Summary: All 75 stations occupied: 66 standard & 9 SCCOOS 20m isobath stations
Data Links: 1210NH CTD Cast Files; Final bottle-corrected CTD csvs, plots, & metadata;
Cruise Dates: 19 October - 05 November 2012 (Fri - Mon)
Load Dates: 16 - 18 October 2012 at MarFac, Pt Loma (Tues - Thurs)
Offload Date:  06 Nov 2012 (Tues)
Ship: SIO RV New Horizon; (CalCOFI NH Layout)
Station plan: 75 Standard (66 CalCOFI + 9 SCCOOS); Predicted Schedule & Station Plan.htm (spreadsheet; .xls)
Cruise Instructions: NOAA-SWFSC Cruise Instructions (pdf)
Cruise Map:
Contacts: James Wilkinson, Chief Scientist, SIO-IOD
  Amy Hays, NMFS (Fisheries Technical Coordinator)

Please note that the anomalies are based on 50-year harmonics and that these data are direct from the CTD and have not gone through thorough quality control checks. They are presented to give a general impression of current conditions. Final data plots will be published after all data are processed.


General Processing Notes for CalCOFI 1210NH CTD Data
Download 1210 CTD raw cast files zipped Download 1210 FinalQC CTD + bottle data with data quality codes
CTD sensor corrections derived by comparing 4 secs of CTD sensor data (prior to bottle closure) to bottle samples
Dual T, S, & O2 Primary Sensor Secondary Sensor  
Salinity offset (bottle - CTD salinity; > 350m only; Seabird SBE4) 0.00010  0.00482
Oxygen (Seabird SBE43 as Primary;
RINKO (voltage 6 & 7) as 2nd O2 on casts 5 - 24, 26, 36 - 52,  62 - 72
Altimeter on voltage 6 on casts 1 - 4, 25, 27 - 35, 53 - 61, 73 - 75
y = 0.8858x - 0.0959
R² = 0.9989
No RINKO regression available, data were pre-processed
Single sensors
Nitrate - ISUS 4sec ave voltage vs Bottle Nitrate (Satlantic MBARI-ISUS v2) y = 29.289x - 10.384
R² = 0.9868

Fluorometer - Seapoint #3069 used casts 001 - 021  (failed cast 021, 3600m)
                          Seapoint #2483 used casts 022 - 075

y = 1.3284x + 0.0126

R² = 0.8791


y = 8.9123x² + 2.1153x + 0.01

R² = 0.8878

Primary CTD O2 Sensor vs Bottle O2
MBARI-ISUS Voltage vs Bottle NO3
Seapoint Fluorometer (#3069) vs Chl-a Seapoint Fluorometer (#2483) vs Chl-a

General CTD Notes
RINKO oxygen sensor run as secondary O2 mounted vertically for casts 001-067, then mounted horizonatally. CTD files only contain Seabird 43 oxygen data as primary O2. RINKO data are available and may be imported into the CTD csvs (programming required- stayed tuned).
CalCOFI 1210NH had problems with bottle tripping and closure confirmations. Solutions attempted after using the deck unit only to trip bottles: switching to the backup CTD computer, from primary Windows XP CTD PC to backup Windows 7 CTD PC - still no comfirmations; new CTD to Carousel cable installed after cast 6 appeared to solve the problem. But the problem reappeared so what finally solved the issue was rewiring the termination - 4-individual-wire termination resulted in the solution. Only used the black & white wires only; red & green were not used. One wire for signal and shield for ground.

Casts affected - 004 93.3 28.0; 005 93.3 30.0; 006 93.3 35.0

2017 note on RINKO data: it was discovered during the 2017 reprocessing, that casts 005, 007, & 026 had pressure-to-depth calculation errors in the downcast RINKO data provided by ODF. These data have been corrected in the 'finalQC' CTD.csvs.
Cast 005: the miscalculation occurs at 260m; Cast 007: miscalculations at 42-43m; Cast 026: miscalculations at 246-247m.

08Mar2017 other than the RINKO error mentioned above, the reprocessing adds data-quality code columns and data codes on bad or missing data ("9"), or questionable data ("8"). Data values should not have changed from the previously published final CTD data. But the column number on updated CTD.csvs has changed from 65 to 82.
Refer to the CTD.csv data format webpage: 65-column index; 82-column index

Cast notes - (unusually) significant issues this cruise with non-confirmation of bottle closures:
Cast 004 93.3 28.0 - downcast & upcast in two files; upcast restarted after 3 bottles tripped; 4 - 24 used for 515 to surface, duplicate 100m was non-confirm re-trip.
Cast 005 93.3 30.0 - first real issue with non-confirmations; deck unit to trip bottles; bottle #12 (85m) no response at all - hit 2x. ISUS data loss ~440-450m upcast, estNO3_StaCorr data edited
Cast 006 93.3 35.0 - bottle #1 (515m) no confirm
Cast 007 93.3 40.0 - new carousel to ctd cable installed, no apparent problems
Cast 009 93.3 50.0 - ISUS failed on downcast @195m-515m, estNO3_StaCorr data edited; possible battery not charged issue; extra mrk at #5 - edited
Cast 012 93.3 70.0 - bottle #1 no closure mistrip; carousel cleaned post-cast
Cast 013 93.3 80.0 - two bottles tripped at 515 - #1 & #2, #2 lid not closed properly - bottle #2 switched out; new ISUS battery cable installed
Cast 014 93.3 90.0 - big rolls, CTD wire tension spiking to 2500+, error lights flashed on deck unit between 170-125m upcast
Cast 016 93.3 110 - no confirm on bottle #6 (230m), #7 tripped at 230m, mrk edited
Cast 017 93.3 120.0 - calm night; upcast profiles different from downcast
Cast 021 90.0 90.0 - deep cast - Seapoint fluorometer flakey post-cast, switched back to old reliable Seapoint; non-confirm bottle #12 so #13 tripped at 170m; other depth spacing adjusted for the lose of one bottle ie 140, 125, 112 = 140, 120
Cast 022 90.0 80.0 - non-confirm back! #5 (270m) & #6 (230m) but no extras tripped - bottles were closed
Cast 024 90.0 60.0 - non-confirm bottle #4, #5 tripped too; salt run offset by 1 bottle starting at #7; -0.2 added to Pr offset; bad 515m bottle O2
Cast 026 86.7 45.0 - non-confirms #8 (170m), #10 (100m), #13 (70m) but bottles seemed to close at appropriate depths
Cast 027 86.7 40.0 - #14 (100m), #15 (85m), #16(75m), #18 (50m) non-confirms; #8 (270) bottom lid ajar - bad water samples; ISUS V bad 120m-190m downcast, estNO3_StaCorr data edited
Cast 028 86.7 35.0 - rebooted PC, 100% confirmations; another -0.2 added to Pr offset
Cast 034 90.0 30.0 - catastrophic failure of bottle closure - prodo cast aborted; restarted after nets, bottle #9 (140m) non-confirm
Cast 035 90.0 35.0 - bottle #1 (440m) non-confirm but closed at the right depth (O2 draw temp indicates)
Cast 037 - ISUS bad V 110-120m upcast, estNO3_StaCorr data edited
Cast 039 86.7 55.0 - bottle #11 (100m) non-confirm
Cast 041 86.7 70.0 - extra bottle tripped accidentally at 60m (#15)
Cast 044 - ISUS bad V 500-515m downcast, estNO3_StaCorr data edited
Cast 045 - ISUS bad V 450-475m upcast, estNO3_StaCorr data edited
Cast 047 - ISUS 515m voltage bad on up & downcast, estNO3_StaCorr data edited
Cast 048 - ISUS V bad 115-130m & 380-400m upcast, estNO3_StaCorr data edited
Cast 050 83.3 70.0 - #1 bottle not closed
Cast 065 80.0 90.0 - #12 = #11 data so #12 (85m) mistripped
Cast 066 80.0 100.0 - extra bottles tripped at #12 & #16 (for some unknown reason RAJ)
Cast 068 76.7 90.0 - RINKO oxygen sensor mounted horizontally (vertical up till now); ISUS dropout at 470m downcast, estNO3_StaCorr data edited
Cast 069 - ISUS V Bad 80-110m downcast
Cast 071 - bottle !3 515m salt looks bad
Cast 073 76.7 51.0 - O2 primary sensor bio-fouling on upcast; #16 surface bottle non-confirm, extra tripped to be safe
Cast 074 76.7 49.0 - #4 (30m) top not closed properly

2017 Updates - Re-merged the CTD asc files with sta.csvs to generate new CTD.csvs with data quality code columns.
The original cruise-corrected coefficients from comparison to final data were not changed so CTD data from the
older zip archive (20-1210NH_CTDFinal.zip May 2015) and this updated archive should be the same.
Station-corrected are calculated dynamically and with the use of data codes to exclude bad or questionable data.
The "stacorr" oxygen, chlorophyll, and nitrate may have changed slightly. Please review the cast-specifics outlined
below for details on quality codes. The combined upcast and downcast db-csvs have been updated as well. All primary
and secondary plots were redone using the new csvs for quality-control.
The data problems listed in the original notes have not be corrected except bad data have been removed or data coded
as questionable or bad. Most issues were with the ISUS nitrate sensor but there were a few casts with other problems.

Specific cast notes 2017:
Cast 004: during the upcast, the cast had to be restarted so the two separate CTD upcast asc files were merged. The
downcast also had significant ISUS sensor drop-outs that were edited out of the downcast csv and data coded.

Cast 005: The upcast had ISUS sensor drop-outs from 458-437m, these data were edited out of the upcast csv and data coded.

Casts 009-012: ISUS battery was not powering the sensor so there are no data; data codes have been added.

Cast 037: ISUS signal loss 133-118m on upcast; bad data removed and missing depths data coded.

Cast 044: very slight hiccup in ISUS data at depth in both downcast and upcast files. 502-516m downcast ISUS data
removed and data coded; 516-515m upcast ISUS data removed and data coded.

Cast 045: ISUS signal loss 482-437m on upcast; bad data removed and missing depths data coded. Recommend cruise-corrected
NO3 estimate instead of station-corrected NO3 estimate. Csv plots display cruise-corrected NO3 estimates.

Cast 047: mild problem in ISUS data at depth in both downcast and upcast files. 514-515m downcast ISUS data
removed and data coded; 515-513m upcast ISUS data removed and data coded.

Cast 048: upcast-only ISUS signal loss from 393-378m & 134-119m; bad data removed and missing depths data coded.

Cast 065: data look like they may improve if loopedit was used. SIO-CalCOFI does not typically apply loopedit to
our CTD data since we use bottles to correct the CTD data. Bottle samples are collected when the CTD is stopped
at specific depths. Loopedit would filter these data out since the CTD is not moving (relatively speaking).

Cast 069: downcast ISUS data dropouts between 75-111m; data removed and data codes added.

Cast 073: downcast looks fine but upcast may have had a bio-fouling problem. Upcast salinity, and oxygen data do
not agree with bottle samples very well. Cast 074 primary & secondary sensor data look normal.

JRW 03/07/2017


On CalCOFI 1210NH, a RINKO optode oxygen sensor was deployed on 51 CTD-Rosette casts. Along with the RINKO sensor, a Seabird SBE43 oxygen sensor functioned as the primary oxygen sensor for the cruise. There were 75 stations in total - on 24, an altimeter was needed so the RINKO sensor was disconnected & dummy plugged. On casts 005 - 024, 026, 036 - 052, 061 - 067, the RINKO was mounted vertically; on casts 068 - 072, the RINKO was mounted horizontally.

RINKO oxygen values were very close to Winkler titration oxygen sample values. Comparison of RINKO oxygen data to processed non-bottle corrected SBE43 oxygen data were significantly different (~-0.6 ml/L). Bottle-corrected SBE43 oxygen values, which SIO-CalCOFI considered the best data, did not significantly differ from either RINKO or bottle values (>0.1ml/L). Based on these very preliminary comparisons, if bottle oxygen calibration samples are not available, the RINKO optode oxygen sensor would provide significantly better data than the SBE43.

CalCOFI 1210NH Rinko O2 & Bottle-Corrected SBE43 O2 vs Depth
Plot file containing all 51 oxygen plot comparisons: 1210RINKOvsSBE43plots.zip
RINKO Compared to processed SBE43, not bottle-corrected RINKO Compared to processed SBE43 & SBE43 bottle-corrected
Average diff = 0.000, StDev = 0.1541 Average diff = -0.001, StDev = 0.1379


October 11, 2012 F/SWC1:AEH

1210 Cruise TrackVESSEL: R/V New Horizon (SIO) Cruise 1210-NH.
CRUISE DATES: October 19 – November 5, 2012.
PROJECT: CalCOFI Survey, Fisheries Resources Division.
ITINERARY: Depart San Diego, California at 0800 on October 19, 2012.
Calibration of the Simrad EK60 echosounders will be performed at the beginning of the cruise (requiring 4 - 6 hours). The ship will
anchor in San Diego Bay, San Diego, and calibrate. After small boat transfer of calibration team, the ship will proceed to the
first CalCOFI station 93.3/26.7 (position 32° 57.4'N/117° 18.3'W) and begin a standard CalCOFI pattern (see attached cruise track).
The vessel will return to San Diego, California on November 5, 2012.


  1. To continue an ongoing assessment of pelagic fish stocks between Morro Bay and La Jolla, California.
  2. To monitor environmental conditions within the CalCOFI survey area.
  3. To conduct continuous underway sampling of surface waters. Temperature, salinity and chlorophyll will be automatically logged by computer with the output from the GPS navigational unit.
  4. To record current profiles throughout the duration of the cruise with the Acoustic Doppler Current Profiler.
  5. To measure optical profiles within the California bight. The optical profile measurements will include pigment concentration and particle absorption.
  6. To record continuous acoustic targets obtained with the Simrad EK-60 scientific sounder.


  1. Each standard CalCOFI station will include the following:
    • A CTD/Rosette consisting of 24 10-liter hydrographic bottles will be lowered to 500 meters (depth permitting) to measure physical parameters and collect water at discrete depths for analysis of: oxygen concentration, salinity, nutrients, chlorophylls and phytoplankton.
    • A CalBOBL (CalCOFI Bongo) standard oblique plankton tow with 300 meters of wire out, depth permitting, using paired 505 µm mesh nets with 71 cm diameter openings. A self-contained LOPC (Laser Optical Particle Counter) will be mounted in the port side opening during each tow. The technical requirements for this tow are: Descent rate of 50 meters per minute, ascent rate of 20 meters per minute. All tows with ascending wire angles lower than 38° or higher than 51° in the final 100 meters of wire will be repeated. Additionally, a 45° wire angle should be closely maintained during the ascent and descent of the net frame.
    • A Manta net (surface) tow, using a 505 µm mesh net on a frame with a mouth area of 0.1333 m².
    • Weather observations.
    • A Pairovet (vertical) plankton tow will be taken at all stations inshore of, and including station 70. The Pairovet net will be fished from 70 meters to the surface (depth permitting) using paired 25 cm diameter 150 µm mesh nets. The technical requirements for Pairovet tows are: Descent rate of 70 meters per minute, ascent rate of 70 meters per minute. All tows with wire angles exceeding 15° during the ascent will be repeated.
    • A PRPOOS (Planktonic Rate Processes in Oligotrophic Ocean Systems) net tow will be taken at all stations on line 90.0 and 80.0 as well as stations out to and including station 70.0 on lines 86.7 and 83.3. These stations are occupied as part of the LTER(Long Term Ecological Reserve) project. The mesh of the PRPOOS net is 202 µm and the tow is a vertical cast up from 210 meters.
    • At about 1100 hours on each day of the cruise a primary productivity CTD cast consisting of six 10-liter hydrographic bottles will be carried out. The cast arrangement will be determined by a Secchi disc observation. The purpose of the cast is to collect water from 6 discrete depths for daily in situ productivity experiments. Measurements of extracted chlorophyll and phaeophytin will be obtained with a fluorometer. Primary production to be  measured as C14 uptake in a 6 hour in situ incubation. Nutrients will be measured with an auto-analyzer. All radioisotope work areas will be given a wipe test before the departure of the SIO technical staff.
    • A light meter(secchi) will be used to measure the light intensity in the euphotic zone once a day with the primary productivity cast.
    • During transit between stations, a bird observer and three mammal observers will be recording location and species of various sea birds and marine mammals.
    • During transit between most daylight stations, an acoustic hydrophone array will be towed off the stern with a cable/winch to record sounds from marine mammals. Upon approaching a station, a sonobuoy will be deployed one nautical mile prior to stopping for station work.
    • A MOHT(Oozeki) pelagic trawl will be deployed on approximately 16 night/day time CalCOFI stations within the standard CalCOFI grid(lines 76.7 to 93.3). This will encompass both adaptive and non-adaptive sampling in conjunction with the EK-60. The Oozeki is a fixedframe trawl with a 5.5 m² mouth opening that can be towed at speeds up to 4-5 knots. It is designed to capture a variety of organisms including krill, late larval and juvenile fishes, and micronekton. The Oozeki data will be used to ground truth the EK-60 acoustic data as well as collect samples of juvenile fishes for the study of sardine recruitment processes.

1. Supplied by scientific party:

  • 37% Formalin (SWFSC)
  • Sodium borate (SWFSC)
  • 30 cc and 50 cc syringes (SWFSC)
  • Canulas (SWFSC)
  • Pint, quart and gallon jars (SWFSC)
  • Inside and outside labels (SWFSC)
  • CalCOFI net tow data sheets (SWFSC)
  • 71 cm CalCOFI Bongo frames (SWFSC)
  • 71 cm CalCOFI 505 µm mesh Bongo nets (SWFSC)
  • CalCOFI 150 µm calvet nets and codends (SWFSC)
  • CalCOFI pairovet frames (SWFSC)
  • 333 µm mesh codends (SWFSC)
  • Inclinometer for bongo tows (SWFSC)
  • Digital flowmeters (SWFSC)
  • 75 lb Bongo weights (SWFSC)
  • 170 lb hydro weight (SWFSC)
  • CalCOFI Manta net frames (SWFSC)
  • 60 cm CalCOFI 505 µm mesh Manta nets (SWFSC)
  • Standard CalCOFI tool boxes (SWFSC)
  • Bucket thermometers and holders (SIO)
  • Hand held inclinometer (SIO)
  • Oxygen titration rig with reagents (SIO)
  • Oxygen flasks (SIO)
  • Guildline Portasal (SIO)
  • Salinity bottles (SIO)
  • Standard sea water (SIO)
  • Data sheets for scheduled hydrographic work (SIO)
  • Weather observation sheets (SIO)
  • CTD and rosette (SIO)
  • 10 liter hydrographic bottles (SIO)
  • Isotope van (SIO)
  • LTER van (SIO)

2. Supplied by R/V New Horizon:

  • Hydro winch with ¼" cable for standard Bongo, Pairovet and Manta tows
  • Oceanographic winch w/.322" conductive cable
  • J-frame w/blocks to accommodate .322" conductive cable and ¼” mechanical cable
  • A-frame w/block to accommodate Oozeki .580" trawl wire
  • Constant temperature in main lab set at 22°C ±1°C (71.5°F ±2°F)
  • Winch monitoring system
  • 12 kHz Knudsen precision depth recorder
  • Acoustic Doppler Current Profiler


  1. At the completion of the cruise an inspection will be made of scientific working and berthing spaces by the Master or his designated representative. The scientific party is responsible for the condition and cleanliness of spaces assigned to the scientific party.
  2. The Cruise Leader will hold a pre-cruise meeting aboard the vessel before departure.
  3. All dates and times recorded will be in Pacific Standard Time.

Date: 2 October 2012
Prepared by: Amy E. Hays
Approved by:
Francisco Werner, Ph.D.
Science & Research Director
Southwest Fisheries Science Center

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