Marine

Burrow Counting with Dean Anthony Notaro on the Nephrops norvegicus Underwater TV Survey


Dean joined the survey with Coaching By way of Analysis Surveys (TTRS), a collaboration between  the Marine Institute and Strategic Marine Alliance for Analysis and Coaching (SMART) for scholar trainee-ships on the Nationwide Analysis Vessels, Celtic Explorer and Celtic Voyager.

CV19002 Labadie Financial institution UWTV Survey of the Nephrops norvegicus 8-day analysis cruise on the RV Celtic Voyager from the twenty first to twenty eighth of August by Dean Anthony Notaro

What its all about: Time stamped picture of Nephrops norvegicus on the UWTV survey.
Hey, my identify is Dean Anthony Notaro and I just lately accomplished a MSc in Marine Biology at College School Cork (UCC). I undertook my undergraduate diploma in Science, a Double Honours program combining Biology and Laptop Science, at Maynooth College (NUIM). Upon commencement of my undergraduate diploma, I labored in varied software program improvement roles in each Dublin and Montréal, Canada, earlier than returning to UCC to review Marine Biology.

Since altering careers into the marine sciences, I’ve been on the lookout for alternatives to extend my organic sampling and surveying expertise. Due to SMART Sea College and the Marine Institute (MI), I’ve been invited to take part, as one of many scientific crew members on the Nephrops norvegicus Beneath Water TV (UWTV) Survey, as a part of the Coaching By way of Analysis Surveys (TTRS) scheme. The Nephrops survey, will present me with a chance to realize offshore scientific expertise, that may complement my research and beforehand gained expertise.

For this weblog, I wish to offer you an perception into the daily duties and my total expertise as one of many six scientists on board. Firstly, I wish to introduce the crew and description the goals of the survey and the tools that we use all through.

Scientific Staff

The crew consists of six scientists: Dr. Jonathan White (Chief Scientist), Mikel Aristegui (MI), Marcin Blaszkowski (MI), Dermot Charge (MI), John Energy (MI) and Dean Anthony Notaro (UCC). Groups are break up up into three groups of two, with two four-hour surveying shifts scheduled per day.

Survey Goals

Nephrop burrows should be appropriately recognized by skilled scientists and precisely counted from UWTV footage to assist calculate the abundance of Nephrops in designated “practical items”, the seafloor grounds which Nephrops inhabit. Knowledge gathered from this survey might be utilized in assessing the standing of Nephrops shares and advising on their future administration.

Due to this fact goals of this survey are:


  1. Get hold of 2019 information of Nephrops burrow densities from roughly 100 stations within the Labadie Financial institution Nephrops fishing grounds. This information will then be in comparison with information collected from earlier survey years.
  2. Acquire environmental information utilizing the the sledge mounted Conductivity, Temperature and Depth probe and a deck deployed Day Seize for sediment evaluation.
  3. Collect ancillary data (presence/absence) on different macro benthic organisms and demersal fish species from the UWTV Footage.

Survey Gear

The UWTV sledge used for this survey (Determine 1 and a pair of) homes a forward-facing HD digital camera mounted at a 70 diploma angle to the seafloor, lasers (2 x 3 laser beams) for measuring the sector of view, lamps for illuminating the seafloor and a CTD probe to log the conductivity (salinity), temperature and depth on the survey stations. A restoration line can be hooked up to retrieve the sledge if it turns into indifferent or misplaced.  Extra payload features a multibeam echosounder to scan the seafloor for boulders and rocks and even wrecks that would harm the sled and its excessive tech payload.
Determine 1. UWTV sled on deck of the RV Celtic Voyager.
Determine 2. UWTV sled being deployed over the  stern of the RV Celtic Voyager.

Counting Burrows with R

A software program interface for counting burrows is used to evaluation and annotate the recorded video. Developed in “R” by Mikel, who was good sufficient to provide us an summary of its improvement and display the software program’s performance, it permits reviewers to label the Nephrops burrows.  Whereas taking part in again recorded video the pc cursor is positioned over a burrow and with a easy mouse-click a circle is added across the burrow and the rely routinely incremented by 1, sending the knowledge to a CSV file which is later loaded into the survey database. The GPS coordinates of video observe are additionally recorded and might be mapped in GIS. The interface additionally permits the person to report ancillary data, as an example the presence/absence of sea pens, squat lobsters (Determine 3) and fish (Determine 4).  The interface automates the method used beforehand, simplifying a number of work for the scientists reviewing the footage. Initially, scientists would use “clickers” to rely the burrows and write down counts utilizing pencil and paper, with information subsequently typed into the database manually.
Determine 3. UWTV footage capturing Squat Lobster (Galathea squamifera) on the seafloor.

Determine 4. UWTV footage capturing lesser-spotted Dogfish (Scyliorhinus canicular).

Day 1

I boarded the RV Celtic Voyager from Horgan’s Quay within the Port of Cork (Determine 5) round 11 am on the twentieth of August. On boarding I used to be greeted by a P&O crew member, who kindly confirmed us to our cabins and took our related documentation and signed us onboard as seafarers. The primary day consisted of normal introductions with the survey crew and a number of the vessel crew and familiarisation of the vessel. Figures 6 and seven present the dry lab the place a lot of the management work and communications for the UWTV survey is carried out.
Determine 5. RV Celtic Voyager docked at Horgan’s Quay, Port of Cork.
Determine 6. Dry lab searching the starboard home windows.
Determine 7. Port aspect of Dry lab.
Checking out and putting in tools took up the primary quarter of the day. After setup, I had the chance to look at the skilled scientists perform reference counts of Nephrops burrows.  Reference counts of beforehand recorded footage are made by every scientist earlier than the Nephrops surveys, to validate burrow counts of survey footage and be certain that each member of the survey crew counting the burrows, is doing so persistently.

For the second half of the primary day, depth and high quality testing of the brand new digital camera tools was carried out. For this, we sailed out from Cork Harbour in the direction of the Labadie Nephrops grounds and selected places the place depth was round 60m-70m.  This took us three makes an attempt, as the primary two places we stopped at contained a rocky seafloor and have been unsuitable to get the UWTV sledge secure on the seafloor. The third location was chosen in an space beforehand surveyed and identified to comprise a extra stage terrain extra appropriate for the UWTV sledge. On efficiently getting the sledge secure on the seafloor, a 20-minute tow was carried out. At round 11pm, I acquired my first glimpse of Nephrops on the seafloor and what can be forward for the rest of the survey (Determine 9).

Determine 8.  Nephrops norvegicus rising from a burrow
Determine 9. Nephrops norvegicus on the Labadie Financial institution (not Rio de Janeiro)

Day 2

Day 2 began off a bit slower, we remained docked in port resulting from poor climate circumstances at sea. Extra reference counts have been carried out by lead scientists and I took the chance to learn up and discuss to different crew members on Nephrops burrow identification. After some run-through of Nephrops burrow identification, I practiced burrow relying on the reference footage myself. I additionally spent a while wanting by way of the 20-minute tow photos from our check runs from the day before today and was actually impressed by a number of the photos captured and marine fauna we noticed (Determine 10 and 11).
Determine 10. Picture of Lemon Sole (Microstomus kitt) from UWTV footage.
Determine 11. Positively digital camera shy and presumably an extended tough Dab (Hippoglossoides platessoides) from UWTV footage.

Day 3

We have been woken up by the ship’s engines at round 7am for an early begin and eight hour voyage to our first station. All crew members have been current for the primary few stations, to familiarise ourselves with protocols and the duties required for every survey station throughout our shifts. The primary stations labored effectively with no points getting the sledge all the way down to the seafloor and all of the cameras and sensors returning information.  The seafloor was fairly stage with clear visibility. On profitable completion of the primary shift, to our delight Jonathan shocked us with ice-cream, which was very a lot appreciated. After ice-cream, I took the chance to view some extra footage from the tows on the first few stations (Determine 13).
Determine 12. UWTV nonetheless of the underneath appreciated Gray Gurnard (Eutrigla gurnardus).

Day 4

7 am bathe and breakfast after an eventful night time’s sleep when the rolling of the ship appeared to have picked up a gear. After breakfast, myself and Jonathan headed as much as the dry lab to alleviate the 4am  to 8am shift (Marcin and Dermot). We acquired the replace of occasions with the principle level being that two stations needed to be skipped due to fishing exercise within the space. From the beginning of our shift  there was an extended steam to the primary station and a chance to step exterior and think about a number of the animals dwelling in and across the sea floor (Determine 13).

Determine 13. Widespread Dolphin (Delphinus delphis) travelling alongside the RV Celtic Voyager.

Day 5

The survey is in full swing and we have managed to cowl greater than half the variety of deliberate stations, making good progress. The climate circumstances, to date have been glorious, permitting us to finish, on common one station per hour. For every station it could possibly take roughly half-hour to get the digital camera sledge down onto the seafloor, stabilise it and report footage for 10 minutes earlier than retrieval. Steaming time varies between stations, however on common has been round half-hour for many.

We accomplished our first station by 8:20 am, having began simply earlier than 8 am. After station one, we got here into some technical points with the UWTV sledge, however this was fastened promptly, and we have been quickly off once more, to proceed recording (Determine 14). For many of at this time the crew continued to work by way of burrow counting (Determine 15 and 16) and recording UWTV footage (Determine 17 and 18).

Determine 14. Jonathan with P&O crew  bother capturing the sled after station 1.
Determine 15. Skilled counter Marcin scrutinising UWTV footage.
Determine 16.  Ballyshannon Sham, Dermot Charge checking the stock of accomplished stations.
Determine 17. Mikel conserving it actual, and John driving the sled on the graveyard shift.
Determine 18. Jonathan and Dean on the 8 am – 12 pm shift.



Determine 19. Widespread skate (Dipturus batis) from UWTV footage.
Determine 20. A fish, what species we’re undecided, occupying a burrow entrance.  Could possibly be the consierge?
Determine 21. Octopus swimming alongside the ocean ground.



Determine 22. Dawn over the Labadie Financial institution

Day 6

Day 6, and what a gorgeous morning to get up to. Solar is shining and air is crisp. Right now, as we transfer from station to station, we are going to take some seize samples (Determine 23).  Seize samples are packets of sediment lifted from the ocean ground for onshore evaluation after the survey is accomplished.
Determine 23. Ship’s crew retrieving the Shipek sediment seize.
This afternoon, I’m spending extra time reviewing UWTV footage, with a deal with honing my burrow identification expertise. With the assistance of the professional scientists, I’ve managed to place collectively a montage of some Nephrops burrow sorts (Figures 24, 25, 26).  Nephrops burrow identification is kind of a talent, and difficult for the novice, because it takes a while to get accustomed to totally different burrow sorts and to appropriately determine and distinguish Nephrops burrows from these of different burrow forming fauna.
Nephrops begin growing their burrows roughly 6 – 8 weeks after hatching. They decide on the seafloor, in places the place sediments are beneficial, having the correct quantity of silt and clay. The principle figuring out function of the grownup Nephrops burrow, is the distinct crescent formed entrance (Determine 24). Different burrowing species in the identical setting have usually round entrances, from burrowing vertically. When viewing the footage, I discovered this to be the tough half. It will possibly take a while to resolve if all of the defining options are current, to say that it’s really a Nephrops burrow that you’re taking a look at.
Over time the Nephrops’ preliminary burrow turns into prolonged, with the addition of a  second entrance mirroring the primary one. Relying on the sediment sort wherein the burrows are excavated, these might be discovered a number of centimetres to virtually a meter other than one another. This technique known as a linear burrow system (Determine 25).
Nephrops burrow programs can develop additional by including one other tunnel to the unique linear system. The brand new tunnel added to the system is mostly constructed at 90 levels to the first tunnel and types a “T”- formed system (Determine 26).
Determine 24. Nephrops burrow from UWTV footage, crescent formed entrance.

Determine 25. Nephrops linear burrow system from UWTV footage. Apex of every entrance (black line) pointing in the direction of one another.

Determine 26. Nephrops “T” – formed burrow system from UWTV footage.

Given sufficient time burrow programs can change into much more advanced.  For advanced “T” formed programs,  new asymmetrically developed entrances start to look.   Determine 28 exhibits one of many advanced “T” – formed burrow system we noticed on this survey.
Determine 27. Nephrops complexed “T” – formed burrow system from UWTV footage.

Day 7

At this stage, we’re approaching the ultimate few stations of the Labadie Financial institution Nephrops norvegicus grounds and anticipate to succeed in our ultimate station within the early hours of Tuesday morning. 
Now that we’re nearing the tip of the survey, our work turns more and more in the direction of reviewing the UWTV footage and counting the burrows.  As careworn earlier within the weblog, Nephrops burrows should be confidently recognized and counted precisely for strong estimates of abundance. 
To do that we observe high quality management and assurance procedures on how and what to rely, and the minimal variety of counters required. Certainly one of these is that scientists scrutinise the footage in isolation and independently of one another. After counts have been accomplished, there are extra impartial counts to validate the outcomes and to resolve any variations that will come up between totally different counters. 
Figuring out which stations should be recounted is finished statistically utilizing Lin’s Concordance Correlation.  For correct counting and producing the strong estimates of abundance required by stakeholders, scientists agree on a statistically decided threshold of distinction between their rely outcomes.
Nephrops norvegicus in burrow.

Nephrops norvegicus on the seafloor.
In between steaming from station to station and burrow counting, the crew attempt to get exterior for some recent air and solar. Right now, we have been fortunate, and had the possibility to watch a pod of Dolphins bow driving alongside the RV Celtic Voyager. On this survey, I’ve noticed dolphins swim alongside the vessel most afternoons and evenings, and it may be fairly hypnotising to look at them, and their behaviours. In addition to dolphins, there have been alternatives to watch different marine megafauna, with sea birds, particularly Northern Gannets, Fulmars, Storm Petrels and Manx Shearwaters, following us for a lot of the journey.
Marcin, John and Dean out on deck.
John and Dermot out on deck (after which there was two)
Marcin has all of it to himself
Dean on lookout
For these, Widespread Dolphins, sneakily bow-riding!

Day 8

That is the final day of our nice journey in the middle of which we now have captured over 16 hours of HD video footage of roughly 25,000 metres (13.5 nm) of seabed, representing an space of roughly 10,014 sq. kilometers. Depths have ranged from 70 to 140 meters and we now have seen and archived some fantastic footage from the 100 stations from the Labadie Financial institution Nephrops grounds within the Celtic sea. It has been immense from begin to end!
Míle Buíochos
I wish to thank the Marine Institute and SMART Sea College for offering me with the chance to participate within the UWTV survey. An enormous due to Dr. Jonathan White and John Boyd (SMART) for accepting my software and welcoming me to affix the survey.
Thanks to all of the scientific crew, for sharing their data and enthusiastically answering any questions I had alongside the best way. There are lots of extra causes to thank the crew and I’ve been fortunate to have the chance to work alongside them, and I’ve gained an immense quantity of knowledge and data on this analysis journey.
Lastly, thanks to the ship’s crew who assisted the scientific crew all through, with crusing, sediment grabs, deploying and retrieving UWTV, aiding with any technical points that occurred, in addition to feeding us. Thanks very a lot.
The sheer quantity of labor goes in to planning and organising UWTV surveys, how they work, why they’re so essential and the worth of Nephrops norvegicus to the Irish Fishing Business are simply a number of the many issues I’ve discovered on this survey.  That is with out mentioning the incredible alternative to study a bunch of marine biology and technical expertise from a crew who’re on the absolute prime of their recreation.  It has been an exquisite expertise, and I hope to have extra comparable alternatives sooner or later.
Míle buíchos to everybody who made this such a formative expertise for me,
Dean Anthony Notaro
Conger eel (Conger conger)inspecting the grounds, in all probability not probably the most welcome sight for absolutely anything else on or within the seafloor!
That appears like a boar fish, Capros aper out for a glide
Bantry Bay with Hungry Hill.  We have been something however, thanks Prepare dinner!

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