CRUISE REPORT: AR28
(Updated FEB 2017)









Highlights


                              Cruise Summary Information

               Section Designation  AR28 (DY0052)
Expedition designation (ExpoCodes)  74EQ20160607
                  Chief Scientists  Stefan François Gary / SAMS, PS
                             Dates  2016 JUN 07 - 2016 JUN 24 
                              Ship  RRS Discovery
                     Ports of call  Inchgreen, Scotland - Greenock., Scotland

                                              63°19.11' N
             Geographic Boundaries  6°7.97' W              20°13.01' W
                                              56°40.02' N

                          Stations  89
      Floats and drifters deployed  3 floats deployed
    Moorings deployed or recovered  0

                                 Contact Information:
                                 Stefan Francois Gary
                       Scottish Association for Marine Science
                              Oban, Argyll PA37 1QA, UK
                     +44 (0) 1631 559419 • stefan.gary@sams.ac.uk





















                                     RRS Discovery

                                     Cruise DY052

                                  Glasgow to Glasgow

                                 Extended Ellett Line

                            7th June 2016 - 24th June 2016

                        S. F. Gary and the DY052 Science Team





























                                         SAMS

          Scottish Association for Marine Science Scottish Marine Institute
                           Oban, Argyll, PA37 1QA, Scotland

                              Tel: [+44] (0)1631 559000
                              Fax: [+44] (0)1631 559001
                                    www.sams.ac.uk






Summary

This report describes the events that occurred during DY052, a cruise on the RRS 
Discovery that sailed Glasgow to Glasgow from June 7 to June 24, 2016.

The main objective of the cruise was to occupy the annually repeated hydrographic 
section of the Extended Ellett Line (EEL). The EEL runs from the Sound of Mull via 
Rockall to Iceland. The EEL is is funded by NERC under the National Capability 
Program.

More information on the history and findings of the EEL can be found at 
http://prj.noc.ac.uk/ExtendedEllettLine/ . This was a successful cruise with all 
objectives fulfilled and minimal downtime. Calibrated, processed data from DY052 
will be banked with the British Oceanographic Data Centre (BODC, 
http://www.bodc.ac.uk).

The main objectives for DY052 were:

1)  Hydrographic stations
    71 planned CTD stations + 1 test station. We achieved 89 CTD stations. 

    Speciic measurements:
    • CTD + other electronic instruments + LADCP
    • Bottle salinity
    • Bottle oxygen
    • Bottle nutrients (Nitrate+Nitrite, Phosphate, Silicate)
    • Bottle carbon (alkilinity, DIC)
    • Bottle trace metals
    • Bottle density

2)  Underway  measurements

    • towed hydrophone for any transits greater than 30 minutes
    • meterological and oceanographic underway measurements
    • sail by the locations of the OSNAP moorings in Rockall Trough

3)  Epibenthic sled tows at “Station M” (4 tows)

4)  Argo float deployments (3 floats)












DY052 – Extended Ellett Line 2016
Cruise Report

 1  Personnel
    1.1  Scientific personnel                                                       6
    1.2  Ship’s personnel                                                           6

 2  Cruise narrative                                                                7

 3  Cruise track and station map                                                    9

 4  NMF-SS CTD sensors                                                             12
    4.1  CTD system configurations                                                 12

    4.2  Technical detail report                                                   14
    4.3  Configuration files                                                       14
    4.4  CTD sensor geometry                                                       19

 5  CTD data processing                                                            21
    5.1  Sea-Bird processing                                                       21
    5.2  MSTAR processing                                                          23
    5.3  Oxygen hysteresis correction                                              24
    5.4  Oxygen sample files and oxygen calibration                                25
    5.5  SBE35 temperature sensor data processing                                  27
    5.6  Temperature sensor performance                                            28
    5.7  Conductivity calibration                                                  29
    5.8  Cast anomalies                                                            31

 6  Vessel mounted ADCP                                                            33
    6.1  Synchronization                                                           33
    6.2  Data summary                                                              33
    6.3  Processing                                                                35

 7  Lowered ADCP data processing                                                   40
    7.1  Introduction and data processing                                          40
    7.2  Preliminary quality checks                                                42
    7.3  Initial results                                                           43

 8  Underway data processing                                                       44
    8.1  Daily processing                                                          44
    8.2  Navigation                                                                47
    8.3  Bathymetry                                                                47
    8.4  Surface atmosphere and ocean observations                                 47

 9  Salinity samples & analysis                                                    51
    9.1   Bottle sampling                                                          51
    9.2   Autosal analysis                                                         52
    9.3   MSTAR processing                                                         53

10  Dissolved inorganic nutrients                                                  54
    10.1  Introduction                                                             54
    10.2  Method                                                                   54
    10.3  Data quality assessment                                                  55

11  Determination of dissolved oxygen concentrations by Winkler titration          56
    11.1  Introduction                                                             56
    11.2  Method                                                                   56
    11.3  Summary of results                                                       57

12  Carbon samples                                                                 57

13  Trace metal samples                                                            58

14  Direct density samples                                                         59

15  Epibenthic sled                                                                60
    15.1  Introduction                                                             60
    15.2  Methods                                                                  60
    15.3  Initial results                                                          61
    15.4  Conclusion                                                               62

16  Sampling microplastics in the deep sea                                         62
    16.1  Microplastics in deep sea fauna                                          63
    16.2  Microplastics in deep sea water                                          63

17  Hydrophone and fish finder                                                     64
    17.1  EK60                                                                     64
    17.2  Hydrophone                                                               66

18  Argo float deployment                                                          70

19  Seaglider recovery                                                             71

20  Acknowledgements                                                               72

Appendix A) Ship instrumentation overview                                          73

Appendix B) BODC ship-fitted instrument logging                                    82

Appendix C) Surfmet sensor information                                             87

Appendix D) Scientific systems technician report                                   90






1  PERSONNEL

1.1  Scientific personnel

Stefan François Gary            SAMS, PS
Richard Edward Abell            SAMS
Timothy Brand                   SAMS
James Anothony Cameron Coogan   SAMS
Elizabeth Anne Comer            University of Southampton 
Winifred Martha Courtene-Jones  SAMS
Estelle Dumont                  SAMS
Clare Beth Embling              Plymouth University
Stacey Louise Felgate           SAMS
Martin Stephen Foley            University of Glasgow
Emily Jane Hill                 SAMS
David John Hughes               SAMS
Robert King                     UK MetOice
Ashlie Jane McIvor              SAMS
Emma Slater                     BODC
Jonathan Paul Tinker            UK MetOice
Leah Elizabeth Trigg            Plymouth University
Colin John Hutton               NMF
Jack McNeill                    NMF
Jonathan Barry Short            NMF



1.2  Ship’s personnel

Joanna Louise Cox              Master
Michael Patrick Hood           C/O 
Declan Daniel Anderson Morrow  2/O 
Colin James Leggett            3/O
Andrew Nicholas Lewtas         C/Eng
Geraldine Anne O'Sullivan      2/E
Ian Stuart Meldrum Collin      3/E
Edin Silajdzic                 3/E
Felix Robert Arthur Brooks     ETO
Graham Bullimore               PCO
Samuel Nicholaidis             Cadet
Calum Nathan Deacy             Cadet
Stephen John Smith             CPOS
Thomas Gregory Lewis           CPOD
Robert George Spencer          POD
William Mclennan               SG1A
Raoul John Laferty             SG1A
Craig James Lapsley            SG1A
John Michael Hopley            SG1A
Emlyn Gordon Williams          ERPO
Mark James Ashield             H/Chef
Amy Kerry Whalen               Chef
Jefrey Alan Orsborn            Stwd
Kevin John Mason               A/Stwd




2  CRUISE NARRATIVE
   (All times on ship's time, UK BST)

June 07, J159      08:15 muster stations and boat drill. 09:30 pilot arrived and 
underway shortly thereafter leaving Inchgreen, near Glasgow. Safety briefing for 
science party at 17:30 previous evening. A beautiful day, not as much sun as the 
last two astonishingly beautiful weeks but still very nice. Weather forecast for the 
EEL region looks generally good giving us confidence that we can proceed to the sick 
glider's position in the Iceland Basin for recovery. Pumped sea surface underway 
system switched on at 15:30. Ongoing tests with the VMADCP and EK60 configuration.

June 08, J160      08:30 meeting between ship's team leaders and science team 
leaders. The first CTD test cast was at 09:30 and all went smoothly. After CTD 
recovery, there was a hydrophone toolbox talk for relevant parties. Then, the 
hydrophone was deployed for first time at 11:15.  EA640 and EM122 switched off 
because they interfere with the hydrophone.  Echosounders will be turned on when 
needed for navigation and approaching stations for CTD operations, but of otherwise.

June 09, J161      Fire drill and science party muster at 15:30. Then ire hose 
training for science party. Hydrophone first recovery was after the drill in 
preparation for glider recovery. Glider recovered at about 19:00 then hydrophone 
redeployed and ship underway to first station near Iceland.

June 10, J162      Echosounders back on at noon and hydrophone recovery at 13:00 in 
preparation for first CTD cast on the Extended Ellett Line, CTD 002. Minor technical 
issues with bottle firing, but otherwise all well.  CTD 003 through 005 proceeded 
without any glitches. Hyrdophone not in the water due to short steaming time between 
stations.

June 11, J163      Steady progress for CTD 006 through 011.  Hydrophone deployed 5 
times in between stations as steaming time is now more than 1 hour.

June 12, J164      Steady progress for CTD 012 through 016. Argo float deployed 
immediately after CTD 013. Hydrophone deployed 6 times. Slightly rougher seas than 
previous days, but not enough to interrupt work.

June 13, J165      Steady progress for CTD 017 through 022. Two Argo floats deployed 
directly after CTD 017. The carousel failed during CTD 018 so no bottles were ffired 
on this cast. As this station is not one of the core Extended Ellett Line stations, 
the electronic instruments recorded good data, and it was uncertain how long it 
would take to replace the carousel, this station was not repeated and we progressed 
to the next station. CTD 019, with a new carousel, went without incident and all the 
bottles closed as commanded.

June 14, J166      Completed CTD 023 through 031 and 6 hydrophone tows. Now working 
in over the Rockall Hatton Basin. Cloudy.

June 15, J167      Completed CTD 032 through 040 and 8 hydrophone tows. Still cloudy 
for most of the day but a break in the clouds was well-timed for nice views of 
Rockall.


June 16, J168      During the night, entered the Rockall Trough and made slight 
deviations to sail over OSNAP moorings WB1 and WB2 in between CTD 040, 041, and 042. 
Worked steadily through CTD 049 and 3 hydrophone tows. Sailed over Anton Dohrn 
Seamount.

June 17, J169      Early morning hydrophone tow and CTD 050. Starting at 8AM, back-
to- back epibenthic sled tows at Station M. Both tows were successful. While the 
sled team rested at night, CTD 051 and 052 were done along with 3 hydrophone tows in 
transit.

June 18, J170      Second day of epibenthic sled tows.  Two successful back-to-back 
tows. RRS James Cook came by to say hello. Extra CTD cast, 053, with all bottles 
ffired at the bottom for microplastics sampling at Station M. Then, proceeded to 
next station on EEL with hydrophone in tow. Learned that an OSNAP glider needed 
assistance but it is 3 days’ steam and expected heavy seas in the area until 
Wednesday (J174).  As we are due in port on J177 morning, we cannot recover it.

June 19, J171      Working up the continental slope and across the Scottish Shelf 
for CTD 054 though 068. Tentative plans were made to use the remaining time of DY052 
to go back to the shelf break and make a high-resolution electronics-only section of 
the European Slope Current at the Ellett Line as well as traverse the Rockall Trough 
with hydrophone in tow and extra stations to the north of Anton Dohrn Seamount. 
Weather forecasts suggest that we will not be able to work last year's extra 
stations at 58N on the Rockall Hatton Plateau but the Rockall Trough area should be 
workable. Stations north of Anton Dohrn would help verify the latitudinal extent of 
the Rockall Trough hydrographic observations. Of course, the mention of extra 
stations caused the pumps to not turn on during the start of CTD 065. The cast was 
aborted, the SBE 9+ was replaced, and CTD 065-068 were completed.

June 20, J172      Finished the Extended Ellett Line with CTD 069 through 073 in the 
morning. Steam back out to the open ocean towing the hydrophone over moderate swell 
for electronics-only casts over the shelf break. Completed CTD 074 through 076 at 
the 200 m, 300 m, and 400 m isobaths despite the challenging conditions due to the 
swell.

June 21, J173      Continued with electronics-only CTD casts every 100 m of water 
depth for CTD 077 through 084. Then towed the hydrophone and operated the EK60 and 
ADCPs in the Rockall Trough, sailing over Anton Dohrn Seamount and then north, 
nearly to Rosemary Bank. Swell calmed down substantially over the course of the day.

June 22, J174      Worked extra CTD stations 085 to 087 north of Anton Dohrn 
Seamount, towing the hydrophone in between stations.

June23, J175       Completed the last of the CTD stations, 088 and 089, and steamed 
back to Glasgow with hydrophone in tow. Hydrophone recovered just before reaching 
the continental shelf. Cruise summary meeting at 1400 to discuss the Post Cruise 
Assessment. TechSAS, non-toxic, and all other instruments turned of at 21:00.

June24, J176       Continued compiling the cruise report, running the last samples, 
and cleaning labs. Docked at 16:30 at Ocean Terminal, Greenock.



3  CRUISE TRACK AND STATION MAP

Figure 3.1: DY052 track shaded by Julian day. Black stars indicate the start of each 
            day. Bathymetry is contoured at 500 m intervals at depths greater than 
            500 m in black and at 100 m intervals at depths shallower than 500 m in 
            gray.

Figure 3.2: Map of all 89 CTD casts on DY052 shaded by station number. Every 10th 
            cast is indicated by a thin plus sign. Bathymetry is the same as in 
            Figure 3.1.


Table 3.1: CTD station list

The first column is the CTD station number, followed by the date, time at bottom, 
latitude, longitude and water depth. Water depth, cdep, was computed as described at 
the end of Section 5.2. The max. depth of the CTD and altimeter reading at the 
bottom of the casts, maxd and alt, respectively, are compared to cdep to determine 
the residual, res. Columns 14-20 list the max. wire out, max. pressure, number of 
depths, and number of sampled depths. Comments indicate the historical Extended 
Ellett Line station names for each station, if available. The E: series of stations 
are electronics-only casts at the shelf break on the EEL and the X series are 
stations north of Anton Dohrn.

stn  yy/mo/dd  hhmm  dg   min   lat  dg   min   lon  cdep  maxd  alt  res  wire  pres  nd  sal  oxy  nut  car  Cmnts
---  --------  ----  --  -----  ---  --  -----  ---  ----  ----  ---  ---  ----  ----  --  ---  ---  ---  ---  -----
 1   16/06/08   858  56  53.52   N    9  46.18   W   1912   501  -9  -999   500   507   9   9    9    0    1   Test
 2   16/06/10  1338  63  19.11   N   20  13.01   W    133   124   9    -1   120   125   8   7    7    7    0   IB23S
 3   16/06/10  1606  63  12.93   N   20   4.14   W    674   664  11     2   662   672  12  12   12   13    9   IB22S
 4   16/06/10  1844  63   7.98   N   19  55      W   1041  1032  10     1  1029  1045  15  15   15   15    0   IB21S
 5   16/06/10  2157  63   1.6    N   19  44.37   W   1304  1295   2    -6  1300  1312  17  17   17   17    0
 6   16/06/11   112  62  55.05   N   19  33.2    W   1398  1390  11     2  1385  1408  16  16   16   16    0   IB20S
 7   16/06/11   457  62  40.09   N   19  40.1    W   1681  1672   6    -3  1668  1695  17  17   17   17    0   IB19S
 8   16/06/11   922  62  20.09   N   19  50.12   W   1799  1791   5    -3  1787  1816  19  19   19   19    0   IB18S
 9   16/06/11  1403  62   0.02   N   20   0.13   W   1801  1793   6    -2  1790  1819  18  18   18   18    0   IB17
10   16/06/11  1805  61  45.04   N   20   0.2    W   1791  1783  10     2  1780  1808  18  18   17   18    9   IB16A
11   16/06/11  2218  61  30.05   N   20   0.09   W   2212  2204  10     2  2206  2237  20  20   20   20    0   IB16
12   16/06/12   230  61  15.07   N   20   0.17   W   2369  2362   8     1  2358  2398  20  20   19   20    0   IB15
13   16/06/12   656  61   0.03   N   20   0.11   W   2397  2389   8     1  2382  2426  20  20   20   20    0   IB14
14   16/06/12  1124  60  45.01   N   19  59.99   W   2362  2354   9     2  2350  2390  21  21   20   21    0   IB13A
15   16/06/12  1557  60  30.05   N   20   0.09   W   2526  2519  11     3  2512  2558  21  21   21   21    0   IB13
16   16/06/12  2031  60  15.02   N   20   0.05   W   2641  2634  10     3  2627  2676  21  21   21   20    0   IB12A
17   16/06/13   104  60   0.01   N   20   0.15   W   2718  2711   9     2  2705  2755  22  22   22   21    0   IB12
18   16/06/13   554  59  48.53   N   19  30.04   W   2703  2696   9     2  2689  2740   0   0    0    0    0   IB11A
19   16/06/13  1110  59  40.02   N   19   7.02   W   2671  2664   7     0  2658  2707  21  21   21   22    0   IB11
20   16/06/13  1533  59  31.96   N   18  46.11   W   2715  2709  10     3  2702  2752  22  22   21   22    0
21   16/06/13  1917  59  24.03   N   18  25.05   W   2396  2389  11     4  2390  2426  21  21   19   20    0   IB10
22   16/06/13  2222  59  20      N   18  14.02   W   1844  1837   8     1  1835  1862  18  18   17   18    6   IB09
23   16/06/14   145  59  12.05   N   17  53.05   W   1528  1520  10     2  1515  1540  17  17   16   17    0   IB08
24   16/06/14   416  59   7.01   N   17  40.05   W    980   971  10     1   968   982  15  15   15   16    0   IB07
25   16/06/14   729  58  56.97   N   17  11.11   W    890   882  10     1   880   892  13  13   13   13    0   IB06
26   16/06/14   948  58  52.99   N   17   0.15   W   1155  1147   6    -3  1145  1161  16  16   16   16    0   IB05
27   16/06/14  1243  58  45.41   N   16  45.12   W   1161  1152   8     0  1152  1166  16  16   15   16    0
28   16/06/14  1534  58  39.62   N   16  30.79   W   1204  1195   9     0  1193  1210  15  15   16   15    0   IB04A
29   16/06/14  1827  58  33.93   N   16  15.09   W   1217  1209   9     1  1208  1224  16  16   16   16    0
30   16/06/14  2107  58  29.98   N   16   0.17   W   1186  1178  10     2  1177  1192  16  16   15   16    6   IB04
31   16/06/15    11  58  20.51   N   15  39.96   W   1156  1148   8     0  1145  1162  15  15   14   15    0
32   16/06/15   256  58  14.97   N   15  20.02   W    659   650  10     0   648   657  12  12   12   12    0   IB03
33   16/06/15   542  58   4.29   N   14  57.68   W    558   549  10     1   547   555  11  11   11   11    0
34   16/06/15   827  57  56.94   N   14  34.95   W    442   433   9     0   430   437  10  10   10   10    0   IB02
35   16/06/15  1113  57  48.03   N   14  15.04   W    229   219  10     0   215   221   9   9    8    9    0
36   16/06/15  1341  57  40.05   N   13  54.16   W    150   140   9    -1   137   142   7   7    7    7    0   IB01
37   16/06/15  1601  57  34.96   N   13  38.05   W    114   104  10     0   101   105   6   5    6    5    0   A
38   16/06/15  1756  57  34      N   13  19.99   W    179   169  10     0   166   171   8   8    8    8    0   B
39   16/06/15  2001  57  32.99   N   13   0.02   W    295   285  10     1   281   288   9   9    9    9    0   C
40   16/06/15  2149  57  32.51   N   12  52.1    W   1085  1077   9     1  1075  1090  15  15   15   15    0   D
41   16/06/16    46  57  31.88   N   12  38.13   W   1636  1628  11     3  1624  1650  18  18   18   18    0   E
42   16/06/16   416  57  30.48   N   12  15.18   W   1799  1792   8     1  1789  1816  18  18   18   18   10   F
43   16/06/16   802  57  29.49   N   11  51.08   W   1788  1781   9     2  1780  1805  18  19   19   19    0   G
44   16/06/16  1135  57  28.94   N   11  32.06   W   2011  2004  10     3  2001  2033  19  20   20   20    0   H
45   16/06/16  1421  57  28      N   11  19.07   W    751   742   9     0   741   751  13  14   14   14    0   I
46   16/06/16  1643  57  26.95   N   11   4.99   W    588   579  10     1   576   585  11  11   11   11    0   J
47   16/06/16  1842  57  23.97   N   10  52      W    786   777  10     1   776   786  13  13   13   13    0   K
48   16/06/16  2059  57  22      N   10  40.06   W   2104  2097  10     3  2096  2127  20  19   19   18    0   L
49   16/06/17    16  57  17.94   N   10  23.16   W   2205  2198  10     3  2195  2231  19  19   19   19    0   M
50   16/06/17   341  57  13.98   N   10   3.21   W   2099  2092  10     3  2093  2123  20  20   20   20    0   N
51   16/06/17  2351  57   5.99   N    9  25.05   W   1417  1409  10     2  1406  1427  16  16   16   16    0   P
52   16/06/18   243  57   8.94   N    9  41.9    W   1923  1916   8     1  1913  1942  18  18   18   18   10   O
53   16/06/18  1945  57  14.75   N   10  21.1    W   2234  2227  10     3  2224  2260   1   0    0    0    0   M
54   16/06/19   107  57   4.54   N    9  19.09   W    780   771  11     2   770   780  13  13   13   13    0   Q1
55   16/06/19   238  57   3.05   N    9  13.03   W    315   305  10     1   301   308   9   9    9    9    0   Q
56   16/06/19   406  57   0.1    N    8  59.98   W    135   125  10     0   122   126   6   6    6    6    6   R
57   16/06/19   530  56  57.09   N    8  46.99   W    130   120   9    -1   117   121   7   7    7    7    0   S
58   16/06/19   724  56  53      N    8  29.98   W    129   119  10     0   116   120   7   7    7    7    0   15G
59   16/06/19   841  56  50.27   N    8  20.01   W    133   123  10     0   120   124   6   6    6    6    0   T
60   16/06/19   953  56  48.52   N    8  10      W    128   118   9     0   115   119   7   7    7    7    0   14G
61   16/06/19  1113  56  47      N    8   0      W    123   113   9    -1   110   115   7   7    7    7    0   13G
62   16/06/19  1241  56  45.52   N    7  50.09   W     59    49   8    -2    46    49   4   4    4    4    0   12G
63   16/06/19  1353  56  44.02   N    7  40.13   W     63    53  10     1    50    53   4   4    4    5    0   11G
64   16/06/19  1508  56  44.07   N    7  29.95   W    221   211  10     0   208   214   8   8    8    8    6   10G
65   16/06/19  2035  56  44      N    7  19.96   W    157   148  11     1   145   149   7   0    7    7    0   9G
66   16/06/19  2154  56  44.01   N    7   9.9    W    173   163   9     0   161   165   8   0    8    8    0   8G
67   16/06/19  2322  56  43.98   N    6  59.92   W    137   127  10     0   125   128   6   4    6    6    0   7G
68   16/06/20   106  56  44      N    6  44.92   W     38    28  10     0    27    29   4   0    3    3    0   6G
69   16/06/20   221  56  44.01   N    6  35.9    W     78    68  10     0    67    69   5   0    5    5    0   5G
70   16/06/20   428  56  44.03   N    6  26.88   W     86    76  10     0    75    77   6   3    5    5    0   4G
71   16/06/20   626  56  42.57   N    6  21.9    W     70    60  10     0    58    60   4   0    4    4    0   3G
72   16/06/20   726  56  41      N    6  16.93   W     41    31   8    -2    30    31   3   0    3    3    0   2G
73   16/06/20   845  56  40.02   N    6   7.97   W    171   161   7    -2   160   163   7   8    8    8    0   1G
74   16/06/20  2229  57   2.33   N    9   9.75   W    203   193  12     2   190   195   0   0    0    0    0   E:0200m
75   16/06/21     4  57   2.78   N    9  12.55   W    299   289   9     0   283   292   0   0    0    0    0   E:0300m
76   16/06/21   124  57   3.17   N    9  14.44   W    401   392  10     0   386   396   0   0    0    0    0   E:0400m
77   16/06/21   254  57   3.48   N    9  15.89   W    509   500  10     1   496   505   0   0    0    0    0   E:0500m
78   16/06/21   415  57   3.82   N    9  17.08   W    598   589  10     0   585   596   0   0    0    0    0   E:0600m
79   16/06/21   534  57   4.12   N    9  18.28   W    720   711  11     2   707   719   0   0    0    0    0   E:0700m
80   16/06/21   651  57   4.37   N    9  19.03   W    804   795   9     0   792   804   0   0    0    0    0   E:0800m
81   16/06/21   812  57   4.45   N    9  19.84   W    922   914  10     2   910   924   0   0    0    0    0   E:0900m
82   16/06/21   939  57   4.59   N    9  20.61   W   1023  1015   9     0  1010  1027   0   0    0    0    0   E:1000m
83   16/06/21  1132  57   4.81   N    9  22.15   W   1206  1198   8     0  1195  1213   0   0    0    0    0   E:1200m
84   16/06/21  1349  57   5.24   N    9  24.2    W   1388  1380  10     2  1375  1397   0   0    0    0    0   E:1400m
85   16/06/22  1248  59   0.03   N   11   4.94   W   1951  1944  10     2  1940  1971  19  18   19   19    0   X1
86   16/06/22  1841  58  32.98   N   11   4.92   W   1836  1828  10     2  1825  1854  18  18   17   18    0   X2
87   16/06/22  2343  58   6.03   N   11   5      W   1964  1957   9     2  1953  1984  18  18   18   18   10   X3
88   16/06/23   436  57  39      N   11   4.9    W   1810  1802  10     2  1800  1827  19  18   18   18    0   X4
89   16/06/23   637  57  33.02   N   11   4.94   W    704   695  10     0   693   703  12   8   12   12    0   X5   















4  NMF-SS CTD SENSORS
   J. Short, C. Hutton, E. Dumont

4.1  CTD system configurations

     1) One CTD system was prepared. The initial water sampling arrangement was NMF 
frame 24-way stainless steel frame system (s/n CTD8), and the initial sensor 
coniguration was as follows:

Sea-Bird 9plus underwater unit, s/n 09P-24680-0637
Sea-Bird 3P temperature sensor, s/n 03P-4381, Frequency 0 (primary) 
Sea-Bird 4C conductivity sensor, s/n 04C-3054, Frequency 1  (primary)
Digiquartz temperature compensated pressure sensor, s/n 79501, Frequency 2 
Sea-Bird 3P temperature sensor, s/n 03P-4712, Frequency 3 (secondary)
Sea-Bird 4C conductivity sensor, s/n 04C-3529, Frequency 4 (secondary) 
Sea-Bird 5T submersible pump, s/n 05T-6320,  (primary)
Sea-Bird 5T submersible pump, s/n 05T-6916, (secondary) 
Sea-Bird 32 Carousel 24 position pylon, s/n 32-31240-0423 
Sea-Bird 11plus deck unit, s/n 11P-24680-0589 (main)
Sea-Bird 11plus deck unit, s/n 11P-34173-0676 (back-up/spare)

     2) The auxiliary input initial sensor configuration was as follows:

Sea-Bird 43 dissolved oxygen sensor, s/n 43-2575 (V0, primary) 
Benthos PSAA-916T altimeter, s/n 59494 (V2)
WETLabs light scattering sensor, s/n BBRTD-758R (V3) 
Biospherical QCP Cosine PAR Sensor (UWIRR), s/n 70510 (V4) 
Biospherical QCP Cosine PAR Sensor (DWIRR), s/n 70520 (V5) 
Chelsea Aquatracka MKIII luorometer, s/n 088244 (V6) 
WETLabs C-Star Transmissometer, s/n CST-1759TR (V7)

     3) Additional instruments:

TRDI WorkHorse Monitor 300kHz LADCP, s/n 4275 
NOCS LADCP battery pack, s/n WH005
SBE35 Deep Oceans Standards Thermometer, s/n 35-0037

     4) Changes to instrument suite:

Carousel changed to Sea-Bird 32 Carousel 24 position pylon, s/n 32-60380-0805 prior 
to cast DY052_19.

LADCP s/n 4275 replaced with s/n 13400 prior to cast DY052_051. 
LADCP s/n 13400 replaced with s/n 13399 prior to cast DY052_074.

Sea-Bird 9plus underwater unit, s/n 09P-24680-0637 replaced with Sea-Bird 9plus 
underwater unit, s/n 09P-39607-0803 prior to cast 65. Sea-Bird 9plus configuration 
file DY052_0637_SS.xmlcon was used for CTD casts 001 through
064. DY052_0803_SS.xmlcon was used for CTD casts 065 through 089.

The spare water sampling equipment was the 24-way stainless steel frame system (s/n 
SBE CTD1), and the spare sensors were as follows:

Sea-Bird 9plus underwater unit, s/n 09P-39607-0803
Digiquartz temperature compensated pressure sensor, s/n 93896 
Sea-Bird 9plus underwater unit, s/n 09P-34173-0758
Digiquartz temperature compensated pressure sensor, s/n 90074 
Sea-Bird 3P temperature sensor, s/n 03P-4782
Sea-Bird 3P temperature sensor, s/n 03P-5660 
Sea-Bird 3P temperature sensor, s/n 03P-5700 
Sea-Bird 3P temperature sensor, s/n 03P-5785 
Sea-Bird 4C conductivity sensor, s/n 04C-2571 
Sea-Bird 4C conductivity sensor, s/n 04C-4138 
Sea-Bird 4C conductivity sensor, s/n 04C-4139 
Sea-Bird 4C conductivity sensor, s/n 04C-4140 
Sea-Bird 5T submersible pump, s/n 05T-3085 
Sea-Bird 5T submersible pump, s/n 05T-5301 
Sea-Bird 5T submersible pump, s/n 05T-7371 
Sea-Bird 5T submersible pump, s/n 05T-7514
Sea-Bird 32 Carousel 24 position pylon, s/n 32-34173-0493
Sea-Bird 32 Carousel 24 position pylon, s/n 32-60380-0805

     5) The auxiliary spare sensors were as follows:

Sea-Bird 43 dissolved oxygen sensor, s/n 43-0619 
Sea-Bird 43 dissolved oxygen sensor, s/n 43-0709 
Sea-Bird 43 dissolved oxygen sensor, s/n 43-0363 
Sea-Bird 43 dissolved oxygen sensor, s/n 43-2831 
Benthos PSAA-916T altimeter, s/n 59493
Benthos PSAA-916T altimeter, s/n 62679 
WETLabs light scattering sensor, s/n BBRTD-759R
WETLabs C-Star Transmissometer, s/n CST-1720TR
Chelsea Alphatracka MKII transmissometer, s/n 161-2642-002 
Chelsea Aquatracka MKIII luorometer, s/n 088195
Chelsea Aquatracka MKIII luorometer, s/n 88-2050-095

     6) Additional instruments:

TRDI WorkHorse Monitor 300kHz LADCP, s/n 10607 
TRDI WorkHorse Monitor 300kHz LADCP, s/n 13399 
TRDI WorkHorse Monitor 300kHz LADCP, s/n 13400 
NOCS LADCP battery pack, s/n WH006T

Total number of casts – 089 
Casts deeper than 2000m - 016
Deepest cast - 2710 m on CTD017








4.2  Technical detail report

S/S CTD

Communication errors with carousel noted on cast DY052_018 meaning no bottles were 
fired.
Pumps failed to start at the beginning of cast DY052_65. Deck testing and trouble-
shooting carried out on deck, no faults found with pumps, conductivity cells or 
cabling, hence underwater unit changed.

LADCP

LADCP instruments rotated for testing purposes as all units were recently received 
back from the manufacturer.

AUTOSAL

A Guildline 8400B, s/n 71185, was installed in the Salinometer Room as the main 
instrument for salinity analysis. A second Guildline 8400B, s/n 71126, was installed 
in the Salinometer Room as a spare instrument. The Autosal set point was 24C, and 
samples were processed according to WOCE cruise guidelines: The salinometer was 
standardized at the beginning of the first set of samples, and checked with an 
additional standard analysed prior to setting the RS. Once standardized the Autosal 
was not adjusted for the duration of sampling.

Additional standards were analysed every 24 samples to monitor & record drift. These 
were labeled sequentially and increasing, beginning with number 9001. The standard 
deviation limit of the three Autosal readings that contribute to the final average 
value reported as an observation was set to 0.00002. Autosal readings were repeated 
until all readings for that sample were within the standard deviation limit.

A large drift was noted on 71185 on running of last set of samples (day 172) standby 
value settled at 5994 (from 5988 where it had been steady for the duration of the 
cruise preceding day172), further analysis carried out with instrument s/n 71126.


4.3  Configuration files

Stainless CTD frame:

Casts 001 - 065                                    Casts 065 - 089
------------------------------------------------   ------------------------------------------------
Date: 06/23/2016                                   Date: 06/23/2016
Instrument configuration file:                     Instrument configuration file:
C:\Users\sandm\Documents\Cruises\DY052\Data        C:\Users\sandm\Documents\Cruises\DY052\Data\
\Seasave  Setup  Files\DY052_0637_SS.xmlcon        Seasave  Setup  Files\DY052_0803_SS.xmlcon
Configuration report for SBE 911plus/917plus       Configuration report for SBE 911plus/917plus
CTD                                                CTD
------------------------------------------------   ------------------------------------------------
Frequency channels suppressed : 0                  Frequency channels suppressed : 0
Voltage words suppressed      : 0                  Voltage words suppressed      : 0
Computer interface            : RS-232C            Computer interface            : RS-232C
Deck unit: SBE11plus Firmware                      Deck unit                     : SBE11plus Firmware
Version >= 5.0                                     Version >= 5.0
Scans to average              :1                   Scans to average              :1
NMEA position data added      : Yes                NMEA position data added      : Yes
NMEA depth data added         : No                 NMEA depth data added         : No
NMEA time added               : Yes                NMEA time added               : Yes
NMEA device connected to      : PC                 NMEA device connected to      : PC
Surface PAR voltage added     : No                 Surface PAR voltage added     : No
Scan time added               : Yes                Scan time added               : Yes

 1) Frequency 0, Temperature                        1) Frequency 0, Temperature
    Serial number              : 3P-4381               Serial number              : 3P-4381
    Calibrated on              : 21-Jul-15             Calibrated on              : 21-Jul-15
    G                          : 4.42359050e-003       G                          : 4.42359050e-003
    H                          : 6.44917114e-004       H                          : 6.44917114e-004
    I                          : 2.26674159e-005       I                          : 2.26674159e-005
    J                          : 1.97655514e-006       J                          : 1.97655514e-006
    F0                         : 1000.000              F0                         : 1000.000
    Slope                      : 1.00000000            Slope                      : 1.00000000
    Offset                     : 0.0000                Offset                     : 0.0000

 2) Frequency 1, Conductivity                       2) Frequency 1, Conductivity
    Serial number              : 4C-3054               Serial number              : 4C-3054
    Calibrated on              : 16-Jun-15             Calibrated on              : 16-Jun-15
    G                          : -9.80759366e+000      G                          : -9.80759366e+000
    H                          : 1.42268693e+000       H                          : 1.42268693e+000
    I                          : -2.32442769e-004      I                          : -2.32442769e-004
    J                          : 8.20502779e-005       J                          : 8.20502779e-005
    CTcor                      : 3.2500e-006           CTcor                      : 3.2500e-006
    CPcor                      : -9.57000000e-008      CPcor                      : -9.57000000e-008
    Slope                      : 1.00000000            Slope                      : 1.00000000
    Offset                     : 0.00000               Offset                     : 0.00000

 3) Frequency 2, Pressure, Digiquartz with TC       3) Frequency 2, Pressure, Digiquartz with TC
    Serial number              : 79501                 Serial number : 93896
    Calibrated on              : 06-Jan-15             Calibrated on : 09-Jul-14
    C1                         : -6.052595e+004        C1                         : -8.331332e+004
    C2                         : -1.619787e+000        C2                         : -3.281962e+000
    C3                         : 1.743190e-002         C3                         : 2.216060e-002
    D1                         : 2.819600e-002         D1                         : 2.906000e-002
    D2                         : 0.000000e+000         D2                         : 0.000000e+000
    T1                         : 3.011561e+001         T1                         : 3.005232e+001
    T2                         : -5.788717e-004        T2                         : -3.843669e-004
    T3                         : 3.417040e-006         T3                         : 4.436390e-006
    T4                         : 4.126500e-009         T4                         : 0.000000e+000
    T5                         : 0.000000e+000         T5                         : 0.000000e+000
    Slope                      : 0.99985000            Slope                      : 1.00001000
    Offset                     : -1.66130              Offset                     : -1.35810
    AD590M                     : 1.293660e-002         AD590M                     : 1.289250e-002
    AD590B                     : -9.522570e+000        AD590B                     : -8.106440e+000
    
 4) Frequency 3, Temperature, 2                     4) Frequency 3, Temperature, 2
    Serial number              : 3P-4712               Serial number              : 3P-4712
    Calibrated on              : 21-Jul-15             Calibrated on              : 21-Jul-15
    G                          : 4.40403756e-003       G                          : 4.40403756e-003
    H                          : 6.33214711e-004       H                          : 6.33214711e-004
    I                          : 1.90723282e-005       I                          : 1.90723282e-005
    J                          : 1.14981012e-006       J                          : 1.14981012e-006
    F0                         : 1000.000              F0                         : 1000.000
    Slope                      : 1.00000000            Slope                      : 1.00000000
    Offset                     : 0.0000                Offset                     : 0.0000
 
 5) Frequency 4, Conductivity, 2                    5) Frequency 4, Conductivity, 2
    Serial number              : 4C-3529               Serial number              : 4C-3529
    Calibrated on              : 21-Jul-15             Calibrated on              : 21-Jul-15
    G                          : -9.91877058e+000      G                          : -9.91877058e+000
    H                          : 1.57004159e+000       H                          : 1.57004159e+000
    I                          : -2.20163146e-003      I                          : -2.20163146e-003
    J                          : 2.65000201e-004       J                          : 2.65000201e-004
    CTcor                      : 3.2500e-006           CTcor                      : 3.2500e-006
    CPcor                      : -9.57000000e-008      CPcor                      : -9.57000000e-008
    Slope                      : 1.00000000            Slope                      : 1.00000000
    Offset                     : 0.00000               Offset                     : 0.00000

 6) A/D voltage 0, Oxygen, SBE 43                   6) A/D voltage 0, Oxygen, SBE 43
    Serial number             : 43-2575                Serial number              : 43-2575
    Calibrated on             : 31-Jul-15              Calibrated on              : 31-Jul-15
    Equation                  : Sea-Bird               Equation                   : Sea-Bird
    Soc                       : 4.41200e-001           Soc                        : 4.41200e-001
    Offset                    : -4.67000e-001          Offset                     : -4.67000e-001
    A                         : -4.32580e-003          A                          : -4.32580e-003
    B                         : 2.14910e-004           B                          : 2.14910e-004
    C                         : -2.87190e-006          C                          : -2.87190e-006
    E                         : 3.60000e-002           E                          : 3.60000e-002
    Tau20                     : 1.00000e+000           Tau20                      : 1.00000e+000
    D1                        : 1.92634e-004           D1                         : 1.92634e-004
    D2                        : -4.64803e-002          D2                         : -4.64803e-002
    H1                        : -3.30000e-002          H1                         : -3.30000e-002
    H2                        : 5.00000e+003           H2                         : 5.00000e+003
    H3                        : 1.45000e+003           H3                         : 1.45000e+003
 
 7) A/D voltage 1, Free                             7) A/D voltage 1, Free
    
 8) A/D voltage 2, Turbidity Meter, WET Labs,       8) A/D voltage 2, Turbidity Meter, WET Labs,
    ECO-BB                                             ECO-BB
    Serial number             : BBRTD-758R             Serial number              : BBRTD-758R
    Calibrated on             : 3 June 2013            Calibrated on              : 3 June 2013
    ScaleFactor               : 0.002903               ScaleFactor                : 0.002903
    Dark output               : 0.043100               Dark output                : 0.043100
 
 9) A/D voltage 3, Altimeter                        9) A/D voltage 3, Altimeter
    Serial number             : 59494                  Serial number              : 59494
    Calibrated on             : 29 November 2012       Calibrated on              : 29 November 2012
    Scale factor              : 15.000                 Scale factor               : 15.000
    Offset                    : 0.000                  Offset                     : 0.000
            
10) A/D voltage 4, PAR/Irradiance,                 10) A/D voltage 4, PAR/Irradiance, 
    Biospherical/Licor                                 Biospherical/Licor
    Serial number             : 70510                  Serial number : 70510 
    Calibrated on             : 01-Jun-15              Calibrated on              : 01-Jun-15 
    M                         : 1.00000000             M                          : 1.00000000
    B                         : 0.00000000             B                          : 0.00000000
    Calibration constant      : 20161290300.00000000   Calibration constant       : 20161290300.00000000 
    Multiplier                : 1.00000000             Multiplier                 : 1.00000000
    Offset                    : -0.05051050            Offset                     : -0.05051050
             
11) A/D voltage 5, PAR/Irradiance,                 11) A/D voltage 5, PAR/Irradiance, 
    Biospherical/Licor, 2                              Biospherical/Licor, 2
    Serial number             : 70520                  Serial number              : 70520 
    Calibrated on             : 01-Jun-15              Calibrated on              : 01-Jun-15 
    M                         : 1.00000000             M                          : 1.00000000
    B                         : 0.00000000             B                          : 0.00000000
    Calibration constant      : 19531250000.00000000   Calibration constant       : 19531250000.00000000 
    Multiplier                : 1.00000000             Multiplier                 : 1.00000000
    Offset                    : -0.05251338            Offset                     : -0.05251338
             
12) A/D voltage 6, Transmissometer,                12) A/D voltage 6, Transmissometer, 
    WET Labs C-Star                                    WET Labs C-Star
    Serial number             : 1759TR                 Serial number              : 1759TR 
    Calibrated on             : 22-Dec-2015            Calibrated on              : 22-Dec-2015 
    M                         : 21.3083                M                          : 21.3083
    B                         : -0.1705                B                          : -0.1705
    Path length               : 0.250                  Path length                : 0.250
             
13) A/D voltage 7, Fluorometer, Chelsea Aqua 3     13) A/D voltage 7, Fluorometer, Chelsea Aqua 3 
    Serial number             : 088-244                Serial number              : 088-244
    Calibrated on             : 6 August 2014          Calibrated on              : 6 August 2014
    VB                        : 0.236800               VB                         : 0.236800
    V1                        : 2.151000               V1                         : 2.151000
    Vacetone                  : 0.305900               Vacetone                   : 0.305900 
    Scale factor              : 1.000000               Scale factor               : 1.000000 
    Slope                     : 1.000000               Slope                      : 1.000000
    Offset                    : 0.000000               Offset                     : 0.000000 
             
Scan length                     45                 Scan length                      45
 	
 
LADCP script file:

; Append command to the log file: "C:\adcp\ladcp.log"
$lC:\Users\SANDM\Documents\DY052 ladcp data\log files\ladcp.log
;
$P  *************************************************************************
$P  **********   LADCP  Deployment  downward looking ADCP.   DY052  **********
$P  *************************************************************************
; Send ADCP a BREAK
$B
; Wait for command  prompt  (sent  after  each command)
$W62
;Set Baud rate to 9600,8,N,1 
cb411
$w62
;**Start**
; Display real time clock setting 
tt?
;Display unused Memory 
rs?
$d5
$w62
;Display number of deployments 
ra?
$d5
$w62
;Run predeployment tests 
pa
pt200 pc2
$d5 a
$w62
; Set to factory defaults 
CR1
$W62
; Save settings as User  defaults  
CK
$W62
; Name data file 
RN DY052
$W62
;Set Profiling mode 15 
WM15
$w62 
TC2
; Set one ping per  ensemble.  Use  WP  if LADCP  option  is not  enabled. 
LP1
$W62
;Set time per burst  to  2.8sec  
TB 00:00:02.80
$w62
; Set zero second  between  pings  
TP  00:00.00
$W62
;set time per ensemble to  1.3s 
TE 00:00:01.30
$w62
; Set to record 25 bins. Use WN if LADCP  option is not enabled.  
LN25
$W62
;Set depth bin to 800cm 
LS0800
$w62
;set blank after transmit to zero 
LF0
$w62
;set narrow bandwidth 
LW1
$w62
;set ambiguity velocity to 400cm/s (radial) 
LV400
$w62
;set as master 
SM1
$w62
;set	Synch  Before/After Ping/Ensemble Bottom/Water/Both 
SA011
$w62
;disable channel b break interrupts 
SB0
$w62
;set synch delay (1/10 msec) 
SW5500
$w62
;set synch interval to zero SIO
$w62
;set Sensor Source (C;D;H;P;R;S;T) 
EZ0011101
$w62
;set Coord Transform (Xform:Type; Tilts; 3Bm; Map) 
EX00100
$w62
;set Flow Ctrl (EnsCyc;PngCyc;Binry;Ser;Rec) 
CF11101
$w62
;save as user defaults CK
$w62 CS
$d3
$l
$P  *************************************************************************
$P  ****  Please  disconnect  ADCP  and  Remember  to  rename  log file! ****
$P  *************************************************************************









4.4  CTD sensor geometry


                 Cruise       DY052
                 Technician   J. Short
                 Date         23 June 2016
                 CTD type     24-way s/s frame, 10L water samplers, SBE 9/11+


                                          ID   Vertical distance from pressure
                                                       sensor (m)
                                          ---  -------------------------------
                                          A                 1.25
                                          B                 0.17
                                          C**               0.17
                                          D                 0.07




Fitted Sensors***:

                                                               Comments    Cali-          Last 
Manufacturer          Sensor/Instrument       Serial No.        (Casts    bration      calibration 
                                                              installed)  applied?**      date
--------------------  ----------------------  --------------  ----------  ----------  --------------
SBE 11plus V2         CTD deck unit           11P-24680-0589  All casts     Y         10 March 2004            

SBE 9plus             CTD Underwater Unit     09P-24680-0637  001 - 064     Y         6 January 2015            
                                                (Ti)
NOCS                  Stainless steel         SBE CTD8        All casts     N/A       N/A            
                        24-way frame
Paroscientific        Digiquartz Pressure     79501           All casts     Y         6 January 2015            
                        sensor
SBE 3P                Primary Temperature     3P-4381 (Ti)    All casts     Y         21 July 2015            
                        Sensor
SBE 4C                Primary Conductivity    4C-3054(Ti)     All casts     Y         16 June 2015            
                        Sensor
SBE 5T                Primary Pump            5T-6320         All casts     N/A       N/A            

SBE 3P                Secondary Temperature   3P-4712(Ti)     All casts     Y         21 July 2015            
                        Sensor
SBE 4C                Secondary Conductivity  4C-3529 (Ti)    All casts     Y         21 July 2015            
                        Sensor
SBE 5T                Secondary Pump          5T-6916         All casts     N/A       N/A            

SBE 32                24-way Carousel         32-31240-0423   All casts     001-018   N/A            

SBE 43                Dissolved Oxygen        43-2575         All casts     Y         31 July 2015            
                        Sensor
Benthos PSA-916T      Altimeter               59494           All casts     Y         29 Nov. 2012            

WETLabs BBRTD         Light Scattering        BBRTD-758R      All casts     Y         3 June 2013            
                        Sensor
WETLabs C-Star        Transmissometer         CST-1759TR      All casts     Y         22 Dec. 2015            

CTG Aquatracka        Fluorometer             088244          All casts     Y         6 August 2014            
  MKIII
Biospherical QCP      Irradiance              70520           All casts     Y         1 June 2015 
  Cosine PAR            Sensor (DWIRR)            
Biospherical QCP      Irradiance              70510           All casts     Y         1 June 2015 
  Cosine PAR            Sensor (UWIRR)            
OTE                   10L Water               1 through 24    All casts     N/A       N/A            
                        Samplers
TRDI Workhorse        ADCP                    4275            001-050                                 
  Monitor            
TRDI Workhorse        ADCP                    13400           051-73                                 
  Monitor            
TRDI Workhorse        ADCP                    13399           074-089                                 
  Monitor            
Deep Ocean Standards  SBE 35                  35-0037         All casts            
  Thermometer            
***Please include details of LADCP, CTD carousel and deck unit in addition to CTD and auxillary sensors.
** Were the manufacturer’s calibrations applied during NMF-run Sea-Bird processing?


Spare Sensors***:

                                                               Comments    Cali-          Last 
Manufacturer          Sensor/Instrument       Serial No.        (Casts    bration      calibration 
                                                              installed)  applied?**      date
--------------------  ----------------------  --------------  ----------  ----------  --------------
SBE 11plus            CTD deck unit           11P-34173-0676     N/A        Y         10 March 2004  
SBE 9plus             CTD Underwater Unit     09P-39607-0803  065-089       Y         9 July 2014
                                                (Ti)
Paroscientific        Digiquartz Pressure     93896           065-089       Y         9 July 2014
                        sensor
SBE 3P                Temperature Sensor      3P-5660            N/A        Y         21 July 2015            
SBE 3P                Temperature Sensor      3P-4782            N/A        Y         17 September 2015            
SBE 3P                Temperature Sensor      3P-5700            N/A        Y         17 September 2015            
SBE 3P                Temperature Sensor      3P-5785            N/A        Y         17 September 2015            
SBE 4C                Conductivity Sensor     4C-4138            N/A        Y         17 September 2015            
SBE 4C                Conductivity Sensor     4C-4139            N/A        Y         14 July 2015            
SBE 4C                Conductivity Sensor     4C-4140            N/A        Y         21 July 2015            
SBE 4C                Conductivity Sensor     4C-2571            N/A        Y         17 September 2015            
SBE 5T                Pump                    5T-3085            N/A        N/A            N/A            
SBE 5T                Pump                    5T-5301            N/A        N/A            N/A            
SBE 5T                Pump                    5T-7371            N/A        N/A            N/A            
SBE 5T                Pump                    5T-7514            N/A        N/A            N/A            
SBE 32                24-way Carousel         32-0493 (Ti)       N/A        N/A            N/A            
SBE 32                24-way Carousel         32-60380-0805    19-089       N/A            N/A            
                                                (Ti)
SBE 43                Dissolved Oxygen        43-0709            N/A        Y          21 August 2015            
                        Sensor
SBE 43                Dissolved Oxygen        43-0619            N/A        Y          9 September 2015            
                        Sensor
WETLabs C-Star        Transmissometer         CST-1720TR         N/A        Y          16 April 2015            
CTG MKII Alphatracka  Transmissometer         161-2642-002       N/A        Y          3 September 2014            
CTG Aquatracka MKlll  Fluorimeter             88-2050-095        N/A        Y          15 September 2014            
Guildline Autosal     Salinometer             71126              Main       N/A        Service 19 January 2015 
&            
  8400B                                                                                  Alignment 19 January 
2015            
Guildline Autosal     Salinometer             71185           Spare (used   N/A        Service 20 January 2015 
&
  8400B                                                       for last 6                 Alignment 20 January 
2015            
                                                              salinity 
                                                              crates)
Benthos PSA-916T      Altimeter               59493              N/A        Y          25 March 2013            
Benthos PSA-916T      Altimeter               62679              N/A        Y          27 March 2014            
WETLabs BBRTD         Light Scattering        BBRTD-759R         N/A        Y          3 June 2013            
                        Sensor
OTE                   10L Water Samplers      1D through 24D     N/A        N/A            N/A            
Deep Ocean Stan-        SBE 35                35-0037            N/A         
  dards Thermometer            


Sea-Bird processing:

The table below lists the Sea-Bird processing routines run by NMF staff (if any). 
Note this is only the modules that were run by NMF, not by scientific staff.

Module             Run?  Comments          
-----------------  ----  ----------------------------------------------
Configure           N
Data Conversion     Y    As per BODC guidelines Version1.0 October 2010 
                         (Beam Transmission, mS/cm Conductivity)          
Bottle Summary      Y    As per BODC guidelines Version1.0 October 2010          
Mark Scan           N
Align CTD           Y    As per BODC guidelines Version1.0 October 2010 
                         (dissolved oxygen advanced 6 seconds)          
Buoyancy            N
Cell Thermal Mass   Y    As per BODC guidelines Version1.0 October 2010          
Derive              Y    As per BODC guidelines Version1.0 October 2010      
                         (appended file name)          
Bin Average         Y    As per BODC guidelines Version1.0 October 2010         
                         (appended file name)          
Filter              Y    As per BODC guidelines Version1.0 October 2010 
                         (appended file name)          
Loop Edit           N    Not applicable.          
Wild Edit           N    No pressure spikes observed.          
Window Filter       N
ASCII In            N
ASCII Out           Y    As per request from NMF Sea Systems for sound 
                         velocity profiles,  periodic processing only.          
Section             N
Split               N
Strip               Y    As per BODC guidelines Version1.0 October 2010          
Translate           N
Sea Plot            N
SeaCalc II          N    


Field calibrations

The table below details any calibrations against independent (bottle) samples that 
were applied by NMF staff

Sensor serial no.  Coefficients
-----------------  ------------

 


5  CTD DATA PROCESSING
   Stefan Gary, Emma Slater, and Estelle Dumont


The CTD data processing on DY052 closely mirrored that of DY031. Updated extracts of 
the DY031 cruise report are included here for completeness and expanded to reflect 
this cruise.

The CTD used on DY052 had two independent sets of temperature, T, and conductivity, 
C, sensors, each with its own pump. The first pair of T and C sensors, T1 and C1, 
were mounted close to the bottom, outermost corner of the CTD “in” within a small 
metal frame to protect the sensors from any bumps during deployment and recovery 
(Chapter 4). The second pair of sensors, T2 and C2, were mounted near the bottom of 
the CTD frame, under the Niskin bottles, and inside of the SeaBird 9+ underwater 
unit. We chose to report the results from the primary sensors because previous 
experience (see DY031 cruise report) has shown that in-mounted sensors result in 
cleaner data that are less impacted by turbulent eddies spun off from the CTD frame 
and sensors attached to the frame. Furthermore, the CTD oxygen sensor was mounted on 
the same pump line as the primary temperature and conductivity sensors.


5.1  Sea-Bird processing

The first stage of processing of the CTD data was with the Sea-Bird Electronics 
SeaSave software package. Each step is outlined below.

Data Conversion - The Data Conversion tool converted the raw frequency and voltage 
data to engineering units as appropriate by applying the manufacturer's calibrations 
stored in the CON file and saved both downcast and upcast to an ASCII format file. 
This process can include the oxygen hysteresis correction using SBE parameters but 
we opted to do the oxygen hysteresis correction separately, described below. Two 
files are created during the data conversion step; the .cnv data file and the .ros 
rosette file.

It is essential that the output variables from Data Conversion include scan and 
pressure temperature, latitude and longitude:

# name 0 = timeS: Time, Elapsed [seconds]
# name 1 = depSM: Depth [salt water, m]
# name 2 = prDM: Pressure, Digiquartz [db]
# name 3 = t090C: Temperature [ITS-90, deg C]
# name 4 = t190C: Temperature, 2 [ITS-90, deg C]
# name 5 = c0mS/cm: Conductivity [mS/cm]
# name 6 = c1mS/cm: Conductivity, 2 [mS/cm]
# name 7 = sal00: Salinity, Practical [PSU]
# name 8 = sal11: Salinity, Practical, 2 [PSU]
# name 9 = sbeox0V: Oxygen raw, SBE 43 [V]
# name 10 = sbeox0Mm/Kg: Oxygen, SBE 43 [umol/kg]
# name 11 = sbeox0ML/L: Oxygen, SBE 43 [ml/l]
# name 12 = CStarTr0: Beam Transmission, WET Labs C-Star [%]
# name 13 = lC: Fluorescence, Chelsea Aqua 3 Chl Con [ug/l]
# name 14 = turbWETbb0: Turbidity, WET Labs ECO BB [m^-1/sr]
# name 15 = altM: Altimeter [m]
# name 16 = scan: Scan Count
# name 17 = ptempC: Pressure Temperature [deg C]
# name 18 = pumps: Pump Status
# name 19 = latitude: Latitude [deg]
# name 20 = longitude: Longitude [deg]
# name 21 = lag: 0.000e+00

Align - Next, the Align CTD option aligns the oxygen sensor in time relative to 
pressure and writes the output to a new file.

In the Sea-Bird processing suite, the CTD align function will shift the oxygen 
sensor output in time relative to the temperature and salinity sensors to account 
for the additional length of hose between the T and S sensors and the oxygen sensor. 
Each water sample in the CTD will pass through the T and S sensors first and then 
the oxygen sensor and then the pump. In addition to the impact of geometry, this 
correction also helps to address the response time of the oxygen sensor. As the 
response time of the sensor may change with temperature, the first 7 casts were all 
reprocessed with 2, 4, 6, 8, and 10 second shifts of the oxygen sensor time series 
as well as applying the default Sea-Bird oxygen hysteresis correction.

To evaluate the best time alignment of the oxygen sensor, the oxygen-pressure 
relationship for the up and down casts were separated based on the deepest pressure 
measurement and then independently bin averaged into 2 dbar bins. The absolute value 
of the oxygen difference (µmol/kg) between each corresponding upcast and downcast 
bin was computed and the median of these differences, over each cast, was used to 
evaluate the impact of the alignments. Three of the 7 casts exhibited the lowest 
median difference between up and down cast with a 6 second alignment with other 
casts exhibiting the lowest median differences at 2, 4, and 10 seconds.

Since the most casts agreed with a 6 second alignment time, we chose this value for 
the Sea-Bird oxygen alignment. 6 seconds also corresponds to the default value in 
the Sea-Bird software as well as our estimate, by eye, of which alignment produced 
the least deviations between the up and downcast plots. Finally, it is important to 
note that the metric used here to evaluate the alignment shift was not particularly 
sensitive – its variability from alignment time to alignment time was very small 
compared to its uncertainty in light of the variability within each cast.

Cell Thermal Mass - The next step is the Cell Thermal Mass correction for the 
conductivity because there is a time lag during which the conductivity cell is 
flushed, so its temperature is not precisely the same as the temperature measured by 
the temperature sensor. This last step creates a new file (dy052_NNN_actm.cnv). All 
the Sea-Bird data files were copied to the DY052 ship's public server, and copied to 
the MSTAR workstation using the shell script ctd_linkscript.


5.2  MSTAR processing

MSTAR uses some template files to define the variables in sample files 
(sam_dy052_varlist.csv) and CTD variable names (ctd_dy052_renamelist.csv and 
ctd_dy052_renamelist_out). These were edited at the start of the cruise.

At this stage, the CTD data are ready to be read into MSTAR for additional 
processing. The standard MSTAR CTD data processing suite was applied to the CTD data 
for each station. First an empty sample file was created with msam_01. The 
converted, aligned, and thermal mass corrected data from SeaSave in .cnv format were 
copied into MSTAR with mctd_01 and the variables were renamed with mctd_02a and the 
oxygen hysteresis correction was applied (see below), along with creating a backup 
of the data, with mctd_02b.

The original 24 Hz data were averaged to 1 Hz and the salinity was computed from 
temperature, pressure and conductivity with mctd_03. The suite of mdcs_01, mdcs_02, 
and mdcs_03g were used to collect station position and time information from the 
TechSAS position data stream and put it in each station file as well as select the 
exact start and end of the cast.  The .dcs files created for each cast store the 
cast start and stop independently of the rest of the cast data and can be used for 
other purposes, for example matching SBE35 timestamps with a particular cast.

Once the cast timing was determined, mctd_04 was used to average the data to 2 dbar 
levels and the mir_01, mir_02, mir_03, and mir_04 suite were used to collect bottle 
firing information in the .bl file created by SeaSave, extract data from the cast to 
represent the instrument measurements at the time of bottle firing, and paste this 
bottle-specific data to the sample file. The mwin_01, mwin_02, and mwin_3 suite of 
scripts was used to collect wire out from the TechSAS winch data stream and paste 
this information into the sample file.

Once this first round of MSTAR processing was executed, the CTD data were ready for 
manual inspection and quality control. The script mctd_checkplots was used to check 
for large spikes, significant differences between primary and secondary sensors, 
deviations from the expected T-S relationship, and any potential station-to-station 
drifts in the sensors. Spikes observed via a graphical user interface in 
mctd_rawedit were changed to NaN. Throughout the cruise there was the manual removal 
of conductivity spikes due to the ingestion of particles into the conductivity cells 
of the primary and secondary sensors. Spikes were defined by an anomalously low 
conductivity value over just a few scans (usually 1-10 scans at 24 Hz), that was not 
reflected by a similar dip in temperature. With the spikes removed for a particular 
station, mctd_02b, mctd_03, mctd_04, mir_03, and mir_04 were run again and the data 
(with spikes removed this time) were bin averaged and overwritten in the 24 Hz, 1 
Hz, 2dbar, and sample files.

Casts 65-73 exhibited noisy oxygen data where the signals were amplified in both 
directions. These points were removed from the raw files. It was not known what the 
cause for this was and the cables were checked for loose connectivity. From cast 74 
onwards this noise was not observed as prolifically. As stated below in Section 5.8, 
during cast 18 the CTD data acquisition was restarted at the bottom of the down 
cast. Large spikes in the oxygen signal were removed from the bottom of the 
downcast.

mctd_makelists was run to create ascii listings used in LADCP processing, and for 
providing key CTD variable to chemists. This step was very helpful as data were 
ready to be imported into ODV for quick plots to check, for example, the validity of 
the oxygen calibration on a nearly cast-by-cast basis.

Water depth for each station was determined by adding the range to the bottom, 
estimated as 10 m, to the pressure at the bottom of each cast as stored in the dcs_ 
file for each cast. To within a couple meters, every cast ended about 10 m of the 
bottom. The only exception to this was CTD001, which was a partial depth cast to 
about 500 m in 1912 m of water. The depth as recorded in the CTD001 log sheet is the 
reported value for the water depth in this case. The script populate_station_depths 
will read the station_depths_dy052.txt file and convert it to a .mat file. Then, 
mdep_01.m reads the .mat file containing water depth in the variable bestdeps and 
pastes this information into headers of all CTD files.


5.3  Oxygen hysteresis correction

To account for the hysteresis of the oxygen sensor, we need to do a trial and error 
modification of the parameters for the hysteresis correction. This analysis was done 
with CTD016 because it was one of the deepest stations (~2680 m) during the cruise 
and early in the cruise. The standard Sea-Bird correction parameters were applied to 
a subset of the other deep stations and also compared to the hysteresis correction 
determined here with good agreement.

The first step in the process was to save the results using the default Sea-Bird 
oxygen hysteresis correction (-0.033, 5000, 1450). Then mctd_02b and mctd_03 were 
run without any hysteresis correction at all and the resulting 1 Hz file was also 
saved.

When comparing no correction with the SBE default correction at the depths of 
Labrador Sea Water (~3-4 °C), the SBE defaults help to reduce the gap between the 
upcast and the downcast from about 1.5 µmol/kg to about 1.0 ?mol/kg. Furthermore, 
the hysteresis correction causes the value of the oxygen in the LSW to be shifted by 
about 3 µmol/kg, roughly 1.2% of the measurement value.

To get better agreement between the up and down casts in the deepest water, we used 
plot_oxygen_profiles.m to quantify the differences between the upcast and the 
downcast. Given the recommended range for the hysteresis correction parameters and 
trailing various combinations of parameters, we chose the values -0.02, 5000, and 
2000 to get the up and downcast to within about 2 µmol/kg of each other below about 
500 m and within about 0.3 ?mol/kg in the depth range of Labrador Sea Water. These 
selected values are an improvement over uncorrected profiles as well as the default 
Sea-Bird hysteresis correction. Visual inspection with a range of deep oxygen casts 
showed that these parameters were valid for several casts. All oxygen sensor data 
were then reprocessed with the mctd_02b, mctd_03, mctd_04, mir_03, and mir_04 
pipeline.


Figure 5.1: Difference between up and down cast oxygen on CTD016 for raw 
            (blue), default Sea-Bird (red) and parameters for this cruise 
            (black).



5.4  Oxygen sample files and CTD oxygen calibration

Once the bottle oxygen values had been measured they were written into spreadsheets 
for ingesting into MSTAR. The files provided by the oxygen team, one for each CTD 
cast, conformed to the naming convention Oxy_StationNNN.csv, with NNN replaced by 
the zero-padded station number. The headers for the columns in each text file were:

botnum,statnum,sampnum,tixa,botoxya,Flag,tixb,botoxyb,Flag 
number,number,number,degC,umol/l,a,degC,umol/l,b

where the 'a' and 'b' values allow for 2 samples drawn from a single Niskin bottle.


These files were used by oxy_linkscript to create a symbolic link for each oxygen 
bottle file with a name expected by MSTAR: oxy_dy052_NNN.csv. Each text file was 
then read and copied into a cast-by-cast netcdf file with moxy_01 whose output is 
oxy_dy052_NNN.nc. A subset of the data was manually checked for accurate data 
transcription. The next step is to paste the oxygen-only netcdf bottle file into the 
sample file for that station with the script moxy_02. As the laboratory analysis of 
oxygen results in concentrations of µmol/L, the draw temperature measured at the 
time of taking the oxygen sample and CTD salinity was used to compute the density of 
the sample and thus convert the µmol/L to µmol/kg in the script msam_oxykg. The 
result is written in the sample file for each cast into the variable botoxy. Oxygen 
data from the individual cast sample files were then pasted into the master sample 
file, sam_dy052_all.nc, which contains all the bottle data from the whole cruise, 
with msam_updateall.

The master sample file itself was created by first copying the sample file from the 
first cast, sam_dy052_001.nc, to sam_dy052_all.nc and then using msam_append_dy052. 
The master sample file was then used as the source data for generating diagnostic 
plots showing the relationship between bottle oxygen and ctd oxygen 
(ctd_evaluate_oxygen) (Figure 5.2) and residuals between bottle oxygen and CTD 
oxygen (Figure 5.3). All CTD data were grouped into one of two subsets: before and 
after cast 65. As noted in Chapter 4, when the pumps did not turn on at the 
deployment of cast 65, the cast was initially aborted, the SBE 9+ underwater unit 
was replaced, and the cast was restarted. As the oxygen sensor sends its output 
voltage through an analog, not digital, data acquisition port in the SBE9+, a change 
in the analog amplifier resulted in a different gain applied within the new SBE9+ 
relative to the previous SBE9+. The result was a shift in the magnitude of the 
oxygen measured by the CTD system (Figures 5.2 and 5.3). It's important to note in 
Figure 5.2 that casts 74-84 were run electronics only.  Figure 5.3 shows that when 
accounting for the change in SBE9+ underwater unit, the oxygen sensor was stable in 
time. What appears as a possible temporal drift from casts 65-89 is really a 
temperature-based variation because the waters for CTD 065-073 were much shallower 
warmer than for CTD 084-089.


Figure 5.2: The relationship between bottle oxygen and CTD oxygen. Plus, signs  
            denote points that were used in determining the calibration and 
            open circles are points that were excluded from the calibration 
            because their respective residuals (Figure 5.3) lie outside 2 
            standard deviations of the mean. Subset 1 is the data before the 
            change in the SBE9+ unit.

Figure 5.3: Residuals of bottle oxygen relative to CTD oxygen plotted with CTD 
            cast number. Plus signs denote points that were used in 
            determining the calibration and open circles are points that were 
            excluded from the calibration because their respective residuals 
            lie outside 2 standard deviations of the mean. The mean for each 
            subset is shown with a solid red line and the 2 standard deviation 
            envelope is shown with the dashed lines.


From the best it lines in Figure 5.2, the slope and intercept for CTD 001 – 064 were 
determined to be 1.01335 and 10.99686 µmol/kg, respectively. For CTD 065- 089, the 
slope and intercept were 0.92960 and 21.07409 µmol/kg, respectively. After applying 
these slopes and intercepts to the CTD oxygen data, the residuals were plotted again 
in Figure 5.4 and it was found that a small pressure adjustment was needed. A piece-
wise linear adjustment was determined by computing the average residuals in 3 zones: 
the upper 100 m (-0.97109 µmol/kg); from 900 m to 1100 m (0.19834 µmol/kg); and 
below 2500 m (5.72306 µmol/kg).  These residuals, together with the corresponding 
pressures of 0 dbar, 1000 dbar, and 2655 dbar were used to create the red lines in 
Figure 5.4. A linearly interpolated adjustment, using these three points, was 
applied to all CTD oxygen data based on the pressure of each data point.

The final result of the calibration and adjustment process is shown in Figures 5.5 
and 5.6. After this process, the mean residual is 0.039 ± 2.7 µmol/kg. The 
variability reported here is one standard deviation of all residuals.

The oxygen calibration and adjustment was applied in mctd_oxycal, which is a wrapper 
script for oxy_apply_cal which stores the exact parameters of the calibration. These 
scripts were run in a loop over all CTD casts once the calibration was determined.


Figure 5.4: Residuals between bottle oxygen and CTD oxygen plotted with 
            pressure after the calibration was applied but before the pressure 
            adjustment was applied. The red line indicates the piecewise 
            linear pressure-based adjustment that will be applied.

Figure 5.5: As in Figure 5.4 but after the pressure adjustment was applied.

Figure 5.6: Relationship between bottle oxygen and CTD oxygen after both the 
            calibration and the pressure adjustment were applied.



5.5  SBE35 temperature sensor data processing

There were three temperature measurements on each CTD cast; two SBE3P temperature 
sensors continuously recording temperature for the whole cast at 24 Hz and one SBE35 
sensor that was triggered by the firing of each bottle. When triggered, the SBE35 
was set to average over 9 measurement cycles and each measurement cycle is about 1.1 
s, so SBE35 measurements at the bottle stops represent averages over approximately 
10 s windows. The SBE35 did not collect data at other times.

In contrast to the real-time data acquisition of the SBE3P sensors, the SBE35 stores 
all of its data internally. After the cast, the sensor uploads its data via the CTD 
deck unit. The upload process is manually initiated by the CTD operator and due to 
the limited memory of the SBE35, data may be overwritten if not downloaded 
regularly. The SBE35 data are stored as a series of ASCII files, usually one for 
each cast, in cruise/data/ctd/ BOTTLE_SBE35. As the data download process is manual, 
the following anomalies were noted:

CTD003 – 14 samples on the SBE35 but only 13 bottles fired. This is due to a test 
ire on deck before the cast.

CTD015 – SBE35 data pointer not reset to 1 from the previous cast. CAP ASCII file by 
hand to remove the data from the previous cast and reset the bottle numbers to be 
consistent with just cast 15.

CTD016 – Error during data download, only the first bottle was recorded. CTD018 – No 
bottles fired due to carousel failure so no SBE35 data.

CTD025 – Error in saving data capture file resulting in some of the header 
information in the .asc file being copied into the data capture file. Manual edits 
to the capture file so it can be in the same format as the other data files but no 
data loss.

CTD028 - SBE35 data pointer not reset to 1 from the previous cast. CAP ASCII file 
modified by hand to remove the data from the previous cast and reset the bottle 
numbers to be consistent with just cast 28.

CTD032 – Only 13 data scans logged because bottles 8 and 9 fired too close together 
in time. Both bottles fired at the same depth.

CTD036 – Data pointer not reset after download after cast 35, so CTD035 data 
included in this file. Manually removed CTD035 data and reset the bottle numbers 
after this data was ingested in MSTAR. In the process, confirmed that manual edits 
are not necessary as MSTAR can detect duplicate data (see below).  No data lost.

CTD037, 038 – data missing.

CTD045 – Data for this cast appended to CTD044 (data pointer not reset, no data 
lost). No manual changes made to original files since MSTAR edits out data 
duplication.

CTD047 – Only data from the deepest bottle was recorded (similar to CTD016). CTD058 
to 061 – Data not downloaded and overwritten by subsequent casts.

CTD067 – Data pointer not reset from previous cast. Manually removed previous casts 
data and renumbered the firing index.

CTD073 – Data point not reset from previous cast, no data lost. No manual changes 
made to original files since MSTAR edits out data duplication.

CTD074 to 084 no bottles fired so no SBE35 data.

MSTAR will ingest SBE35 data via the msbe35_01 and msbe35_02 pipeline where SBE35 
data are read from the ASCII files and pasted into the sample file, respectively. 
The first step reads in all the SBE35 data from all casts and checks each SBE35 data 
time stamp with the cast start and stop times in the .dcs file so SBE35 data is 
automatically sorted by cast (please see MSTAR processing, above). Due to this 
functionality, occasionally forgetting to reset the SBE35 data pointer during the 
data download does not have an impact on how the data are ingested into the MSTAR 
database. A subset of the SBE35 data were manually inspected, including all casts 
where the data pointer was accidentally not reset and a handful of normal casts, to 
check that data were transcribed accurately and no anomalies were noted. Once SBE35 
data are pasted on the sample files, the master sample file must be updated with 
msam_updateall.


5.6  Temperature sensor performance

Figures 5.7 and 5.8 show the differences between each temperature sensor for all 
bottle stops and bottle stops below 1000 dbar, respectively. All sensors performed 
reliably and no temporal drift was detected in any sensor relative to the others. 
The median differences between the primary and secondary SBE3P sensors and the SBE35 
are -0.0009°C (SBE35 cooler) and +0.0012°C (SBE35 warmer), respectively. The median 
difference between the primary and secondary CTD sensors was 0.0021°C. As all three 
sensors are factory calibrated to an accuracy of 0.002°C and given the overall noise 
(on the order of at least 0.001°C) in the sensor-to-sensor comparisons, there is no 
firm basis for deciding whether either SBE3P sensor should be adjusted relative to 
the SBE35. Taking the SBE35 as the reference temperature measurement, both SBE3P 
sensors are within the 0.002°C accuracy limit for WOCE quality data.

Sensor mounting position does play a role in the observed temperature differences.  
In particular, the secondary SBE3P, T2, was mounted immediately next to the SBE35 
while the primary SBE3P, T1, was mounted on the fin of the CTD. To minimize the 
impact of vertical gradients, the SBE35 itself was mounted horizontally, adjacent to 
the SBE9+ underwater unit in the bottom section of the CTD frame. In Figures XX and 
YY, the upper and lower quantiles for the distribution of temperature differences is 
tighter for SBE35 minus T2 than SBE35 minus T1, suggesting that the uncertainty in 
the temperature difference is smaller for sensors that are mounted more closely 
together. Furthermore, CTD053 with all bottles fired near the bottom at ~2200 m in 
the relatively homogeneous Labrador Sea Water, is a unique opportunity to repeatedly 
sample nearly uniform water. Consistent with the overall results, for CTD053, T1 was 
0.0009 ± 0.0002 °C warmer and T2 was 0.0014 ± 0.0001 °C cooler than the SBE35.

Since these median temperature differences, observed under nearly ideal conditions, 
are consistent with the median differences over the whole cruise, we conclude that 
the temperature sensors performed consistently.


Figure 5.7: Temperature differences between each of the three sensors for all 
            bottle stops. The histogram bin intervals are at 0.0005 °C, the 
            precision of all three sensors. Solid red lines are the lower 
            (25%), middle (50%, i.e. median), and upper (75%) quantiles of the 
            differences between the sensors.  Dashed red lines are the 5% and 
            95% quantiles.

Figure 5.8: Same as Figure 5.7 except only for temperature data at bottle 
            stops below 1000 dbar.



5.7  Conductivity calibration

The calibration of the CTD conductivity sensors was achieved by directly comparing 
conductivity from Niskin bottle salinity samples measured in the laboratory (Chapter 
9) with a subset of data from the primary and secondary conductivity sensors, C1 and 
C2, respectively, taken at the time of bottle closure. The WOCE precision limit for 
salinity is 0.002 PSU, which, depending on temperature, translates to approximately 
0.0015 to 0.0023 mS/cm in conductivity difference or the range from 0.99995 to 
1.00005 in conductivity ratio. The calibration steps are similar for the primary and 
secondary conductivity sensors but both sensors were calibrated separately. The 
residuals between the bottle data and the primary and secondary sensors are compared 
to check for any possible temporal drifts or pressure effects on the conductivity 
calibration.

The conductivity sensors showed differences from around 0.004 PSU on the beginning 
casts to around 0.009 PSU towards the end of the cruise. The station-by-station 
correction determined by comparing the bottle conductivities with CTD conductivities 
will be detailed below and any calibrations were applied after spikes were removed 
during MSTAR processing (Section 5.2).

As with oxygen, the conductivity calibration is essentially two steps. The first 
step is a linear it between bottle conductivity and C1 and C2. The second step is a 
correction based on the residuals from the first step (usually to correct for 
pressure effects or temporal drifts). We attempted applying different linear fits to 
subsets of the data, grouped by station. However, in the end, we chose to apply a 
single linear it over all the data because of large temporal discontinuities in the 
salinity offsets that arose with different linear its being applied over different 
subsets of the stations. Figures 5.9 and 5.10 show the initial, uncalibrated 
differences between CTD and bottle data for C1 and C2, respectively. In general, for 
both conductivity sensors, there does not seem to be a pressure effect. However, 
both conductivity sensors exhibit temporal drifts with the drift in C1 being bigger 
than C2.


Figure 5.9: Uncalibrated CTD primary conductivity residuals and ratios 
            compared to the corresponding bottle conductivities.

Figure 5.10: Same as Figure 5.9 except for the secondary CTD sensor.


Once a linear it, using standard practice to force the intercept to zero, was 
applied, new residuals were computed and are displayed in Figures 5.11 and 5.12 for 
C1 and C2, respectively. These residuals are the basis for the station by station 
conductivity adjustment was applied to the data to compensate for the temporal 
drift. As shown in Figures 5.11 and 5.12, a parabolic it does not sufficiently 
capture the range of the drift, so a piecewise linear adjustment was applied on a 
station-by-station basis instead. The final salinity residuals calculated from the 
calibrated conductivity data are shown in Figures 5.13 and 5.14. Table 5.1 summaries 
the parameters for the calibrations applied to the two sensors as well as the 
resulting estimates for the overall accuracy of the calibrations.


Figure 5.11: Conductivity residuals plotted with station number after the 
             linear calibration it was applied on the primary conductivity 
             sensor. The piecewise linear adjustment is shown by the bold red 
             line. A quadratic it for the adjustment, which was not used, is 
             shown with a blue line.

Figure 5.12: Same as Figure 5.11 except for the secondary conductivity sensor.

Figure 5.13: Salinity residuals between bottle salinity and CTD-derived 
             salinity from the primary instru-ments after calibration slope 
             and station-by-station adjustments were applied. Red plus signs 
             are residuals outside of ± 3 standard deviations.

Figure 5.14: Same as Figure 5.13 except for the secondary conductivity sensor.


Table 5.1: Summary of parameters and performance of conductivity calibration. 
           The symbol C' represents conductivity residuals, C' = Cbottle – 
           CCTD. All conductivities are in units of mS/cm and all salinity are 
           in practical salinity units. The mean conductivity residuals from 
           stations 1-6, 10-20, and 85-89 were used to determine the endpoints 
           of the red lines in Figures 5.11 and 5.12 – the linear conductivity 
           adjustments that were applied to each sensor to account for the 
           temporal drift of the sensors.

  Calibration parameter     Primary Conductivity     Secondary Conductivity          
--------------------------  --------------------  ----------------------------
mean(abs(C')) no calibra-     0.0032 ± 0.0016           0.0027 ± 0.0012          
tion [mS/cm], removing ± 
     3 std residuals        

  Slope (intercept = 0)        1.0000832788               0.9999343064          

mean(abs(C')) after slope     0.0013 ± 0.0014           0.0011 ± 0.0013
        applied                    

    Mean C' stn 1:6             -0.0022095                -0.0012403             
        Mean 

     C' stn 10:20               -0.0004107          0 (no adjustment applied)          
  
   Mean C' stn 85:89             0.0013027          0 (no adjustment applied)            

   mean(abs(C')) after        0.0010 ± 0.0013           0.0010 ± 0.0014          
   adjustment applied    

   mean(abs(S')) [PSU]        0.0010 ± 0.0014           0.0011 ± 0.0014          

   mean(abs(S')) after        0.0009 ± 0.0009           0.0009 ± 0.0009          
    removing ± 3 std      

   mean(abs(S')) after        0.0006 ± 0.0006           0.0006 ± 0.0006
  removing ± 3 std and 
     below 1000 dbar.    


The calibration slopes and temporal adjustments in Table 5.1 were applied to the 
data in MSTAR with the wrapper script mctd_condcal, which, in turn, calls 
cond_apply_cal, a script designed to hold the exact parameters of the conductivity 
calibration. The calibration was applied to the 24 Hz data for each station which 
then had to be reprocessed with mctd_03, mctd_04, mir_03, and mir_04 to recreate the 
calibrated 1Hz, 2dbar, and sample files.


5.8  Cast anomalies

This section details some overall cast anomalies that had implications for one or 
more streams of the CTD data.

CTD002 – bottles had to be fired manually due to a PC setup error. Operator fired 9 
bottles, but when the package came up on deck, only 8 bottles had closed. The same 
setup error resulted in the Seabird .bl file not being created so we had to turn to 
the operator logsheet and the SBE35 time stamps to figure out the bottle firing 
order.

On the logsheet for cast 2, the first two bottles were commanded to ire at the 
bottom with less than 1 minute spacing between them. Then, bottles were fired about 
every 2 to 4 minutes for the duration of the cast because no other bottles were 
fired at the same depth and the bottles were spaced pretty closely together (max 
spacing ~25 m). The SBE35 sampling timestamps were of by a couple minutes from the 
CTD logsheet probably due to a slight offset in the SBE35 clock. However, the 
spacing between SBE35 timestamps are all about 2 to 4 minutes. This means that the 
initial double ire at the deepest level was not registered by the SBE35. Assuming 
that the bottle closing carousel operated in sync with the SBE35, either the first 
or the second bottle did not ire and the rest of the bottles closed one after the 
other.

As all the samples will be logged in MSTAR based on cast number and (Niskin) bottle 
number, we don't need to make any special considerations for the labelling of 
samples. We do, however, need to reconstruct the Seabird .bl file so that MSTAR 
knows what scans to use when constructing sub-samples of the sensor data to compare 
to the bottle data for calibration.

To reconstruct the .bl file, the following information is required: bottle firing 
sequences, bottle positions, firing times, first scan and the last scan.  It was not 
possible to use the SBE35 for the bottle firing times as the SBE35 internal clock is 
offset to the CTD. It could however be used as a guide. In order to assimilate the 
bottle firing times, plots were created of scan vs depth from the .cnv file. This is 
shown in Figure 5.15. Here we could see where the CTD had stopped in the water 
column to ire a bottle. Using the plot and zooming in we got the first scan number 
(when the scans settled at the firing depth).


Figure 5.15: CTD depth versus data scan to identify when the bottles fired on 
             CTD cast CTD002. Red circles indicate the scan numbers that were 
             used to reconstruct the .bl file for CTD002 and indicate a best 
             estimate for when the bottles were fired.


The normal firing procedure is to wait 30 seconds before firing a bottle at a 
desired depth, however when we calculated the first and last scan numbers, this 
seemed too short for the time the CTD stayed at these firing depths. We therefore 
assumed a minute was left before firing a bottle and this resulted in a more 
realistic scan number.

To calculate the scan number, we needed to know the frequency of the CTD output. The 
CTD is recording at 24Hz. Therefore, to include a 60 second wait, 1440 (60 *24=1440 
scans) was added from the initial first scan from looking at Figure 5.15.

In order to obtain the last scan number, we looked at the other .bl files and this 
showed the number of scans from start to end that are averaged for each bottle and 
this was 36 scans (1.5 seconds). Therefore, after calculating the first scan (from 
looking at the plot and adding the waiting time) we added 36 to get a last scan 
number.

The first and last scan number was then added to Figure 5.15 in red. These scans it 
nicely into the middle of where the CTD has stopped so we are confident this 
approach has worked. We then worked out the times of these firings and checked them 
against the operator log as a sanity check.

CTD018 – Carousel Failure, so no bottles were fired. CTD data acquisition was 
restarted at the bottom of the cast when computer and manual attempts to ire bottles 
failed, to no avail. The down and up casts were manually stitched together after the 
standard Sea-Bird processing (convert, align, cell thermal mass) but before the 
MSTAR processing steps. The carousel was replaced with a new unit and operated well 
on subsequent casts.

CTD021 - reported Niskin 11 was leaking slowly. CTD029-031 – reported Niskin 09 was 
leaking slowly.

CTD053 – all bottles fired at bottom for micro-plastics study. CTD062 – Pumps took 
10 minutes to start.

CTD065 – Initially aborted as pumps failed to turn on. Sea-Bird 9plus unit replaced 
with S/N 0803 and cast redeployed. The sensors remained the same.

CTD071 – Pumps did not work on first attempt with possibility of air trapped in the 
system. CTD brought back on deck to re-lush with seawater. Second attempt 7 minutes 
to start.




6  VESSEL MOUNTED ADCP
   Liz Comer


6.1  Synchronisation

The processing method described here is very much the same as that in DY031 but some 
sections may be updated or edited. The Discovery has two VMADCPs; the 150 kHz and 
the 75 kHz. Both were switched on at the start of DY052. There are many acoustic 
instruments on the ship, such as the EM122 Deep Water Multibeam Echosounder, EM710 
Shallow Water Multibeam Echosounder, SBP120 Sub-bottom Profiler, EA640 Single Beam 
Echosounder, EK60 Multi-frequency Echosounder (‘fish-finder’) and the Kongsberg SU16 
Synchronisation Unit (K- Sync). The VMADCP’s were triggered and running as normal 
with K-Sync.


Figure 6.1: Screenshot of K-Sync setup.



6.2  Data summary

Whilst processing the OS75 data it was noticed that it produced significant amounts 
of poor quality bins and the instrument was not producing any data throughout the 
water column regularly. This is still to be fully investigated but likely to be 
caused by either bubbles near the mounted instrument or interference with other 
acoustic instruments. However, when on-station the OS75 produces reasonable data, 
with a good data quality. The percent good data images in Figures 6.2 and 6.3 show 
that the OS150 and OS75 are preforming at similar levels with better data quality 
over shallow regions and lower data quality in adverse weather conditions. The OS75 
has a larger spread of percent good data which is seen in a visual inspection of the 
bottom images.


Figure 6.2: The top image shows a timeseries of the percent good data for the 
            OS 75 kHz and the bottom shows its column-by-column average over 
            time.

Figure 6.3: The top image shows a timeseries of the percent good data for the 
            OS 150 kHz and the bottom shows its column-by-column average over 
            time.


Multiple re-starting events at the beginning of the cruise, for both the instruments 
but more so in the OS 75 kHz, is due to the setup of the command file. Towards the 
end of the cruise it was noticed that the VMADCP automatically collects bottom 
tracking data when in shallow enough water, therefore, the bottom tracking command 
file did not need to be activated manually. All raw data has been kept from both 
instruments. The successfully processed files are given in the tables below. Any 
gaps in the record correspond to when raw data files were not successfully 
processed, usually due to short files during the testing of the instrument setup.


Table 6.1: Data file information for the 75 kHz VMADCP.

           File no.      Start       End      Comments  
           --------  -----------  ----------  --------
              01       7/6 19:03   8/6 07:37   BT on  
              36       8/6 14:24   8/6 14:49   BT on  
              37       8/6 14:50   8/6 15:52
              38       8/6 15:52  10/6 12:23
              39      10/6 12:24  10/6 15:00   BT on  
              40      10/6 15:00  11/6 14:04
              41      11/6 14:04  12/6 14:27
              42      12/6 14:27  13/6 13:57
              43      13/6 13:57  14/6 14:01
              44      14/6 14:01  15/6 12:06
              45      15/6 12:06  15/6 15:21   BT on  
              46      15/6 15:22  15/6 15:54
              47      15/6 15:54  15/6 18:47   BT on  
              48      15/6 18:48  16/6 13:59
              49      16/6 13:59  17/6 14:53
              50      17/6 14:53  18/6 00:15
              51      18/6 00:16  18/6 14:13
              52      18/6 14:13  19/6 14:23
              53      19/6 14:23  20/6 13:58
              54      20/6 13:58  21/6 14:09
              55      21/6 14:09  22/6 13:57
              56      22/6 13:57  23/6 14:38
              57      23/6 14:38  23/6 19:54  



Table 6.2: Data file information for the 150 kHz VMADCP.

           File no.      Start       End      Comments  
           --------  -----------  ----------  --------
              24       7/6 19:39   8/6 06:25  BT on
              30       8/6 14:45  10/6 12:22
              31      10/6 12:23  10/6 14:59  BT on
              32      10/6 15:00  11/6 14:04
              33      11/6 14.04  12/6 14:26
              34      12/6 14:26  13/6 13:57
              35      13/6 13:57  14/6 14:00
              36      14/8 14:01  15/6 12:05
              37      15/6 12:05  15/6 15:20  BT on  
              38      15/6 15:21  15/6 15:53
              39      15/6 15:53  15/6 18:46  BT on
              40      15/6 18:47  16/6 13:58
              41      16/6 13:59  17/6 14:53
              42      17/6 14:53  18/6 14:12
              43      18/6 14:12  19/6 14:23
              44      19/6 14:23  20/6 13:58
              45      20/6 13:58  21/6 14:09
              46      21/6 14:09  22/6 13:57
              47      22/6 13:57  23/6 14:38
              48      23/6 14:38  23/6 19:53  
              


6.3  Processing

Data processing followed the usual paths:

Stage A: Initial Processing

i) Copy data from the ship server:

cd data
cd vmadcp cd v150

Remove the directory and data with the largest sequential number. You need to do 
this because the linkscript also copies data that is still being collected, creating 
a new incomplete rawdataNNN directory, and if a directory is already present it does 
not get updated with new data. To copy the most up to date data (once the logging 
has been restarted) it is necessary to remove the directory with the largest 
sequential number before running vmadcp_linkscript*.

e.g. for file 128:
/bin/rm ./rawdata/*128*
/bin/rm -r rawdata128
/bin/rm -r dy052128nbenx 

Now copy the new data files: 

vmadcp_linkscript150


This script redistributes raw data from rawdata to rawdataNNN; rawdataNNN is 
automatically created if necessary (may need to edit movescript so that it parses 
the file names correctly). Now do the same for the os75:

cd data
cd vmadcp cd v75
/bin/rm ./rawdata/*128*
/bin/rm -r rawdata128
/bin/rm -r dy031128nbenx vmadcp_linkscript75

The following steps are repeated for each v150 and v75 data file.

ii) Create a new directory containing all the output files:

cd v150 (or v75)
adcptree.py dy052NNNnbenx --datatype enx

iii) Copy calibration files into the directory for each data file (there is a 
template file called q_py.cnt in data/v150 and data/v75):

cd dy052NNNnbenx 
cp ../q_py.cnt .

Generally, only the dbname and datadir for each NNN need to be updated. 

For information, an example q_py.cnt file is

# q_py.cnt is
## comments follow hash marks; this is a comment line
--yearbase 2016
--dbname dy052001nnx
--datadir /local/users/pstar/cruise/data/vmadcp/v75/rawdata001
#--dataile_glob "*.LTA"
--dataile_glob *.ENX
--instname os75
--instclass os
--datatype enx
--auto
--rotate_angle 0.0
--pingtype nb
--ducer_depth 5
#--verbose
# end of q_py.cnt
# end of q_py.cnt

At the start of the cruise check yearbase, dbname, os75 or os150 and datatype enx 
(glob ENX). dbname should be of form dy052NNNPTT where P is n for narrowband, b for 
broadband. In order to achieve the deepest measurements, the instrument should be 
operated in narrow unless there is a good reason to choose broad. TT is “nx” for 
ENX; “ns” for ENS; “nr” for ENR; “lt” for LTA; “st” for


STA. Standard processing is to process ENX. Traditionally, dbname must not exceed 11 
chars. So, if we use 9 for dy052NNNn, there are only two left to identify ENX, ENS, 
LTA, STA. Without calibration informa-tion, the angle can be left as zero. The 
transducer depth was changed for this file in cruise DY052 to 7. It must be an 
integer.

iv) Process in CODAS (with no calibration)

quick_adcp.py --cntile q_py.cnt

v) To access data in Matlab type in the command line:

>> m_setup
>> codaspaths
>> cd edit
>> gautoedit

The gautoedit utility allows you to view the data and do a quick check for quality. 
Note that the JDAY on the plots is our DOY minus 1. Alter the time step and tick the 
list of variables to plot on the figures (including using depth as x axis), then 
click the "show now" button in order to get plots up on the screen.

Gautoedit does allow you to clean up data but this was not done on DY052. See DY031 
and JC086 cruise reports or CODAS documentation for more information.

Stage B: Finding and correcting the ADCP misalignment angle (the calibration)

Find the calibration information

The calibration information can come from BT (bottom track) or WT (water track) 
files. The latter are generated during sharp turns in the ship's track, especially 
coming on or of station.

Any calibration information produced can be found in the "cal" directories of the 
processing directories (eg dy052001nbenx/cal/*/*out). Note that a calibration is not 
always achieved, for example if the ship has made no manoeuvres while the ADCP is in 
water tracking mode, so there may be no *out file). Note also that additional 
calibration information may be saved after lags are applied after the gautoedit 
process (not done on DY052). Tables 6.3 and 6.4 summarize the DY052 calibration 
information.


Table 6.3: Calibrations from bottom-tracking and water-tracking for v150.

File       Time        BT/   Amp     Mean    STD    Phase    Mean    STD  
           (DoY)       WT   Median                  Median
----  ---------------  ---  ------  ------  ------  ------  ------  ------
024    163.67-164.31   BT   0.9991  0.9990  0.0039  0.2628  0.2609  0.2291
027                    BT   0.9991  0.9990  0.0039  0.2628  0.2609  0.2291
031    161.52-161.62   BT   0.9981  0.9994  0.0067  0.3461  0.5980  0.5760
037    166.51-166.24   BT   0.9970  0.9967  0.0022  0.1317  0.1505  0.2267
039    166.67-166.78   BT   0.9988  0.9993  0.0027  0.1189  0.0724  0.2313
Mean                        0.9984                  0.2245
WT    mean of all files             1.0007  1.0019          0.2968  0.2753


Table 6.4: Calibrations from bottom-tracking and water-tracking for OS75.

File       Time        BT/   Amp     Mean    STD    Phase    Mean    STD  
           (DoY)       WT   Median                  Median
----  ---------------  ---  ------  ------  ------  ------  ------  ------
001    158.80-159.24   BT   1.0151  1.0156  0.0035  0.7339  0.7572  0.2113  
036    159.61-159.61   BT   1.0179  1.0179  0.0028  0.4561  0.4561  0.1566  
039    161.52-161.62   BT   1.0148  1.0121  0.0086  0.8307  0.7586  0.7533  
045    166.51-166.64   BT   1.0136  1.0146  0.0044  0.6542  0.6484  0.4104  
047    166.67-166.78   BT   1.0144  1.0148  0.0032  0.6012  0.5379  0.2832  
Mean                        1.0152                  0.6552
WT    mean of all files             1.0199  1.0209          0.6196  0.6077  


ii) Select the most reasonable looking values of the amplitude and phase.

Reasonable might mean the values from a large file, or from BT rather than WT, or an 
average of all the median values produced. One can take into account values from 
previous cruises on the same ship, as long as the ADCP has not been refitted since 
then. On DY052 we chose the mean of the BT median values (bottom row of Tables 6.3 
and 6.4) which is consistent with the method from last year’s cruise (DY031). It is 
also useful to note that the BT median shows a similar value to the BT mean and is 
consistent from file to file.


iii) Apply the calibration

The calibration application is repeated for both ADCPs and for each data file. The 
calibration was applied by manually putting the amplitude and phase coefficients 
determined above into the control files ("q_pyrot.cnt"), one for each instrument. If 
required, different values for groups of files can be manually specified, in 
particular for cases where there are different EA values in the command files. An 
example q_pyrot.cnt with calibration coefficients contains:

# q_pyrot.cnt for OS 150 DY052
## comments follow hash marks; this is a comment line
--yearbase 2016
--rotate_angle 0.2245
--rotate_amp 0.9984
--steps2rerun rotate:navsteps:calib
--auto
# end of q_pyrot.cnt

Still in directory dy052NNNnbenx, apply the final calibration only once. Adjustments 
are cumulative so if this step is done twice the cal is applied twice.

quick_adcp.py --cntile q_pyrot.cnt


Stage C: Merge VMADCP data into MSTAR

i) Still in directory dy052NNNnbenx open a Matlab window and type into its command 
line:

>> mcod_01

This step produces an empty output file os75_jr265NNNnnx.nc.

>> mcod_02

This step will grab water speed and ship speed from the VMADCP files and get all the 
variables onto an NxM grid.

ii) Append individual files using:

>> mcod_mapend

This script will append individual files to create a single cruise file ("_01"). 
This script expects the files to have the same bin number and bin depths.  On DY052 
we did this after every VMADCP file was processed. If this is done periodically, the 
new .nc file needs to be manually added to the ‘nc_iles’ text file, which contains a 
list of all the processed ones.


iii) Create .mat files specific to each CTD stations

>> mcod_03
>> mcod_stn_out(‘ctd’,nnn,75)


In the above, nnn is the CTD cast number. This script will generate the .mat files 
in: ~/cruise/data/vmadcp/dy052_os75

The final step is to make the data available for LADCP processing. Create symbolic 
links to the .mat files in /ladcp/ix/data/SADCP with the format 
‘os75_dy052_ctd_nnn.mat’. The VMADCP data will now be available for comparison with 
LADCP data and for providing a constraint on the processing. During LADCP 
processing, the .mat files are automatically picked up by the ‘process_cast’ script 
(Chapter 7).







7  LOWERED ADCP DATA PROCESSING
   Jonathan Tinker and Stefan Gary


This chapter builds on the LADCP processing carried out during DY031, the 2015 EEL 
cruise. As such, the LADCP section of the DY031 cruise report was the starting point 
for this section and is updated here to reflect the data pipeline during DY052.


7.1  Introduction and data processing

Data from the LADCP instrument was processed as soon as possible between stations to 
allow early detection of any problems with the ADCP workhorse. The final processing 
relied on the processed CTD casts, and the processed VMADCP (which also relied on 
the processed CTD casts), and so LADCP was at the end of the chain of processing.

Data quality were checked in WinADCP by the CTD operators (Colin Hutton, Estelle 
Dumont, and Jon Short) immediately after download from the LADCP. They copied the 
data files and the pre-deployment log text files from the LADCP PC onto the 
DY052/Public server. The instruments performed well and there were no problems. The 
LADCPs had just been recalibrated at the factory and so they were rotated out prior 
to casts 51 and 74 (Chapter 4).

Processing was via the Lamont-Doherty IX.8 software. The processing was performed in 
three steps, each with additional supplementary data to further constrain the LADCP 
results:

The data from the LADCP were processed in isolation, including bottom tracking from 
the LADCP.
The pressure, temperature, salinity, and lon/lat data from the CTD were included in 
the processing.
Data from the vessel mounted ADCP (VMADCP, or in the IX software, referred to as 
SADCP) were compared to the result from step 2.

Data from the VMADCP were included as a constraint, along with bottom tracking, GPS, 
and CTD data, in the LADCP processing.

At sea, a Linux link script was run followed by Matlab processing and as Matlab 
wrote the output file to the same directory each time (DL_BT), the files were then 
moved to DL_LADCP, DL_CTD, and DL_VM_ADCP_75 for steps 1, 2 and 3, respectively. 
Step 4 was performed ashore and during that step, all the processed data were 
written directly to the directory DL_BT_GPS_CTD_SADCP.

Bold text denotes commands to enter at the X-window/terminal prompt. ‘>>’ preceding 
bold text indicates commands to be entered in the Matlab window.

Step 1: Processing without any auxiliary data

a) Move to the appropriate location on the Unix system. The linkscript creates a new 
directory for that cast and creates a symbolic link with the filename structure that 
the processing expects.

cd ~/cruise/data/exec 
lad_linkscript_ix_dy052

b) Open Matlab window, move to the processing directory, setup paths, and process 
the cast:

>> m_setup
>> mcd ladcp
>> cd ix/data
>> ixpath
>> process_cast(nnn)

c) Copy output files to the correct location 

The previous step put the output into
~/cruise/data/ladcp/ix/data/DL_BT/processed
The output includes a number of ps files, and a .mat file of the format nnn.mat 
(where nnn is the zeropadded cast number i.e. 001). The .mat file includes a 
structure called dr which will not include the fields ctd_t, or u_sadcp. These data 
should be moved to ../../DL_LADCP/processed

mv  ~/cruise/data/ladcp/ix/data/DL_BT/processed/nnn*
~/cruise/data/ladcp/ix/data/DL_LADCP/processed/nnn*


Step 2: Processing with CTD and GPS

a) Created Linux link files:

cd ~cruise/data/ladcp/ix/data/raw 
ladctd_linkscript_ix

b) Process in Matlab using the same series of steps as in Step 1.

c) copy to the correct location

The .mat files will now have a ctd_t field, but still no u_sadcp field

mv  ~/cruise/data/ladcp/ix/data/DL_BT/processed/nnn*
~/cruise/data/ladcp/ix/data/DL_CTD/processed/nnn*


Step 3: Processing compared to VMADCP

a) Created link files:

cd ~cruise/data/ladcp/ix/data/raw 
ladvmadcp_linkscript_ix

b) Process in Matlab

c) copy to the correct location


The .mat files will now have both ctd_t field and u_sadcp ields

mv  ~/cruise/data/ladcp/ix/data/DL_BT/processed/nnn*
~/cruise/data/ladcp/ix/data/DL_VM_ADCP_75/processed/nnn*



Step 4: Processing with all constraints, including VMADCP

Post cruise, it was found that the variable ps.sadcpfac was set to 0 in 
set_cast_params.m which effectively removed the VMADCP from processing the LADCP 
data but still loaded the VMADCP data for comparison with the LADCP. To rectify this 
omission, all LADCP data were processed again, this time including the VMADCP data 
by setting ps.sadcpfac = 1 in set_cast_params.m. All data processed at this level 
were written to DL_BT_GPS_CTD_SADCP/processed and the *.lad, *.mat, and *.ps files 
were retained. This final level of processing, including the VMADCP and other 
constraints, is the data submitted to BODC along with the raw data files.

For all processing ashore, the geomagnetic database was updated from IGRF11 (used at 
sea) to IGRF12 (http://www.ngdc.noaa.gov/IAGA/vmod/igrf.html). All LADCP profiles 
were visually inspected to check for consistency with the VMADCP constraint (at the 
top of the profile) and the bottom tracking constraint (at the bottom of the 
profile).


7.2  Preliminary quality checks

Some of the figures generated by the processing script are particularly useful to 
provide early indication of poor quality data, possible faults, and incorrect 
transfer of the raw data. Use the paper log file (“LADCP_QC_JT.xlsx”) to note the 
following points, and then compare to the CTD logs where necessary. The following is 
a list of what was looked at in each of the figures generated by the Matlab 
processing.

Figure 1: Make sure that the bottom track velocities (bottom part of the plot on the 
          left-hand side) match those of the water track (plot on the left-hand side). 
          Also, check if time and depth of the cast indicated in Figure 1 match with 
          the corresponding logged data.

Figure 2: Check the performance of the four beams from the bottom-left plot. This 
          figure also indicates the CTD heading direction. This can represent valuable 
          information for the CTD operator, in case it is spinning excessively.

Figure 4: Compare profiles from down and up casts and check if they are both complete. 
          If not, this could indicate a fault. This figure also indicates the depths 
          of the cast, which can be checked against logged information.

Figure 11: This figure provides a list of processing errors and warnings.

For each cast, these figures (from the CTD processing) were assessed and logged in 
the log sheet “LADCP_QC_JT.xlsx”: for figure 1, the profile was compared to the 
bottom track, the start and stop time was noted, and the max depth; figure 2, the 
number of spins (heading time-series) and beam performance (that they were similar 
to one another etc.); figure 4, that the top and bottom profile match (lower left 
panel), and the bottom depth (bottom at: - middle panel); figure 11, any other 
errors. The depths and times were then compared to the CTD logs.

Cast 068: did not process at the first stage (without CTD or VMADCP) as there was 
insufficient data.

Processing was completed for every cast at the second stage (with CTD). 

For processing with the VMADCP data, the following anomalies were noted:

Cast 001: was not processed with the VMADCP, as there was no VMADCP data.
Cast 061, 062, 068, 070-072 did not have sufficient VMADCP data to create a 
constraint for the LADCP data.


Specific error messages from the LADCP processing:

Cast 002: shifted ADCP timeseries by 122 seconds
Cast 005: Battery voltage is low : 36.8 V
Cast 006: Battery voltage is low : 34.8 V 
Cast 007: Battery voltage is low : 34.2 V 
Cast 008: Battery voltage is low : 32.9 V
Cast 037: shifted ADCP timeseries by 17 seconds 
Cast 060: shifted ADCP timeseries by 37 seconds 
Cast 061: shifted ADCP timeseries by 45 seconds
Cast 062: all SADCP values removed because of low weight 
Cast 063: all SADCP values removed because of low weight
          large V bottom track bias 0.11082
Cast 070: all SADCP values removed because of low weight 
Cast 071: all SADCP values removed because of low weight


7.3  Initial results

Some Matlab functions and scripts were created to allow for an initial data 
analysis. These are found at:
cd  /home/mstar/Desktop/DY052/LADCP/

The main script,

>>  JT_plotting_LADCP_proc_comp

shows the LADCP data with each level of processing (Figure 7.1) and the effect each 
level of processing has (Figure 7.2). We found that the CTD and GPS data had an 
appreciable effect on the results. The VMADCP constraint also had an impact, but 
less so than the CTD.


Figure 7.1: Lowered ADCP data with different stages of processing. Velocity shading is 
            in units of m/s. The vertical axis is depth (m) and the horizontal axis is 
            distance along the section starting in Iceland (km).

Figure 7.2: Effect of each stage of processing on LADCP. The top row is the 
            differences between LADCP only and LADCP + CTD + GPS. The bottom row is 
            the differences between LADCP + CTD + GPS and LADCP + CTD + GPS + VMADCP. 
            Velocity shading is in units of m/s. The vertical axis is depth (m) and 
            the horizontal axis is distance along the section starting in Iceland (km).



 
8  UNDERWAY DATA PROCESSING
   Robert King

The underway observations include data-streams from navigation, echo sounding 
bathymetry, meteorological observations, and sea surface observations.

Much of the processing has followed the steps used during last year's Extended 
Ellett Line cruise (DY031) with some changes to account for changes in data-streams. 
Extracts of these notes are based on the previous Ellett line cruise DY031.


8.1  Daily processing

The daily processing for DY052 involved the following steps:

1)  The techsas link script was run to create a directory of symbolic links to the 
    netCDF files in the TechSAS stream.

~/mstar/dy052/data/exec/techsas_linkscript_dy052.sh

For the first two days (20160607-08) of DY052, an error in the server configuration 
meant that TechSAS netCDF files were spread across two folders. This script was 
hard- coded to copy the different dates from the appropriate network location. Also, 
for some early dates in the cruise duplicate files with time-stamps offset by 1-
second were present. This may have been caused by data-streams being 
paused/restarted.
The link script removes the unnecessary duplicates.

There was also an intermittent problem with some of the TechSAS netCDF files which 
required close inspection. Occasionally, the final (few) elements of the time 
variable would be set to zero (the ill value specified in the netCDF file) which 
would cause the underway and CTD processing to fall-over. A short script to identify 
the files was written and a work-around added to the linking script which removes 
the offending elements from all variables. See 
techsas_linkscript_dy052_check_bad_data.sh and techsas_ 
linkscript_dy052_bad_data.sh. This was not automated further as the number of 
trailing zeroes varied and once was not the final value. It would be better in 
future to adapt MSTAR to deal with masked times in the netCDF files.

In total, for each date there were 18 unique files produced from the different 
streams:

CLAM-CLAM_DY1.CLAM
cnav-CNAV.GPS
EA600-EA640_DY1.EA600
gyro-GYRO1_DY1.gyr gyro-SGYRO_DY1.gyr
Light-DY-SM_DY1.SURFMETv2
lgskippervdvbw-SkipLog.winch 
MET-DY-SM_DY1.SURFMETv2
positon-Applanix_GPS_DY1.gps 
position-Seapath330_DY1.gps 
satelliteinfo-Applanix_GPS_DY1.gps 
satelliteinfo-CNAV.gps
satelliteinfo-Seapath330_DY1.gps 
SBE45-SBE45_DY1.TSG
shipattitude-Applanix_TSS_DY1.att 
shipattitude_aux-Applanix_TSS_DY1.att 
Surf-DY-SM_DY1.SURFMETv2
wamos-WaMoS.wamos

Note that the EM120 echo sounder was not logging in TechSAS.

2) To confirm that the linking script properly updated the available data-streams to 
   process a full day, in MatLab run

>> mtlookd  
   # Num     Start      StartJD            EndJD 
   Cycles    Date      StartTime          EndTime     EndDate               DataStream
----------  --------  ------------      ------------  --------  -------------------------------------
   1415366  16/06/05  157 09:00:01  to  174 02:09:38  16/06/22  CLAM-CLAM_DY1.CLAM  
   138561   16/06/07  159 12:00:42  to  173 14:47:04  16/06/21  EA600-EA640_DY1.EA600
   1526145  16/06/05  157 09:00:01  to  174 02:09:40  16/06/22  Light-DY-SM_DY1.SURFMETv2
   1526145  16/06/05  157 09:00:01  to  174 02:09:40  16/06/22  MET-DY-SM_DY1.SURFMETv2
   1372783  16/06/05  157 09:00:01  to  174 02:09:40  16/06/22  SBE45-SBE45_DY1.TSG
   1526145  16/06/05  157 09:00:01  to  174 02:09:40  16/06/22  Surf-DY-SM_DY1.SURFMETv2
   1529700  16/06/05  157 09:00:01  to  174 02:09:39  16/06/22  cnav-CNAV.GPS
   1530481  16/06/05  157 09:00:00  to  174 02:09:40  16/06/22  gyro-GYRO1_DY1.gyr
   6969347  16/06/05  157 09:00:00  to  174 02:09:40  16/06/22  gyro-SGYRO_DY1.gyr
   3583650  16/06/05  157 09:00:00  to  174 02:09:41  16/06/22  logskippervdvbw-SkipLog.winch
   1444081  16/06/05  157 09:00:00  to  174 02:09:39  16/06/22  position-Applanix_GPS_DY1.gps
   1431040  16/06/05  157 09:00:00  to  174 02:09:39  16/06/22  position-Seapath330_DY1.gps
   1444081  16/06/05  157 09:00:00  to  174 02:09:39  16/06/22  satelliteinfo-Applanix_GPS_DY1.gps
   1529700  16/06/05  157 09:00:01  to  174 02:09:39  16/06/22  satelliteinfo-CNAV.gps
   1431040  16/06/05  157 09:00:00  to  174 02:09:40  16/06/22  satelliteinfo-Seapath330_DY1.gps
   1530479  16/06/05  157 09:00:00  to  174 02:09:38  16/06/22  shipattitude-Applanix_TSS_DY1.att
   1530481  16/06/05  157 09:00:00  to  174 02:09:39  16/06/22  shipattitude_aux-Applanix_TSS_DY1.att
    3303    16/06/08  160 15:48:01  to  174 02:03:59  16/06/22  wamos-WaMoS.wamos  


3) To extract the appropriate 24 hours of data from each stream run 
   m_dy052_daily_processing(nnn) where nnn is the Julian Day. This script calls the 
   routine mday_00_get_all and mday_00 for each data stream, skipping any streams not 
   present for the current cruise. The output will be a series of daily files with the 
   raw data from each stream (e.g., attposmv_dy052_d157_raw.nc) which will be stored 
   in the following directories within /home/mstar/dy052/data/

         /em120
         /log_skip
         /met/*
         /nav/*
         /sim
         /tsg
      
The daily processing script does some further processing of specific streams:

mgyr_01 is used to remove any data cycles with non-monotonic times from the ship 
gyro data-stream (nav/gyros)

msim_01 is used to run a median clean and 5-minute averaging of the EA640 echo 
sounder data. The corresponding routine for the EM122 (mem120_01) was not run as the 
EM122 sounder was not logging during this cruise.

msim_plot is used to interactively remove spikes from the echo sounder derived 
depths. Additional files were saved to log which data were rejected. This script was 
edited to explicitly ignore EM122 for DY052. The script relies on a lower resolution 
bathymetry file being available in ~cruise/data/tracks/. This is used to provide a 
comparison for the echo sounder data.

mmet_01 is used to correct the units of wind speed stored in the netCDF header. 
Although the header originally reported the speed in knots, comparison against the 
on- boar live streams showed that the units were in fact m/s.

Finally, the script runs mday_02_run_all to append the daily file onto the cruise 
master file for each stream (e.g., nav/gyros/gyp_dy052_01.nc).

4) Once a TSG salt crate has been run through the AutoSal, calibration of the underway 
   salinity can start.

Further details on individual streams is given below.


8.2  Navigation

As part of the routine daily processing six navigation streams were extracted from 
TechSAS (attposmv, cnav, gyropmv, gyros, posmvpos, seapos). Note that there is 
duplicated information among some of the streams. The posmvpos is the master 
position source. The master file pos_dy052_01.nc contains the full and final cruise 
archive. There was no editing of positional information, except for the removal of 
any non-monotonic times with the routine mgyr_01

Finally, mbest_all was used to run a series of scripts to produce the master bestnav 
file (nav/posmvpos/bst_dy052_01.nc). This uses posmvpos for position, and merges on 
heading so that there is a complete file containing position, heading, course and 
speed made good, and distance run. The data are reduced to a 30-second time base and 
heading is properly vector averaged. This is the definitive cruise navigation file. 
In order to avoid the problem of housekeeping variables like distrun across daily 
files, the bestnav processing is rerun from the start of the cruise each time it is 
required. There is therefore only ever one bst_dy052_01.nc file.


8.3  Bathymetry

On DY052 the EA640 echo sounder was activated when not towing the hydrophone. The 
EM120 sounder observations were not recorded in TechSAS. Since the echo sounder was 
only in operation when not towing the hydrophone, most of the data will correspond 
to time spent stationary at CTD stations.

As part of the daily processing (m_dy052_daily_processing), the bathymetry data from 
EA640 was cleaned of gross errors. Only spikes widely discrepant with the lower 
resolution bathymetry from cruise/data/tracks/n_atlantic.mat were  removed.

Some ~50m spikes were left in place. The constant magnitude of the spikes suggests 
that these could be caused by interference from other instruments.


8.4  Surface atmosphere and ocean observations

The ‘met’ streams are divided into three TechSAS streams: met/surfmet, met/surlight, 
and met/surftsg. The SeaBird SBE45 thermosalinograph data (in surftsg) is also 
logged in separate data stream (in the directory cruise/data/tsg or mexec 
abbreviation M_TSG).



SurfMet

Ship speed, position and heading from the bst navigation file were merged onto the 
wind data in the surfmet stream.

The absolute wind speed is calculated and vector averaged with mtruew_01.m. As with 
bestnav processing, this is rerun for the entire cruise each time the data are 
updated. The output files from this processing are

data/met/surfmet/met_dy052_true.nc 
data/met/surfmet/met_dy052_trueav.nc

The latter file is reduced to 1-minute averages, with correct vector averaging when 
required. In order to avoid ambiguity, variable units are explicit in whether wind 
directions are ‘towards’ or ‘from’ the direction in question.

As stated earlier, mmet_01 is used to correct the units of wind speed stored in the 
netCDF header. Although the header originally reported the speed in knots, 
comparison against the on-board live streams showed that the units were in fact m/s.

SurfLight

PA irradiance and thermal-IR data are found in the surflight stream, which also 
contains surface pressure. These streams were ingested and stored, but no further 
processing was undertaken.

SurfTSG

The daily processing creates two sets of raw files and two concatenated cruise 
master files related to the underway thermosalinograph (TSG) stream:

data/met/surftsg/met_tsg_dy052_d???.nc
extracted from TechSAS data stream Surf-DYS-SM_DY1.SURFMETv2 including variables 
time, temp_h, temp_m, cond, luo, trans

data/tsg/tsg_dy052_d???.nc
extracted from TechSAS data stream SBE45-SBE45_DY1.TSG 
including variables time, temp_h, temp_r, cond, sndspeed, salin

It was found that the surftsg steam was not logging the temperatures (temp_h and 
temp_m) or conductivity (cond). The temperatures were logged as constant values 
while the conductivity variable contained data which did not correlate with the 
expected values. The cruise SST, Jack McNeil, explained that this was a known fault 
with the current set-up of the surftsg stream.

Although the temperature and conductivity were not logged in the surfmet stream, it 
does contain valid observations of the fluorescence and transmissance.

Thermosalinograph (TSG, SurfTSG)

The TSG stream, however, contains the logged temperatures, conductivity, and derived 
salinity. The salinity values were recalculated from the housing temperature and 
conductivity (using mtsg_make_sal.m) to confirm that the salinity values stored in 
the files was reliable and the conductivity units (S/m) as reported in the netCDF 
attributes.

We therefore use the TSG stream in the thermosalinograph calibration (unlike last 
year's cruise DY031 where the SurfTSG stream was used). Calibration used the 
followed steps:

1) Edit mtsg_cleanup.m to hardcode the times when the pumps were switched of, such as 
   the stat and end of the cruise, and any periods of the maintenance. This routine 
   will be run later as part of mtsg_medav_clean_sal.m.
2) Run mcd('M_TSG') to move to the TSG directory within MatLab.

3) Run mtsg_indbad_dy052.m to interactively remove spikes and bad data from the 
   temp_h, cond and salin variables. The commands to select periods to be marked as 
   bad are explained on running the routine. Note the use of 'n' to store the start 
   and end of the bad data and move on to the next segment. The output file with bad 
   times is appended every time this routine is run, so can be done throughout the 
   cruise.
      Input: data/tsg/tsg_dy052_01.nc 
      Output: data/tsg/bad_time_limits.mat

During the spike removal for DY052, a regular feature was noticed (see Figure 8.1): 
approximately every 12 hours, the housing temperature (temp_h) logged by the SBE45 
would sharply increase by ~1.5K (over 1 minute) and decrease back to the background 
level over a period of ~10 minutes. On several occasions this was followed by a 
smaller magnitude signal (around 15 minutes later) with the same features. Although 
this feature was not observed in the remote temperature (temp_r), it was present in 
the conductivity and salinity. These data were therefore excluded from the final 
data-set using mtsg_indbad.


Figure 8.1: The remote temperature (top), conductivity (middle) and salinity reported 
            by the TechSAS TSG stream. The left-hand plot shows a single occurrence of 
            the possible discharge-related feature, while the right-hand plot shows 
            the same feature reappearing on a ~12 hourly cycle.  These data shown are 
            prior to any spike removal or median averaging.


4) Run mtsg_medav_clean_cal_dy052.m to create 1-minute median-binned data and remove 
   known bad data identified in the previous step (the times stored in 
   bad_time_limits.mat).
      Input:  data/tsg/tsg_dy052_01.nc
      Output:  data/tsg/tsg_dy052_01_medav_clean.nc
5) Check for updates to the TSG salinity bottle samples, in data/ctd/BOTTLE_SAL/. When 
   new crates have been processed run cruise/data/exec/modsal_unix_dy052 (in a 
   terminal) to convert the csv file from a Mac format to a unix compatible format 
   (this just adds end-line characters), unless the csv file was created on linux. You 
   may first need to create the CSV file from the AutoSal-produced spreadsheet using 
   Excel or LibreCalc.


   Also, to this file, add a sample number for each underway salinity sample using 
the 
   format DDDHHMMSS (recorded in the underway logsheets) for TSG samples, and sample 
   number 99#### for standards, where #### is the bottle number.
      Input: data/ctd/BOTTLE_SAL/tsg_dy052_nnn.csv 
      Output: data/ctd/BOTTLE_SAL/tsg_dy052_nnn.csv_linux

6) Run mtsg_01_dy052.m to convert TSG salinity bottle samples from ASCII to netCDF. 
   First the routine had to be updated with a cruise specific bath temperature. For 
   DY052, the same settings were used as had been agreed for the CTD salt sample 
   processing. This step can be run as each TSG crate has been processed.
      Input: data/ctd/BOTTLE_SAL/tsg_dy052_nnn.csv_linux 
      Output: data/ctd/tsg_dy052_nnn.nc
      Output: data/ctd/tsg_dy052_all.nc

7) Run mtsg_bottle_compare_dy052.m to merge the clean 1-minute data onto bottle 
   samples. This should first be run with the switch at the top of the script set to 
   uncalibrated. Individual bottle residuals are plotted, as well as a smoothed time 
   series of the residuals, (see Figure 8.2) which can then be used as a slowly-
   varying adjustment to the TSG salinity in the next step.
      Input:  data/ctd/tsg_dy052_01_medav_clean_cal.nc
      Output: data/tsg/tsg_dy052_01_medav_clean_cal_botcompare.nc


Figure 8.2: Left: Salinity difference (PSS-78) between underway bottle measurements 
            and the SBE45 salinity measurement at each sample time (black crosses) and 
            a smoothed it (magenta line). The red crosses show data-points rejected 
            from the smoothed it. Right: Uncalibrated salinity from the SBE45 (blue 
            line) along with the individual bottle samples (red crosses).

8) Run mtsg_apply_salcal_dy052.m to smooth the differences in botcompare, interpolates 
   and adds them to the uncalibrated salinity data. You can run 
   mtsg_bottle_compare_dy052.m after this to check the residuals are acceptable.
   calls mtsg_salcal_dy052.m
      Input: data/met/surftsg/met_tsg_dy052_01_medav_clean.nc
      Input: data/met/surftsg/met_tsg_dy052_01_medav_clean_botcompare.nc 
      Output: data/met/surftsg/met_tsg_dy052_medav_clean_cal.nc

9) Rerun mtsg_bottle_compare_dy052.m to merge the clean 1-minute data onto bottle 
   samples. This should now be run with the switch at the top of the script set to 
   calibrated. Individual bottle residuals are plotted, as well as a smoothed time 
   series of the residuals, (see Figure 8.3) which can then be used as a slowly-
   varying adjustment to the TSG salinity in the next step.
      Input: data/ctd/tsg_dy052_all.nc
      Input:  data/tsg/tsg_dy052_01_medav_clean.nc
      Output: data/tsg/tsg_dy052_01_medav_clean_botcompare.nc

10) Run met_tsg_av_addnav_dy052.m to merge with navigation data (lat and long) on 
    variable time. Run mbest_all.m prior to this to update the best navigation file 
    bst_dy052_01.nc.
      Input: data/tsg/tsg_dy052_01_medav_clean_cal.nc 
      Input:  data/nav/posmvpos/bst_dy052_01.nc
      Output: data/tsg/tsg_dy052_medav_clean_cal_nav.nc (final file)


Figure 8.3: Left: Salinity difference (PSS-78) between underway bottle measurements 
            and the calibrated SBE45 salinity measurement at each sample time (black 
            crosses) and smoothed it (magenta line). The red crosses show data-points 
            rejected from the smoothed it. Right: Calibrated salinity from the SBE45 
            (blue line) along with the individual bottle samples (red crosses).



 
9  SALINITY SAMPLES AND ANALYSIS
   Estelle Dumont, Jon Short, Colin Hutton, and Stefan Gary


9.1  Bottle sampling

The 24 Niskin bottles on the CTD rosette were sampled for laboratory determination 
of conductivity in order to calibrate the CTD conductivity sensors. Salinity samples 
were drawn from each unique depth. When 2 bottles were fired at the same depth only 
one bottle was sampled. Salt bottle samples were collected after oxygen and carbon 
into glass bottles with plastic inserts and caps. Some bottles on the Scottish Shelf 
east of Barra were not sampled due to the strong salinity signals on the shelf and 
to reduce Autosal operator workload when arriving in port. For each sample, the 
bottle and cap was rinsed three times and then filled with sample. The neck, 
threads, and cap were carefully dried, to prevent salt crystals from forming around 
the opening, and the insert and cap were put on the bottle for storage. Filled salt 
bottles were placed in the Autosal lab and allowed a minimum of 24 hours to reach 
the ambient lab temperature before analysis on the Autosal. The salinity samplers 
were Liz Comer, Martin Foley, Dave Hughes, Rob King, Emma Slater, and Jon Tinker.


9.2  Autosal analysis

These samples were subsequently analysed on two Guildline Autosal salinometers 
(serial number 71185 and 71126) using NMF software in Labview for the automated 
reading of the digital output of the Autosal. The Autosals were standardized during 
mobilization and no adjustments to the resistance knob were made thereafter. 
Handwritten paper logs were kept of the Autosal readings as a backup but were not 
needed during the cruise. The Autosal water bath was maintained at 24˚C.  The room 
temperature fluctuated slightly (between 20 and 22˚C) during the first two days of 
analysis, until the engineers fixed the temperature-control unit, leaving a more 
stable room temperature of approximately 20.5˚C for the remainder of the cruise.  
The first Autosal (S/N 71185) failed on the 29th June, and the last few crates were 
analysed on Autosal S/N 71126. The Autosal operators for DY052 were Jon Short, Colin 
Hutton and Estelle Dumont.

Over the course of the cruise, 41 crates of 24 bottles and 82 OSIL standard seawater 
bottles (SSW) were processed for the CTD discrete salinity sampling. An additional 4 
crates of salt samples taken from the underway system were also analysed. On the 
first day seawater standards from batch P158 (K1 =  0.99970, 34.988 PSU) were used, 
then P159 (K15 = 0.99988, 34.995 PSU) for the rest of the cruise. A standard was run 
at the start and end of each crate to check for any drift of the salinometer. When 
several crates were run in sequence, only one new bottle of standard run between 
crate.  For the first two days, the same standard bottle was analysed at the start 
and end of each crates. However, after some discussion this practice was 
discontinued and new standards were always used.

The Autosal standard seawater measurements appear to have been more variable in the 
first two days of operation than the rest of the cruise.  After this, the nearly 
constant temperature in the Autosal laboratory resulted in good instrument 
stability.  An offset for each cast was determined from the standard seawater 
reading offsets (Figures 9.1 and 9.2).


Figure 9.1: Autosal standards offset readings for each cast. Black + symbols are the 
            measured – nominal values for each SSW observation in Guildline counts 
            (Autosal display units, double the conductivity ratio) and the 
            corresponding conductivity and salinity differences. Black dots indicate 
            the average of the SSW measurements associated with each cast, an average 
            of up to 4 measurements if a cast was split between two crates.  The red 
            line in the top panel is the offset adjustment applied to each cast when 
            the salinity bottle data were read into MSTAR (see Table 9.1 and Section 
            9.3, below). The red dashed lines are plus or minus 0.00003 Guildline 
            counts relative to the solid red line, a rough approximation to the 
            uncertainty in the average of the SSW observations contributing to each 
            data point. The standard deviation limit for the three Autosal readings 
            that are averaged to create each bottle observation is 0.00002 (Chapter 4) 
            and the RMS combination of the two such uncertainties results in 0.000028 
            Guildline counts.

Figure 9.2: Similar to Figure 9.1 except the autosal standards are plotted by date of 
            analysis rather than CTD cast number. The red line in the top panel is the 
            mean conductivity ratio offset over the whole cruise and the dashed lines 
            are plus or minus two standard deviations relative to the mean.


9.3  MSTAR processing

All the analysed bottle salinities were read into MSTAR via the msal_01, msal_02, 
msam_updateall pipeline.  The first step in this process requires applying an 
adjustment to each bottle salinity based on the Autosal offsets determined from the 
observations of standard seawater. The purpose of this adjustment is to account for 
any long-term drift or temporal offset in the laboratory salinometer while also 
taking into account any errors in the standards. As such, offsets were applied to 
groups of casts and occasionally to single casts with no more than 0.00002 Guildline 
counts steps for each change (Table 9.1, next page).  Offsets were informed by the 
average offset for each cast (black dots in Figure 9.1) but the final decision was 
made by examining the offsets by eye. All values were rounded to the nearest 10-5 
Guildline count.

The exceptionally high standard run on a crate containing bottles form casts 9 and 
10 was ignored. Note that two dots appear for this standard in Figure 9.2 because 
this was one of the standards run in the first two days, so the same standard 
seawater bottle was analysed twice. The four cases of exceptionally low standards 
run for casts 3-5, 10-11, 28-29, and 60-70 are most likely do to incomplete flushing 
of de-ionized water from the Autosal conductivity cell as all of these standards 
were run after a relatively long pause in analysis when the Autosal was stored with 
de-ionized water in the conductivity cell.

Once the adjustment was applied to each observation, the CISRO Seawater Toolbox, 
version 3.2, was used to compute the corresponding conductivity with sw_sals. Since 
the Autosal laboratory was maintained at nearly constant temperature and the Autosal 
lights were blinking continuously, the bath temperature of the Autosal was taken to 
be constant at 24 °C.


Table 9.1: Conductivity ratio offsets that were applied to all laboratory CTD bottle 
           conductivity ratio observations on a cast-by-cast basis. Note that in 
           Figures 9.1 and 9.2 the Autosal display is in general a bit higher than 
           the nominal reading, so the adjustment is negative to bring the value 
back 
           down towards the nominal value of the standard.

           Start CTD  End CTD  Offset [Guildline counts = 2 x Cond. Ratio x10-5]
           ---------  -------  -------------------------------------------------
               1        13                            -2  
              14        29                            -3  
              30        30                            -4  
              31        31                            -5  
              32        47                            -6  
              48        48                            -4  
              49        49                            -3  
              50        50                            -2  
              51        52                             0  
              54        54                            -1  
              55        57                            -2  
              58        64                            -1  
              67        74                            -2  
              85        85                            -3  
              86        86                            -4  
              87        89                            -5  



10  DISSOLVED INORGANIC NUTRIENTS
    Tim Brand


10.1  Introduction

The basic water column dissolved nutrients, phosphate, silicate (reactive silica) 
and total oxidized nitrogen, TON, (nitrate+nitrite) were analyzed from 72 (out of a 
possible 73) CTD casts along the Extended Ellett line and 5 stations along a N-S 
transect approaching the Anton Dohrn seamount.

Samples were drawn at every unique depth at which the Niskin bottles were closed.


10.2  Method

Samples were collected in 50ml acid pre-cleaned polythene vials directly from the 
CTD spigots without the use of a tube and using a single half-full rinse prior to 
collection. Samples were always analyzed within 24 hours of collection and stored in 
low light conditions at room temperature prior to analysis if analysis time exceeded 
8 hours after collection time. Measurement was conducted using a Lachat QuikChem 
8500 low injection autoanalyser (Hach Lange) using the manufacturers recommended 
methods: Orthophosphate, 31-115-01-1-G; Silicate, 31-114-27-1-A and Nitrate/Nitrite, 
31-107-04-1-A. After analysis, the 50ml tubes were double rinsed with the ship’s DI 
water and reused for subsequent CTD sample collection.

Samples were measured in triplicate to identify instrument precision. Individual 
stock standard solutions of nitrate, phosphate and silicate were prepared in 
deionised water immediately prior to the cruise from oven dried (60C) salts. A 
primary mixed working standard solution was prepared each day from the stock 
solutions using the ship’s DI water and the calibration standard solutions were 
prepared by the instruments autodiluter facility using OSIL Low Nutrient Sea Water 
for dilution, (OSIL, http://www.osil.co.uk, Batch LNS 23 24, Salinity 35). Seven 
calibration standards and blank seawater were run at the start of each batch of 
samples (between 21 and 42 samples) followed by a drift standard run in triplicate 
at the end of the batch.
Calibration drift determined was accounted for in the calculation of the sample 
result (arithmetic methodology assumes linear calibration drift correction from 
start to finish of sample batch).

A standard reference solution prepared from nutrient standard solutions supplied by 
OSIL containing 1 µMPO4, 10 µMSiO2 and 10 µMNO3 was run at the start, during and end 
of the entire analysis to check accuracy of the dried salt derived standards.


10.3  Data quality assessment

Analytical precision was gathered by running each sample in triplicate and regularly 
yielded relative standard deviations (S.D.) of better than 2% for phosphate and 
nitrate and better than 5% for silicate. The method detection limit (MDL) of each 
nutrient was calculated as 3 x S.D. of 7 replicates of the blank low nutrient sea 
water. This yielded MDL’s of PO4, 0.02uM, SiO2, 0.48uM, and NO3+NO2, 0.03uM. 
Accuracy, determined by analysing the independent OSIL reference standard solutions 
at the beginning and end of the cruise showed a 103.3+/- 1.8% recovery for 
phosphate, 97.9 +/- 3.3% recovery for silicate and a 101.7 +/- 1.1% recovery for 
nitrate+nitrite.

Recovery percentages have not been factored into the final results.






11  DETERMINATION OF DISSOLVED OXYGEN CONCENTRATIONS BY WINKLER TITRATION.
    Richard Abell, James Coogan, Winnie Courtene-Jones and Ashlie McIvor.


11.1  Introduction

Dissolved oxygen concentrations were measured in 1111 seawater samples collected 
during DY052. Sampling and analysis were performed 24hrs a day from every CTD cast 
using Winkler photometric auto-titration. Methodologies followed those documented in 
GO-SHIP protocols (Langdon, 2010) and based on the standard methodologies of 
Carpenter 1965 adapted for large scale hydrographic studies (e.g. Culberson, 1991 
and Dickson, 1995).

Prior to analytical session the titration was standardised using an OSIL 0.01N 
iodate standard. Precision of the analysis was estimated using duplicate 
measurements of samples collected from same the Niskin bottle (11% of samples 
collected, 1? = 0.17%). 4% of the data was rejected either due to poor analysis or 
sampling issues.


11.2  Method

Seawater samples were drawn from Niskin bottles via a short length of silicon tubing 
without allowing air bubbles to enter the individually calibrated sampling bottles. 
Excess seawater (at least three times the bottle volume) was flushed through the 
sample bottle to both clean it and remove any air bubbles. Samples were fixed 
immediately upon addition of 1ml of 3M MnCl2 and 1ml of 8M NaOH + 4M NaI. The 
temperature of the sample during fixing was recorded using a digital thermometer 
(±0.1°C) in a separate sample bottle. Reagents were dispensed below the surface of 
the sample so as not to introduce air bubbles and ensure all reacting species were 
contained within the sample. Ground glass lid stoppers were added tightly, again 
ensuring no air bubbles were trapped within the sample. Samples were shaken 
vigorously and transferred to a dark cool storage space in the lab. After half an 
hour samples were re-shaken and allowed to settle and equilibrate with lab 
temperature for at least 1 hour.

Before every analytical session the titrant (0.1M Na2S2O3) was standardised using a 
commercially purchased OSIL 0.001667M KIO3 standard. During the course of the 
analytical sessions the drift in titre concentration was small (~ 0.0002M). Reagent 
blanks were also measured during standardisation following the methodologies of 
Carpenter (1965) and subtracted during the titration calculation.

Prior to analysis 1 ml of 5M H2SO4 was added to samples followed by a Teflon coated 
magnetic stirrer. End points reached by the auto burette were recorded.









11.3  Summary of results


Figure 11.1: Dissolved Oxygen profiles measured during DY052 from Iceland (left) to 
             Scotland (right) (Ocean Data View, R. Schlitzer, 2011). The top panel 
             shows saturation highlighting the plankton blooms encountered, 
             particularly strong above the Rockall Hatton Plateau. Middle panel shows 
             oxygen concentration in the upper 250m and lower panel the full depth 
             profile.




References

Carpenter, J.H. 1965. The Chesapeake Bay Institute technique for the Winkler dissolved 
    oxygen method. Limnol.and Oceanogr. 10:141-143.

Culbertson, C.H. 1991. Dissolved Oxgen. WHPO Publication 91-1.

Dickson, A.D. 1995. Determination of dissolved oxygen in sea water by Winkler 
    titration. WOCE Operations Manual, Part 3.1.3 Operations & Methods, WHP Oice 
    Report WHPO 91 – 1.

Langdon. C. 2010. Determination of dissolved oxygen in seawater by Winkler titration 
    using the amperometric technique. The GO-SHIP Repeat hydrography manual: A 
    collection of expert reports and guidelines. IOCCP report No.14.



 
12  CARBON SAMPLES
    Stacey Felgate


Water samples were collected from 8 initial EEL stations (IB22, 1B16A, 1B9, 1B4, F, 
O, R & 10G) and an additional 1 station in the Anton Dohrn deep (X3). At each of 
these stations, 6 samples were collected from depths representative of water mass 
features:

1. Bottom
2. Bottom – 50 m
3. Mid-way between bottom and OMZ
4. OMZ
5. Mid-way between OMZ and surface
6. 2nd from surface

Additional samples were taken at high priority stations (IB22, 1B16A, F, O & X3) in 
order to obtain a higher resolution, with 3-4 extra samples taken to provide a 
profile spaced as evenly as possible within the top 1200 m. Accepted bubble-free 
water sampling techniques were used in all cases. Samples were collected into 250 ml 
glass stoppered bottles. Once collected, samples were poisoned by removing 2.5 ml 
water and adding 0.050 ml Mercuric Chloride solution (7 g/100 ml). Bottles were 
sealed using PVC tape, and stored in a chilled room at 9 °C. Analysis will be 
conducted at the Scottish Association for Marine Science under the supervision of Dr 
Kirsty Crocket.

The carbon samples were taken to coincide with the trace metal samples (Chapter 13) 
and so the sampling scheme for the carbon samples is identical to that of Table 
13.1.

It is of possible note that the paper used to stop the glass stoppered bottles from 
sealing pre-sampling in some cases became attached inside the bottle neck and was 
problematic to remove, potentially leading to some contamination of the samples. In 
particular, this affected the later sampling stations.



 
13  Trace Metal and Nd ISOTOPE SAMPLING
    Emily Hill


A total of 82 samples for rare earth element (REE) analysis and 7 samples for Nd 
analysis were collected along the EEL transect from 9 stations: IB22S, IB16, IB9, 
IB4, F, O, R, 10G and X3. The deepest sample from each station was sampled twice 
from a duplicate niskin bottle for reproducibility purposes. Stations and niskin 
bottles sampled for REEs and Nd isotopes are shown in Tables 1 and 2 respectively.


Table 13.1: CTD no and station names for REE samples

            CTD no.  EEL station        niskins sampled
            -------  -----------  ---------------------------
              003       IB22S       1 2 3 4 5 6 7 8 10 12
              010       IB16       1 2 5 7 8 9 13 14 17 18
              022       IB9            1 2 3 5 8 11 18
              030       IB4            1 2 3 4 5 9 16
              042       F         1 2 3 4 6 8 10 11 13 15 18
              052       O         4 5 6 7 8 10 12 14 15 17 21
              056       R                1 2 3 4 5 6 8
              064       10G              1 2 3 4 5 6 8
              087       X3         1 2 3 4 7 9 12 13 15 17 18

                              
Table 13.2: CTD no and station names for Nd samples

            CTD no.  EEL station        niskins sampled
            -------  -----------  ---------------------------
               49         L                   22
               50         M                   18
               51         N                 5 8 11
               52         O                   2 3

          
REE samples: 250ml bottles were used to collect seawater from the appropriate 
niskin. Once sampling was completed, seawater was filtered in a clean lab through 
47µm polycarbonate filters and poured into 50ml spin tubes. The seawater was then 
acidified on board with 2ml/L of concentrated UpA hydrochloric acid. The samples 
were then placed into the fridge until disembarkation and will be analysed for REE 
composition at SAMS.

Nd samples: Seawater was filtered directly from the niskin using an AcroPak filter 
and 10L were collected in a cubitainer. Samples were then acidified with 20ml of 6M 
hydrochloric acid and placed into the fridge until disembarkation. Neodymium 
isotopic analysis will be carried out at the National Oceanographic Centre in 
Southampton.




14  DIRECT DENSITY SAMPLES
    Emma Slater

Density samples were taken where bottles were also sampled for salinity, nutrients 
and carbon data. Aluminium bottles were used to sample the density. Replicate 
samples were taken from the deepest bottle to check measurement precision.

The sampling method consisted of:

1. Sample immediately after salinity.
2. Rinse bottle three times.
3. Fill to neck (allowing gap for thermal expansion of cold water) and cap bottle 
   tightly by screw cap.
4. Soak in freshwater for a few seconds to wash away seawater on the bottle and cap.
5. Put bottle in the box upside down.
6. Store the box at room temperature.

The following CTD stations were sampled:

           Cast     Site                    Niskin number
          ------  ---------  -----------------------------------------------
          CTD001  Shakedown                 1 (duplicated)
          CTD003    IB22S       1 (duplicated), 3, 4, 5, 6, 7, 8, 10, 12
          CTD010    IB16A            1, 5, 7, 8, 9, 13, 14, 17, 18
          CTD022     IB9             1 (duplicated), 3, 5, 8, 11, 18
          CTD030     IB4             1 (duplicated), 3, 4, 5, 9, 16
          CTD042      F      1 (duplicated), 3, 4, 6, 8, 10, 11, 13, 15, 18
          CTD052      O      5 (duplicated), 6, 7, 9, 10, 12, 14, 15, 17, 21
          CTD056      R              1 (duplicated), 3, 4, 5, 6, 7
          CTD064     10G             1 (duplicated), 3, 4, 5, 6, 8
          CTD087     X3       1 (duplicated), 3, 4, 7, 9, 12, 13, 15, 17, 18          


A duplicate sample at the deepest depth on cast CTD010 was not taken in mistake. 
These bottles will then be sent to Hiroshi Uchida at JAMSTEC for direct analysis of 
density.



 
15  EPIBENTHIC SLED DEPLOYMENTS
    Dave Hughes


15.1  Introduction

SAMS biological sampling in the Rockall Trough dates from 1973. As David Ellett 
established his hydrographic survey line the late John Gage decided to use one of 
the Ellett stations – ‘M’ – as a regular benthic sampling station, located near the 
foot of Anton Dohrn seamount at 2,200 m depth. Over the period from 1973-1994 
regular samples were obtained from Station M with the Woods Hole Oceanographic 
Institution (WHOI) pattern epibenthic sled. The historical samples span a time frame 
of >20 years, during which there have been noticeable changes in the surface 
phytoplankton productivity. Since the end of John Gage’s sampling programme in 1994 
the issue of climate change and its impacts has become one of the most important 
research themes in biological oceanography and long-term time series measurements 
have correspondingly grown in importance. Very few deep-sea benthic time series 
exist, and none extend back as far as the SAMS historical samples from Station ‘M’. 
The deep-sea benthic group at SAMS, now led by Dr Bhavani Narayanaswamy, therefore 
decided to carry out a community- level analysis of macrofaunal composition of the 
historical samples, and to initiate a renewed sampling programme at Station ‘M’ 
using the same gear and methods as originally used by Gage. The WHOI epibenthic 
sleds were refurbished at SAMS, Oban in late 2012 and deployed on the 2013 and 2015 
EEL cruises (see James Cook 086 and Discovery 031 cruise reports). Possible changes 
in the macrobenthic community at Station ‘M’ are currently being investigated with 
analysis of the 2013 and 2015 samples to provide a > 40 year time span record for 
this gear and position. Cruise DY052 has enabled a further set of sled tows to be 
carried out, extending the benthic time series to 2016.


15.2  Methods

Two of the original WHOI-pattern sleds, used by John Gage, were rigged as in 2013 
and 2015 with identical net meshes of 0.5 mm for both main and extension nets 
(Figure 15.1).  The sleds are fished with the door open and fishing stops when the 
door is closed by a timer mechanism.  The door closure at the end of the tow 
prevents both over-washing of the trapped sample and incorporation of planktonic 
fauna during the recovery. As far as possible, deployment procedures followed the 
method used for the historical samples. Sled deployment, towing and recovery 
protocols are described in detail in the cruise report for Discovery 031.


Figure 15.1:  Epibenthic sled


After washing on stacked 4 mm, 0.5 mm and 0.42 mm sieves (Figure 15.2) the retained 
material is placed in suitable sample buckets with 4% buffered formaldehyde in 
filtered seawater. The largest volume of material is retained on the 0.5 mm sieve 
and constituted between 3 and 6 litres of washed material per sled (Figure 15.3). 
This large volume is impractical to be processed as a unit so sub-sampling is 
carried out. This is achieved in the laboratory in an agitated water column which 
allows the fauna to settle out at random between eight segments in a collecting 
chamber. The same sub-sampler has been in use since 1974. Historically, final 
screening was carried out on a 0.42 mm and a 0.425 mm sieve (Figure 15.4) so the 
original sieves were employed for comparison with historical data.


Figure 15.2: Stacked sieves

Figure 15.3: Sample collected on 0.5 mm sieve.

Figure 15.4: Sample collected on 0.42 mm sieve.



15.3  Initial results

Four successful sled tows were carried out. In all cases the sled door- closing 
mechanism worked perfectly, retaining the benthic sample as intended. The only minor 
technical mishap was the detachment of one of the pair of towing bridles on the 
first sled tow, caused by an insufficiently-secured shackle. However, the sled was 
held firm by the second bridle and was recovered on board without difficulty.

On the first tow the collected sediment filled the extension net but did not extend 
into the main net contained within the sled frame. The following three tows were 
longer in duration and collected larger volumes of sediment, filling the extension  
net and up to approximately one-third of the main net. This represents approximately 
200 litres of sediment per tow, requiring about six hours for sieving on deck, 
sample  fixation and labelling.

The table below gives the ship’s positions at the start and end of each sled tow. 
The starting position was recorded at the time at which the sled was considered to 
have reached the seabed (from length of wire paid out). The end coordinates were 
taken at the time of sled door closure, immediately before the beginning of haul-in.


      SAMS
led  sample          Position at                  Position at          Tow duration 
tow  number         start of tow                   end of tow          (bottom time)
---  ------  ---------------------------  ---------------------------  -------------
 1  ES_1693  57° 20.018’ N  10°22.082’ W   57°20.791’ N   10°21.603’ W       49 mins  
 2  ES_1694  57° 18.987’ N  10°23.234’ W   57°19.908’ N   10°22.613’ W  1 hr 30 mins    
 3  ES_1695  57° 18.582’ N  10°22.809’ W   57°19.787’ N   10°21.051’ W  1 hr 33 mins  
 4  ES_1696  57° 17.386’ N  10°22.842’ W   57°16.133’ N   10°22.014’ W  1 hr 20 mins  


The epibenthic sled is not designed to collect larger benthic animals (megafauna), 
although some specimens are fortuitously caught up and recovered in the nets. 
Representative specimens of the species caught were frozen individually for 
laboratory analysis of microplastic particles in gut contents (see Section 16). The 
sieve residues will contain large numbers of benthic macrofauna, ranging in size 
from approximately 0.42 mm to >1 cm body length, consisting principally of various 
species of polychaete worms, bivalves, isopod and amphipod crustaceans, and other 
minor groups. On return to the laboratory these animals will be extracted from the 
sediment, identified and counted for comparison with the macrofauna recorded from 
Station ‘M’ in the 2013, 2015 and historical samples.


15.4  Conclusion

The 2016 epibenthic sled deployments proved highly successful and achieved the 
desired replicated sampling of Station ‘M’ to further extend the benthic time 
series. Analysis of these new samples will begin on return to SAMS and will require 
several months’ work in the laboratory.




16  SAMPLING MICROPLASTICS IN THE DEEP SEA
    Winnie Courtene-Jones

Microplastics are small pieces (most commonly fragments, fibres or beads) of 
plastics, less than 5mm in diameter. Microplastics occur in the environment from the 
fragmentation of larger items of plastic debris or are manufactured to be of small 
size for use as ‘scrubbers’ or as a precursor for other products. Due to the 
persistent nature of microplastics these accumulate in the environment, and have 
been identified in a range of marine ecosystems. The work carried out during this 
cruise compliments the deep sea epibenthic operations undertaken by the Scottish 
Association for Marine Science, and furthermore represents the first efforts to 
quantify microplastics in deep sea macro-invertebrates and in deep sea water.




16.1  Microplastics in deepsea fauna

Samples were collected using an epibenthic sled as described in Chapter 15. Sled 
sediment was processed by systematically washing small quantities through stacked 
sieves of mesh sizes 4mm, 500µm and 420µm. Once at this stage additional sample 
processing was carried out for those macrofauna retained on the 4mm sieve (Figure 
16.1). Invertebrates were wrapped individually in aluminium foil and placed in pre-
cleaned sealable containers separated to group level (e.g. gastropods, bivalves 
etc.) as shown in Figure 16.2. These containers were labelled for each sled trawl 
and specimens were frozen in a -20°C freezer.

To mitigate against and control for contamination, samples of all ropes used on the 
epibethic sled, along with fibres from the net and net cover were taken.

Additionally, samples from ropes used on the winch and on the ship deck and 
surrounding areas were also taken. The water filter system fitted to the ship’s 
underway water intake was tested for efficiency by running the water through a 80µm 
mesh filter for 2 hours before sampling commenced and once all operations were 
completed. All containers were cleaned with 70% ethanol and wiped clean with non-
shedding paper, followed by rinsing in deionised water.

Before operations and between each sled haul, the ships deck was washed with a high-
pressure fire hose to remove any debris from the deck. Between processing sediment 
from each sled deployment sieves were washed thoroughly.


Figure 16.1: Ophiomusium lymani (left) and Hymenaster sp. (right) shown on a 4mm 
             sieve.

Figure 16.2: Invertebrate specimens individually wrapped in aluminium foil in clean 
             sealable container



16.2  Microplastics in deep sea water

Immediately after the final epibenthic sled was completed a CTD cast was deployed at 
position 57° 14.74 N, 10° 21.09 W. All 24 niskin bottles from the rosette were fired 
at bottom depth of 2224 m. Once on deck, care was taken to remain downwind of the 
CTD to avoid contamination. Water filters were made by securing 80µm mesh gauze to a 
length of rubber tubing, all tubing and gauze was cleaned with deionised water and 
inspected under a microscope before use to ensure they were clean and free from 
contaminants.

Each niskin bottle spigot was cleaned using deionised water and immediately after 
the tube containing filter was fitted to the spigot. The air tap was opened to allow 
water low and the spigot was fully opened. Water was allowed to flow through the 
mesh until each the bottle was completely empty (Figure 16.3). The rubber pipe was 
carefully removed, avoiding any contact with the mesh filter and placed on the next 
cleaned spigot. This was repeated for each of the 24 bottles; in total 240 litres of 
water were filtered. Once complete mesh was paced into sterile petri dishes, sealed 
with electrical tape and labelled.


Figure 16.3: Rubber pipe with 80µm mesh gauze screen fitted to the niskin bottle 
             spigot, allowing for water filtration directly from the CTD to analyse 
             microplastics in deep sea water.



 
17  HYDROPHONE & EK60
    Clare Embling and Leah Trigg


17.1 EK60

Deployment

The EK60 (ER60) was switched on and recording according to the schedule given in 
Table 17.1.


Table 17.1: EK60 logged data during DY052

       Deployment         Deployment     Frequencies switched  Depth range 
       start (UTC)         end (UTC)          on & logged        (logged) 
     ----------------  ----------------  --------------------  -----------
     08/06/2016 19:57  12/06/2016 14:40    18, 38, & 70 kHz        200m 
     18/06/2016 14:34  19/06/2016 17:57         18 & 38 kHz       2000m
     20/06/2016 23:13  23/06/2016 10:46         18 & 38 kHz       2000m


The 18 and 38 kHz frequencies were selected due to interest in the deep scattering 
layer (DSL), higher frequencies do not transmit deep enough to detect the DSL. The 
EK60 was uncalibrated during this cruise, and there is no evidence that it has ever 
been calibrated (this should be done if this is going to be used to produce useful 
data for analysis). The EK60 was synchronised with the other echosounders (ADCP, and 
depth sounders) using the synchronisation unit.


Initial results

We were primarily interested in the mesopelagic deep scattering layer, which was 
clearly visible in daylight hours (Figure 17.1). This showed clear internal waves in 
the deep scattering layer around Rosemary Bank and Anton Dohrn seamount (Figure 
17.2).

Since no log was kept for when the echosounders were on or off, we didn’t have a 
record of which EK60 transceivers were on or off, however the recorded EK60 files 
provided a record (though it wasn’t always recording when switched on) by viewing 
them in EchoView (Figure 17.3).

The EK60 data was poor in high swell, which varied depending on the direction of 
travel (see Figure 17.4), and frequency (38kHz was generally worse than 18kHz).


Figure 17.1: EK60 18kHz, 70 dB echogram for waters between Anton Dohrn and the shelf 
             break (57° 17.500’ N, 10° 21.009’W to 57° 14.755’ N, 10° 21.009’W), 
             colour scale: red = highest backscatter, yellow/green = moderate 
             backscatter, blue = low backscatter. The mesopelagic deep scattering 
             layer is between around 300-500m, and apparent fish schools just below 
             100m.

Figure 17.2: EK60 data for 18kHz at 70dB, on the approach to Rosemary Bank. Colour 
             scale: red = highest backscatter, yellow/green = moderate backscatter, 
             blue = low backscatter. Fish schools around 200m depth, and the deep 
             scattering layer 400-500m, with clear internal waves in both layers.

Figure 17.3: Example of EK60 data recorded at 4 different frequencies over the 
             Icelandic Shelf (for the 200m data). There was no record of which 
             frequencies were switched on but this suggests that the 18, 38 and 70kHz 
             transceivers were switched on, while higher frequencies were switched 
             off.

Figure 17.4: EK60 18kHz at 70dB, showing the effect of swell and direction on the 
             return of signal to the receiver. The ship turned at the point where the 
             EK60 return improved substantially.


Recommendations for future EK60/ADCP working simultaneously

The ER60 when reset would automatically switch to default settings, which was 200m 
(& set to operate at certain frequencies? Why was the 70kHz echosounder turned on?).

1. Recommend that the default settings are set to the desired combination (in this 
   case 2000m depth, and only on 18 and 38 kHz), and being logged to an appropriate 
   folder for the cruise, and with an appropriate file name (in this case DY052 
   directory, and DY052 file name with the date and time stamp in the filename).
2. Log every time any of the echosounders are turned on or off, since this wasn’t 
   recorded, so it wasn’t known, making it difficult to determine interference from 
   other devices (either for the EK60 data, the ADCP data, or the hydrophone).


17.2  Hydrophone

Specification & deployment

The hydrophone array is built by and on loan from Thom Gordon, Vanishing Point 
(www.vanishingpoint.org.uk). The array comprises of ~340m of tow cable, and a 5m 
long oil-filled (Isopar M) polyurethane tube streamer containing the hydrophone 
elements and pre-amplifiers, comprising:

   i. Two Magrec HP03 hydrophone/pre-amp units, each consisting of spherical 
      hydrophone elements feeding broadband preamplifiers (Magrec HP/02). The preamps 
      have a low-cut filter set at 2kHz and the units have good frequency response 
      between 2-150 kHz. The two elements are spaced 30cm apart.
  ii. Two Benthos AQ4 elements with matching Magrec HP02 preamplifiers.  These have a 
      low cut filter in the preamp set to -3dB at 100Hz. The elements are flat to 
      15kHz, and sensitivity is reasonable up to 30kHz. The two elements are spaced 3m 
      apart.

The high frequency elements (HP03) were connected to a SAIL DAQ card (St Andrews 
Instrumentation Ltd), which was set via the PAMGUARD software to a gain of 24dB, and 
sampling rate of 500kHz. The medium frequency elements (AQ4) were connected via a 
Behringer Ultragain Pro Mic 2200 amplifier unit set to a gain of 20dB, and a 
Fireface 400 sound card, connected to a second computer running PAM-GUARD, sampling 
at 48kHz.

All logging of the hydrophone data was carried out via PAMGUARD, with automatic 
recordings of all elements for 2 minutes every 15 minutes, continuous running of 
click detectors (to monitor for sperm whales from the medium frequency and beaked 
whales on the high frequency computers). The high frequency computer was connected 
to the NMEA GPS feed so that all data was GPS referenced. Listening stations were 
carried out every 15 minutes, where noise levels, sperm whale and dolphin sounds 
were scored on a loudness level from 0 to 5. Environmental data such as sea state 
and swell was recorded at least every hour. The data were stored in a SQLite 
database (Version 3.0.6). Deployment and retrieval times were logged.

For the majority of deployments the 10 and 12kHz bottom-detection echosounders 
(EM122 and EA640) were switched of during each tow since it was difficult to hear 
sounds over these specific echosounder pings (due to the long ping duration). Other 
echosounders that were on for the majority of the time during hydrophone deployment, 
and that can be detected by the hydrophone (but didn’t interfere with listening or 
detecting whales) were: EK60 18kHz and 38kHz (and ~8-12th June the 70kHz EK60 
echosounder was on, we aren’t sure when it was turned off); ADCP 75kHz and 150 kHz.

The hydrophone was best deployed at speeds of 8 knots or greater, thrown to the side 
of the ship, out of the propeller wash. Lower speeds and the hydrophone would tend 
to be sucked into the propeller wash. The hydrophone was suspended when towed, as 
shown in Figure 17.5, to avoid chafing. Retrieval could be carried out at 8 knots 
(or higher). Deployment/retrieval took generally less than 10 minutes. It could be 
towed in most weather conditions (we were not restricted by weather during the whole 
survey).


Figure 17.5: Hydrophone deployment


Deployment dates and times are given in Table 17.2.


Initial results

Sperm whales were heard in highest densities in the Rockall Trough between Anton 
Dohrn Seamount and the shelf edge (Figure 17.6). Pilot whales were also heard on 
several occasions, along with dolphin whistles of unidentified species (Figure 
17.6). Sightings of cetaceans included a in whale and pilot whales close the shelf 
edge, beaked whales over Anton Dohrn, sperm whale blows in the Rockall Trough, and 
common dolphins over the Scottish Shelf (harbour porpoises and seals were also seen 
on the transit out from Glasgow in the Firth of Clyde). Feeding buzzes were heard 
most frequently in the Rockall Trough.


Table 17.2:  Hydrophone deployment dates, times and locations of tows for DY052

Tow  Deployment start (UTC)  Start location  Deployment end (UTC)  End Location
 1       08/06/2016            59.909486N,        09/06/2016        60.016971N,
         10:15                  9.812368783W      15:21             17.72408W
 2       09/06/2016            60.2432293N,       10/06/2016        63.27944N,
         18:30                 18.307422W         12:36             20.19403116W
 3       11/06/2016            62.908538N,        11/06/2016        62.697693N,
         02:28                 19.5536695W        03:53             19.666148
 4       11/06/2016            62.63822683N,      11/06/2016        62.3444773N,
         06:24                 19.677538W         08:23             19.8511788W
 5       11/06/2016            62.320106N,        11/06/2016        62.0500553N,
         10:52                 19.840990W         12:40             19.9858898W
 6       11/06/2016            61.958163N,        11/06/2016        61.787148N,
         15:35                 20.0068358W        16:50             20.016376W
 7       11/06/2016            61.7284833N,       11/06/2016        61.5068452N,
         19:25                 19.996575W         21:00             20.0543002W
 8       11/06/2016            61.4740752N,       12/06/2016        61.2617553N,
         23:50                 20.001409W         01:13             20.0145228W
 9       12/06/2016            61.2284153N,       12/06/2016        61.0207365N,
         04:03                 20.0038193W        06:32             20.0252082W
10       12/06/2016            60.9885783N,       12/06/2016        60.7536117N,
         08:40                 19.9945105W        10:18             20.0266323W
11       12/06/2016            60.728479N,        12/06/2016        60.5310748N,
         13:07                 20.0011095W        14:26             20.012301W
12       12/06/2016            60.472649N,        12/06/2016        60.26216N,
         17:35                 20.0006965W        19:05             20.016863W
13       12/06/2016            60.2355786N,       12/06/2016        60.017331N,
         22:10                 19.9951076W        23:35             20.0007075W
14       13/06/2016            59.9787752N,       13/06/2016        59.830212N,
         02:55                 19.9545875W        04:30             19.5540903W
15       13/06/2016            58.8041403N,       13/06/2016        59.6606223N,
         07:40                 19.4761653W        09:05             19.1651018W
16       13/06/2016            59.6600111N,       13/06/2016        59.5191036N,
         12:55                 19.097477W         14:07             18.8130315W
17       13/06/2016            59.5202646N,       13/06/2016        59.41316116N,
         17:05                 18.7304968W        18:10             18.45244W
18       13/06/2016            59.315564N,        14/06/2016        59.20298917N,
         23:39                 18.18604817W       00:43             17.914186W
19       14/06/2016            59.096403N,        14/06/2016        58.95738917N,
         05:15                 17.6212978W        06:50             17.209390W
20       14/06/2016            58.8762345N,       14/06/2016        58.7767955N,
         10:54                 16.9805848W        11:44             16.8158258W
21       14/06/2016            58.7448531N,       14/06/2016        58.6760283N,
         13:52                 16.7223595W        14:32             16.5730163W
22       14/06/2016            58.6456885N,       14/06/2016        58.580774N,
         16:38                 16.4807238W        17:20             16.314874W
23       14/06/2016            58.4905478N,       14/06/2016        58.3444608N,
         22:10                 15.9772622W        23:27             15.6854245W
24       15/06/2016            58.3281035N,       15/06/2016        58.2403023N,
         01:12                 15623214W          02:15             15.3625168W
25       15/06/2016            58.2339468N,       15/06/2016        58.08091N
         03:44                 15.294005W         05:05             14.98620783W
26       15/06/2016            58.0601667N,       15/06/2016        57.964145N,
         06:30                 14.9280872W        07:48             14.6167625W
27       15/06/2016            57.9409608N,       15/06/2016        57.779978N,
         09:17                 14.5651178W        10:40             14.2816325W
28       15/06/2016            57.787626N,        15/06/2016        57.6734976N,
         11:53                 14.214811W         13:05             13.949283W
29       15/06/2016            57.654582N,        15/06/2016        57.5551235N,
         14:15                 13.8808351W        15:17             13.6841893W
30       15/06/2016            57.5747448N,       15/06/2016        57.5551946N,
         16:28                 13.607319W         17:14             13.3878293W
31       15/06/2016            57.565438N,        15/06/2016        57.5466975N,
         18:28                 13.2961463W        19:16             13.0679003W
32       16/06/2016            57.507057N,        16/06/2016        57.4745835N,
         05:26                 12.219757W         06:53             11.8695643W
33       16/06/2016            57.492637N,        16/06/2016        57.4736415N,
         09:28                 11.8229017W        10:33             11.5474093W
34       16/06/2016            57.360527N,        16/06/2016        57.3016882N,
         22:20                 10.6386306W        23:10             10.4162808W
35       17/06/2016            57.287414N,        17/06/2016        57.23268217N,
         01:40                 10.3460687W        02:37             10.086367W
36       17/06/2016            57.2345718N,       17/06/2016        57.2494665N,
         05:04                 10.0863357W        06:09             10.3996428W
37       17/06/2016            57.3368818N,       17/06/2016        57.1104776N,
         19:35                 10.3461253W        22:40              9.473409W
38       18/06/2016            57.10591517N,      18/06/2016        57.135087N,
         00:55                  9.4568512W        01:41              9.68108383W
39       18/06/2016            57.15109217N,      18/06/2016        57.237797N,
         03:59                  9.7329448W        06:25             10.4226367W
40       18/06/2016            57.2400888N,       19/06/2016        57.0857526N,
         20:47                 10.313108W         00:05              9.37001W
41       19/06/2016            56.9452637N,       19/06/2016        56.8962548N,
         06:00                  8.74824317W       06:58              8.5077205W
42       20/06/2016            56.7292728N,       20/06/2016        56.9663103N,
         12:05                  6.868674W         20:26              8.8243558W
43       21/06/2016            57.0918553N,       22/06/2016        58.9577948N,
         14:40                  9.4289605W        11:29             11.1043031W
44       22/06/2016            58.9675251N,       22/06/2016        58.5723246N,
         14:50                 11.0820335W        17:30             11.0517836W
45       22/06/2016            58.5338156N,       22/06/2016        58.1391488N,
         19:51                 11.0811305W        22:29             11.0524755W
46       23/06/2016            58.07435N,         23/06/2016        57.65926167N,
         00:59                 11.08240683W       03:44             11.079971W
47       23/06/2016            57.539857N,        23/06/2016        58.8696855N,
         07:17                 11.06649467W       13:58              9.5427556W  	
		       
                         
Figure 17.6: Loudness of sperm whale clicks (coloured, sized dots), and locations of 
             whistles (stars) from the towed hydrophone array. Size of sperm whale 
             dots and colour indicates loudness of the clicks (a proxy for proximity 
             to the ship) on a scale from 0 (absent) to 5 (very loud).          
                         
                  
The noisiest location was in the shallow area close to Rockall, in this area the 
propeller noise reverberated a lot of the bottom making it difficult to hear 
animals. Also, the EM122 and EA640 bottom echosounders were switched on which, 
combined with the propeller noise made it impossible to hear anything except for the 
ship.

Ship noise primarily comprised of the propeller noise, and some associated 
cavitation, quietest in deep water, and at slower speeds. There was also water noise 
suggesting that the hydrophone was quite close to the surface (the hydrophone could 
have benefitted from a little weight to bring it down in the water column a little). 
The medium frequency channel was quite crackly in rougher weather conditions, these 
were recorded as clicks in the click detector, and overloaded the buffer when the 
crackling was severe (resulting in a cut-out of the audio signal). The high 
frequency elements did not suffer from this problem, and the recordings are much 
cleaner (this is the data provided to BODC). Other occasional noises included 
propagation of noise from the needle drill (heard on the hydrophone), another ship 
(in shelf waters), and occasional ‘chirp’ sounds of unknown source.


Recommendations for future hydrophone deployment

* Deploy the hydrophone at a minimum of 8 knots, and throw to the side away from the 
  propeller wash.
* Ensure that the echosounders with long ping durations are turned off during 
  hydrophone steaming.
* Keep a clear record of which echosounders are on, and when.
* Request needle drill use avoided during hydrophone tows.
* Ensure any sightings of cetaceans are reported to the hydrophone team for recording 
  and for species ID for any recorded vocalisations


18  ARGO FLOAT DEPLOYMENT
    Stefan Gary


Three Argo floats were deployed during DY052 according to the standard Argo float 
deployment instructions, i.e. plugs removed, lowered over back rail on a line 
through a hole in the plate, line removed from the float as it drifted away. All 
floats were in pressure activation mode. No anomalies in the deployment were noted. 
The last two floats were deployed at nearly the same location to test the RBR versus 
the standard version.

S/N:       7575, standard Apex
Time:      0828 UTC
Day:       164 (June 12)
Depth:     about 2400 m Conditions: calm
Position:  Just after CTD013, a.k.a. IB14 
           60 deg 59.988 N
           20 deg 0.04434 W

S/N:       7576, standard Apex
Time:      0230 UTC
Day:       165 (June 13)
Depth:     about 2700 m Conditions: calm
Position:  Just after CTD017, a.k.a. IB12
           59 deg 59.900 min
           20 deg 00.314 min

S/N:       7626, RBR Apex
Time:      0244 UTC
Day:       165 (June 13)
Depth:     about 2700 m Conditions: calm
Position:  Just after CTD017, a.k.a. IB12
           59 deg 59.510 min
           19 deg 59.316 min



 




19  SEAGLIDER RECOVERY
    Estelle Dumont


One Seaglider, SG550 (‘Eltanin’), belonging to the MARS pool and operated by SAMS, 
was recovered during DY052.

The glider had been deployed in the Hebrides on the 11th February 2016, and was 
planned to travel along the Extended Ellett Line and back, with recovery planned in 
the Hebrides in August. She was equipped with a Seabird CT sail, Aanderaa oxygen 
optode, and a Wetlabs puck measuring fluorescence, C-DOM and backscatter. Eltanin 
successfully completed her journey to Iceland, however she suffered an early battery 
failure on the way back while traversing the Icelandic Basin. She was put into 
recovery by the SAMS pilot on the 29th May, and left to drift at the surface 
awaiting recovery during DY052. During this time she was set to regularly transmit 
her position (every 6 hours) to the primary base station based at SAMS.

By the time Discovery set sail Eltanin had drifted slightly East of the Extended 
Ellett Line, North-West of the Hatton Bank, and it was decided to recover her on the 
passage leg to Iceland. The glider call interval was decreased to 3 hours then to 
one hour during the night prior to recovery on the 9th June 2016. As Discovery was 
approaching the glider the call interval was decreased to 10 minutes. She was 
spotted in the water from the bridge around 17:00 UTC, and the ship manoeuvred 
alongside. The pilot checked the internal pressure, humidity and battery levels 
prior to recovery, and deemed the glider safe to recover. After a few attempts, the 
crew managed to lasso a rope around the tail of the glider (under the rudder) using 
a telescopic pole and soft rope, while the SAMS team tried to help holding the 
glider still with another telescopic pole. The glider was lifted her on deck using 
the auxiliary winch on the starboard side.

Full recovery details:
SAMS Mission    #18 - Recovery 
Glider:         SG550 - Eltanin 
Glider mission: 1 (for SAMS)
Project:        Extended Ellett Line #5
Date:           09-Jun-16 18:10 UTC
Location:       60° 12.3’ N, 18° 16.9’W
Vessel:         RRS Discovery
Cruise:         DY052
Weather:        Wind force 3 / 4, sea state slight, rain 
Pilot:          Estelle Dumont, Loic Houpert
Field team:     Estelle Dumont, Stefan Gary

Following the cruise, Eltanin will be returned to the MARS glider team for 
refurbishment and evaluation of the battery failure. At this stage, a fault in the 
battery pack manufacturing seems the most likely cause.

The full mission’s raw data can be viewed at: vocal.sams.ac.uk/gliders, and is 
available from BODC. Delayed-mode data will be submitted to BODC within the next few 
months. The full glider technical mission report will also be finalised within the 
next few months and will be available from BODC and SAMS.


Figure 19.1: SG550 in the water; recovery hoop and lasso; SG550 being lifted on 
board.



20  ACKNOWLEDGEMENTS


DY052 was a very successful cruise thanks to excellent teamwork and good weather. We 
would like to thank the Master, Jo Cox, for her support during the trip. Also, many 
thanks are extended to the whole ship's crew. The skill and professionalism of the 
bridge officers, the engineers, the catering staff and the ABs was very much 
appreciated.

We would also like to thank the science party for their positive attitude and hard 
work. Special thanks are extended to the CTD/Autosal operators who sailed on DY052: 
Jon Short, Colin Hutton, and Estelle Dumont; whose experience, skills, and careful 
attention to detail helped keep things moving along smoothly.

Many thanks are extended to Laura Wedge, Krys Szczotka, Jade Garner, Sally Heath, 
Rolly Rogers (NMF) and Collin Griffiths (SAMS) for assistance with cruise planning; 
Stuart Cunningham, Loïc Houpert, Rich Dale (SAMS), Penny Holliday, and Brian King 
(NOC) for assistance with setting up and using the MSTAR software; and Thom Gordon 
for loaning the hydrophone.



























                         National
                         Oceanography Center
                         NATURAL ENVIRONMENT RESEARCH COUNCIL













                              National Marine Facilities


                            Ship Instrumentation Overview
                                    RRS Discovery
                                    IMO: 9588029
                                   MMSI: 235091165
                                   Call Sign: 2FGX5

                              Cruise: DY052 (Ellet Line)
                                   by Jack McNEILL

                           7th of June - 25th of June 2016














                                NERC    SCIENCE OF THE
                                        ENVIRONMENT



   This document describes systems maintained by NERC Scientific Systems Technicians



Revision History

                      Date     Version     Description       Author
                   ----------  -------  -------------------  ------
                   2015.03.12    1.0      First draught        JM
                   2015.06.04    1.1        Corrected          ZN
                   2016.06.17    1.2    Updated & Corrected    JM









Questions?

Jack McNEILL NMF/SE/SSS
341/33 National Marine Facilities National Oceanography Centre Waterfront Campus 
Southampton
SO14 3ZH
+44(2380)596151
E-mail:  jmn@noc.ac.uk  or nocs_nmfss_shipsys@noc.ac.uk


Table of Contents

1   Introduction                                                                    73
1.1   Datalogging & Data Storage                                                    73
1.2   TechSAS                                                                       73
1.3   RVS Level C                                                                   73

2   Attitude & Positioning Instruments                                              74
2.1   Applanix POS MV V4 (Primary Science GNSS and Attitude Sensor)                 74
2.2   Kongsberg Seapath DPS330 (Secondary Science GNSS and Attitude Sensor)         74
2.3   iXBlue PhINS (Photonic Inertial Navigation System)                            74
2.4   CNav 3050 GPS, GLONASS, Galileo GNSS                                          75

3   Hydroacoustics                                                                  75
3.1   Kongsberg-Simrad                                                              75
3.2   Sonardyne Transponder Beacons & Software                                      76
3.3   Teledyne-RDI Ocean Surveyor ADCP                                              76
3.4   Sound Velocity Sensors                                                        77

4   MetOcean                                                                        77
4.1   OceanWaves WaMoS II Wave Radar                                                77
4.2   NMFSS SurfMet (Surface Water System and Meteorological Monitoring System)     77
4.3   Meteorological Instruments (Met)                                              77
4.4   Surface Water Sampling Instruments (SWS)                                      77
4.5   DartCom HRPT L-Band Polar Orbiter Weather Satellite Imaging System            78

5   Data Displays                                                                   78
5.1   NMFSS-SSS SSDS (Ship Scientific Display Screens)                              78
5.2   OLEX 3D Seafloor Hydrographic Mapping and Visualisation Software              79


1  Introduction

The new RRS Discovery is broadly similar to the RRS James Cook and has a similar 
arrangement of instruments and sensors. This document provides a brief overview of 
what’s on board; where it is; what it does; what its inputs and outputs are; and 
gives an indication of where to get more information. Datasheets for all instruments 
are provided on the Cruise disc.


1.1  Datalogging & Data Storage 

Datalogging software and storage is provided on a platform common to both RRS 
vessels (RRS Discovery and RRS James Cook), and managed by NERC's NMFSS Ship 
Scientific Systems group.


1.2  TechSAS

TechSAS is an integrated technical and scientific sensors acquisition system and is 
the primary datalogger on both vessels. The system allows monitoring and accurate 
time-stamping of each individual instrument with a graphical output

TechSAS saves data in the self-describing NetCDF (Network Common Data Format) format 
that can be easily read via MatLab or using freely available NetCDF libraries. 
TechSAS also broadcasts the logged data across the ship’s network in UDP pseudo-
NMEA0183 (i.e.: "NMEA-like") packets. Separate NetCDF documentation is available 
that explains the logged variables.


1.3  RVS Level C

Level-C is a data management programme, written in C for its Sun SPARC environment. 
The Level-C system logs the TechSAS UDP packets in the Level-C binary format as flat 
files (colloquially known as “streams”).

Level-C has a number of little programmes inside it that allow the flat files to be 
viewed, edited, and exported rapidly in a range of formats, e.g.: CSV; ASCII text 
file, at custom intervals and averaging periods.

Another feature is the display of meteorological, depth, and navigation data (as 
with the SSDS software running on the wall-mounted HP touchscreens around the ship).

The NMFSS Science Systems Technician can generate reports from the Level-C system.




2  Attitude & Positioning Instruments

The new RRS Discovery has some of the same sensors as the RRS James Cook, and some 
new ones.


2.1  Applanix POS MV V4 (Primary Science GNSS and Attitude  Sensor)

A combined GNSS receiver and attitude (i.e.: gyrocompass, and conventional motion) 
sensor that provides data about: attitude; heave; position; and velocity. The GNSS 
aspect is for use with Multibeam Echosounder systems.

The POSMV is logged to the TechSAS Datalogger. The datalogger produces two files for 
its configured file period (usually 24hrs).

These files are:
* POSMVPOS.POS - NetCDF File Containing Positional Data (Heading, Latitude, Longitude)
* POSMVATT.ATT - NetCDF File Containing Attitude data (Roll, Pitch, Heave)

Please note that the position output is the position of the ship's common reference 
point (the cross on the top of the POSMV MRU in the gravity room).


2.2  Kongsberg Seapath DPS330 (Secondary Science GNSS and Attitude) 

This is a secondary Science GNSS and attitude sensor. The position output is the 
position of the ship's common reference point (the cross on the top of the POSMV MRU 
in the Gravity Meter Room).




2.3  iXBlue PhINS (Photonic Inertial Navigation System)

A surface inertial navigation system that uses a FOG (Fibre-Optic Gyro) to output 
accurate position, attitude, and velocity data.


2.4  CNav 3050 GPS, GLONASS, Galileo GNSS

GNSS and RTCM Satellite Corrections Receiver. The position output is the position of 
the antenna. This GPS is not referenced to any other systems. It is primarily used 
to provide RTCM differential corrections to the other GPS systems. Please note that 
the position output is the position of the antenna. This GPS is not referenced to 
any other systems.




3  Hydroacoustics

RRS Discovery has both vessel-mounted and smaller deployable transponders.

3.1  Kongsberg-Simrad

Simrad, now part of Kongsberg, is the supplier of the heavy artillery of 
echosounders.

3.1.1  EM122 Deep Water Multibeam  Echosounder

This 12kHz echosounder is rated to 11,000m, but probably up to 8,000m for good 
quality data. The EM122 it is viewed and operated via SIS (Seafloor Information 
Service).

3.1.2  EM710 Shallow Water Multibeam  Echosounder

This 70-100kHz echosounder is rated to 2,000m, but in reality you might consider 
switching to the EM122 between 600-1500 metres. Within this range, the EM710 gives a 
broader swathe, with less detail, so which one you use depends on what data you need 
to generate.

3.1.3  SBP120 Sub-Bottom Profiler

The SBP120 is a 6kHz-8kHz extension to the EM122 Deep Water Echosounding Profiler 
(the receiver part).

3.1.4  EA640  Single-beam Echosounder

The EA640 is a special version of the EA600 commissioned for the RRS Discovery, 
pretty much identical to the EA600 and can operate at either 12kHz or 10kHz as 
required. The performance of each varies with output power (e.g.: 1kW or 2kW) and 
pulse lengths. They both have a wide bandwidth that overlaps, and can be run at the 
same time.

3.1.5  EK60 Multi-Frequency Echosounder (“Fish Finder”)

The EK60 has 18, 38, 70, 120, 200, and 333 kHz transducers fitted to the starboard 
drop keel. Equipment to calibrate the system is carried onboard.
Specifications  Ek60_brochure_english_reduced.pdf
Location dy###_data_disc/cruise_reports/instrument_data_sheets/



3.1.6  Kongsberg-Simrad SU16 Synchronisation Unit  (K-Sync)

Running several acoustic systems simultaneously on ships with several acoustic 
instruments can cause interference between the systems, which may reduce the data 
quality. This unit and associated software lets you synchronise the pings of 
different acoustic equipment, (providing that they operate at different 
frequencies!). This system lets the SST control the timing of the instruments and by 
controlling the triggering of each instrument's transmission.

Specifications  Operator Manual.pdf
Location dy###_data_disc/cruise_reports/instrument_data_sheets/k-sync/
	

3.2  Sonardyne Transponder Beacons & Software

There are two hull-mounted transponders on the RRS Discovery. The Starboard side 
USBL is a 7000 directional bis head for improved performance in deeper water; the 
Port side USBL is a 5000 standard head. The USBL transponder spars are extensible & 
retractable and project more or less vertically down from the aft half of the hull 
between the Drop Keels and the Propellers. The software used is Ranger 2.

Inputs Vertical Reference Units (VRUs), Gyro Compass; DGPS (Surface Positioning); 
GPS (Time Synchronisation). Transponders (1km-depth Wide-band Sub-Mini – WSM), and 
3km- depth DP Transponder.

Outputs it logs data itself into a file that can be taken away; can also output a 
data string to TechSAS (in this case, you only get the position of one beacon at a 
time in the water, you can put this info into the Level-C system and plot some data 
from it; it outputs to the OLEX 3D- seafloor mapping software that provides a visual 
display). It can also output DP telegram format data.


3.3  Teledyne-RDI Ocean Surveyor ADCP

The ADCP transducers are located in the hull, in blisters, in a forward-aft 
configuration approximately 6m below the water line. There are two systems that 
operate at two frequencies: 75 kHz; and 150kHz. Both the heads have a rotation 
relative to the ship's centre line of -45°. The software used for configuring and 
datalogging with the ADCP is called VmDAS (Vessel Mounted Data AcquisitionSystem). 
VmDAS gets data from the ship's attitude sensor and uses that to convert ship 
velocities into earth co-ordinates.

VmDAS can be configured either by loading or editing a command file; or by changing 
settings on the interface. Users should be aware that it's possible to 
simultaneously load and use a command file, and adjust settings using the interface, 
which can lead to command conflicts, in which case the interface overrides the 
command file. Data is logged to local hard-disc, and then create a back-up on the 
server. Set-up file is editable when starting the VmDAS software.

3.3.1  Teledyne Ocean Surveyor 75KHz Vessel Mounted ADCP (VMADCP)

Inputs: GPS; Gyrocompass; iXSea PhINS so it can calculate accurate speed and 
direction of currents. It is recommended that the EM710 is not used at the same time 
as the OS75 Range: 520-650m (Long-range/Low quality); 310-430m (Short range/High 
quality).

3.3.2  Teledyne Ocean Surveyor 150 kHz Vessel Mounted ADCP  (VMADCP)

Inputs: the same as for the 75kHz
Range: 325-350m or 375-400m (Long Range/Low Quality); 200-250m or 220-275m (Short 
Range/High Quality).



3.4  Sound Velocity Sensors

Discovery has a hull-mounted AML Micro X Probe, and a portable Valeport Midas SV 
Profiler. The Valeport uses DataLogExpress datalogger software and have a maximum 
depth of 5000m.
The Kongsberg SIS software has a new application called MDM for bringing the saved 
profiles in.


	

4  MetOcean

RRS Discovery has the same MetOcean instruments and sensors as the RRS James Cook, 
except the Temperature/humidity probe different on the RRS James Cook it’s Vaisala 
HMP45A on the RRS Discovery it’s HMP155.


4.1  OceanWaves WaMoS II Wave Radar

WaMoS is an X-Band nautical RADAR with a range of 100m to 4km. It can only generate 
data in above a minimum wind speed of 3ms-1. It detects open wave spectra. Sea state 
is calculated from detected backscatter of µwave “sea clutter” in real time. The 
system can detect wavelengths from 15 m – 600 m and covers periods from 4 sec-20 
seconds. At coastal sites, WaMoS II can only measure the spatial wave field beyond 
the wave breaking zone.  There is a WaMoS computer in the Met Lab, where it stores 
processed radar images. Data is logged in WaMoS's own format. Summary wave 
information is available in one of the ASCII files generated.


4.2  NMF SurfMet (Surface Water System and Meteorological Monitoring) 

SurfMet comprises two sets of scientific instruments: Meteorological; and Surface 
Water Sampling, along with ADCs and a PC hosting SurfMet data conversion software 
that passes data to the Data Systems for event  logging.

4.3  Meteorological Instruments (Met)

The Meteorological part of the system comprises a range of instruments located near 
the forward mast about 10 metres above sea level.


4.4  Surface Water Sampling Instruments (SWS)

The Surface Water part of the SurfMet system collects seawater (known as “non-toxic" 
or "underway" water) from the upper 5.3 metres of the ocean, and passes it through 
the following instruments:


The instrument called the..  ..measures..                  ..in..    ..to calculate..
---------------------------  ----------------------------  --------  ----------------
SeaBird 45                   Temperature and conductivity  Seawater  Salinity
Thermosalinograph 

SeaBird 38                   Change in resistance via a    Seawater  Temperature
Digital Oceanographic        thermistor
Thermometer          

WetLabs WetStar WS3S         Reflected light frequency     Seawater  Marine floral 
Fluorometer                  difference between beams of             density via 
                             light passed through water              fluorescence

WetLabs WetStar CST          Photon quanta (received       Seawater  Particulate 
Transmissometer              light)                                  density



TSG flow is approx 1.6 litres per minute whilst fluorometer and transmissometer flow 
is approx 20 l/min. Flow to instruments is degassed using a debubbler (outlet) with 
10 l/min inflow; waste flow is usually around 8-10 l/min (adjusted to maintain 
balance, but at a low rate to keep the TSG flow rate to around 1.6 l/min).


4.5  DartCom HRPT L-Band Polar Orbiter Weather Satellite Imaging System 

The DartCom system comprises a 1.2m Parabolic Dish enclosed in a Radome. It receives 
signals from satellites that take images of cloud coverage. These images can be used 
to see  the type of atmospheric and weather conditions  nearby.


	



5  Data Displays

Software for displaying useful science-related information is provided around the 
ship.


5.1  NMF/SE/SSS SSDS (Ship Scientific Display Screens)

These touchscreens located around the ship display a range of data from scientific 
and non- scientific systems: Gyro information; GPS information from CNAV; sensor 
information from SurfMet; Depth from EA640; and winch information. Waypoints to 
stations can also be entered on the ETA tab, and propagated around the network to 
the other screens.


5.2  OLEX 3D Seafloor Hydrographic Mapping and Visualisation Software 

OLEX is a 3-D seafloor map visualisation software that has a shared seafloor data 
files, and installed on a dedicated PC. OLEX receives data from navigation, depth, 
multibeam, and ship positioning systems (it can also position data from USBL). Olex 
provides rapid visualisation of multibeam data, as well as showing where in the 
world the ship is.

































                         National
                         Oceanography Center
                         NATURAL ENVIRONMENT RESEARCH COUNCIL













                              National Marine Facilities


                          BODC Ship-Fitted Instrument Logging

                                    RRS Discovery
                                    IMO: 9588029
                                   MMSI: 235091165
                                   Call Sign: 2FGX5

                              Cruise: DY052 (Ellet Line)
                                   by Jack McNEILL

                           7th of June - 25th of June 2016













                                NERC    SCIENCE OF THE
                                        ENVIRONMENT



   This document describes systems maintained by NERC Scientific Systems Technicians



Revision History


                     Date     Version      Description         Author
                  ----------  -------  ----------------------  ------
                  2015.05.05    1.0    First draught             JM
                  2015.05.15    1.1    Format changes & fixes    JM
                  2016.06.18    1.2    Template update           JM





Questions?

Jack McNEILL NMF/SE/SSS
341/33 National Marine Facilities 
National Oceanography Centre 
Waterfront Campus 
Southampton
SO14 3ZH
+44(2380)596151
E-mail:  jmn@noc.ac.uk  or nocs_nmfss_shipsys@noc.ac.uk

 







Table of Contents

   1  Ship-fitted instruments:                                              82
   2  Bestnav hierarchal ordering                                           83
   3  Relmov source:                                                        84
   4  RVS data processing                                                   84
















1  Ship-fitted instruments:

The following table lists the logging status of ship-fitted instrumentation and 
suites.

Manufacturer  Model     Function/data types  Logged?            Comments
------------  --------  -------------------  -------  --------------------------------
Meinberg      M300      GPS network time        N     Not logged but feeds 
              Lantime      server (NTP)               times to other systems

Trimble/      POS MV    DGPS and attitude       Y     Secondary DGPS         s/n 
Applanix      v4                                      5421 IMU36 s/n 2236_423154

C-Nav         3050      DGPS and DGNSS          Y     Primary correction

Kongsberg     Seapath   DGPS and attitude       Y     Primary DGPS  No attitude 
Seatex        330                                     logged, only position

iXBlue        PhINS     Inertial Navigation     Y     TechSAS logging module in 
                        System                        development. Attitude input to 
                                                      the ADCPs s/n PH-832; logged raw 
                                                      data from 2016/06/13/23.04

Sonardyne     Ranger 2  USBL                    N     n/a
              USBL     

Sperry Marine           Ship gyrocompasses      Y     "gyro_s" message in Level-C
                        x2

Kongsberg     EA640     Single beam echo        Y     s/n 420041 Software version 
Maritime                sounder (hull)                2.5.0.2f Logged via TechSAS & 
                                                      CLAM2014

Kongsberg     EM122     Multibeam echo-         N     s/n 123       SIS version 4.1.3
Maritime                sounder (deep)

Kongsberg     EM710     Multibeam echo-         N     s/n 211       SIS version 4.1.5
Maritime                sounder (shallow)

Kongsberg     SBP120    Sub-bottom profiler     N     n/a
Maritime 

Kongsberg     Simrad    Scientific echo-        Y     n/a
Maritime      EK60      sounder (fisheries)

Kongsberg     K-Sync     Acoustic Synchro-      N     See cruise report for systems
Maritime                 nisation Unit                synchronised  version 1.7.0     
                                                      SU version 1.5.1

NMFSS         CLAM2014   CLAM system winch log  Y     Constant hourly logging

NMFSS         SurfMet    Meteorology suite      Y     dy052_surfmet_sensor_ 
                                                      information.docx for sensor 
                                                      details

NMFSS         SurfMet    Hydrography suite      Y     dy052_surfmet_sensor_ 
                                                      information.docx for sensor 
                                                      details

OceanWaveS    WaMoS II   Wave Radar             Y     Logged locally and in TechSAS, 
                                                      not GmbH   requested, so no 
                                                      large raw data files.

Teledyne RDI  Ocean      VM-ADCP                Y     Deck unit s/n 1813 VMDas version 
              Surveyor                                1.46.5 Inteference from EM710 
              75                                      affects data
                 
Teledyne RDI  Ocean      VM-ADCP                Y     Deck unit s/n 28550 VMDas 
              Surveyor                                version 1.46.5 
              150 

Microg        Air-Sea    Gravity                N     Not fitted 
Lacoste       System II



2  Bestnav hierarchal ordering:

The following table lists the order of navigational systems in the bestnav process 
for positional fix.

                   Rank  Order of positional fixes  Comment
                   ----  -------------------------  --------
                     1   Kongsberg Seapath 330      spathpos
                     2   Applanix POSMV v5          posmvpos
                     3   C&C Tech. C-Nav 3050       gps_cnav

Units of dist_run: nautical miles.



3  Relmov source:

The following table lists the navigational systems that are used in the relmov 
process for ship’s motion.

                 Navigational source of ship’s motion  Comments
                 ------------------------------------  --------
                 Sperry Marine gyro                    gyro_s
                 Skipper Speedlogger                   log_dysk



4  RVS data processing:

The following table lists the RVS Level-C processing programs that were run.

               Programme  Run?  Comments
               ---------  ----  --------------------------------
               bestnav     Y    Data from: 
                                  • 16 159  15:42  on Discovery1
                                  • 16 164  10:18  on Enterprise

               prodep**    N    Using Carter Table Corrections

               protsg      N

               relmov      Y    Data from: 
                                  • 16 159  15:42  on Discovery1
                                  • 16 164  10:18  on Enterprise

               satnav      N

               windcalc    Y    Data from: 
                                  • 16 159  15:42  on Discovery1
                                  • 16 164  10:18  on Enterprise


**Please state if sound velocity probes used for depth correction instead of prodep.



 













                         National
                         Oceanography Center
                         NATURAL ENVIRONMENT RESEARCH COUNCIL












                              National Marine Facilities


                              SurfMet Sensor Information
                                    RRS Discovery
                                    IMO: 9588029
                                   MMSI: 235091165
                                   Call Sign: 2FGX5

                              Cruise: DY052 (Ellet Line)
                                   by Jack McNEILL

                           7th of June - 25th of June 2016















                                NERC    SCIENCE OF THE
                                        ENVIRONMENT



   This document describes systems maintained by NERC Scientific Systems Technicians


Revision History

                       Date     Version       Description     Author
                    ----------  -------  -------------------  ------
                    2015.03.12    1.0       First draught       JM
                    2015.06.04    1.1         Corrected         ZN
                    2016.06.17    1.2    Updated & Corrected    JM







Questions?

Jack McNEILL NMF/SE/SSS
341/33 National Marine Facilities 
National Oceanography Centre 
Waterfront Campus 
Southampton
SO14 3ZH
+44(2380)596151
E-mail:  jmn@noc.ac.uk  or nocs_nmfss_shipsys@noc.ac.uk


 
                       Seawater System Parameter             Value
                       ------------------------------------  -----
                       Pumped seawater flow rates (ml/min):  1500
                       Anemometer orientation on bow (deg):  0°
                       Seawater intake depth (m):            5.5

Fitted Sensors:

Manufacturer  Sensor               Serial No.    Comments (e.g. port)  Calibration  Last calibration 
                                                                         applied?      (DD/MM/YYYY)
------------  -------------------  ------------  --------------------  -----------  ------------------------
Surface SV    AML Micro X-Series   10626/204242  Drop Keel SV                        2015.09.30
Skye          PAR SKE510           28556         Starboard                  No       2015.09.11 (2yr)
Skye          PAR SKE510           28561         Port                       No       2015.04.30 (2yr)
Kipp & Zonen  TIR CM6B             962276        Starboard                  No       2014.11.13 (2yr)
Kipp & Zonen  TIR CM6B             973134        Port Inv:240004209         No       2015.03.19 (2yr)
Gill          Windsonic Option 3   071121        Starboard Inv:250004845    No       N/A (tested 2015.09.28)
Vaisala       HMP155 Temp./Hum.    K0950057      Met Platform               No       2015.01.19
Vaisala       PTB110 Air Pressure  M1750058      Met Platform               No       2016.04.29
Vaisala       PTB110 Air Pressure  G0820001      Mast Battery Room          No       2016.01.21
Wet Labs      WS3S Fluorimeter     WS3S-246      Inv:240002938              No       2015.09.01
Wet Labs      CST Transmissometer  CST-1131PR    Inv:24000####              No       2016.04.13 (2yr)
Sea-Bird      SBE38 Temperature    3854115-0491                             No       2015.06.25
Sea-Bird      SBE45 TSG            4548881-0231  Installed & freshwater-    No       2015.07.02 (1yr
                                                 tested on 2015.10.05                from 2015.10.05)



Spare Sensors on-board not fitted:

Manufacturer  Sensor               Serial No.    Comments (e.g. port)  Calibration  Last calibration 
                                                                         applied?      (DD/MM/YYYY)
------------  -------------------  ------------  --------------------  -----------  ------------------------
Surface SV    AML Micro X-series   10156/204889                                     2015.09.17
Skye          PAR                  28558                                            2015.09.11
Kipp & Zonen  TIR                  962301                                           2015.08.25
Kipp & Zonen  TIR                  973135                                           2015.08.25
Gill          Windsonic Option 3   71123         Inv.: 250004845            No      N/A (Tested 2015.03.10)
Vaisala       HMP155Temp./Hum.     K0950058                                         2015.01.16
Wet Labs      WS3S Fluorimeter     WS3S-117                                         2015.09.16
Wetlabs       CST Transmissometer  CST-1132PR                                       2014.09.29 (2yr)
Sea-bird      SBE38 Temperature    3854115-0488                                     2015.11.09
Sea-Bird      SBE38 Temperature    3853440-0416                                     2015.08.10
Sea-Bird      SBE45 TSG            4548881-0229                                     2015.08.13 (valid for 1y 
                                                                                    from 2015.10.20)
Valeport      Midas SVP            22356                                            2015.09.23 (2yr)
Valeport      Midas SVP            41603                                            2015.04.28 (2yr)


 






































                         National
                         Oceanography Center
                         NATURAL ENVIRONMENT RESEARCH COUNCIL













                              National Marine Facilities


                         Scientific Systems Technician Report
                                    RRS Discovery
                                     IMO: 9588029
                                   MMSI: 235091165
                                   Call Sign: 2FGX5

                             Cruise: DY052 (Ellett Line)
                                   by Jack McNEILL

                          8th  of June - 24th  of June 2016













                                NERC    SCIENCE OF THE
                                        ENVIRONMENT




   This document describes systems maintained by NERC Scientific Systems Technicians


 

Revision History

                         Date     Version  Description    Author
                      ----------  -------  -------------  ------
                      2016.06.11    1.0    First draught    JM
                      2016.06.23    1.1    Final            JM




Questions? 
Jack McNEILL 
NMF/SE/SSS
341/33 National Marine Facilities 
National Oceanography Centre 
Waterfront Campus 
Southampton
SO14 3ZH
+44(2380)596151
E-mail:  jmn@noc.ac.uk  or nocs_nmfss_shipsys@noc.ac.uk

 	



Table of Contents

  1  Overview                                                                       90
     1.1  Itinerary & Maps                                                          90
     1.2  Deployed Equipment                                                        90
     1.3  Personnel                                                                 91

  2  Requested Services                                                             92
     2.1  TechSAS & Hydracoustics                                                   93
  3  Data Acquisition Performance                                                   93
     3.1  Ship Scientific Datasystems                                               93

     3.2  Position & Attitude                                                       93
     3.3  Instrumentation                                                           94
     3.4  Hydroacoustics                                                            95
     3.5  Third Party Equipment                                                     97



1  Overview
The Ellet Line 2016, the previous Ellet Line was DY031 in 2015. The next two cruises 
are both OSNAP cruises with a stopover in Reykjavik.


1.1  Itinerary & Maps

Event        Date:YYYYMMDD/Day:hhhh  Summary                          Lat. & Lon.
-----------  ----------------------  -------------------------------  ----------------------
Start Date:  20160606/Mon:1400BST    Transit to Port Glasgow          12 hours by car
Sail Date:   20160607/Tue:0800UTC    Departed from PG at 07.00BST     55° 57.1’N 4° 47.2’ W
Transit:     20160608/Wed            Vastermanaeyar Is. near Iceland  63° 18.9’N 20° 12.7’ W     
Station:     20160612/Sun            Due south along Ellet Line       62° 54.1’N 19° 34.8’ W
Station:     20160615/Wed            Rockall Bank, Argo deployments   59° 57.7’N 19° 58.5’ W    
Station:     20160617/Fri            ESE towards Anton Doern seamt.   57° 34.4’N 13° 41.8’ W    
Station:     20160618/Tue            Rendezvous with RRS James Cook
Station:     20160619/Sun            Glider pickup                    57° 26.9’N 11° 03.2’ W
Station:     20160620/Mon            Barra Islands                    56° 43.4’N 7° 40.2’ W
Station:     20160621/Tue            Isle of Coll & Ardnamurchan      56° 44.2’N 6° 26.6’ W
Station:     20160622/Wed            Out again to Rockall-Hatton      57° 55.2’N 11°04.7’ W
Transit:     20160623/Thu:0900       Return to PG via Inner Hebrides  n/a
Dock Date:   20160624/Fri:1800       Moored alongside Port Glasgow    55° 57.1’N 4° 47.2’ W
End Date:    20160625/Sat            Handover to ZN for DY053, DY054  


Weather Map

Figure 2: Mostly calm and clear.

 	



Geographic Map

1.2  Deployed Equipment

The equipment deployed for is as follows:
• Networking:
  o Servers, Computers, Displays, Printers, Network Infrastructure
  o A public network drive for scientists, updated via Syncback
• Datasystems:
  o IFREMer TechSAS logged data and converted it to NetCDF format
  o NetCDF Format given in: dy052_netcdf_file_descriptions.docx
  o Logged Instruments given in: dy052_instrument_logging.docx
  o Data was also logged to NERC/RVS Level-C format, also described in:
  o dy052_netcdf_file_descriptions.doc
  o NERC software: Level-C; SurfMet Express; CLAM2016; SSDS3
  o Olex
• Hydroacoustics
  o Kongsberg echosounders (EM122, EM710, EA640, EK60)
  o Teledyne RDI (OS75, OS150)
• Telecommunications
  o GNSS & DGNSS (POS MV, PhINS; KB Seapath 330; CNAV 3050)
  o OceanWaves WaMoS II Wave Radar
  o DartCom Polar Ingester
  o NESSCo V-Sat; Thrane & Thrane Sailor 500 Fleet BroadBand
• Instrumentation
  o SurfMet MetOcean system: SWS Underway & Met Platform instrumentation


1.3  Personnel

Technicians


NERC Staff
  Senior Project Support (STO)   Jon        SHORT     jos@noc.ac.uk
  Scientific Systems Technician  Jack       McNEILL   jmn@noc.ac.uk
  Sensors & Moorings Technician  Colin      HUTTON    chut@noc.ac.uk

Guest Technicians
  SAMS Oceanographic Technician  Estelle    DUMONT    sa01ed@sams.ac.uk

Remote Technical Support
  Scientific Systems Technician  Martin     BRIDGER   mart@noc.ac.uk
  Scientific Systems Technician  Zoltan     NEMETH    zome@noc.ac.uk
  Scientific Systems Technician  Mark       MALTBY    mma@noc.ac.uk
  Scientific Systems Technician  Lisa       SYMES     lisa.symes@noc.ac.uk
  Teledyne RDI                   Kevin      GRANGIER  kevin.grangier@teledyne.com
  Teledyne RDI                   Loïc       MICHEL    loic.michel@teledyne.com  


Crew

Deck
  Captain                        Jo         COX
  Chief Officer                  Mike       HOOD
  2nd Mate                       Declan     MORROW
  3rd Mate                       Colin      LEGGETT
  Chief Petty Officer, Deck      Greg       LEWIS
  Chief Petty Officer, Science   Steve      SMITH
  Petty Officer, Deck            Bob        SPENCER
  Petty Officer, Science         Steve      SMITH
  Seaman Grade 1A                Willie     McLENNAN
  Seaman Grade 1A                Raoul      LAFFERTY
  Seaman Grade 1A                John       HOPLEY
  Seaman Grade 1A                Craig      LAPSLEY
  Deck Cadet                     Sam        NICHOLAIDIS

Engine
  Chief Engineer                 Andy       LEWTAS
  2nd Engineer                   Geraldine  O’SULLIVAN
  3rd Engineer (Fwd)             Ian        COLLIN
  3rd Engineer (Aft)             Edin       SILAJDIC
  Engine Room Petty Officer      Emlyn      WILLIAMS
  Engine Cadet                   Calum      DEACY

Auxiliary
  Electro-Technical Officer      Felix      BROOKS

Hotel
  Purser                         Graham     BULLIMORE
  Head Cook                      Mark       ASHFIELD
  Cook                           Amy        WHALEN
  Steward                        Jeff       ORSBORN
  Assistant Steward              Kevin      MASON  


Crew changes due on Saturday June 25th in Port Glasgow.


 	
Scientists

Job Title                Hon.  Forename  SURNAME          Institution  E-Mail Address
-----------------------  ----  --------  ---------------  -----------  --------------------------------
PSO                      Dr    Stefan    GARY             SAMS         sa01sg@sams.ac.uk
Cetacean Researcher      Dr    Clare     EMBLING          Plymouth     clare.embling@plymouth.ac.uk
Sr Marine Biogeochemist        Tim       BRAND            SAMS         sa01tb@sams.ac.uk
Sr Benthic Ecologist     Dr    David     HUGHES           SAMS         sa01dh@sams.ac.uk
Marine Chemist           Dr    Richard   ABELL            SAMS         sa01ra@sams.ac.uk
Met Office Scientist     Dr    Jon       TINKER           Met Office   jonathan.tinker@metoffice.gov.uk
Met Office Scientist     Dr    Rob       KING             Met Office   robert.r.king@metoffice.gov.uk
Data Scientist                 Emma      SLATER           BODC         emmer@bodc.ac.uk
PhD Student                    Liz       COMER            Southampton  ec10g10@soton.ac.uk
PhD Student                    Leah      TRIGG            Plymouth     leah.trigg@plymouth.ac.uk
PhD Student                    Winnie    COURTENE- JONES  SAMS         sa01wcj@sams.ac.uk
MSc Student                    Martin    FOLEY            Glasgow      2039728f@student.gla.ac.uk
UG Student                     Ashlie    McIVOR           UHI          13000201@uhi.ac.uk
UG Student                     James     COOGAN           UHI          14003393@uhi.ac.uk
UG Student                     Emily     HILL             UHI          emily.hill94@hotmail.co.uk
UG Student                     Stacey    FELGATE          UHI          13002514@uhi.ac.uk  

Figure 6: Scientist List



2	Requested Services

• Project Consumables: Stationery; Stationery Tools; Insulation Tape; Cables; Tags; 
  Ties; Labels; Workshop Tools; Printer Ink.
• Telecoms, Network & Computing infrastructure: VSat; FBB; Exinda; Vigor; Cisco 
  Switches & WAPS; BlackBox; DiscoFS; AMS; Squid; Desktop Computers; Printers.
• Datasystems: TechSAS; Level-C; CLAM; Olex; SSDS; VNC Nettops; Display PCs.
• Instruments: PySurfMet; PML's Live pCO2;
• Hydroacoustics:
  o K-Sync
  o 150 kHz hull mounted ADCP system
  o 75 kHz hull mounted ADCP system
  o EM122 multi-beam echosounder for Sondes (CTDs)
  o EA640 single-bottom echosounder for Sondes (CTDs)
  o EK60 fish-finder echosounder (18kHz)
• SurfMet
  o Meteorology monitoring package
  o Pumped sea water sampling system
  o Sea surface monitoring system
• Ship scientific computer networking infrastructure


2.1  TechSAS & Hydracoustics

All acoustics, Wave Radar, TechSAS, Level-C (both Discovery1 & Enterprise), SWS 
(Underway), PCO2, POSMV software & PHINS logging, was turned off by 201606232100, as 
we approached the Irish EEZ on the return to Port Glasgow. This was done at the 
request of the PSO.




3  Data Acquisition Performance

All times given are in UTC.


3.1  Ship Scientific Datasystems

Data were logged and converted into NetCDF file format by the TechSAS datalogger. 
The format of the NetCDF files is given in the file: 
dy052_netcdf_file_descriptions.docx. 
The instruments logged are given in dy052_ship_instrumentation_overview.docx.
Data were additionally logged in the RVS Level-C format, which is also described in:
    dy052_netcdf_file_descriptions.docx.


3.2  Position & Attitude

The main GNSS and attitude measurement system, Applanix POS MV was run throughout 
the cruise. Kongsberg Seapath 330 is not set up to log to TechSAS yet. iXBLue PhINS 
was logged from 2016.06.13:23.05 UTC.

3.2.1  Kongsberg Seapath 330

The Seapath is the vessel’s primary GNSS, it outputs the position of the ship’s 
common reference point in the gravity meter room. Seapath position and attitude was 
used by the EM122 (and by the EM710 when it was on). The system was turned off by 
the ETO on 2016.06.16:1520, and restarted on 2016.06.15:1842. Seapath Position and 
Heading was logged from 2016.06.8:13:28 in TechSAS.

3.2.2  Applanix POSMV

The POSMV is the secondary scientific GNSS, and is used on the SSDS displays around 
the vessel. TechSAS and Level-C only attitude data from the POSMV was logged from 
2016.06.8:13:28 in TechSAS.

A TechSAS data logging module for the iXSea PHINS and Seapath 330 is under 
development.

3.2.3  C&C Technologies CNAV 3050

The POSMV is the tertiary scientific GNSS, and is located on the bridge. TechSAS and 
Level- C only attitude data from the CNAV was logged from 2016.06.8:13:28 in 
TechSAS.

3.2.4  PhINS

PhINS supplies the ADCP OS75 and OS150 with position and attitude data. iXBLue PhINS 
was logged from 2016.06.13:23.05 UTC.


3.3  Instrumentation

3.3.1  SurfMet & SBE45

Following changes to the serial connections, SurfMet ran without any malfunctions. 
dy052_surfmet_sensor_information.docx for details of the sensors used and the 
calibrations that need to be applied.
Calibration sheets are included in the directory:
\Ship_Fitted_Scientific_Systems\MetOcean\SurfMet_metocean_system\SurfMet_calibration
_sheets\fi tted\
Data are available in NetCDF in: \Ship_Fitted_Scientific_Systems\TechSAS\SURFM
The non-toxic water supply was active from before 2016.06.07:1536-1631.
TechSAS files are generated from 2016.06.07:09.00 to 2016.06.24:0?00. Data in Level-
C starts from 2016.06.08:13:28.

3.3.1.1  SurfMet: Surface Water System & SBE45

The system operated normally throughout the cruise, in fact the flow rate was more 
stable than it has been in previous cruises.

SBE45 Thermosalinograph files now contain Conductivity, Temperature, and
There was some data loss on 2016.06.16:2000-2400 approximately; this is indicated by 
the slightly smaller file size in TechSAS around that time. NetCDF shows a restart 
time of 2016.06.15:18.54. Data in Level-C starts from 2016.06.08:13:28.

3.3.1.2  SurfMet: Met Platform System

No problems. The HMP155 temperature sensor (K0950056) on the Met Platform was 
replaced at the start of the cruise on 2016.06.06 (with K0950057).

3.3.1.3  SurfMet: PySurfMet.

The software operated normally throughout the cruise.

3.3.2  WaMoS II Wave Radar

Not requested, but logged locally, and in TechSAS. When data is logged, a summary of 
its output is given in the PARA*.ems files.

3.3.3  Gravity Meter

Not installed on the ship for this cruise.


3.4  Hydroacoustics

Generally worked well, apart from the OS75 VMADCP, which suffered from interference 
from an as yet unknown source (i.e.: apparently not from an echosounder at a similar 
frequency). Data is available in: \Ship_Fitted_Scientific_Systems\Hydroacoustics

3.4.1  Kongsberg EA640

10kHz and 12kHz both run in synch with K-Sync. Both transducers were turned off and 
on frequently to accommodate the 2kHz-250kHz passive hydrophone deployed off the 
back deck. Not normally logged, but logged mainly after June 11th and from the 13th.

3.4.2  Kongsberg EM710

Not requested, but some data logged, at the start of the cruise, and turned off long 
before reaching Iceland. This echosounder was not calibrated with an SVP dip, and 
was run purely to ensure the system is in good working order and to add data to the 
Olex map, and to provide depth for CTD Rosette deployments. Data logged from 
2016.06.07:1559-1905 and 2008, and 2016.06.19:1409-2126. This was mainly to collect 
diagnostic data, but was turned off for periods to investigate possible interference 
with OS75 VMADCP. EM710 turned off again at 2016.06.21:1625 along with the SBP.

3.4.3  Kongsberg EM122

Not requested, but some data logged, at the start of the cruise, and turned off long 
before reaching Iceland. This echosounder was not calibrated with an SVP dip, and 
was run purely to ensure the system is in good working order and to add data to the 
Olex map, and to provide depth for CTD Rosette deployments.

3.4.4  Kongsberg SBP120

Not requested, tested briefly 2016.06.21:0132-1623, no usable data logged.

3.4.5  Kongsberg EK60

18kHz and 38kHz transducers were both run to collect data on the deep-scattering 
layer. 

Data were logged from 2016.06.08:20.03 and restarted at 2016.06.11:1524; restarted 
again at 2016.06.15:1850 and from 2016.06.17:1959 and 2016.06.18:1434
38KHz was turned off on 2016.06.17:1959

Logged data are available in: \Ship_Fitted_Scientific_Systems\Hydroacoustics\EK60



3.4.6  Sound Velocity Profiles

Used manual setting of 1500m/s in the swathe. The opportunity to do an SVP dip was 
overtaken by other events, and there was no pressing science requirement to do this.

3.4.7  Teledyne RDI Ocean Surveyor  ADCPs

ADCPs received GNSS data from the iXBLue PhINS system. There are no known faults on 
the VMADCPs or K-Sync, tests were done and passed at the start and end of the 
cruise.

Command files were applied according to details provided by e-mail and discussed 
prior to the cruise.

Data recorded from the OS75 before 2016.06.08:22.26 seems suboptimal, and may seem 
more optimal after this date and time, but there is no firm conclusion on this yet.
Data is available for the OS150 from 2016.06.08:14.17.

3.4.7.1  Ocean Surveyor 75kHz

No faults. The system operated normally throughout the cruise.
Data available at: \Ship_Fitted_Scientific_Systems\Hydroacoustics \OS75kHz
Data logged from 2016.06.07:20.00, for testing and tweaking the command file.
Data logged from 2016.06.08:22.00 with bottom tracking turned off in narrowband, 64 
bins, 16m bin Size and 8m blanking distance, as requested by Dr Penny Holliday.
From the UHDAS processed data, it looks like when on DP, bubbles from the Aziprops 
contributed part of the interference seen. Another component of interference can be 
weather, this is evident in the latter few days of the cruise when the ship 
travelled WNW again.
On the morning of the 20th, there was a lot of noise being put into the water from 
many echosounders being turned on (not the SBP120) during that watch. There is no 
clear evidence of any interference from any other similar frequency source, such as 
EM710.

3.4.7.2  Ocean Surveyor 150kHz

No faults. The system operated normally throughout the cruise.
Data available at: \Ship_Fitted_Scientific_Systems\Hydroacoustics\OS150kHz
I used to 64 bins of 4m bin size, on narrowband mode; 8m blanking distance. The 
maximum number of bins is 128, the more you use, the slower the ping rate. There was 
no limited or no data in depths >1000m, which is to be expected.

Bottom tracking was turned on over near the coast of Iceland and Vastermannaeyjar, 
over Rockall Bank, and on the Hebridean shelf.

3.4.8  Sonardyne USBL

Not requested; no data logged.


3.5  Third Party Equipment

3.5.1  NMF/SE/Sensors & Moorings: CTD, LADCP,  Salinometer

Jon Short has provided a CTD cruise report in the following location in the Data 
Disc:
\Specific_Equipment\CTD\documents






CCHDO DATA PROCESSING NOTES


*  File Online Carolina Berys
dy052.pdf (download) #78da4
Date: 2016-10-20
Current Status: unprocessed


*  File Submission Carolina for Stefan Gary
dy052.pdf (download) #78da4
Date: 2016-10-20
Current Status: unprocessed
Notes
Cruise Report from 
https://www.bodc.ac.uk/data/information_and_inventories/cruise_inventory/report/16032/


*  File Online Carolina Berys
prelim_dy052_cchdo_submission.tar.gz (download) #ef0fe
Date: 2016-10-20
Current Status: unprocessed


*  File Submission Stefan Gary
prelim_dy052_cchdo_submission.tar.gz (download) #ef0fe
Date: 2016-07-27
Current Status: unprocessed
Notes
AR28 annual repeat of Extended Ellett Line
RRS Discovery, June 7- June 24 2016
Please see README.txt in the compressed file for more information.

This is a PRELIMINARY data submission to comply with the data submission within 5 
weeks of the end of the cruise for high-frequency GO-SHIP sections.

I intend to submit a completed data set within the 6 month time frame.

This is my first time submitting to CCHDO, please let me know about data format 
preferences for the final submission.
