General practices & notes on CalCOFI's Seabird 911/911+ CTD-Rosette
CalCOFI CTD data, particularly the thermodynamic properties, are computed by Seasoft based on EOS-80. Temperatures, typically from the primary temperature sensor, are merged with bottle sample data into station files which produce the hydrographic database and other data products, Hydrographic Reports, figures, IEHs. CTD sensor salinities, and oxygen values may also replace bottle measurements on mistrip, interpolated standard levels (in place of calculated interpolations) or missing samples.
Currently (May 2014) no TEOS-10 calculation for absolute salinities are calculated.
Algorithms used for calculation of derived parameters in Data Conversion, Derive, Sea Plot, SeaCalc III [EOS-80 (Practical Salinity) tab], and Seasave are identical, except as noted in Derived Parameter Formulas (EOS-80; Practical Salinity), and are based on EOS-80 equations.
For formulas for the calculation of conductivity, temperature, and pressure, see the calibration sheets for your instrument.
Formulas for the computation of salinity, density, potential temperature, specific volume anomaly, and sound velocity were obtained from "Algorithms for computation of fundamental properties of seawater", by N.P. Fofonoff and R.C Millard Jr.; Unesco technical papers in marine science #44, 1983.
Please note, the processing methods described use SIO-CalCOFI-developed software (DECODR & BtlVsCTD) to merge and correct Seabird 911+ CTD data with bottle samples. The Seasoft portion of our data processing protocol follow their recommended settings for our 911+ v2 CTD & deck unit.
"Sta.csvs" are bottle data collected at each station cast combined with 1m binavg CTD data from matching bottle depths (~20). Preliminary comparisons & plots of CTD sensor data versus bottle data are generated after each cruise. These comparisons are used to point-check the bottle data and QC the CTD sensor data. Once final bottle data are generated, eliminating fliers & mistrips, a final comparison of 1m binavg CTD to bottle data is performed. This generates final CTD data csv files for each cast that contain 1m binavg Seasoft-processed CTD sensor data, bottle-corrected Seasoft-processed CTD sensor data, and final bottle data.
The CTD temperatures are Seasoft-processed with no additional corrections applied. CTD salinities are corrected using bottle samples from depths >350m, where the profile is near vertical - offset are typically very small (<0.001). CTD SBE43 oxygen data are significantly improved using bottle oxygen samples for calibration; a linear regression is applied to bottle-correct SBE43 O2 profiles. Fluorometer and ISUS-NO3 sensor data require bottle data to generate regressions and convert their voltages to quantitative measurements. Transmissometer & PAR data are collected, processed using Seasoft and not QC'd further.
Seabird's CTD data processing software suite, Seasoft, is available for free at seabird.com JRW 06/2019
CTD Data Processing Quick Guide (rev Jun 2019)
see sections below for more information & settings - these instructions reference SIO-CalCOFI inhouse software which merges CTD & bottle data then applies regression corrections to sensor data based on sensor vs calibration sample plots. CTD data compared to bottle data are 4-second averages prior-to-bottle-closure.
1. Data Conversion... (SBE): Match CON or XMLCON files accordingly.
1a. Calculate transmissometer M & B values from deck tests if not done during the cruise, edit/update tranmissometer .xmlcon coefficients to derive beam attenuation coefficients and % light transmission.
2. Window Filter... (SBE): To smooth profiles & reduce spikes (median filter: 9 for all except cosine 500 for ISUS Voltage, usually setup on V6).
3. Filter... (SBE): Filter B = 0.15 on Pressure only.
4. Align CTD... (SBE): Oxygen sensors only (4 seconds).
5. Cell Thermal Mass... (SBE): Default settings.
6. Derive... (SBE): Match CON or XMLCON files accordingly.
7. ASCII Out... (SBE): Select desired variables (see figure below for selection example), check output HDR for errors. DatCNV overwrites the existing .hdr files with new .hdr from embedded information. If the hdr information was keyed-in incorrectly during the cast and the .hdr file was corrected (cast or line.station number, for example) post-cast. The correction is lost when DatCNV generates a new hdr from the .hex file. Hexediting the .hex file, done carefully with a hex editor, will eliminate this problem.
7a. Sta.csvs updated with .btl data (for 4sec depth value) then 1m .asc data followed by bottle data (salt, O2, chl, nutrients)
8. Step 1... (BTLvsCTD): Individual station BL files and recent preliminary sta.csvs (ieh option still works), unaveraged CTD asc files are required.
9. CSV to .XLS... (Excel): Open the YYMM_CCTD.CSV generated by BtlVsCTD Step 1 in Excel then save as an XLS file.
10. Salt... (Excel): Calculate BTL-CTD offsets (>350m), remove outliers, derive means & statistics.
11. Oxygen... (Excel): Calculate regressions for both oxygen sensors Sbeox0/1ML/L vs. BTL_O2.
11a. Oxygen (Excel): Calculate regressions for both oxygen sensors Sbeox0/1uM/KG vs. BTL_O2.
12. Nitrate... (Excel): Calculate regression for ISUS vs. BTL_NO3.
13. Chlorophyll... (Excel): Calculate regression for FLSP vs. BTL_CHL.
14. Split... (SBE): Apply the split to the derived CNV files.
15. Bin Average... (SBE): Bin by Depth in 1 meter increments.
16. ASCII Out... (SBE): Select correct variables.
Generating CTD.csvs for point-checking and plots
17. Step 2... (BTLvsCTD): ASC- HDR with current sta.csvs (or IEH) and corrected Events file in folder.
18. Plot Profiles... (Matlab): Plot up cast CSV data with bottles from BTLvsCTD Step 2.
18a. Zip & post preliminary CTD+Bottle csvs with metadata files online.
18b. Copy preliminary CTD+Bottle csvs to dataserver for GTool point-checking.
For Final CTD data, repeat steps 8 - 18 using final data sta.csvs
19. Step 1... (BTLvsCTD): Regenerate comparisons using final sta.csvs (or IEH).
20. Coefficients... (Excel): Recalculate final regressions and coefficients.
21. Step 2... (BTLvsCTD): Regenerate final CTD.CSV files.
22. Plot Profiles... (Matlab): Create final up and down cast profiles with bottles.
23. Misc... (BTLvsCTD): Rename ASC/HDR files, column voltages (optional), and create ZIP files.
24. Database... (Access): Import files into annual database (usually done by JLW).
25. Data Upload... (WinScp): Upload files to sio-calcofi.ucsd.edu in correct folders.
Recent Changes
2013 - large data files warehoused on sio-calcofi.ucsd.edu, includes CTD data & underway data
201108 - new sta.csv format replaces 00/20/ieh
5-5-11 Removed Check on Tau Correction during Step One CNV creation.
5-6-11 No longer plotting downcast without bottles
CalCOFI's primary hydrographic instrument is a Seabird 911+ CTD equipped with dual temperature, conductivity and oxygen sensors mounted on a 24-10L bottle rosette. Additional CTD sensors mounted on the rosette frame include a fluorometer, transmissometer, nitrate sensor, PAR, pH and altimeter.
The CTD-Rosette is lowered into the ocean measuring a suite of seawater properties throughout the water column. Occupying the same stations (specific GPS locations) four times a year - Winter, Spring, Summer, Fall - we measure physical & biological properties: temperature, salinity, oxygen, fluorescence (chlorophyll), nutrients, and productivity from surface to 500m. Additional measurements from seawater samples collected using the rosette are combined with CTD sensor data, filling out the dataset. These seasonal measurements are published in Cruise Data Reports & added to our time-series database, both available online.
The CTD-Rosette is electronically tethered to the ship using a winch with conductive wire. This allows a computer on the ship to control the CTD and monitor the temperature, conductivity, oxygen sensor arrays plus single fluorometer, transmissometer, altimeter & nitrate sensors. As the CTD-Rosette is lowered to 500m, the temperature, salinity, oxygen, chlorophyll, nitrate, and other measurements are displayed real-time & stored on the ship's computer. Depending on the downcast profiles, mainly the depth of highest chlorophyll & mixed layer, bottles are closed at standard depths as the CTD-Rosette is brought back to surface. The seawater samples collected will be analysed & used to calibrate the various sensors or provide measurements that cannot be measured electronically.
A Sea-Bird Electronics 911plus V2 CTD collects vertical profile data at every CalCOFI station. In addition to being a dual TCO (temperature, conductivity, and oxygen) system, the CTD also interfaces with a transmissometer, fluorometer, PAR/SPAR meters, altimeter, nitrate, and pH sensor. Connected to a shipboard data-acquisition computer through an electronically-conductive winch wire, sensor data are collected and displayed real-time using Seasave V7 on a Windows PC. The CTD is normally lowered to terminal depth of 515 m, bottom-depth permitting, but is routinely deployed within meters from the seafloor at nearshore SCCOOS and basin stations. To ensure high resolution sampling in areas with significant hydrological and biological gradients a speed of ~30 m/min is used for the first 100 m then ~60 m/min to depth without stopping. During retrieval, the CTD is paused for at least 20 seconds at target bottle depths to adequately flush each 10 liter sample bottle prior to closure. Seawater samples are analyzed onboard (e.g., salinity, oxygen, nutrients, chl) and are used to correct measured CTD values.
Setting up and using the ISUS with Seabird CTD
1). Connect the ISUS Analog Out port to a 6-pin CTD port – we use voltage channel 6 on a universal Y-cable, allowing pH to occupy channel 7. Map that port in Seasave as user-polynomial; under the user-polynomial, enter: A0 = - 7.1168, A1 = 27.155.
These are linear regression coefficients from an earlier CalCOFI (1501NH).
2). Connect the battery cable to the ISUS fifteen minutes prior to deployment to "warm-up". This improves data quality & stability.
3). SIO-CalCOFI uses a 10m charging cable strung from an AC adapter in the wetlab to the battery mounted on the CTD-rosette. Between casts, the battery is left mounted on the rosette and charged. This method has improved the reliability of the ISUS to have adequate power for the full cast, provided the battery has been charged between deployments. Occasionally, the CTD operator forgets to unplug the ISUS and it logs deck data until discovered - usually next station, draining the battery & filling the ISUS internal memory.
The original method was swapping batteries every three 500m cast then charging inside the ship. The Wetlabs 12v lead-acid batteries usually lasted ~3.5 hours before requiring removal and charging. Charging takes 12-15hrs so three primary batteries were rotated.
Regardless of charging method, be sure to unstopper the battery's vent plug to allow hydrogen emissions. Re-stopper, greasing lightly if necessary, before mounting the fresh battery on rosette. When charging on the rosette, protect from seawater intrusion by keeping the vent-plug closed but vent the battery before deployment.
4). Remove the ISUS on casts deeper than 1000m. The 512kb memory allows storage of ~75 casts without the need to download data and purge the memory. Data are downloaded by connecting the ISUS to a Windows laptop’s serial port. If the ISUS memory is full, the sensor will still work but the sensor data profile will "stair-step" significantly.
SeasaveV7 on Windows 7 CTD Operator's Cookbook