by whole-image analysis of 

still frames sampled at 30-sec intervals. 

The results of 15 towed-diver surveys conducted at Midway Atoll in the Hawaiian Archipelago during a mass coral bleaching event in 2002 

are presented to exemplify the method and are compared to quantitative results derived from more 

conventional methods of benthic biotic assessment. 

Towed-diver surveys bridge a gap between largescale mapping efforts using satellite data and smallscale, roving diver assessments, providing a mesoscale spatial assessment of reef habitats. The spatial coverage afforded by towed-diver surveys provides more comprehensive data to managers concerning the extent, intensity, differential taxonomic 

response, and bathymetric correlates of bleaching 

than does data derived from conventional, site-specific surveys alone. 

Key Learnings 

• Towed-diver surveys are an effective method 

for assessing benthic communities over large 

spatial scales. 

• The value of towed-diver survey results is 

enhanced when compared with results of 

more conventional survey methods (e.g., belt 

transect) at specific sites. 

• Limitations of the method must be balanced 

with its advantages before implementation. 

INTRODUCTION 

The manta tow technique, in which snorkel 

divers are towed behind a small boat, is a versatile 

method that has been adapted to census specific 

benthic targets including crown-of-thorns starfish 

Acanthaster planci (e.g. Chesher 1969, Moran and 

De’ath 1992), introduced algal species (Rodgers 

and Cox 1999), and derelict fishing gear (Donohue 

et al. 2000). Manta tows have also proved useful 

for broader benthic habitat characterization (e.g. 

Kenchington 1978, Miller and Müller 1999, Lopez 

Victoria et al. 2000). A primary advantage of the 

manta tow technique in habitat characterization is 

that it enables efficient survey coverage of large 

areas of reef benthos; a disadvantage is the lack of 

27

fine taxonomic resolution that can be observed and 

recorded compared to surveys conducted by freeswimming divers (Carleton and Done 1995). The 

technique has not customarily included a photographic or videographic component (Bass and 

Miller 1996) that provides a permanent record of 

the benthos and that is suitable for quantitative 

image analysis. 

Technological advances in videography over the 

past decade have catalyzed the development and 

evaluation of protocols designed to quantitatively 

assess reef benthos using computer-assisted image 

analysis (Vogt et al. 1997, Osborne and Oxley 1997, 

Page et al. 2001). Most field studies have involved 

video surveys of multiple, short (10-50 m) transects 

by free-swimming divers (e.g. Aronson et al. 1994, 

Lybolt and Eaken 2000, Ninio et al. 2000, Crabbe 

and Smith 2002), from which randomly or regularly selected frames have been assessed for benthic 

composition and abundance by the projection of 

random points on the image (e.g. Carleton and Done 

1995, Miller and Müller 1999). While such surveys 

enable reliable, site-specific habitat description, they 

generally sample but a single habitat, and they do 

not capture the transitions by which habitat characteristics change over larger spatial scales. 

Carleton and Done (1995) coupled the use of a 

manta tow with a camcorder mounted on the mantaboard in an underwater housing so as to record a 

portion of the benthic survey area; the observer maneuvering the manta-board was equipped with 

SCUBA rather than snorkel gear. Though the authors report the potential of the technique for sampling on the scale of kilometers, the actual lengths 

of reported surveys were confined to 200 meters 

and, despite the SCUBA capacity of the observer, 

were conducted to maximum depths of 3 meters. 

No protocol by which the tow path could be 

georeferenced was described, an important procedure for linking image to position over large, geomorphic spatial scales. 

In 1990, the Honolulu Laboratory of NOAA 

Fisheries inaugurated the use of SCUBA-diver-controlled towboards equipped with videographic 

equipment to assess benthic variables deemed important to lobster habitat on three emergent banks 

in the Northwestern Hawaiian Islands (Parrish and 

Polovina 1994). Since that time the Honolulu Laboratory has continued to develop an integrated 

towed-diver survey methodology in response to 

advances in videographic and georeferencing technology and has adapted the method for mesoscale 

assessment of coral reef benthic habitats. Our methodology differs from other techniques widely used 

and reported in that: (a) towed divers regularly 

survey the reef benthos to the accepted limit of 

conventional SCUBA, (b) the tow track is mapped 

through the concurrent recording of GPS positions 

and depth data, and (c) the data extraction and 

analysis regime includes percent cover quantification of all identifiable components within sampled 

frames rather than a point sampling strategy. In this 

paper we present the main components of our integrated methodology, provide a case study of data 

collected and processed using this methodology 

during a mass coral bleaching event at Midway Atoll 

in the Hawaiian Archipelago (Aeby et al. 2003, 

Kenyon et al. 2004), and compare results with data 

derived from more conventional belt-transect surveys. 

MATERIALS AND METHODS 

Personnel allocation 

Four people are utilized to conduct each toweddiver survey: two SCUBA divers, a coxswain to 

drive the surface boat, and an additional crew member to deploy and retrieve the towboards, operate 

GPS units, and record the time at which 

videorecording begins and ends. Efficiency is enhanced by the four people composing two teams 

of two divers, such that surface personnel and divers 

switch roles at the end of each tow survey. One 

member of each dive team maneuvers a towboard 

dedicated to recording observations concerning the 

benthic habitat (“habitat” towboard), while the other 

28

member of the dive team maneuvers a towboard 

dedicated to recording observations of ecologically 

and economically important fish taxa (“fish” 

towboard). This paper focuses on protocols pertinent to benthic habitat characterization. 

Towboards and accessory instruments 

Constructed of marine-grade plywood and 

coated in epoxy resin, towboards are equipped with 

a digital video camera recorder inside an underwater housing with a wide-angle port and color-correction filter, mounted to maintain a viewing angle 

perpendicular to the bottom. The videocamera automatically records the date and time on the imagery. On each side of the camera bracket, a waterproof, battery-operated laser pointer is mounted, 

with the inter-laser distance calibrated to project 

two red dots in the field of view that are 20 centimeters apart. A depth gauge, digital watch, and 

alarm chronograph set to emit an auditory signal 

every 5 minutes after activation are mounted on a 

separate bracket. The camera clock and digital 

watch are synchronized with the clock of the GPS 

unit used onboard the towboat. Plexiglas strips affixed to the towboard allow insertion of a vinyl data 

sheet for recording written information pertinent 

to the overall tow as well as quantitative visual estimates of benthic composition integrated over 5­

min periods. An SBE 39 temperature recorder (SeaBird Electronics, Inc.) mounted on the towboard 

electronically records depth, temperature, and time 

at 5-sec intervals. While conducting the videotaped 

survey, the diver maneuvers the habitat towboard 

to maintain an estimated distance of 1 meter above 

the substrate. A simple telegraph is operated by the 

diver who maneuvers the fish towboard to maintain communication with the tow boat, using several prearranged acoustic signals based on dots 

(short tones) and dashes (long tones). 

Each towboard is separately connected to the 

towboat transom by an adjustable-length (typically 

60 m long), 3/8”inch low-stretch buoyant line. 

Rather than being directly attached to the towboard, 

the tow line connects to a short bridle with a stainless steel swivel shackle that allows the diver to 

disconnect the towboard from the tow line if the 

towboard becomes grounded and cannot be quickly 

freed by the diver. Each towboard has a 5-m-long 

trailing line for the divers to grab if they become 

detached from the towboard. Divers receive special training in the risks associated with conducting 

surveys. A standard video survey (< 21 m depth) is 

50 minutes long. At greater depths (21 – 27 m) the 

time is adjusted according to no-decompression limits. 

Coordination with Collection of GPS 

Tow Track Data 

To georeference all data collected during a tow, 

a GPS receiver is programmed to record longitude 

and latitude coordinates every 5 seconds onboard 

the tow boat. When the divers are ready to begin 

videorecording, a prearranged acoustic signal is sent 

to the tow boat, where the crew member marks a 

waypoint indicating the start point of the videotape recording. The coxswain attempts to drive 

along a predetermined isobath using a bathymetric 

chart, depth sounder, and shoreline features (when 

present) as a guide while maintaining a speed of 

2.5 - 3.5 km/hour (1.7 - 2.5 knots). At the end of 

the benthic survey, before beginning an ascent to 

the safety stop, another coded signal is sent to the 

tow boat to record the time and place at which the 

video recording ended. 

The primary GPS positioning error is the difference between the location of the GPS unit 

onboard the tow boat and the divers, typically some 

55 meters behind the tow boat. To reduce this 

source of error, a series of tows were conducted to 

determine a model that addresses the “layback” 

difference between the position of the videocamera 

and the position of the GPS unit on the tow boat. 

Normal survey protocols were conducted, with the 

addition of a surface snorkeler being towed directly 

above the towboard divers while wearing a backpack containing a GPS unit inside a waterproof bag. 

The coxswain maneuvered the tow boat over a series of courses that varied in frequency and amplitude of curvature to mimic the most conservative 

and the most extreme deviations of the divers’/ 

29

snorkeler’s position from the coordinates recorded 

by the GPS unit on the tow boat during regular 

surveys. 

Tape Processing and Data Extraction 

The quantitative analysis of each benthic videotape begins with the capture of single, still frames 

as the tape is simultaneously played through a computer and a high-resolution monitor. The high-resolution monitor assists with identification of benthic 

characters that may be difficult to distinguish on 

the lower-resolution computer screen. If the frame 

is too blurry because of momentary excessive speed, 

or more than an estimated 5% of the benthos cannot be identified due to shadow, the analyst toggles 

forward frame by frame until the next frame that is 

suitable for analysis is reached. A sampling interval 

of 30 sec was selected as best optimizing the joint 

interests of reproducible results, inter-frame distance, and time required to complete the analysis. 

Each captured still frame is next imported into 

SigmaScan® Pro (SPSS ScienceTM) for tracing 

benthic components using a stylus and graphics 

tablet. The benthic area (cm2

) captured within the 

frame is determined using the projected pair of red 

laser dots known to be 20 cm apart, and is used as 

the denominator in the percent cover calculations 

for benthic components within that frame. For 

frames in which the dots have not been imprinted 

because of laser malfunction, the number of pixels 

composing the still image is used as the denominator in percent cover calculations. The number of 

benthic categories that can be identified from still 

frames varies according to the geographic locality 

surveyed; the variation is attributable to different 

coral faunas. Categories that are consistent among 

geographic locality include macroalgae, turf algae, 

coralline algae, invertebrates other than coral, sand, 

rubble, carbonate pavement, rock, and unencrusted 

(recently dead) coral. A spreadsheet called up within 

the SigmaScan® Pro program receives the computed area (in cm2

 or pixels) of each member of 

each benthic category as the analyst completes its 

tracing with the stylus. Tracing proceeds until only 

Figure. 1 Location of Midway Atoll in the Hawaiian Archipelago 

one category present within the frame remains. 

These values are then imported into a Microsoft® 

Excel spreadsheet that has been preformatted with 

formulas for the calculation of percent cover of each 

category of imported data. The percent cover of 

the remaining untraced category is computed by 

subtracting the sum of the other categories from 

100. Lastly, the time-stamp for the still frame is 

manually entered. The percent cover data and time 

stamp from each frame-specific Excel spreadsheet 

are then compiled into a master spreadsheet from 

which the quantitative habitat data can be summarized over whatever time/spatial interval is desired. 

GIS Data Ingestion, Processing, and Display 

GPS data are downloaded directly into GIS 

using a custom-designed (Hoeke, unpublished) 

ArcView© extension. Data are downloaded as (1) 

track data files, containing a position and time stamp 

every 5 sec, and (2) waypoint data files, defining 

locations of the start and end of the videotaped 

survey. The customized extension then performs a 

number of calculations and allows for editing and 

quality control of the data including (1) a layback 

calculation to rectify the position of the towboard, 

(2) merging all track files for a single day, (3) sorting and trimming track files based on waypoint files, 

interpolating for lost GPS data if necessary, (4) 

calculating sequential dive numbers, local time, and 

other attribute fields, (5) adding temperature and 

depth data, matching SBE 39 and GPS time stamps, 

and (6) calculating sequential segments for each 

tow; using segment lengths of 30 sec and 5 min to 

correlate with the intervals over which analytical 

and in situ data are compiled, respectively. The 

30

extension then adds video analysis data (30-sec 

segments) and in situ observational benthic data (5­

min segments) as separate files. These separate files 

are spatially represented as polyline files, where each 

segment of analysis/observation data is a separate 

polyline. The nodes of these polylines match the 

nodes in the track file. The attribute tables (*.dbf) 

of the analysis/observation tables are tied to the 

track file’s attributes by the dive number and the 

respective segment number. The resulting 

georeferenced observations can be mapped in conjunction with IKONOS-acquired imagery and 

viewed on spatial scales of resolution varying from 

33 m (the average separation between sequential 

frames) to the entire length of a tow (i.e. several 

kilometers). 

Case Study: Midway Atoll 

Midway Atoll (28o

15’N, 177o20’W) is one of 

the northwestern-most atolls in the Hawaiian Archipelago (Fig. 1). Between 20 and 25 September 

2002, 15 towed-diver surveys were conducted at 

Midway Atoll to assess a mass coral bleaching event 

(Aeby et al. 2003, Kenyon et al. 2004). Video analysis was conducted by a single analyst. The categories of live coral that could be recognized in recorded videotapes were Pocillopora, massive/encrusting Porites, Porites compressa, Montipora, 

and other live coral (e.g., Pavona, Fungia). For 

each category, percent cover of bleached and unbleached coral were separately quantified. Incidence 

of bleaching was computed as the percentage of 

coral cover that was bleached. To examine the correlation between depth and incidence of bleaching, 

each sampled still frame was paired with its depth 

using concurrent time stamps on the video and 

depth recorder. 

Comparison with Belt Transect Data 

Between 19 and 25 September 2002, belt 

transects enclosing 50 m2

 or 100 m2 at each of 20 

sites were conducted according to the methods of 

Maragos et al. (2004), in which the number of colonies as well as the number with bleached tissue was 

tallied by genus. Incidence of bleaching was computed as the percentage of colonies with bleached 

tissue. To examine the correlation between depth 

and incidence of bleaching, for each site the percentage of all colonies with bleached tissue was 

paired with that site’s depth. 

31

RESULTS 

Towed-diver Surveys 

The distance between sample frames captured 

at 30-sec intervals depends upon the tow speed; 

the average distance ranged from 19.2 m to 38.6 m 

(mean = 33.0, n = 20 tows). The average benthic 

area captured in laser-scaled frames was 10,907 cm2 

(SE = 119, n = 700). Towed divers surveyed 37.5 

km of benthic habitat within 3 atoll zones (forereef, 

backreef, channel) (Table 1, Figure 2), from which 

1129 frames were analyzed, for a total analysis area 

of 1231 m2

. The videotape from a standard 50-min 

tow over a habitat with a diversified benthos (e.g. 

backreef) requires approximately 16 hours for complete analysis, from capturing still frames to summarization. Coral cover was low (<12%) in all 3 

zones (Table 1). Incidence of bleaching was highest on the backreef, lowest on the forereef, and 

moderate in the broad channel along the northwest 

exposure (Table 1, Fig. 2). Bleaching was most 

prevalent in Pocillopora and Montipora, with a low 

incidence of bleaching in Porites (Table 1). There 

was a significant negative correlation between the 

incidence of bleaching and depth (rs = 0.50, n = 

1129, p = 0.00). 

Comparison with Belt Transect Data 

Belt-transect divers surveyed 1450 m2

 of 

benthic habitat in 4 zones (Table 1). Incidence of 

bleaching was highest on the backreef, lowest on 

the forereef, and moderate in the channel and on 

lagoon patch reefs (Table 1, Figure 2). Bleaching 

was most prevalent in Pocillopora and Montipora, 

with no bleaching observed in Porites (Table 1). 

There was a significant negative correlation between the incidence of bleaching and depth (rs

 = 

0.73, n = 20, p = 0.00). 

Figure. 2 Locations of towed-diver and belt transect surveys at 

Midway Atoll, using IKONOS-acquired imagery as a basemap. Sites 

and track segments are shaded according to incidence of bleached 

coral; values presented for towed-diver surveys are averages 

computed over sequential 5-min intervals. 

CONCLUSIONS AND 

RECOMMENDATIONS 

Towed-diver surveys provide an efficient 

method for recording spatial variability in benthic 

communities on coral reefs when conducted by 

experienced divers trained in the safety considerations that pertain to this advanced diving technique. 

A primary strength of towed-diver surveys is 

their ability to assess the major benthic components 

and condition of reef habitats over spatial scales 

substantially greater than can be observed and documented by free-swimming divers. In the present 

study at Midway Atoll, belt-transect divers examined more benthic area than was analyzed from 

towboard videos (1450 m2

 vs. 1231 m2, respectively); however, results from towed-divers were 

derived over a survey length of 37.5 km (Table 1), 

while results from belt transects were derived over 

transect lengths totaling 725 m. Because the 

samples (still frames) from towed-diver surveys are 

spread over a long curvilinear dimension, whereas 

belt transect surveys are concentrated at specific 

sites (Figure 2), towed-diver surveys provide a 

broader spatial assessment of large reef systems with 

variable habitats. The primary conclusions gener32

ated from both methods are congruent: (1) incidences of bleaching were highest on the backreef, 

lowest on the forereef, and moderate in other atoll 

zones; (2) Pocillopora and Montipora were highly 

susceptible to bleaching whereas Porites evidenced 

little bleaching; and (3) there was a significant negative correlation between depth and the incidence 

of bleaching. In receiving corroboration from the 

similar results generated through belt-transect surveys, towed-diver surveys allow extrapolation to 

broader spatial scales. 

Because they are powered by a surface boat, towed 

divers are able to survey in sea conditions that are 

too extreme for roving divers or their support skiff 

to safely work in, e.g. high swell, strong current, 

or poor anchorage. They provide a permanent visual record that is amenable to re-sampling by different analysts, or to re-analysis when more automated, image-recognition technologies are developed. Inclusion of a GPS receiver on the towing 

boat allows georeferencing the survey path, and 

incorporation of a layback model improves the accuracy of positioning the recorded imagery, thereby 

providing a basis for ground-truthing satellite and 

aerial remote sensing imagery (e.g. Andréfouët 

et al. 2002, Bainbridge and Reichelt 1988). The 

method is particularly useful for assessing remote 

areas that can only be visited infrequently and for 

short durations. 

A primary limitation of interpreting visual information from a towed camera is the loss of taxonomic resolution compared to the capacity of roving diver classifications. Field equipment as well as 

computer equipment needed to analyze imagery is 

expensive, realistically limiting this method to programs with large budgets. Image analysis is timeconsuming. Field and computer personnel require 

special training, the former to ensure safety and 

accuracy, the latter to ensure consistency and reproducibility. Interested researches should weight 

the advantages and limitations of towed-diver surveys before investing in and implementing the 

method. 

ACKNOWLEDGMENTS 

We thank more than two dozen fellow NOAAcertified divers for building the safety record of 

towed-diver surveys, the officers and crew of the 

NOAA ship Townsend Cromwell for logistic support and field assistance, and Greta Aeby for sharing belt transect data. Permission to work at Midway Atoll National Wildlife Refuge was granted by 

the Pacific Remote Islands Wildlife Refuge Complex, U.S. Fish and Wildlife Service, Department 

of the Interior. Will Smith, of the Hawaii Coral Reef 

and Monitoring Program of the University of 

Hawaii’s Hawaii Institute of Marine Biology, and 

Michael Coyne, of the Biogeography Program of 

NOAA’s National Ocean Service, assisted with surveys from which a layback model was derived. 

Funding from the Office of Habitat Conservation 

at NOAA Fisheries as part of the NOAA Coral Reef 

Conservation Program has supported this work 

since 2001, with particular encouragement and facilitation from Tom Hourigan. 

REFERENCES 

Aeby, G. S., J. C. Kenyon, J. E. Maragos, and D. 

C. Potts.

2003. First record of mass coral bleaching in 

the Northwestern Hawaiian Islands. Coral Reefs 

22:256. 

Andréfouët, S., R. Berkelmans, L. Odriozola, T. 

Done, J. Oliver, and F. Müller-Karger. 

2002. Choosing the appropriate spatial resolution for monitoring coral bleaching events using 

remote sensing. Coral Reefs 21:147-154. 

Aronson, R. B., P. J. Edmunds, W. F. Precht, D. 

W. Swanson, and D. R. Levitan.

1994. Large-scale, long-term monitoring of 

Caribbean coral reefs: simple, quick, inexpensive 

methods. Atoll Research Bulletin 421:1-19. 

33

Bainbridge, S. J., and R. E. Reichelt. 

1988. An assessment of ground truth methods 

for coral reef remote sensing data. Proceedings 

of the 6th International Coral Reef Symposium 

2:439-444. 

Bass, D.K., and I. R. Miller. 

1996. Crown-of-thorns starfish and coral 

surveys using the manta tow and scuba search 

techniques. Long-term Monitoring of the Great 

Barrier Reef SOP No. 1, Australian Institute of 

Marine Science, 33 p. 

Carleton, J.H., and T. J. Done. 

1995. Quantitative video sampling of coral reef 

benthos: large-scale application. Coral Reefs 

14:35-46. 

Chesher, R.H. 

1969. Acanthaster planci: Impact on Pacific 

coral reefs. Final report to the U.S. Department 

of the Interior. Westinghouse Electric Corporation Research Laboratories, Pittsburgh PA, 

151 p. 

Crabbe, M.J.C., and D. J. Smith. 

2002. Comparison of two reef sites in the 

Wakatobi Marine National Park (SE Sulawesi, 

Indonesia) using digital image analysis. Coral 

Reefs 21:242-244. 

Donohue, M.J., R.C. Boland, C.M. Sramek, and 

G.A. Antonelis.

2001. Derelict fishing gear in the Northwestern 

Hawaiian Islands: diving surveys and debris 

removal in 1999 confirm threat to coral reef 

ecosystems. Marine Pollution Bulletin 

42(12):1301-1312. 

Kenchington, R.A. 

1978. Visual surveys of large areas of coral 

reefs. In Stoddart, D.R., and R.E. Johannes, R.E. 

(eds.), Coral Reefs: Research Methods, 

UNESCO, Paris, p. 149-162. 

Kenyon, J.C., G.S. Aeby, R.E. Brainard, J.D. 

Chojnacki, M. Dunlap, and C.B. Wilkinson. 

2004. Mass coral bleaching on high latitude 

reefs in the Hawaiian Archipelago. [Abstract]. 

Tenth International Coral Reef Symposium, 

Okinawa, Japan, p. 135. 

Lopez, V. M., J.M. Diaz, and J. C. Marques. 

2000. Coralline formations of Tortugilla Island 

(Colombian Caribbean). Boletin Investigations 

Marinas 29:51-58. 

Lybolt, M., and D. Eaken. 

2000. A tested protocol for video sampling of 

benthic habitats. In Hallock, P. and L. French 

(eds.), Diving for Science in the 21st Century. 

American Association of Underwater Science, 

Nahant, Massachusetts, p. 26. 

Maragos, J.E., D.C. Potts, G. Aeby, D. Gulko, J. 

Kenyon, D. Siciliano, and D. VanRavenswaay. 

2003. The 2000-2002 rapid ecological assessment of corals (Anthozoa) on shallow reefs of 

the Northwestern Hawaiian Islands, Part 1: 

species and distribution. Pacific Science 

58(2):211-230. 

Miller, I., and R. Müller. 

1999. Validity and reproducibility of benthic 

cover estimates made during broadscale surveys 

of coral reefs by manta tow. Coral Reefs 18:353-

356. 

Moran, P.J., and G. De’ath. 

1992. Suitability of the manta tow technique 

for estimating relative and absolute abundances 

of crown-of-thorns starfish (Acanthaster planci 

L.) and corals. Australian Journal of Marine and 

Freshwater Research 43:357-78. 

Ninio, R., M. Meekan, T. Done, and H. 

Sweatman. 

2000. Temporal patterns in coral assemblages 

on the Great Barrier Reef from local to large 

spatial scales. Marine Ecology Progress Series 

194:65-74. 

34

Osborne, K., and W.G. Oxley. 

1997. Sampling benthic communities using 

video transects. In English, C., C. Wilkinson, and 

V. Baker (eds.), Survey manual for tropical

marine resources. Australian Institute of Marine 

Science, Townsville, p. 363-376. 

Page, C., G. Coleman, R. Ninio, and K. Osborne. 

2001. Surveys of sessile benthic communities 

using the video technique. Long-term Monitoring 

of the Great Barrier Reef SOP 2, 

49 p. 

Parrish, F.A., and J.J Polovina. 

1994. Habitat thresholds and bottlenecks in 

production of the spiny lobster (Panulirus 

marginatus) in the Northwestern Hawaiian 

Islands. Bulletin of Marine Science 54(1):151-

163 . 

Rodgers, S.K., and E.F. Cox. 

1999. Rate of spread of introduced 

Rhodophytes Kappaphycus alvarezii, 

Kappaphycus striatum, and Gracilaria salicornia 

and their current distributions in Kâne’ohe Bay, 

O’ahu, Hawai’i’ Pacific Science 53(3):232-241. 

Vogt, H., A.R.F. Montebon, and M.L.R. Alcala. 

1997. Underwater video sampling: an effective method for coral reef surveys? Proceedings 

of the 8th International Coral Reef Symposium 

2:1447-1452. 

35 
The Use of Digital Video Recorded 

During Towed Diver Surveys to 

Estimate Reef Fish Assemblages 

Over a Large Spatial Scale 

Brian Zgliczynski 

Coral Reef Ecosystem Division 

Pacific Islands Fisheries Science Center 

2570 Dole Street 

Honolulu, HI 96822-2396 

Email: brian.zgliczynski@noaa.gov 

Towed-diver surveys can be used to conduct 

rapid assessments of large areas of reef in a short 

period of time, which can be critical when working at remote sites. Compared to traditional dive 

surveys, which have limited spatial coverage, the 

towed diver surveys are more effective at estimating abundance and density of large mobile 

fishes. Rare or uncommon fishes not encountered 

during conventional surveys are more likely to be 

observed during towed-diver surveys because of 

the larger area covered. While conventional 

SCUBA surveys are often impacted by adverse 

environmental conditions, towed divers are less 

affected and can therefore survey sites where 

wind, current, and swell are challenging. The 

towed-diver video analysis permits more detailed 

assessment of larger-bodied fishes, including the 

ability to more precisely enumerate the numbers 

of individuals within large aggregations of fishes 

observed during the in situ surveys. Additionally, 

a video record of the habitat is available to 

describe benthic characteristics (i.e., physiographic zones, habitat types, and habitat complexity). Towed-diver surveys involve towing 

two SCUBA divers behind a boat at a constant 

speed (~1.5 knots; Fig. 1). Each diver maneuvers 

one of two towboards that are connected to the 

boat by a bridle and towline and outfitted with 

various survey equipment including digital still or 

video cameras. The divers fly the towboards 

approximately 1 m above the substrate to keep 

the records consistent. One of the towboards 

carries a magnetic switch telegraph system, 

which allows the tow-divers to relay simple prearranged acoustic signals to the surface support 

team. The latitude and longitude 

coordinates of the survey track are recorded 

using a global positioning system allowing data 

to later be geo-referenced. 

Laboratory analyses of the digital videos 

recorded during towed diver fish surveys are 

conducted by viewing 40% of a tape for fishes 

20-50 cm total length (TL), and viewing 100% of 

a tape for fishes >50 cm TL. Tapes are viewed in 

ten 5-min segments (towed-diver survey time 

dependent) and fishes are recorded within an 

estimated 10 m-wide swath. Fishes are identified 

to species level, where possible, and sizes are 

estimated according to one of nine size categories (20, 35, 50, 75, 100, 150, 200, 250, and 

300 cm TL), the latter using habitat cues and, in 

certain cases, size-specific behaviors and colorations. Habitat classification information is also 

recorded during video analysis by assigning a 

specific value for the physiographic zone, habitat 

type, and complexity that is viewed during each 

1-minute sub-segment. 

Figure 1. One diver (forward) records the benthos and another diver 

(rear) records fish during towed-diver surveys using underwater 

videography at Pathfinder Reef in the Commonwealth of the 

Northern Marianas Islands. Photo: S. Holzwarth 

36

Botcam –


Bottom Fish Camera Bait Station


Daniel Merritt 

Coral Reef Ecosystem Division 

Pacific Islands Fisheries Science Center 

2570 Dole Street 

Honolulu, HI 96822-2396 

Email: Daniel.Merritt@noaa.gov 

Since 1997, the National Marine Fisheries 

Service (NMFS) in Hawaii has been collaborating 

with the Hawaii Undersea Research Laboratory 

(HURL) to conduct visual surveys of commercially important bottom fish species including 

snappers, groupers and jacks. Using HURL’s 

deep diving manned submarines, the Pisces IV 

and V, biologists Christopher Kelley (HURL), 

Robert Moffitt (NMFS) and others have conducted ongoing surveys of bottom fish at depths 

from 150 m to 300 m. These surveys employ bait 

to attract fish to the area of the submarine but 

use no external light source, which is known to 

discourage certain target species. Building upon 

this previous work, HURL and NMFS’ Pacific 

Islands Fisheries Science Center are developing 

an autonomous bottom camera bait station 

(Botcam) designed to be deployed in 200-400 m 

depths which automatically releases bait and 

records video (Fig. 1). This presentation reviews 

a prototype Botcam system delivered by Sound 

Ocean Systems, Inc., Redmond, Washington, and 

discusses future design directions and considerations. 

Figure 1. Prototype Bottom Camera Bait Station (Botcam) system 

deployed inapproximately 30 feet of seawater off the south shore of 

Oahu, Hawaii. Photo by K. Wong. 

37

SEAMAP Reef Fish Survey 

of Offshore Banks 

Christopher T. Gledhill, Kevin R. Rademacher 

and Paul Felts 

Mississippi Laboratories 

Southeast Fisheries Science Center 

P.O. Drawer 1207 

Pascagoula,MS 39568-1207 

Email: Christopher.T.Glendhill@noaa.gov 

The objective of the Southeast Fisheries 

Science Center’s annual Southeast Area Monitoring and Assessment Program (SEAMAP) offshore reef fish survey is to provide an index of 

the relative abundances of fish species associated 

with topographic features (banks, ledges) located 

on the continental shelf of the Gulf of Mexico 

(Gulf) in the area from Brownsville, Texas, to the 

Dry Tortugas, Florida (Fig. 1). The offshore reef 

fish survey was initiated in 1992, with sampling 

conducted during the months of May to August 

from 1992 to 1997, 2001 to 2002, and 2004. No 

surveys were conduced from 1998 to 2000 and 

2003. The 2001 survey was abbreviated due to 

ship scheduling. 

Figure 1. Bathymetry along the continental shelf of the Gulf of 

Mexico with the primary sample units (blocks) employed by the 

SEAMAP offshore reef fish survey. 

The survey area is large; therefore a twostage sampling design is used to minimize travel 

times between sample stations. The first-stage or 

primary sampling units (PSUs) are blocks 10 

minutes of latitude by 10 minutes of longitude 

(Fig. 17). The first-stage units are selected by 

stratified random sampling, with stratum boundaries defined by geographic region (four regions: 

South Florida, Northeast Gulf, Louisiana-Texas 

Shelf, and South Texas), and by reef habitat area 

(Blocks # 20 km2 reef, Block > 20 km2 reef). 

There are a total of seven strata. The ultimate 

Figure 2. The SEAMAP camera pod. 

38 
sample sites (second stage units) within a block 

are selected randomly 

The SEAMAP reef fish survey currently 

employs four Sony VX2000 DCR digital 

camcorders mounted in Gates PD150M underwater housings (Fig. 2). The housings are rated 

to a maximum depth of 150 m. The four Sony 

VX2000 camcorders are mounted orthogonally 

at a height of 30 cm above the bottom of the pod 

(Fig. 18b). A chevron (or arrow) fish trap with 

1.5-inch vinyl-clad mesh is used to capture fish 

for biological samples. At its greatest dimensions, 

the trap is 1.76 m in length, 1.52 m in width and 

0.61 m in depth. A 0.4 m by 0.29 m blow-out 

panel is placed on one side and kept closed using 

7-day magnesium releases. The magnesium 

releases are examined after each soak and replaced as needed. The trap is deployed at a 

randomly selected subset of video stations. Both 

the camera pod and fish trap are baited with 

squid. The camera pod soaks for 30 minutes 

while the trap soaks for 1 hour. 

One video tape from each station is randomly 

selected for viewing. Tape viewers examine 

20 minutes of the selected video tape, identify, 

and enumerate all species for the duration of the 

tape. Identifications are made to the lowest 

taxonomic level and the time when each fish 

enters and leaves the field of view is recorded. 

This is referred as a time in - time out procedure 

(TITO). Tapes are viewed from the time when 

the view clears from any silt plume raised by the 

gear when it landed. Less than 20 minutes may be 

viewed if the duration when water is not clear 

enough to count fish is less than 20 minutes, or if 

the camera array is dragged. Three estimators of 

relative abundance are available from the video 

data: 1) presence and absence; 2) maximum 

count (each fish of each taxon is counted each 

time it appears on the screen); and, 3) a minimum 

count (the greatest number of a taxon that appears on screen at one time). The minimum count 

is the same at the MAXNO used by Ellis and 

Figure 3. Still image captured from video showing laser dots on a 

scamp (Mycteroperca phenax) and red porgy (Pagrus pagrus). 

DeMartini (1995). Presence and absence (frequency of occurrence) and minimum count 

estimators are advantageous because they avoid 

the potential of multiple counting of fish. Lasers 

mounted 10 cm apart are used to obtain estimates of fish length (Fig. 3). 

Not all fish can be identified from the videotape. 

Often, identification to species level depends on 

observing fish behavior. Identification can be 

improved with the use of higher resolution 

cameras (High Definition video or digital still 

cameras.) Few fish are hit by the lasers so size 

information is limited. Stereo video or still 

cameras would enable the measurement of all 

fish. The tape viewing procedure is time-consuming. On average, a single viewer can process 

video from three sites (60 minutes of tape) in a 

40-hour week. Automation of the viewing procedure using pattern recognition would make 

the survey data available to stock assessment 

scientists in a more timely fashion. 

39

Underwater Video Research at the 

Northeast Fisheries Science Center 

William Michaels 

Northeast Fisheries Science Center 

166 Water Street 

Woods Hole, MA 02543-1026 

Email: william.michaels@noaa.gov 

Underwater video operations are conducted 

routinely aboard Northeast Fisheries Science 

Center’s (NEFSC) research cruises in support of 

NOAA Fisheries Strategic Goals such as Stock 

Assessment Improvement Plan (SAIP) and 

Essential Fish Habitat (EFH). Underwater video 

has been deployed on survey sampling gear 

(trawls and dredges) to examine gear performance and selectivity for SAIP. Underwater 

video research is also underway to verify acoustic 

seabed classification, which provides the 

framework for identifying and monitoring EFH. 

Underwater video has been implemented to 

improve acoustic population estimates by direct 

verification of acoustic targets and explains the 

variability of the estimates as a function of fish 

behavior (Fig.1). 

For example, in-situ video observations of 

herring behavior with their tilt angle measurements in conjunction with their individual acoustic target strength measurements confirms that 

variability in their acoustic population estimates 

vary primarily with their behavioral patterns (Fig. 

2). Low light CCD and ICCD video cameras are 

utilized to reduce fish avoidance. In situ underwater video has also provided a means to link 

laboratory measurements and theoretical modeling of herring backscatter with the empirical 

results from surveys. Efforts are underway to 

develop an advanced integrated fisheries opticalacoustic-environmental sensing profiler via 

portable fiber-optic winch system for improving 

NEFSC fisheries and habitat acoustic survey 

operations. Existing technological limitations of 

integrated optical-acoustical survey operations to 

resolve include accurate synchronization of video 

Figure 1. A multipurpose low-light video camera array configured to 

obtain in situ tilt angle measurements of Atlantic herring. 

Figure 2. Herring observed swimming with an upward tilt using CCD 

video cameras at low-light levels (1 x 10-4 lux). 

streams and acoustic data logging, real-time 

optical recognition and processing, video and 

metadata management for integrated marine 

habitat mapping, limited dynamic range, and 

minimization of fish avoidance. 

40

Video Scallop Stock Assessment 

in Alaska 

Gregg Rosenkranz 

Alaska Department of Fish and Game 

Division of Commercial Fisheries 

211 Mission Road 

Kodiak, AK 99615 

Email: gregg_rosenkranz@fishgame.state.ak.us 

The Alaska Department of Fish and Game 

began working on methods for video assessment 

of weathervane scallop stocks in 2000. The 

primary objective of the program is to collect 

fishery-independent data on scallop populations 

that will aid in management of the resource. 

Video was chosen because the capture efficiency 

of scallop dredges is variable and difficult to 

estimate. 

Our equipment consists of a towable aluminum sled equipped with a watertight pressure 

tube that houses a mini-DV camcorder, an 

underwater 12 volt battery, and four 75-watt 

lights (Fig. 1a). The camcorder is aimed toward 

the substrate through a glass dome port on one 

end of the pressure tube, and video is recorded 

on the sled only. Tows of 15 minutes duration at 

a target speed of 1.5 knots are made at randomly 

selected stations inside beds defined from logbook effort data from the commercial fishery. 

Two reviewers count scallops by watching the 

video after the survey at regular playback speed 

without pauses. 

A subset of tows is reviewed a second time 

using pause and slow-speed playback to obtain 

the most accurate counts possible, allowing us to 

estimate bias in the original counts (Fig. 1b). 

Observed scallop densities are converted to 

scallop count estimates using area-swept methodology. Scallop shell height measurements obtained from still images captured from video are 

used in conjunction with shell height-meat weight 

data from limited dredge tows to convert the 

a 

b


Figure 1a.) Launching the video sled used for the scallop survey; b.)


view of the seabed showing three scallops.


scallop counts estimates to meat weight biomass 

estimates. To date, surveys have been conducted 

in the eastern Gulf of Alaska, Shelikof Strait, and 

in the Bering Sea north of Unimak Island. 

We hope to upgrade the system to live video 

feed in the near future. This would increase 

efficiency by allowing us to collect more useable 

video footage per vessel day. 

41

Use of Video for Inshore 

Rockfish Stock Assessment 

Chris Grandin 

Department of Fisheries and Oceans 

Pacific Biological Station 

3190 Hammond Bay Road 

Nanaimo, British Columbia V9R 5K6 

Canada 

Email: grandinc@pac.dfo-mpo.gc.ca. 

The Pacific Biological Station’s inshore 

rockfish group in western Canada uses two 

video-based methods to assess stocks in the 

inside waters of British Columbia’s west coast: 

towed cameras, and manned submersibles. 

The two types of towed camera arrays used 

on this study both have the same physical layout 

(Fig. 1a). A video overlay unit is used to overlay 

the video signal with sensor data, GPS coordinates (at surface), and time. This enables the 

application of data analysis methods such as line 

transect density estimation for stock assessment. 

The manned submersible we use is Nuytco’s 

Aquarius, a 2-observer, 1-pilot craft, which is 

shown in Figure 1b with the layout of the cameras and communications used for the September 

2003 survey. 

To create a database of the habitat conditions 

and fish observations, most researchers follow 

some manual method such as pausing the tape 

each time a surface substrate changes or when a 

fish is seen, then insert the time and species/ 

substrate type into a database. We decided early 

on that because of the amount of tape we had to 

analyze, a better method was needed. DVlog 

software was created to not only automatically 

store the data into a database on a button press 

but to also control the DV tape deck remotely. 

The buttons can be re-assigned to different 

species and substrate types on the fly (Fig. 2). A 

person is still needed to view the tape, but the 

amount of work that person needs to do has been 

a 

b 

Figure 1a.) The delta wing towed camera; b.) the Aquarius submersible. 

greatly reduced. For more information on DVlog 

or if you want a copy of the software please 

email me (grandinc@pac.dfo-mpo.gc.ca.). 

Our analysis techniques include line transect 

density estimation using the program DISTANCE 

which is available on the web (http:// 

www.ruwpa.stand.ac.uk/distance/) and we are 

42

exploring the use of neural networks to determine habitat preference by species. At this point, 

the neural network is a simple three-layer perception classification model using the video indicators substrate type, relief, complexity, and depth 

as inputs to the network and the species as the 

output. The output appears as a probability that 

the species will be seen given the habitat conditions. 

With this network we have so far only 

reached a rate of 75% correct classification when 

compared with training data but as more data is 

collected and new networks are tried we hope to 

improve this. The ultimate goal is to use remotely 

sensed data as inputs and have a prediction of 

species and perhaps even density in real time. 

Figure 2.The graphical user interface for Dvlog, the video processing software used for the rockfish assessment project. 

43

Use of Stereo-video Photography in 

Remote Camera and Diver Transect 

Assessments of Fish Populations 

Euan Harvey and James Seager 

School of Plant Biology 

University of Western Australia 

Perth, Australia 

Email: euanh@cyllene.uwa.edu.au 

Mark Shortis 

Science, Engineering and Technology Portfolio 

RMIT University, Melbourne, Australia 

Email: mark.shortis@rmit.edu.au 

Stuart Robson 

Department of Geomatic Engineering 

University College 

London, United Kingdom 

Email: srobson@ge.ucl.ac.uk 

Mike Cappo 

Australian Institute of Marine Science 

Townsville, Queensland, Australia 

Email: mcappo@aims.gov.au 

We have used stereo-video to assess demersal 

fish assemblages in two ways; firstly a diver-held 

stereo-video system and secondly in baited 

remote underwater video stations. 

Diver-held, stereo-video system 

Underwater Visual Census (UVC) by 

SCUBA divers is one of the most popular 

techniques for assessing the diversity, abundance 

and length frequency of shallow water reef fish 

assemblages. However, UVC is not as easy as it 

sounds. Divers need to identify and count all the 

species they see, decide if a fish is inside or 

outside the sample unit and often estimate the 

lengths of individual fish. UVC suffers from many 

biases, of which inter-observer variability is 

probably of the greatest concern. For this reason 

we have constructed several stereo-video systems 

which can be operated and maneuvered by a 

SCUBA diver. The use of stereo-video minimizes 

biases, and inter-observer variability associated 

with length estimates of fish (See Harvey et al. 

2001a,b, 2002a). The latest version of the system 

uses SONY TRV 900E video cameras in watertight acrylic housings (Fig. 1). 

The watertight housings are mounted on a 

base bar 75 cm apart. Using this system we can 

measure the lengths of fish on the video to within 

Figure 1. A diver-held stereo-video camera system. A SCUBA diver swims the camera system recording observations and comments 

directly onto one of the videotapes using a full-face mask containing a microphone (right). 

44

Figure 2. Two stereo BRUVS ready for deployment.These systems use off-the-shelf single CCD Sony HandiCams in PVC housings with 

acrylic ports. 

several millimeters of their real length (see 

Harvey et al. 2002b). To date we have measured 

the lengths of fish ranging from 23 mm through 

to 270 mm at distances of 0.5 m to 9 m from the 

cameras. We also use the stereo-video measurements to define whether a fish is inside or outside 

the borders of our sampling unit. Deciding 

whether a fish is inside or outside a sampling unit 

is very important and can drastically alter the 

estimates of density or relative abundance 

(Harvey et al. 2004). 

The system is neutrally buoyant in water, can 

be operated by any competent diver and deployed 

from small boats. Harvey et al. (2001a, 2002a) 

have shown that measurements of the lengths of 

fish from a stereo-video are more accurate and 

precise than estimates from novice and experienced scientific divers. Similar results were 

recorded for distance estimates (Harvey et al. 

2004). Using stereo-video measurement software 

(Shortis and Robson 2004) inexperienced people 

can make very similar measurements as experienced operators. This has major implications for 

the involvement of volunteers in monitoring 

programs. 

Stereo-video in Baited Remote Underwater Video 

Stations (BRUVS) 

Baited underwater video cameras were first 

used for assessing the abundances of juvenile 

tropical snappers (Ellis and DeMartini 1995), and 

abyssal scavengers (Priede et al. 1994,1996). 

Since then baited video techniques have become 

popular in a variety of forms (Babcock et al. 

1999, Willis and Babcock 2000, Willis et al. 

2000, 2003; Cappo et al. 2003, 2004; Denny et 

al. 2004). 

Some of the advantages of baited cameras 

include the ability to non-destructively sample 

demersal fish assemblages from a wide range of 

habitats across many depths, both during the day 

and at night time. Camera stations also attract 

many species and size classes that are disturbed 

by SCUBA divers in shallower waters. Video 

recordings serve as a permanent record for 

identification and simultaneously provide information on habitat and on the behavior of fish 

towards each other and towards the gear. Stereo 

baited remote underwater video stations (stereo 

45

Figure 3. A screen dump of the VMS interface. 

BRUVS) (Fig. 2) have several advantages over 

single-camera BRUVS. 

Stereo BRUVS facilitate non-extractive fish 

measurements of the lengths of fish over a broad 

range of sizes. Similarly, the distances between 

individuals can be measured as well as the speed 

at which they swim (distance between point A 

and B over a time period). Because it is possible 

to measure distance, one of the main advantages 

of stereo BRUVS is the ability to define a sampling area/volume and decide whether a fish is 

inside or outside of the unit. The inability of 

single BRUVS to measure distance means that 

changes in water visibility over time and location 

will greatly affect the area sampled and the ability 

to draw conclusions from spatial and temporal 

comparisons of data sets. 

Stereo-video Measurement Software 

We used a Vision Measurement System 

(VMS) (Shortis and Robson, 2004) purpose-built 

stereo photo comparator to analyze stereo-video 

imagery. Images from calibrated video cameras 

are loaded into the software either as single 

images or video streams (.avi). They are synchronized using flashing diodes, which are visible in 

the field of view. Measurements of the x,y,z 

location of a point are made by locating the 

cursor over the area of interest and clicking with 

a mouse (Fig. 3). 

The software is presently being further 

developed. Our ultimate aim is the real time 

automated recognition and measurement of the 

lengths and volumes of fish and other target 

organisms. We continue to make small incremental steps towards this goal that decrease process46

ing time, which can be lengthy, and a major 

limitation of the technology. 

Field Applications to Date 

There have been thorough tests of the accuracy, precision and calibration of the hand-held 

stereo-video system using plastic fish silhouettes 

(Harvey et al. 1996, 2002b) and on fast-swimming tuna in fish cages (Harvey et al. 2003). 

These have been followed by field tests in tropical and temperate habitats, including coral reefs, 

algal reefs, seagrass beds and soft substrata 

ranging in depth from 3 m through 110 m. Fish, 

sharks and rays from a variety of families have 

been successfully measured and counted. 

Citations 

Babcock R.C., S. Kelly, N. T. Shears, J. W. 

Walker, and T.J. Willis. 

1999. Changes in community structure in 

temperate marine reserves. Mar. Ecol. Progr. 

Ser. 189:125-134. 

Cappo, M., E. Harvey, H. Malcolm, and P. 

Speare. 

2003. Advantages and applications of novel 

“video-fishing” techniques to design and 

monitor Marine Protected Areas, p. 455-464. 

In Beumer, J.P, A. Grant, and D.C. Smith 

(eds.), Aquatic protected areas – What works 

best and how do we know? Proceedings of the 

World Congress on Aquatic Protected Areas. 

Cairns, Australia; August 2002. 

Cappo, M., P. Speare, and G. De’ath. 

2004. Comparison of baited remote underwater video stations (BRUVS) and prawn (shrimp) 

trawls for assessments of fish biodiversity 

in inter-reefal areas of the Great Barrier Reef 

Marine Park. J. Exp. Mar. Biol. Ecol. 302:123-

152. 

Denny, C.M., T. J. Willis, and R. C. Babcock. 

2004. Rapid recolonization of snapper 

(Pagrus auratus: Sparidae) within an offshore 

island marine reserve after implementation of no 

take status. Mar. Ecol. Progr. Ser. 272:183-190. 

Ellis, D. M., and E. E. DeMartini. 

1995. Evaluation of a video camera technique 

for indexing the abundances of juvenile pink 

snapper, Pristipomoides filamentous, and other 

Hawaiian insular shelf fishes. Fish. Bull., U.S. 93: 

67-77. 

Harvey, E. and Shortis, M. R. 

1996. A system for stereo-video measurement 

of sub-tidal organisms. Marine Technology 

Society Journal, 29(4):10-22. 

Harvey, E. S., D. Fletcher, and M. Shortis. 

2001a. A comparison of the precision and 

accuracy of estimates of reef-fish lengths made 

by divers and a stereo-video system. 

Fish. Bull., U.S. 99:63-71. 

Harvey, E. S., D. Fletcher, and M. Shortis. 

2001b. Improving the statistical power of 

visual length estimates of reef fish: A comparison 

of estimates determined visually by divers with 

estimates produced by a stereo-video system. 

Fish. Bull., U.S. 99(1):72-80. 

Harvey, E. S, D. Fletcher, and M. R. Shortis. 

2002a. Estimation of reef fish length by 

divers and by stereo-video. A first comparison of 

the accuracy and precision in the field on living 

fish under operational conditions. Fish. Res. 57/3: 

255-265. 

Harvey, E. S., M. R. Shortis, M. Stadler, and 

M. Cappo.

2002b. A comparison of the accuracy and 

precision of digital and analogue stereo-video 

systems. Mar. Tech. Soc. J. 36(2):38-49. 

47

Harvey, E. S., M. Cappo, M. Shortis, J. 

Buchannan, and S. Robson. 

2003. The use of an underwater stereo-video 

system for measuring the lengths of caged Southern Blue Fin Tuna. Fish. Res. 63 (3):315-326. 

Harvey, E. S, D. Fletcher, M. R. Shortis, and 

G. A. Kendrick. 

2004. A comparison of underwater visual 

distance estimates made by SCUBA divers and a 

stereo-video system: Implications for underwater 

visual census of reef fish abundance. Mar. 

Freshw. Res. 55: 573-580. 

Priede, I.G., P. M. Bagley, A. Smith, S. Creasey, 

and N. R.Merrett. 

1994. Scavenging deep demersal fishes of the 

Porcupine Seabight, north-east Atlantic: observations by baited camera, trap and trawl. J. Mar. 

Biol. Assoc. UK 74:481-498. 

Priede, I.G., N. R.Merrett. 

1996. Estimation of abundance of abyssal 

demersal fishes; a comparison of data from trawls 

and baited cameras. J. Fish. Biol. 49(Suppl. 

A):207-216. 

Shortis, M. R., and S. Robson. 

2004. VMS Reference and User Guide. 

Geometric Software P/L, 15 Maranoa Crescent, 

Coburg 3058 AUSTRALIA (http:// 

www.geomsoft.com.au). 

Willis, T.J., R.B. Millar, and R.C. Babcock. 

2000. Detection of spatial variability in 

relative density of fishes: comparison of visual 

census, angling, and baited underwater video. 

Mar. Ecol. Progr. Ser. 198:249-260. 

Willis, T.J., and R.C. Babcock. 

2000. A baited underwater video system for 

the determination of relative density of carnivorous reef fish. Mar. Freshw. Res. 51:755-763. 

Willis, T. J., R. B. Millar, and R. C. Babcock. 

2003. Protection of exploited fishes in temperate regions: high density and biomass of 

snapper Pagrus auratus (Sparidae) in northern 

New Zealand marine reserves. J. Appl. Ecol. 40: 

214-227. 

48

Video Mosaics

Yuri Rzhanov

Center for Coastal and Ocean Mapping

University of New Hampshire

24 Colovos Road

Durham, NH 03824

Email: yrzhanov@cisunix.unh.edu

Underwater imagery is collected at a short 

range due to limited visibility and strong attenuation of visible light, making it difficult to 

observe and evaluate features larger than those 

fitting in a single frame (including clusters of 

small features for density estimation). Relatively 

low accuracy of underwater navigation systems 

(> 10 cm) does not allow for utilizing the positioning information in assembling separate 

images in a mosaic because the mosaic typically 

has sub-centimeter or even sub-millimeter resolution. Video footage, however, is acquired at a 

temporal and spatial rate that guarantees high redundancy between consecutive frames. Pairwise 

registration of frames calculates the transformation relating those frames, and thus, recovery of 

camera motion in image space is possible with 

high accuracy. Cascading the transformations, 

video sequences can be assembled in images of 

a scene greatly exceeding the scene of any single 

frame (Fig. 1).

 Image redundancy – multiple coverage of the 

same area from different positions – facilitates 

detection of objects moving with respect to the 

steady background. These objects, depending on 

the objectives, can be either removed from the 

scene, or extracted and registered in a database 

for future processing (e.g., expert identification 

or pattern recognition).

 Requirements for collection of imagery suitable for creating mosaics are formulated. Camera motion models are presented in the order of 

increasing complexity: translational, rigid affine, 

perspective, and full bathymetric. Choice of 

model depends on actual camera motion, strength 

of 3D content of sea bottom, available computational resources, etc.

 Presence of laser caliper spots in the individual 

video frames helps to estimate relative distances 

and hence to find mapping between real and pixel 

spaces for both video frames. On the other hand, 

a set of laser spots is a strong, almost steady 

(within a frame) feature that may seriously hinder 

the registration process. Techniques for laser-spot 

detection and removal are presented. 

An examples of a mosaics is shown in Figure 

26 from the imagery acquired by digital still or 

video camera; hand-held, or mounted on a sled, 

towed body, AUV, or manned deep submersible 

vehicle. 

Figure 1. A video mosaic of a coral reef.

49
High Resolution Underwater 

Imaging and Image Processing for 

Identifying Essential Fish Habitat

Scott M. Gallager, Hanu Singh, Sanjay Tiwari, Jonathan Howland, Paul Rago, and William Overholtz

Woods Hole Oceanographic Institution

Woods Hole, MA 02543

Email: sgallager@whoi.edu 

and

Richard Taylor and Norman Vine

Northwest Atlantic Fishing Community

We currently use a towed digital habitat mapping camera system (HabCam, Fig. 1) developed 

with funding from the Northeast Consortium 

together with the SeaBED autonomous undersea vehicle (AUV;Fig. 2) to collect, process and 

classify high resolution digital imagery of fish 

populations and the seafloor. HabCam has the 

capability to collect accurately geo-referenced 

images while towing at 4 knots, providing a continuous stream of bottom images through a fiber 

optic cable to the surface. On deck, a real-time 

processor merges the images into a continuous 

ribbon followed by classification of habitat and 

biotic community. SeaBED can be deployed for 

up to 12 hours while optically and acoustically 

imaging the bottom, but the data must be downloaded and processed post facto (Fig. 29). 

We have been developing automated classification methods to allow the large volume of 

data to be sorted into more useful information. 

The associations between substrates and species 

in conjunction with other factors such as depth 

and current are then used to develop maps of 

habitat types at multiple scales. The final goal is 

to make the collected data readily available to all 

interested parties, including fishery managers, 

fishermen, marine researchers, and the public via 

the internet in an easily navigated and readily 

understood manner. 

There are five basic steps in processing images for characterizing habitat: 1. Image 

Acquisition, 2. Image Correction and EnhanceFigure 1. Habitat Mapping Camera System (HabCam) as 

configured during March 2003 cruise.

ment, 3. Target Segmentation, 4. Feature Extraction, and 5. Target Classification. 

Image acquisition of benthic habitat begins 

with balanced white light (for color imaging) 

illumination with sufficient intensity to achieve 

color saturation while minimizing illumination of particulates between the target plane and 

camera. For moving imaging platforms (1-4 

knots), short exposures (2-50 μsec) are critical to 

achieve images free from motion blur. MechaniFigure 2. SeaBED AUV during a deployment off Puerto Rico to 

map coral habitat.

50
cal and electronic shutters are usually not sufficiently fast to provide short exposures thereby 

requiring strobes or triggered LED array light 

sources. 

Today’s reasonably inexpensive CCDs and 

CMOS imaging chips can provide 2,000 × 2,000 

pixels with 12-bit resolution at 30 frames per 

second (fps). Considerably higher resolution 

can be obtained albeit at a slower frame rate, the 

tradeoff and limitation being bandwidth of the 

recording device. It is important to simplify the 

imaging geometry as much as possible. To this 

end, the camera placed on an orthogonal axis 

relative to the image plane optimizes the ability to correctly calibrate the imaging system and 

provide the uniform illumination. 

Image correction and enhancement involves 

balancing the light field to remove light gradients and color correction to account for greater 

attenuation of light at longer wavelengths. Both 

processes can be accomplished through various forms of homomorphic digital filtering and 

by making some assumptions or measurements 

about the spectral characteristics of the water. 

Target segmentation is perhaps the most critical and difficult process when studying benthic 

habitat. Typically, the complex background is 

very mottled and the organisms are by design, 

cryptic in nature. We are exploring new methods 

of segmenting benthic images into different hoFigure 3. Benthic images taken on Georges Bank (courtesy P.

Valentine).

mogeneous textures and identifying boundaries 

that separate the different regions. Our method of 

“texture segmentation” uses wavelet coefficients 

of Gabor wavelets to define features of an image. 

The wavelet coefficients provide a joint time-frequency characterization of the image. The basic 

idea behind Gabor wavelets is to decompose 

images into multiple-oriented spatial frequency 

channels. The channel envelopes (amplitude and 

phase) are then used to form the feature maps. 

We also define color features that are constructed 

from the color distribution angles of an image. 

Images are segmented automatically using Gabor 

wavelets and texture energy gradients. 

Finally, we define an average measure 

(composed of all features calculated at all orientations) that is rotation invariant. The rotationinvariance is necessary because a homogeneous 

texture should be recognizable as such when 

viewed from any orientation. For example, the 

spatial frequency of an image of small gravel 

would be higher than that for an area of cobble, 

the smaller particle sizes having more edges. 

Areas are differentiated further where there is 

partial gravel or cobble and mostly sand or mud. 

Orientation-invariance is necessary for targets 

such as flounders, so that they are recognized 

without regard to the direction they are pointing 

when encountered. In order to perform segmentation, we next define an energy function which 

is based on the gradient (composed of the two 

partial derivatives) in feature space at each point 

of the image. Depending on the level of contrast, 

lighting and content of a large benthic region of 

interest, a threshold value of this energy function 

is chosen, and areas of the image with energy 

value larger than the threshold are deemed to be 

the boundaries separating regions of different 

homogeneous textures. 

Feature extraction is actually performed in 

wavelet space using the Gabor coefficients 

calculated during the segmentation process. 

Color angles and morphological information 

(size, shape, etc.) are also part of the feature 

51
Figure 4. Image ribbon taken by SeaBed AUV on Stellwagen Bank.

vector for each image to be classified. Finally, to 

classify the different homogeneous textures, we 

use classifiers called Support Vector Machines 

(SVMs). SVMs have the advantage that they are 

capable of learning in high dimensional feature 

spaces (which ours tend to be) with a small 

training set. They accomplish this by simultaneously minimizing a bound on the empirical error 

and the complexity of the classifier. Given a 

pattern space of inputs, SVMs operate by finding hypersurfaces in the space that attempt to 

split the different patterns from each other. The 

SVM algorithm formulates the training problem 

as one that finds, among all possible separating 

hypersurfaces, ones that maximize the distances 

between the closest elements of each pair of 

adjacent patterns (Fig. 3). 

When an image ribbon is created from many 

sub-images, we can begin to see large scale 

textures that are not readily identifiable in individual sub-images. Areas of the composite 

image abundant in one kind of “texture element” 

(whether it is a inanimate background object or 

an organism) will present a different large-scale 

texture pattern than another part of the image 

abundant in another texture element. Thus, mud, 

sand, small gravel, shell aggregations, reefs, and 

aggregations of cobble/boulder, scallop, or sand 

dollar, all present different large scale homogeneous texture patterns (Fig. 4). 

Our current benthic classification scheme 

includes the following: 

• mud/sand without emergent biological 

structure.

• mud/sand with emergent biological structure. 

• small gravel (< 2 cm) without emergent/ 

attached biological structure.

• small gravel (< 2 cm) with emergent/attached 

biological structure. 

• shell aggregations and/or reefs w/out 

emergent/attached biological structure.

• shell aggregations and/or reefs with 

emergent/attached biological structure.

• cobble/boulder without emergent/attached 

biological structure. 

• cobble/boulder with emergent/attached 

biological structure.

While realizing that substrate is a continuum, 

we find that there are qualitative differences 

between habitats of mud and sand and the species that live there (Fig. 5). Accordingly we 

seek to differentiate these bottom types and the 

associated biota. The categories listed here are 

segmented using the approach described above 

and displayed by pseudo-coloring the original 

mosaic as a function of texture type. Associations with specific targets (e.g., larval and juvenile fish, echinoderms, hydrozoans) and texture 

category are made through discriminate analysis. 

52
Inclusion of diverse habitats in the analysis allow 

for more robust training of the SVMs, providing 

information about the greatest number of environments immediately useful to fishery managers 

and for future study by benthic habitat researchers. 

The techniques described here may be used 

in a variety of habitats both benthic and pelagic, 

in stereo imaging systems, or wherever difficult 

background lighting situations necessitate the 

need for advanced image processing. 

Figure 5. Transect data from the western edge of Georges Bank 

extracted from images taken by HabCam. The substrate is composed of shell fragments, sand, and gravel. The blue line represents abundance of living sea scallops and the yellow line is dead 

(upside down) scallop shell. The transect at top is about 5 km in 

53
Archiving, Annotating and


Accessing Video as Data


Judith Connor 

Monterey Bay Aquarium Research Institute 

7700 Sandholdt Road 

Moss Landing, CA 95039 

Email: conn@mbari.org 

Scientifically useful, high-quality video data 

can be challenging to analyze and archive for use 

in ocean science. Over the past 16 years, the 

Monterey Bay Aquarium Research Institute 

(MBARI) has processed over 15,000 videotapes 

as a record of remotely operated vehicle (ROV) 

dives. The ROVs have high-resolution video 

cameras and the images are recorded on digital 

videotapes and archived as a centralized institutional resource. 

To provide access to the images and data, 

MBARI has developed a set of three software 

applications (with knowledge base, annotation 

and query components) for annotation and 

access. The knowledge base, a hierarchical list of 

over 3,500 biological, geological and technical 

terms, is the foundation of the system. 

The annotation software references the 

knowledge base, providing consistent spelling 

and information about objects seen on the video. 

Columns at the top of the annotation graphical 

user interface (GUI) (Fig. 1) show timecode, 

observations, and associations. 

Physical data relating to the selected row is 

available on the right side of the screen. The GUI 

has quick buttons (below the columns) for special 

functions such as samples taken, population 

number, or close-up image, as well as video tape 

Figure 1. Graphical user interface with the video archiving software. 

54 
deck controls. The horizontal list of Sebastes 

species at the bottom of the GUI functions as 

quick buttons that can easily be changed for an 

individual user’s preferences. Annotation can be 

done in real time on the ship or later in the 

laboratory. The system supports frame capture of 

still images off the video stream to outline the 

highlights of each dive. The software can be used 

for everything from simple annotations to outlining the general fauna in an area, to very detailed 

documentation of each organism, geological 

features, and other habitat characters. 

The query component has a graphical user 

interface that allows users to extract data from 

the database to identify the location of video 

sequences and show the distribution of species or 

other objects from the database, frame grab 

images and physical data collected concurrent 

with the video. Complex queries can be made by 

constraining temporal, spatial, or physical parameters (e.g., season, location, or depth) from a 

pull-down menu on the GUI. 

The software components were written in the 

Java programming language to run on multiple 

platforms and maintain compatibility between 

shipboard and office environments. This should 

maximize utility of the software for future external users who adopt the system because they can 

add the appropriate species, geological features 

and equipment seen in their own regions. Castor, 

an open-source, data-binding framework for 

Java, is used in the annotation and knowledge 

base components to perform object-to-relational 

mapping. Data used in the MBARI Video Annotation and Reference System (VARS) are stored 

in Microsoft SQL Server databases. 

We expect to disseminate the full software 

system royalty-free to the research community in 

2005 to help meet the challenges inherent in 

archiving video data. For more information or to 

express interest in testing the program, contact 

MBARI. 

55 
Remote Sensing Using Laser 

Projection Photogrammetry 

for Underwater Surveys

Thomas H. Jagielo,

Washington Dept. Fish and Wildlife

600 Capitol Way N

Olympia, WA 98501

Email: jagiethj@dfw.wa.gov

Washington Department of Fish and Wildlife 

researchers have combined the Laser/Video 

Photogrammetric System with precision navigation to provide an efficient tool for producing 

quantitative benthic survey data. In addition to 

the roll/pitch motion reference sensor, CCD video camera and three microlasers utilized in the 

original system, a Doppler velocity log (DVL), 

ring laser gyro (RLG), ultra-short baseline sonar 

(USBL) and Integrated Positioning System (IPS) 

software were added to provide more precise 

navigation. This precision allows for geo-referencing, and hence mosaicking of user-specified 

sized areas within an image along a transect survey. Two additional lasers were also added to test 

for improvement of scale measurements. Custom 

software is used to automatically process video 

data at user-selected distance intervals. The software locates the reference lasers in an image and 

optical triangulation is used to compute range to 

a bottom plane in the field-of-view. 

Using this information and measurements 

recorded from the motion sensor, the spatially 

variant magnification is determined over the 

entire field-of-view using a simple algorithm. As 

a result, a variety of parameters are estimated 

using image-processing techniques including: 

perspective overlays, range to a point or location, scale in any region of the image, and area 

measurements. This paper briefly reviews the 

original system, describes the enhancements, and 

summarizes data from two cruises. In the most 

recent cruise during October 2003 the system 

was deployed in the Channel Islands National 

Marine Sanctuary located off the coast of southern California. 

Figure 1. A view of the camera system attached to the Delta

minisub.

Mounted onboard the submersible Delta 

(Fig. 1), the system collected numerous hours 

of video and navigation data from survey transects (Fig. 2). Data were collected from both 

randomly sampled sites and selected areas where 

groundtruth targets were placed. 

Methods to improve these results are also 

discussed. Deployment of a third generation 

system is expected in 2005 onboard an AUV. 

We expect the final system will prove valuable 

Figure 2. A view of the bottom with the quadrate superimposed.

Note the square meter target on the bottom and the three reference laser points (red dots).

56
for estimating the abundance of commercially 

and recreationally exploited groundfish species 

within a study area using stratified random video 

transect methods. 

This unobtrusive, direct-observation technique affords a means to estimate the density of 

certain benthic fish species in high relief areas 

that are not accessible to routine trawl survey 

methods. Differences in fish densities between 

trawlable and untrawlable habitats have clear 

implications for estimation of abundance for a 

number of fish species including rockfish. 

57
Development of a Diver-held 

Stereo Video Camera 

Chris Boynton and Ken Voss 

University of Miami 

Department of Physics 

P.O. Box 248046 

Coral Gables, FL 33124 

Email: chris@physics.miami.edu 

Email: voss@miami.rsmas.miami.edu 

After having reviewed the existing literature, 

we determined that no underwater stereo video 

system with sufficient resolution for quantitative 

analysis was commercially available. To develop 

such a camera, our idea was to perform experiments that would help us determine the required 

system parameters, so simultaneous with this, we 

investigated which still cameras would be suitable 

for the purpose. These experiments required us 

to develop calibration software and data handling 

software. Our camera requirements were as 

follows: 

• Ability to be computer controlled, or at least 

externally triggered, to allow simultaneous 

images to be obtained. Computer control 

would be useful to allow the images to be 

logged as pairs. 

• Firewire interface to allow images with 

sufficient spatial resolution to be downloaded 

quickly to a computer for processing. 

• Sufficient pixel resolution. 

In our search, we found an existing system 

that could be adapted to our use and provide a 

great leap forward. This system was a stereo 

video system built by Videre for use in robotics 

(Fig. 1). The system featured dual electronic 

cameras that are read out simultaneously over a 

firewire interface into a computer. The software 

was already developed for calibration of the 

system, and data reduction of the images into 

x,y,z arrays. In addition, software source code 

Figure 1. The diver-held stereo video camera showing the display 

screen and the control keypad. 

was provided for developing applications in 

Windows and Linux. With this system, which 

could be run either as still or video camera with a 

rate less than 

1/30 second, we could achieve a result which we 

did not originally feel was reasonable in this first 

stage; that is, quantitative digital stereo video. 

We took Videre’s system and used it as the 

basis for our design. The camera, digital compass 

and pitch/roll sensor, computer with hard drive 

and 7” display, and a small numeric keyboard are 

all housed in one container approximately 12” × 

8” × 6”. The power for the system comes from 

an external battery (24V, 1.5 –2A). 

The display on the back of the camera system 

(Fig. 34) has information on internal temperature, 

exposure setting, gain, number of frames taken, 

and current operational status of the system. 

Images from each camera are shown in the 

display along with a real-time histogram of the 

images to help in setting exposure. Almost out of 

the figure on the right is the external system 

battery. There is a SEACON 1508 (8 conductor) 

connector on the right side of the case which 

allows another computer to be connected via 

Ethernet (RJ45), to allow data transfer without 

opening the case (We have made an external 

58

network patch cable that goes between the 

SEACON connector and a standard RJ45 

Ethernet network connector). We have been 

extensively testing this system in a pool to work 

out operational problems before going into the 

field. During this testing we have found various 

hardware and software problems that have been 

corrected. We also did an “ergonomic” test in the 

pool, using the system while swimming with full 

dive gear, and this test went well. Calibration 

data was taken during these pool tests, and 

sample images with plastic fish were recorded 

just to test the data collection operations. 

At this point we are ready to do a field test. 

We are currently in the process of arranging a 

test in a nearby location. The main purpose will 

be to simply operate the system in the open ocean 

environment and collect images. These images 

will be reduced manually to test the operation of 

the system qualitatively. In addition we will be 

putting samples with known characteristics into 

the camera’s field of view so we can get quantitative information on operation of the system. 

These first field tests are within the scope of our 

original proposal, and we expect to have these 

completed by the end of October. 

We hope to soon have a system which can be 

calibrated in an absolute manner and provide x, y, 

z coordinates as a combination of arrays. From 

these coordinates, one could easily find distances 

between different points in the array. However, 

since the system has the capability of obtaining 

images in rapid succession, it is obvious that 

some automated data reduction capability must 

be developed. An obvious application would be 

in providing three-dimensional images of specific 

areas in a coral habitat. Simple views would be 

quite easy to obtain, but mosaics of images that 

provide three-dimensional images would be 

somewhat harder to get. 

Citations 

Harvey, E., and M. Shortis. 

1996. A system for stereo-video measurement 

of subtidal organisms, Mar. Tech. Soc. J. 10-22. 

Van Rooij, J,. and J. Videler. 

1996. A simple field method for stereo-photographic length measurements of free swimming 

fish: merits and constraints, J. Exp. Mar. Biol. 

Ecol.15: 237 – 249. 

Woods, A., T. Docherty, and R. Koch. 

1994. Experiences of using stereoscopic video 

with anunderwater remotely operated vehicle. 

Underwater Intervention 1994, San Diego, 

California, February 1994, p.34-38. 

59

A Review of the Use of 

Underwater Video in Australia 

Euan Harvey 

School of Plant Biology 

University of Western Australia 

Crawley, Western Australia, Australia 

Email: euanh@cyllene.uwa.edu.au 

Mike Cappo 

Australian Institute of Marine Science 

Townsville, Queensland, Australia 

Email: mcappo@aims.gov.au 

In September 2000, the Fisheries Research 

and Development Corporation (FRDC) hosted a 

3-day workshop on Rottnest Island, Western 

Australia on the use of underwater video in 

Australian Fisheries (Harvey and Cappo 2001). 

The rationale for the workshop was based around 

the fact that Fisheries Research and Development 

reviews in Australia have identified the need for 

non-destructive, fishery-independent stock 

assessment techniques for both target and nontarget species, and for assessing the benthic 

habitats that many species occupy. There was 

also the need to develop and validate costeffective techniques that facilitate the comparison 

of data collected over a range of temporal and 

spatial scales for benthos, reef and inter-reef 

fishes. To allow robust spatial and temporal 

comparisons of data, techniques need to minimize many of the biases inherent in fisheries and 

benthic habitat assessments. There was also a 

need to standardize the methods and techniques 

that are being used by marine researchers around 

Australia in both shallow subtidal and deepwater 

environments. 

The workshop was attended by 42 participants from research organizations throughout 

Australia including various State fishery agencies, 

the Australian Institute of Marine Science, 

Commonwealth Scientific and Industrial Research Organization (CSIRO), South Australian 

Research and Development Institute and academic institutions. The workshop also benefited 

from contributions by international scientists 

(from the UK, NZ and USA). The aim of the 

workshop was to share the experience and 

expertise of participants who have been using 

video as a tool for sensing the size and abundance of target and non-target fauna in Australian 

fisheries. Workshop proceedings can be viewed 

online at http://www.aims.gov.au/pages/research/ 

video-sensing/report/report_text.html. 

The specific objectives of the workshop were 

as follows: 

1.	 Report on the present national state of 

knowledge regarding the use and applications 

of videography and stereo-videography for 

censusing fish populations and benthic 

habitats; 

2.	 Report on: a) the limitations of stereophotogrammetry and videography from the 

perspective of hardware, software and the 

behavior of fishes and the complexities of 

benthic habitats; b) the opportunities and 

advantages of stereo-photogrammetry and 

videography from the perspective of develop 

ing new techniques and methods for use in 

fisheries stock assessment; 

3.	 Demonstrate the use of stereo-video 

software; 

4.	 Outline further software developments, 

requirements and time lines for the develop 

ment of a fully automated system for process 

ing video records and gain suggestions on 

changes to software architecture and research 

priorities; 

60

5.	 Share the cumulative knowledge of Austra 

lian based research groups experienced in the 

use of underwater video as a sampling tool; 

and 

6.	 Develop multi-disciplinary, multi-agency 

collaborative research projects to refine, 

apply and evaluate the techniques in critical 

fisheries. 

Around Australia, and indeed the world, 

underwater video was and still is seen as a tool 

that can satisfy many of the needs described 

above in both shallow and deepwater research. 

Consequently, underwater video is being quickly 

adopted for the non-destructive sampling of a 

very broad range of organisms. Unfortunately, 

many researchers do not know how to maximize 

the information and data resulting from their 

recordings. Furthermore, while it is very easy to 

record a lot of information, the processing, 

interpretation, image storage and retrieval can be 

laborious, resulting in a bottleneck in data analysis. At that time there was a need to make researchers aware of the possibilities and limitations of underwater videography as a tool and to 

determine the key concerns and research needs 

and wants. This was achieved by involving key 

individuals from State fisheries agencies and 

academic institutions in the workshop. 

The outcomes from the workshop included a 

research and development plan and a set of 

recommendations about research needs and 

priorities. Although these recommendations were 

accepted and supported by the Fisheries Research 

and Development Corporation, no formal outcomes have resulted yet at a national level. 

However, at the level of individual researchers 

and between organizations, there has been 

greater communication resulting in incremental 

development of software, hardware and sampling 

and interpretation processes. In many respects 

this has resulted in informal standardized 

operating protocols and the sharing of equipment 

and knowledge between groups. 

In Australia the historical use of underwater 

video can be divided into four main research 

categories: habitat mapping and monitoring, 

interactions between fishing gear and animals, 

aquaculture and fish ecology, and biology. Since 

the national workshop, and publications by Willis 

et al. (2000), a number of research groups have 

begun using video techniques to assess the 

performance of Marine Protect Areas in terms of 

fish numbers and sizes (see Cappo et al. 2003 for 

review). 

Many research groups in Australia are involved in habitat mapping programs where 

towed or drop video is used as a technique for 

validating habitat classifications from acoustic 

techniques such as sidescan, single beam and 

multi-beam sonars. Notable examples are the 

SEAMAP program (www.utas.edu.au/tafi/ 

seamap), the Great Barrier Reef Seabed 

Biodiversity Project (www.reef.crc.org.au/ 

resprogram/programC/seabed/index.htm) and 

studies of the fish and fish habitats in the Recherche Archipelago (www.marine.uwa.edu.au/ 

recherche). These projects aim to map the distribution, abundance and biomass of seabed communities, determine the richness and uniqueness 

of seabed communities and identify rare and/or 

threatened species, habitats and/or communities. 

Some projects, most notably the work by the 

CSIRO Division of Marine Research, include 

real-time data acquisition on the characteristics of 

seafloor habitats from video footage, as well as 

detailed post-processing of tapes 

(www.marine.csiro.au/). There are also coral reef 

monitoring programs involving fixed video 

transects (www.aims.gov.au/pages/research/reefmonitoring/ltm/mon-sop7/sop7-2001a.html). 

Underwater video has been used in Australia 

to directly observe and assess interactions between fishing gear, target fauna and non-target 

plants andanimals. A major program to understand the effects of trawling on benthic communities is still underway in tropical prawn (shrimp) 

fisheries (see Pitcher et al. 2000). Video imagery 

obtained from within traps has been used to 

61

minimize interactions between the Australian sea 

lion and the western rock lobster (Panulirus 

cygnus) fishery (pers. comm. R. Campbell, 

Department of Fisheries, Western Australia). 

Barotrauma in trapped deep-water snappers has 

been assessed using video techniques 

(www.aims.gov.au/pages/research/video-sensing/ 

papers/lloyd/lloyd_abs.html), and more recently 

in a national strategy determining the fate of linecaught fish after release (http://www.infofish.net/releasefish/). 

Underwater video has much potential for 

assessing food consumption, growth and survival 

in aquaculture, but surprisingly few applications 

in Australian industry 

The benthos beneath fish cages has been 

monitored using video (Crawford et al. 2001) 

and underwater stereo-video is being used to 

measure the lengths and maximum body depths 

of caged tuna (Harvey et al. 2003). 

Within the areas of Australian fisheries 

research, some emphasis has been placed on the 

development of non-destructive, fishery independent sampling techniques. These include underwater visual census with video cameras, comparisons of baited remote underwater video 

(BRUVS) sampling with traditional trawls 

(Cappo et al. 2004), assessing the fate of discarded bycatch (Hill and Wassenberg, 2000), and 

using towed video for assessing the structure 

of spawning aggregations of finfish and the 

relative abundance and distribution of scallops. 

Whilst towed video footage can be converted 

readily to density estimates of target fauna, the 

baited, stationary video approach has yielded 

only estimates of relative density. More research 

is needed to model the sampling area influenced 

by bait plumes to enable direct estimates of 

density. 

Applications of underwater video in Australia 

are growing in number, variety and sophistication 

– partly because of the national workshop funded

by the Fisheries Research and Development 

Corporation. It is hoped that this growth will be 

matched by national investment in hardware and 

software solutions to overcome the “bottlenecks” 

remaining in image processing and tape analysis. 

Citations 

Cappo, M., E. Harvey, H. Malcolm, and 

P. Speare.

2003. Potential of video techniques to monitor diversity, abundance and size of fish in studies 

of Marine Protected Areas. p. 455-464. In 

Beumer, J.P., A. Grant, and D.C. Smith (eds.), 

Aquatic Protected Areas - what works best and 

how do we know?”. World Congress on Aquatic 

Protected Areas proceedings, Cairns, Australia, 

August 2002. 

Cappo, M., P. Speare, and G. D’eath. 

2004. Comparison of baited remote underwater video stations (BRUVS) and prawn (shrimp) 

trawls for assessments of fish biodiversity in 

inter-reefal areas of the Great Barrier Reef 

Marine Park. J. Exp. Mar. Biol. Ecol. 

302(2):123-152. 

Crawford, C. M., I. M. Mitchell, and 

C. K. A. Macleod. 

2001. Video assessment of environmental 

impacts of salmon farming. ICES J. Mar. Sci. 58: 

445-452. 

Harvey, E. S., and M. Cappo. 

2001. Direct sensing of the size frequency 

and abundance of target and non-target fauna in 

Australian Fisheries. 4-7 September 2000, 

Rottnest Island, Western Australia. Fisheries 

Research and Development Corporation. 187 p. 

Harvey, E. S., M. Cappo, M. Shortis, 

J. Buchannan, and S. Robson.

2003. The use of an underwater stereo-video 

system for measuring the lengths of caged southern blue fin tuna. Fish. Res. 63 (3):315-326. 

62

Hill, B. J., and T. J. Wassenberg. 

2000. The probable fate of discards from 

prawn trawlers fishing near coral reefs; A study in 

the northern Great Barrier Reef, Australia. Fish. 

Res. 48:277-86. 

Pitcher, C. R., I. R. Poiner, B. J. Hill, and 

C. Y. Burridge. 

2000. Implications of the effects of trawling 

on sessile megazoobenthos on a tropical shelf in 

northeastern Australia. ICES J. Mar. Sci. 57(5): 

1359-1368. 

Willis, T .J., R. B. Millar, and R. C. Babcock. 

2000. Detection of spatial variability in 

relative density of fishes: comparison of visual 

census, angling and baited underwater video. 

Mar. Ecol. Progr. Ser. 198:249-60. 

63 
Recommendations 

1.	 Formation of an Underwater 

Video Working Group 

Nearly all participants of the workshop were 

fishery biologists who were users rather than 

developers of video technology and, consequently, felt that the exchange of ideas that 

occurred at the workshop provided them with 

ideas to extend their research capabilities or tools 

to increase their video processing efficiency. The 

participants suggested two ways of maintaining 

this exchange: 1) creation of a working group 

with annual meetings and 2) development of a 

NMFS underwater video technology web page. 

Other technologies for sampling fish or their 

habitat, such as acoustics, trawls and other 

fishing gears, have working groups with periodic 

meetings (i.e., the Fishing Technology and Fish 

Behavior Working Group and the Fisheries 

Acoustics Science and Technology Working 

Group associated with the International Council 

for the Exploration of the Sea ) where fishery 

biologists can discuss sampling issues and 

emerging video or related technology with others 

using the same technologies. However, nothing 

like this is available for the scientific application 

of underwater video. The participants therefore 

recommended the formation of the Underwater 

Video Working Group, which would be officially 

sanctioned by NMFS and meet annually to 

consider special topics (e.g., the use of stereo 

video), new technologies and updates of ongoing 

projects. In addition, the working group could 

facilitate collaborative efforts, perhaps the sharing of specialized video equipment, and promote 

funding opportunities (e.g., NOAA Ocean Exploration and National Undersea Research Programs) for the development of new hardware for 

collecting underwater video (i.e. ultra low light 

cameras or stereo cameras) or software (i.e., 

event counters, measurement tools, pattern 

recognition or video databases) that would either 

increase the capabilities of video collection or 

reduce the time required to translate the video 

into readily usable data. In essence, this working 

group would function much like the existing 

NMFS survey standardization working groups 

(i.e., Bottom Trawl Survey Working Group and 

Acoustic Survey Working Group). 

In addition, the workshop participants felt 

that an important addition to a working group 

would be the development of a web page that 

would provide: 1) updates for NMFS programs 

utilizing underwater video, 2) links to suppliers 

of video equipment and processing software, and 

3) a bulletin board capability that would allow 

researchers to quickly query others about their 

specific needs. 

2.	 Develop Technologies for 

Making Video Processing Easier 

The process of analyzing video involves tasks 

such as counting and measuring fish or other 

objects, measuring strip or quadrate area, and 

entering geo- or time- referenced measurements 

into a database. Although there is some commercial software that partially automates this process, workshop participants felt that many improvements to these products are needed to meet 

their specific requirements. In order of importance, the most needed software is 1) event 

logging software that controls the primary 

recording medium (i.e., tape or DVD); 2) video 

database software that allows retrieval of video 

clips using selection criteria such as depth, 

position, or time of day, or, at least, provides 

some sort of library facility for the original 

recordings; and 3) quadrat measurement software 

that can correct for distance from the bottom and 

camera attitude. Workshop participants felt that 

the use of research funds for either of the following two approaches would be fruitful: 1) hire a 

consultant to review the video processing tech64
nology used by other governmental agencies 

(NASA or Department of Defense), the medical 

profession, or industry to determine if the appropriate technologies have been developed but not 

discovered by NMFS fishery biologists, and 2) 

contract for the development of custom software 

that would meet the needs of most of the NMFS 

programs. 

3.	 Technologies that Extend the 

Operating Capabilities of Video or the 

Information Content of the Video 

Several emerging technologies for the collection of video or video-like data were considered 

during the workshop. Of these, two were of 

particular interest. First,in situations, particularly 

for stock assessment, when the use of lights 

would alter fish behavior, technologies such as 

ultra low-light cameras, infrared illuminators or 

DIDSON acoustic cameras may provide an 

acceptable alternative to using visible light. 

Second, in situations when fish length measurements are required, stereo video may be better 

than the 2- and 3-laser reference systems now in 

use. Although some of the technologies considered are commercially available, some are either 

very expensive or require custom development 

and are therefore beyond the reach of small 

research programs. Workshop participants 

therefore felt that there was a need for either 

increased collaboration between NMFS programs 

or actual joint ownership of hardware (e.g., 

similar to the purchase of the autonomous underwater vehicle by the NMFS Advanced Technology Working Group) to allow them to more 

easily examine the utility of different technologies. 

65 

List of Participants

Chris Boynton

University of Miami

Department of Physics 

P.O. Box 248046 

Coral Gables, FL 33124 

chris@physics.miami.edu

Ph. (305) 284-2323

Fx. (305) 284-4222

Judith Connor

Monterey Bay Aquarium 

Research Institute

7700 Sandholdt Road

Moss Landing, CA 95039

conn@mbari.org

Ph. (831) 775-1728 

Fx. (831) 775-1620

Eric Eisenhardt

Washington Department of Fish 

and Wildlife

600 Capitol Way N

Olympia, WA 98501

eisenepe@dfw.wa.gov

Ph. (360) 586-6129 x 208

Scott Gallagher

Woods Hole Oceanographic Institution 

Woods Hole, MA 02543 

sgallager@whoi.edu

Ph. (508) 289-2783

Fx. (508) 457-2158

Christopher T. Gledhill 

Southeast Fisheries Science Center

Mississippi Laboratories

3209 Frederic Street

Pascagoula, MS 39567

Christopher.T.Gledhill@noaa.gov

Ph. (228) 762-4591 X284

Fx. (228) 769-9200

Chris Grandin

Department of Fisheries and Oceans 

Pacific Biological Station 

3190 Hammond Bay Road 

Nanaimo, B.C., V9T 6N7, Canada

Grandin@pac.dfo-mpo.gc.ca

Ph. (250) 756-7211 

Fx. (250) 756-7053 

Euan Harvey

School of Plant Biology 

University of Western Australia

35 Stirling Highway

Crawley, WA, 6009, Australia

euanh@cyllene.uwa.edu.au

Ph. +61 64882416

Fx. +61 64881001

Rod Hobbs

Alaska Fisheries Science Center

7600 Sand Point Way NE

Seattle, WA 98115

Rod.Hobbs@noaa.gov

Ph. (206) 526-6278

Fx. (206) 526-6615

Tom Jagielo

Washington Department of Fish 

and Wildlife

600 Capitol Way N

Olympia, WA 98501

jagiethj@dfw.wa.gov

Ph. (360) 902-2837

Jean Kenyon

Pacific Islands Fisheries Science Center

1125B Ala Moana Blvd.

Honolulu, HI 96814

Jean.Kenyon@noaa.gov

Ph. (808) 592-7019

Fx. (808) 592-8300

Tom Laidig

Southwest Fisheries Science Center

Santa Cruz Laboratory

110 Shaffer Road

Santa Cruz, CA 95060

Tom.Laidig@ noaa.gov

Ph. (831) 420-3942

Fx. (831) 420-3977

Jeff Lasage

Stennis Space Center

Bay St. Louis, MS 39529

Ph. (228) 688-3650

Fx. (228) 688-1151

67
Bob McConnaughey 

Alaska Fisheries Science Center

7600 Sand Point Way NE 

Seattle, WA 98115

Bob.Mcconnaughey@noaa.gov

Ph. (206) 526-4150

Fx. (206) 526-6723 

Scott McEntire

Alaska Fisheries Science Center

7600 Sand Point Way NE 

Seattle, WA 98115

Scott.McEntire@noaa.gov

Ph. (206) 526-4472,

Fx. (206) 526-6723

Daniel Merritt 

Pacific Islands Fisheries Science Center

1125B Ala Moana Blvd.

Honolulu, HI 96814

Daniel.Merritt@noaa.gov

Ph. (808) 592-7032

Fx. (808) 592-8300

William Michaels

Northeast Fisheries Science Center

166 Water Street,

Woods Hole, MA 02543

William.Michaels@noaa.gov

Ph. (508) 495-2259

Fx. (508) 495-2258

Michael Parke

Pacific Islands Fisheries Science Center

1125B Ala Moana Blvd.

Honolulu, HI 96814

Michael.Parke@noaa.gov

Ph. (808) 592-7017

Fx. (808) 592-7013

Frank Parrish

Pacific Islands Fisheries Science Center 

2570 Dole St

Honolulu, HI 96822

Frank.Parrish@noaa.gov

Ph. (808) 983-5391

Fx. (808) 983-2902

Chris Rooper 

Alaska Fisheries Science Center

7600 Sand Point Way NE 

 Seattle, WA 98115

Chris.Rooper@noaa.gov

Ph. (206) 526-4689

Fx. (206) 526-6723 

Craig Rose

Alaska Fisheries Science Center

 7600 Sand Point Way NE

Seattle, WA 98115

Craig.Rose@noaa.gov

Ph. (206) 526-4128

Fx. (206) 526-6723

Gregg Rosenkranz

Alaska Department of Fish and Game 

211 Mission Road

Kodiak, AK 99615 gregg_rosenkranz@fishgame.

state.ak.us

Ph. (907) 486-1858

Fx. (907) 486-1824

Yuri Rzhanov

Center for Coastal and Ocean Mapping 

University of New Hampshire

24 Colovos Road

Durham, NH 03824

yrzhanov@cisunix.unh.edu

Ph. (603) 862-0075 

Fx. (603) 862-0839

Pete Sheridan

Southeast Fisheries Science Laboratory

Panama City Laboratory

3500 Delwood Beach Rd.

Panama City, FL 32408

pete.sheridan@noaa.gov 

Ph. (850) 234-6541 x203 

Fx. (850) 235-3559

Christy Sims

Alaska Fisheries Science Center

National Marine Mammal Laboratory

7600 Sandpoint Way NE 

Seattle, WA 98115

Christy.Sims@noaa.gov

Ph. (206) 526-6274

Fx. (206) 526-6615

68
David Somerton Brian Zgliczynski

Alaska Fisheries Science Center Pacific Islands Fisheries Science Center

7600 Sand Point Way NE 1125B Ala Moana Blvd.

Seattle, WA 98115 Honolulu, HI 96814

David.Somerton@noaa.gov Brian.Zgliczynski@noaa.gov

Ph. (206) 526-4116 Ph. (808) 592-2816

Fx. (206) 526-6723 Fx. (808) 592-7013

Bradley G Stevens Mark Zimmermann

Alaska Fisheries Science Center Alaska Fisheries Science Center

Kodiak Laboratory 7600 Sand Point Way NE

301 Research Court Seattle, WA 98115

Kodiak,AK 99615 Mark.Zimmermann@noaa.gov

Bradley.G.Stevens@noaa.gov Ph. (206) 526-4119

Ph. (907) 481-1726 Fx. (206) 526-6723

Fx. (907) 481-1703

Allan Stoner

Alaska Fisheries Science Center

2030 S. Marine Science Drive

Newport, OR 97365

Al.Stoner@noaa.gov

Ph. (541) 867-0165

Fx. (541) 867-0136

Waldo Wakefield,

Northwest Fisheries Science Center

2030 S. Marine Science Drive

Newport, OR 97365

Waldo.Wakefield@noaa.gov

Ph. (541) 867-0542

Fx. (541) 876-0525

Mary Yoklavich

Southwest Fisheries Science Center

Santa Cruz Laboratory

110 Shaffer Road

Santa Cruz, CA 95060

Mary.Yoklavich@noaa.gov

Ph. (831) 420-3940

Fx. (831) 420-3977

Harold Zenger

Alaska Fisheries Science Center

7600 Sand Point Way NE

Seattle, WA 98115

Harold.Zenger@noaa.gov 

Ph. (206) 526-4158,

Fx. (206) 526-6723

69