HLY-04-04, SBI Mooring Cruise.  2 Sep – 1 Oct, 2004


Preliminary CTD and Water Sampling Summary

                                                Sarah Zimmermann, WHOI





            A total of 157 CTD stations with bottom depths ranging from 30m--2300m were collected from the Chukchi and western Beaufort Seas.  Water samples were taken at 117 of these stations.  Water sample measurements typically included dissolved oxygen, salinity, nutrients, chlorophyll and phyopigments.  In addition, O18, dissolved organic carbon, particulate organic carbon, total CO2, alkalinity, and radium samples were collected during particular sections.  CTD casts typically went to within 5m of the ocean floor; however, during the eddy survey and on comparison casts for the mooring sensors, it was not necessary to take the CTD to the ocean bottom.



CTD Package

            CTD and water sample data were collected using the USCGC Healy’s Seabird 911+ system operating at 24Hz scan rate, with a 24 position rosette package and 24 12-liter Niskin bottles.  In addition to a dual set of pumped temperature and conductivity sensors, the CTD had a SBE43 oxygen sensor pumped in-line with the primary temperature and conductivity sensors, a WetLabs CST transmissometer, an Aquatraka fluorometer, and a Benthos altimeter.  Fortunately, a backup frame, CTD and auxiliary sensors were also provided because we were required to change out the CTD and the altimeter during the cruise.  See the appendix for sensor serial numbers, calibration dates and position on frame.


CTD Data Acquisition and Processing Procedures

            Upon reaching the station, the rosette was brought out of the hanger, the CTD was powered on and data acquisition started. The transmissometer and fluorometer windows were cleaned immediately before each deployment.  The sensors were soaked for three minutes at 10m after the pumps turned on.  The CTD frame was then raised back to the near-surface (between 2m and 5m) and lowered at 30m/min to 100m and then at 60m/min.  The descent rate was slowed to 30m/min approximately 60m off the ocean floor, and slowed further at 10m off the bottom.  Depending on sea state, maximum CTD depths were within 1 to 5m of the ocean bottom.  The bottom bottle was fired immediately and subsequent bottles were closed after waiting 30 seconds at each stop.  The ‘surface’ bottle was taken at 10m to avoid the extremely large surface gradients and the change in water properties due to ship’s presence (for example, the propeller wash).  The CTD was turned off after the package was landed on deck, the water sampler rinsed with fresh water and the package returned to the heated hanger for sampling.


The CTD data were acquired and processed with Seabird software on a PC platform with further processing using Matlab-based routines.  Acquisition occurred real -time through a conducting cable from the CTD to a PC running Seasave-Win32_V5_31a.  The ship’s GPS position was added to each data scan via the NMEA interface.  Upon completion of the station, the data were copied via the ship’s network to the processing PC.  Seabird’s windows based processing software, SBEDataProcessing-Win32_V5_29b, was then used to produce 1db averaged downcast and upcast profiles.  The standard processing steps followed at sea were: sensor alignment through advancing conductivity; spike removal; a correction for the thermal mass of the temperature sensors; filtering; removal of pressure reversals; calculation of oxygen; averaging to 1 db levels; calculation of other derived properties; and the file separation between downcast and upcast profiles. 


Final processing was completed using Matlab to calibrate, plot and remove spikes in the data.  Both conductivity sensors and the oxygen sensor were calibrated to the water samples and the calibration applied to the down and upcasts.  The data were plotted station by station and density inversions in the downcast identified.  A 0.004 kg/m3 criteria was used to identify density inversions at depths over 10m.   The top 10m were not examined for density inversions.  The inversions were interpolated over in the primary temperature and conductivity sensor data, and the derived properties (salinity, density, theta) were recalculated.  The interpolations are listed in the appendix.  The fluorometer and transmissometer are unprocessed.


CTD and Water Sample Data Files

The file naming scheme starts with a ‘d’ or ‘u’ to indicate downcast or upcast and follows with five digits, ‘dSSSCC.*’,  where SSSCC is a 3-digit station number (SSS) and 2-digit cast number (CC).  Repeat casts (cast 2 and cast 3) were performed to collect radium samples.  Occasionally the repeat cast would be performed out of sequence, ie we moved onto 4 new stations and then came back for the radium cast.


Raw CTD Acquisition Files from Seabird Sea-Save

            SSSCC.dat      raw data

            SSSCC.hdr      header file

            SSSCC.bl        bottle trip scan numbers

            SSSCC.con     configuration file

SSSCC.mrk     mark scan numbers, used to indicate start of down cast, bottom of cast, end of cast.  Also used to mark the comparison stops during the CTD comparison casts where FSI EMCTDs and SBE Microcats were attached to the rosette frame.


Processed CTD Files

            dSSSCC.cnv                down 1 db averaged file is Seabird format

dSSSCC_ct1.csv         down 1 db averaged file is JOSS format, comma delimited, and can be read using EXCEL

            uSSSCC.cnv                up 1 db averaged file in Seabird format

uSSSCC_ct1.csv         up 1 db averaged file in JOSS format, comma delimited, and can be read using EXCEL



Water Sample File

            HLY0404_HY1.csv     water sample file with merged ctd data



CTD Data Quality



            The CTD, rosette and niskin bottles performed well.  The CTD temperature and conductivity sensors performed to their specified accuracy.  The only equipment problems experienced were with leaks in the connections, and the failure of the first altimeter.  The auxiliary-4 CTD bulkhead connector leaked repeatedly even after the cable was changed out.  Due to this, the CTD body was swapped out before station 61, but all the sensors were kept in their same configuration and plugged into the spare CTD.  Removing the CTD with the bad auxillary-4 connector revealed the modem bulkhead connector also had a slow leak.  These connectors were replaced although we never needed to switch back to this CTD.   The altimeter was changed out shortly afterwards for station 64.  It was not reading full scale (~98.5m) when it was over 100m from the ocean floor and during the bottom approach of station 63 the altimeter was reading 4m as the package touched the bottom.  The altimeter base appeared damaged although we had not experienced any event that would have caused this damage.  Perhaps the damage had been received earlier but only now, cycling in the cold and to greater pressure, it became affected by the damage?

The CTD wire was reterminated once, after station 83.  The CTD had swung strongly in the block and in addition to this high-tension event there was an earlier kink in the wire.   As a safety measure it was decided to reterminate the wire.

The CTD touched the bottom during stations 63 and 77, both at slow speed and without any change to the calibrations.

The pumps were frozen at the start of station 111, cast 2.  The CTD was recovered and the pumps thawed before redeployment.   After this the hangar door was lowered further and the gap between door and floor was covered to try and keep the floor at a warmer temperature.  The pumps did not freeze again.

These were the major issues for the CTD, however, the complete list of station comments is included in the appendix.



            On deck pressure was examined for stations 1 to 49 to determine if a mean pressure offset existed.  Typically there was an offset of 0.3db before the cast and –0.2db after the cast.  The CTD is powered up just before the cast, and typically the CTD pressure drifts from 0.4 towards 0 during the pre-cast time on deck.  Based on this, it appears a longer warm-up period could be used and that there is no pressure bias.



            The primary and secondary temperature sensors were compared using the data from the bottle stops.  They show a mean difference of less than 0.0005 degC.  This inter-comparison supports the stated instrument accuracy of 0.001degC without requiring a post-cruise calibration.



            The conductivity sensors were very stable, requiring only one calibration during the cruise and providing the stated accuracy of 0.002 psu.  Stations 1 to 111 were used in the fit.  Surface values were used in the fit to obtain a slope over the range of conductivities; however, the majority of observations discarded by the iterative fitting routine (acceptable residual criteria was less than 2.5 x STD) were from the high salinity gradient water in the upper 50m.


Sensor              Slope               Bias                  STD mS/cm                 Number of Obs

Primary            1.00016            -0.00358         0.0012                         306 of 555

Secondary        0.99959             0.01003         0.0011                         284 of 555




            The oxygen sensor was also quite stable with one calibration performed for the cruise.  The data were calibrated to the water samples, using stations 1 to 96. The calibration method followed the Seabird Application Note Number 64-2.  This method determines two of the six coefficients, Soc and Voffset.  The other coefficients were left at their laboratory calibration settings.  All water samples were used in an iterative fitting routine (acceptable residual criteria was less than 2.5 x STD).   The standard deviation of the calculated oxygen (using the same observations that passed the fitting criteria) was 0.05 ml/l.


Sensor              Soc                  Voffset             STD                             Number of Obs

Oxygen            4.0268e-01      –0.4434           0.006 oxy/phi               422 out of 560

                                                                        0.05 ml/l                       422 out of 560




            The fluorometer data were not processed. 



            The transmissometer data were not processed.  A log of the full scale in-air and blocked in-air readings were measured from 7 September to 16 September.  They show little change over this period.  The full scale in-air reading had a range from 4.56 to 4.8 volts with a more consistent reading after the transmissometer had been powered on for a few minutes.  The blocked reading had a range of 0.048 to 0.056 volts.  The window was cleaned with de-ionized water prior to each cast. 





Water Sample Acquisition and Processing Procedures

Salts, Nutrients, Oxygen, and Water Sample File Preparation

Please see odfhly0404.doc




Dean Stockwell

Chlorophyll samples have been collected from casts covering 106 of the stations occupied during the 2004 SBI Mooring cruise.  Six to nine depths per cast have been sampled and processed.  In addition, samples have been processed from 8 stations, that were collected during underway analysis (Sharon Smith).  Data entry into the data server has been made following quality control checks on spreadsheet information.  Highest chlorophyll concentrations for the cruise (8.2 mg Chl/l) occurred at station 36.  Chlorophyll samples were filtered onto 25 mm GF/F filters and extracted for 24 hours in 90% acetone and determined fluorometrically (Evans and O’Reilly, 1983; Holm-Hansen et al., 1965).


Evans, C.A. and J.E. O’Reilly.  1983.  A Handbook for the Measurement of Chlorophyll a in Netplankton and Nannoplankton.  Biomass Handbook No. 9.  N.O.A.A.


Holm-Hansen, O., C.J. Lorenzen, R.W. Holmes, and J. D. Strickland.  1965.  Fluorometric determination of chlorophyll.  J. Cons. Cons. Int. Explor. Mer 30:3-15.





Jeremy Mathis


Dissolved organic carbon (DOC) samples were taken on all CTD lines and during the eddy survery.  Full depth profiles were conducted with 375 total samples taken.  These samples will be stored frozen until they can be return to the lab for analysis.  Total CO2 and alkalinity samples were taken on all lines at the surface only, with the exception of the eddy profile in which full depth profiles were taken for both.  210 samples were taken for TCO2 and Alkalinity.  Particulate Organic Carbon (POC) samples were taken during the eddy survery.  120 samples were taken at full depth ranges throughout the eddy work and will also be analyzed once returned to lab with the DOC, TCO2 and alkalinity samples.  The main objective of the cruise was to quantify the total carbon transport that occurs in an eddy moving from the shelf break into the Canada Basin and with the excellent high resolution sampling that was conducted in the eddy it is very likely that the objective will be fully accomplished. 






A1       CTD Configuration


Main CTD                                S/N                  Last Cal           Stations

SBE 9+                                                                                   

Pressure                                   0639                                        001 to 060

Primary Temperature                2796                02Jul04            001 to 157

Primary Conductivity                2545                02Jul04            001 to 157

Secondary Temperature            2824                02Jul04            001 to 157

Secondary Conductivity            2568                02Jul04            001 to 157

Oxygen SBE43                        459                  30Jun04           001 to 157

Trans. Wetlabs CST                 CST-390-DR   20Nov03         001 to 157

Fluor. MKIII Aquatracka         088233            21Jan04           001 to 157

Benthos Alt. PSA-916D           872                  default              001 to 064


Change outs:

Pressure                                   0638                5Mar04            061 to 157

Benthos Alt. PSA-916D           843                  default              064 to 157


Main CTD is horizontally mounted at base of CTD frame.  24 bottle rosette with 12 liter Niskin bottles and SBE Rosette.  Oxygen is in line with primary temperature and conductivity. Both T+C pairs have pumped flow.  Fluorometer and transmissometer are not pumped systems.


After swapping out CTD 0639, Jim Schmidt replaced the modem and auxiliary-4 (v6 and v7 channel) bulkhead connectors.  The swap was made because auxiliary-4 connector was leaking, but it was discovered after the swap that the modem connector had also leaked.



Auxiliary Sensor Configuration 1, Stations 1 to 59

Auxiliary 1        V0       Fluorometer

V1       Free

Auxiliary 2        V2       Free    

V3       Free

Auxiliary 3        V4       Transmissometer

V5       Free

Auxiliary 4        V6       Altimeter

V7       Oxygen


Auxiliary Sensor Configuration 2, Stations 60 to 157

Auxiliary 1        V0       Fluorometer

V1       Free

Auxiliary 2        V2       Altimeter         

V3       Free

Auxiliary 3        V4       Transmissometer

V5       Free

Auxiliary 4        V6       Oxygen

V7       Free




Configuration Files


Filename                       Stations                                    Change

Hly0404_1.con            00101 to 05901                       First setup

Hly0404_2.con            06001                                      Changed voltage channels

Hly0404_3.con            06101 to 06401                       Changed pressure housing

Hly0404_4.con            06002 and 06501 to 15701      Changed altimeter




Height from bottom of frame                                                                            


Pressure                                   7”                                

Primary Temperature                3.5”

Primary Conductivity                5.5”

Primary Pump                           6.5”

Oxygen SBE43                        6”

Secondary Temperature            3.5”

Secondary Conductivity            5.5”

Secondary Pump                      6.5”

Trans. Wetlabs CST                 2.75”

Fluor. Aquatracker                   4”

Altimeter                                  2.5”

Bottle bottom                           24.25”

Bottle mid-point                        24.25”+19.5”

Distance between Temperature Sensors            7”

Tubing Lengths in Primary system:

Conductivity to Oxygen            2.5”

Oxygen to Pump                       4.5”

Tubing Lengths in Secondary system:

Conductivity to Pump               6.5”




A2       Individual Station Notes       


Notes from station logsheets and processing:


1301    Did not get within altimeter range of bottom.

1401    Did not get within altimeter range of bottom.

1502    Radium and EMCTD comparison cast. EMCTDs s/n1313(BS7) and s/n1346(BS8).

1503    Radium and EMCTD comparison cast.  EMCTDs s/n1313(BS7) and s/n1346(BS8).

1601    EMCTD comparison cast.  EMCTDs s/n1355(BS3) and s/n1337(BS4).

1701    EMCTD comparison cast.  EMCTDs s/n1337(BS2) and s/n1363(BS4).

1801    EMCTD comparison cast.  EMCTDs s/n1355(BS3) and s/n1341(BS5).

1901    EMCTD comparison cast.  EMCTDs s/n1337 (BS2) and s/n1341(BS5).

2001    MicroCat comparison cast.  Microcats s/n 2131(BS1) and s/n 2132 (BS2).

2101    MicroCat comparison cast.  Microcats s/n 2139(BS6).

            Wire kinked while taking up slack prior to deployment.

2201    MicroCat comparison cast.  Microcats s/n 2135(BS3), s/n2136(BS4), and s/n2137(BS5)

2301    Oxygen sensor not properly soaked.  Only waited at 5m until pump turned on.

2401    Oxygen sensor not properly soaked.  Only waited at 5m until pump turned on.

3001    Niskin 2 closed without waiting for 30second wait so closed  niskin 3 at same depth.  CTD tags will be left for both niskins but water samples should be merged with niskin 3 because they were drawn from this niskin. 

            Surface mark is actually at 30db.

3301    T1-T2 difference looks larger than normal.  May be due to jellyfish tentacles (seen on frame), or due to large swell in shallow water with large gradients.  Later (station ??) a small blob of jelly-fish material freed from tubing between C2 and pump.

3401    Bottom mark is 5m off the bottom of cast.

3801    Did not wait 30 sec on Niskin 3

3901    Niskin1 was deployed with bottom cap closed.  No samples from nikin1 but tag is in file.

4501    Niskin 2 and 3, top vents not closed. 

Gelatinous material removed from tubing between C2 and pump.

Software indicated pump was on while on deck prior to cast.

4601    Prior to cast flushed sensors again.  This time a glob of gelatinous material    appeared in tubing between secondary conductivity cell and pump.  The material was removed, tube re-attached, and cast looked better.

4701    Quite a bit of jellyfish material on frame, including CTD intake.

5001    Originally named 05201.  Filenames and *.hdr changed afterwards.  Bottom depth also added to header file after the cast.

5201    Niskin1 did not close, not sampled.

5603    Mark taken 5 m above max CTD depth.

5801    Ryan noticed altimeter is not reading full scale anymore…off by 5m at surface and bottom depth (altimeter plus ctd depth) are 5m less than the bathymeter and seabeam depth (however it does read +4 of the adcp depth).

Unplugged oxygen and altimeter cable from CTD and found connection had been leaking again.  Cleaned up, reattached and redeployed.

5901    No spare Y-cable available but since the aux-2 bulkhead connector was free we removed Y-cable and plugged altimeter into the aux-2, and left oxygen in aux-4.  New configuration file made: HLY0404_2.con    Altimeter is now changed from V6 to V2 and Oxygen is changed from V7 to V6.

6001    Oxygen data bad.  Yes connection leaked again (aux-4).

Swapped out CTD body (s/n 638 for 639) but kept all the same sensors.  Turns out the modem connection also had corrosion from leaking. No clear problem seen on bulkhead connectors…pins on Aux-4 look slightly bent.  New configuration file: HLY0404_3.con.  The pressure casing we’ve switched to had a blown fuse and bulkhead connector during the last leg.  Rob Palmeres could tell us what happened in particular.  He got it back into working order with MSTs.  Jim Schmidt replaced the aux-4 and modem bulkhead connectors in the removed CTD (s/n639).

6101    Data look good with new pressure housing.

6201    Pump on while on deck before cast.

6301    Bottom contact (at slow speed).  Altimeter read 4m and then touched bottom- altimeter was reading incorrectly.

6401    Careful bottom approach: flat bottom, no ship-rock, altimeter read 6m and then switched to 99.  Did not touch bottom, but expect altimeter has ~ 4m offset.

            Altimeter changed out after cast.

6002    First cast with spare altimeter.  Taken after 6401.  Originally saved as 00602.*  Changed back to 06002.*  No bottles

6501    Altimeter reading fine.

6902    Originally saved file as 0690.* After cast files were renamed back to 06902.*

7401    Auxiliary-4 connector cleaned after cast.  Pins were green, showing seawater had been leaking in.  Connector was examined because V7 was reading non-zero (only oxygen is plugged into this connector so only V6 should have reading).  However, there were no spikes in the data to indicate a problem.

7601    Niskin 3 was closed at an un-intended depth so was not sampled.

7701    Bottom contact.  Ship lost power 8m above bottom.  Ship drift/ wire angle change brought the CTD in contact with the bottom.  The package may have even dragged along the bottom.  Power was restored in ~2 minutes.  Cast was restarted (?) bottom bottle tripped and continued with uptrace as normal.  Primary and secondary conductivity differences were small- does not appear to shifted calibration.

7801    Altimeter went from 4.5 to 98 at bottom.  Maybe due to slope, maybe altimeter problem?  Altimeter was late in finding the bottom (28m off bottom).

8301    Wire stressed during wait at 5m.  A big swell raised package and lowered tension of wire on block and then quickly released package,  putting a shock on the wire.  Data looks spiky and shows 5 m density inversion but this is most likely due to mixing by package/ ship prop in the high gradient water with big swells.  Station 8401 performed next and then it was decided to reterminate wire (outer armor shows slight gaps and there is a kink from an earlier cast ) and go back and repeat this station (calling the repeat 8304).

8304    Follows station 8401, back at station 83.  First cast with reterminated wire.  Looks fine.  Seas have also calmed down slightly.  Voltage channel 7 is free, but shows voltage on this cast.  Aux-4 connector (oxygen plugged in here: V6 and V7) cleaned after cast but does not appear noticeably wet.  Oxygen trace looks fine.  Cast is named 04 to differentiate from naming scheme of radium casts (02 and 03), although there are no radium casts at this station.

8501    Voltage channel 7 shows small noise.  Connector left as is, not checked.

8502    Voltage channel 7 reads 0 all cast but voltage channel 5 now has small noise. Connector left as is, not checked.

8601    Voltage channel 5 shows small noise again.  Connector left as is, not checked.

8701    No more noise on any of the free channels (v1,v3,v5,v7).

9001    Niskin 1 not tripped at right depth (too early, ~10 off bottom).  Not sampled.  2nd mark scan also not at bottom.  3rd mark scan is at bottom.

9601    Did not wait 30 seconds before tripping surface bottle.

11101  Extra tag (24th niskin) not sampled- remove tag.

11102  First dunking the pumps never came on due to freezing.  CTD was brought back into hanger and flushed with warm water and then with warm saline water.  CTD was then redeployed, leaving syringes full of warm saline water on as long as possible, removing just before it was lowered into the water. Initially this was called 11103 but was renamed to 11102.

11201  Paused at 210m for a few minutes on downcast because wire was rubbing side on A-frame.

11601  Initially put into water with syringes still attached.  Brought out, syringes taken off and restarted.

12101  Thermometer for measuring oxygen temperature out of range on very cold water

12502  CTD drifted lower while tripping all the bottles for radium samples.  Niskins 13 and 14 not sampled due to change in depth.  CTD depth readjusted after niskin 14.

12902  Niskin 10 leaking. 

14401  Large number of jellyfish-parts on CTD frame.  May have affected transmissometer.



Notes on Bottles


00101  3                      Did not wait 30 seconds before closing niskin

00201  1                      Did not close.  Lanyard hooked over pin 1 and 24

00201  14                    Did not close.  But closed after tugging on lanyard.

00601  1                      Mistake:  wrong depth, no samples drawn.

01201  2                      Mistake:  wrong depth, no samples drawn.

03801  3                      Did not wait 30 seconds before closing niskin

03901 1                      Deployed with bottom endcap closed

04501  2                      Top vent not closed

04501  3                      Top vent not closed

05201  1                      Tripped but did not close.

09601  9                      Did not wait 30 seconds before closing niskin

12101                          Thermometer for measuring oxygen temperature out of range on very cold water

12902 10                     Niskin leaking




A3       Interpolation List

This list contains the pressure intervals over which the primary temperature and conductivity data were linearly interpolated over.


Station     Start (db)   End(db)

*******  *******    ********

    101           0         9         

    201           0         8         

    501         128       130         

    601           8        10         

    601          19        21         

    603           0         3         

    603         196       197         

    701           5         9         

    701         249       251         

    701         278       280          

    702          14        23         

    702         206       209         

    703           0         5         

    703          48        50         

    801         104       106         

    901         327       330         

    902         339       341         

   1001          28        31         

   1001          38        40         

   1301         153       155         

   1401         456       458         

   1502           7         9         

   1502          71        74          

   1801         771       773         

   2101          13        18         

   2201         308       310         

   2301          33        34         

   2301           9        11         

   3101          11        14         

   4201           4         6         

   4601          11        15         

   4601          35        37         

   4701          52        53         

   4702          21        23         

   4702          50        51         

   4901          30        33         

   4901          34        35         

   4902          33        34         

   5602           0        12         

   5901          10        12         

   5901          19        25         

   6001           6         9          

   6001          10        12         

   6001          17        21         

   6002           5         7         

   6002           9        11         

   6201           4         6         

   6201          66        68         

   6301           9        11         

   6301          67        68         

   6501           4        15         

   6902          11        13         

   6902          16        18         

   7001         180       182         

   7001         194       196          

   7101         160       162         

   7101         206       208         

   7501         358       360         

   7701         478       481         

   7901          39        41         

   8001           5         7         

   8001          61        63         

   8001          23        26         

   8101          12        14         

   8101          45        47         

   8201           4         7         

   8301          19        21         

   8301          42        44         

   8301          45        47         

   8304           8        10         

   8701          55        57         

   8701          62        65         

   8902           6        12         

   9101           8        12          

   9101         111       112         

   9301         119       121         

   9501          15        17         

   9501         135       137         

   9601           7        12         

   9601          16        18         

   9601          46        48         

   9701          66        68         

   9701          69        71         

   9701          89        91         

   9801          32        35         

   9801          45        47         

   9801         144       146          

   9801         241       243         

   9901          29        31         

   9901          32        34         

   9901          36        38         

   9901          40        42         

  10201         171       173         

  10301          10        12         

  10401          33        35         

  10401          36        38         

  10401          39        41         

  10401          42        44         

  10701          10        12         

  10701         588       591         

  10801          11        13         

  11102          10        16         

  11201         213       216         

  11401          10        13         

  11401          19        21         

  11401         130       132          

  11401         180       182         

  11401         187       189         

  11401         119       121         

  11401         126       128         

  11401         234       236         

  11401         243       245         

  11401         258       260         

  11501         117       120         

  11501         125       129         

  11501         132       136         

  11501         141       143         

  11501         149       152         

  11501         175       177          

  11501         228       230         

  11801         212       214         

  11901         175       180         

  11901         210       212         

  11901         283       285         

  11901         290       292         

  12102          11        16         

  12102         227       229         

  12102         280       282         

  12301          43        46         

  12301          58        60         

  12301          62        64         

  12301          80        82         

  12301          85        87         

  12301          89        91         

  12301         105       110         

  12301         237       239         

  12301         245       248         

  12302          45        47          

  12302          52        54         

  12302          56        58         

  12302         302       303         

  12501          61        63         

  12501          65        67         

  12501          69        71         

  12701          14        16         

  12701          38        40         

  12801          51        54         

  13301          18        20         

  13301          20        22         

  13301          24        26         

  13401          23        25          

  13501           9        16         

  13501          16        21         

  13601          10        12         

  13601          23        26         

  13801          35        38         

  13901          28        30         

  13901          40        42         

  13901          43        45         

  14001          38        40         

  14201          34        36         

  14301          34        36         

  14301          32        34         

  14401          34        36         

  14601          37        39         

  14901          41        42         



A4       Seabird Processing Settings

Program/ Module         Function

1          SEASAVE      Acquire raw data.

2          Data Conversion        Convert raw data (*.dat), using the *.con file, selecting ASCII as data conversion format.



Start at scan number of downcast, after the soak.  Store files in   processed/datcnv

            For the *.ros files, use scans marked with bottle confirm bit, 0sec offset, 2sec range duration.


3          Rossete Summary      Average the scans associated with each bottle trip to create CTD bottle stop information.



            Averaged all values.  Derived Oxygen, Oxygen Saturation, Salinity 1 and Salinity 2. Found min/max and STD although this info is not being used in water sample data.


4          Align CTD      Advance sensors relative to pressure, depending on sensor response time.  Typically secondary conductivity is advanced 0.073seconds and oxygen is advanced +2 to +5 seconds.  The primary conductivity is typically already advanced 0.073 seconds by the deck unit.



            Confirmed SBE11 deckunit was already advancing both primary and secondary conductivity by 0.073 seconds so only using align to advance oxygen.

            Advanced oxygen voltage by 3 seconds.


5          Cell Thermal Mass    Perform conductivity cell thermal mass correction to achieve higher salinity accuracy.  This step is necessary when salinity accuracy better than 0.01 PSU is desired in regions with steep gradients. Typical values are alpha = 0.03 and 1/beta = 7.0.



            Chose to adjust Primary Conductivity with Primary Temperature and to adjust Secondary Conductivity with Secondary Temperature.  Used suggested corrections of alpha=0.03 and 1/beta= 7.0


6          Wild Edit         Identify scans that have very different values from their neighboring scans.



            Chose first pass of 10STD and second pass of 20STD using 100 scans per block (about 4 seconds). All scans are used for STD calculation (after loopedit is run, could exclude those flagged data from the STD calculation).   Pressure, T1, T2, C1, C2, OxV, Alt, S1, S2, SndVel, Depth were tested. Did not run procedure on transmissometer,  fluorometer or latitude and longitude.


7          Filter   Low-pass filter pressure with time constant of

0.15 seconds to increase pressure resolution for Loop Edit. Typically pressure is low passed filtered with 0.15 seconds and conductivity is filtered with 0.03



Applied 0.15 second filter to pressure and 0.03 second filter to conductivities.


8          Loop Edit        Mark scans where CTD is moving less than minimum velocity or traveling backwards due to ship roll.



            Scans with speeds less than 0m/s are marked bad.

            Store files in processed/loopedit.

            ‘Exclude marked scans’ is checked, meaning scans previously flagged bad will not be used in loopedit calculation.


9          Derive   Compute oxygen from oxygen signal (SBE 43); also need conductivity (or salinity), temperature, and pressure.



Derive Oxygen ml/l with 1.0 second window size


10        Bin Average   Average data into desired pressure or depth bins.



Pressure averaging, 1db, with interpolation to center the output.  Exclude scans marked bad (wildedit, loopedit)t.  Output the number of scans in each averaged bin.  Process the whole cast, not just the downcast.


11        Derive Compute salinity, density, and other parameters.



            Compute salinity 1 and salinity 2, sound velocity, and depth (using 71 Lat).

            Store files in   processed/derivefull


10        Strip    Remove extra columns.



Reduce file to P,T1, T2, C1, C2, OxV, Fl, Tr, Alt, Oxy, Scans per bin, S1, S2,  Fl,    Alt.  Do not include Latitude, Longitude, SndSpd, and Depth


11        Split     Create a separate file for down and up cast.



Split files into down and uptrace.  Exclude scans marked bad is checked, meaning a scan identified bad in loopedit will not be used to separate the downtrace from the uptrace.