DOI: 10.5061/dryad.8kprr4xwk
title: Oxygen data from Eastern Tropical North Pacific cruises and floats 2021-2022

description: Using standard calibration schemes commercial oxygen optode sensors
 typically yield oxygen concentrations in the range of 2-4 umol/kg under
 anoxic conditions. They are thus unable to detect the roughly 0.1 umol/kg
 levels of oceanic functional anoxia. Here, a modified Stern-Volmer
 equation is used to characterize and calibrate 26 optodes deployed on 16
 autonomous floats in the Eastern Tropical Pacific (ETNP) oxygen deficient
 zone (ODZ) using a combination of manufacturers', laboratory, and
 in-situ data. Laboratory calibrations lasting several months and conducted
 over 2 years show that optodes kept under anoxic conditions drift at rates
 of order 0.2 umol/kg/yr, with much higher drifts in the first month. The
 initial transient is plausibly due to the degassing of plastic components
 of the optodes and might be reduced by replacing these with metal. Oxygen
 concentrations measured by these calibrated optodes in the nearly anoxic
 ODZ core of the ETNP deviated from both the laboratory calibrations and
 ship-based STOX measurements by similar amounts. Thus with current
 sensors, an in-situ anoxic oxygen calibration only once or twice a year is
 needed to maintain an accuracy close to 0.2 umol/kg. An algorithm to find
 the anoxic cores of the ETNP ODZ is developed and used to remove the drift
 in the float optodes to this accuracy. This is an order-of-magnitude
 improvement in the low oxygen performance of the optodes and could be
 implemented on the existing database of Argo oxygen floats to map the
 geography of functional anoxia. This dataset contains the raw float data,
 the float data calibrated using the manufacturers’ schemes and our new
 scheme. The calibration points and our final calibration constants, as
 well as the STOX data used to validate our new calibrations, are included.
description: Data was collected on 10 custom-built profiling 'ODZ'
 floats equipped with oxygen optodes and gas tension devices and on 6
 standard Argo floats with oxygen sensors. Argo data was processed by Argo
 and recalibrated at APL/UW. ODZ float data was processed at APL/UW as
 described in the associated manuscript.
description: # Oxygen data from Eastern Tropical North Pacific cruises and floats
 2021-2022
 [https://doi.org/10.5061/dryad.8kprr4xwk](https://doi.org/10.5061/dryad.8kprr4xwk) ## Description of the data and file structure ## **ODZ Level2.zip** contains scientific data for the ODZ floats converted from raw data using nominal calibrations. Level_2 in NASAspeak. A README, Diagnostic plots, and a Matlab conversion program are included.  The script ***MRVFloatDecode_2023.m*** reads the raw files for the ODZ floats and puts them in a single Matlab file **xo110-.mat** where the first is the float number and the second is the boot number. It makes lots of plots, which I also include. Matlab substructures and variables are: ***CTD*** – Structure containing Seabird 41CT data * P, T, S – pressure [dbar], temperature [deg C], practica salinity as computed by Seabird [psu] * time, mtime – time in Matlab datetime and datenum formats * SA, CT, Sig0 – Absolute salinity [g/kg], conservative temperature [deg C], potential density [kg/m^3] * CC, W, Drag–estimated oil volume [cc], vertical velocity [m/s], Drag force (for ballasting) [N] ***GPS*** – position * time, mtime - time as Matlab datetime, Matlab datnum * lat,lon- location degrees latitude, degrees longitude * nsat, hdop – number of satellites, horizontal dilution of precision ***GTD*** – Gas Tension Sensor * time, mtime - time as Matlab datetime, Matlab datnum, * P, T, S, Sig0 – Pressure [dbar], temperature [deg C], practical salinity [psu], potential density [kg/m^3] * GT – gas tension [mbar] * Tgtd – temperature of GTD [ deg C]  * Ref- time [matlab datenum], temperature [deg C], pressure [mbar] for reference sensor * Other variables are calibration constants and check values. ***SBE5M1,SBE5M2*** - status of pumps. 1 is for optode(1) and GTD. 2 is for reference optod  ***oldGTD*** - One float had an old-style GTD for reference.  ***optode*** - SBE63 optodes (1) is water optode, (2) is reference optode * time, time -time as Matlab datum and date time * SN – optode serial number * red_amp, blue_amp- amplitudes of red and blue LEDs [counts] * red-phase, blue-phase- phases [microvolts] of fluorescence phase. * O2phase- their difference [microvolts] used to compute oxygen * T – optode temperature [deg C] * O2uM – optode’s computed oxygen concentration converted to uMol/kg. * Tctd, S, P, Sig0 – CTD interpolated to optode time - temperature [deg C], practical salinity [psu], pressure [dbar], potential density [kg/m^3] ***ADC, AirPump, AirValve, OilPump,*** ***OilValve*** - structures diagnosing the buoyancy system operations. Scientfically uninteresting. ## ***STOX Oxygen Profiles.zip*** Contains high precision oxygen profiles taken on the two Sally Ride cruises using STOX oxygen sensors. The data is provided as .txt and .mat formats along with miscellaneous data from the CTD. Oxygen measurements from the floats were referenced to STOX oxygen profiles taken from the ship on the two cruises because these provide much more stable and high precision measurements. STOX sensors are described in detail in Revsbech, N. P.; Larsen, L. H.; Gundersen, J.; Dalsgaard, T.; Ulloa, O. and Thamdrup, B. ( 2009) Determination of ultra‐low oxygen concentrations in oxygen minimum zones by the STOX sensor. Limnology and Oceanography: Methods, 7, pp.371-381. DOI:10.4319/lom.2009.7.371. And from their manufacturer [https://unisense.com/products/stox-microsensor/](https://unisense.com/products/stox-microsensor/) STOX data was collected on two cruises of the research vessel, Sally Ride, SR 2114 and SR2011. Data from each CTD cast with a STOX profile is in a separate folder in this archive. In each, the raw data is in a ****.txt*** file and the converted Matlab data is in a ****.mat*** file. MATLAB scripts to read the ****.mat*** file are included in each folder. Data names and units are: Ship Cruise Station Cast Year Month Day Hour Minute * Depth [m] * Latitude [deg]  * Longitude [deg] * Density [sigma-theta,kg/m^3]  * Temperature [ºC]  * Salinity * Beam Attenuation [1/m] * Fluorescence [mg Chla/m3]  * PAR [umol/m2/s] * Oxygen_SBE [µmol/kg]) * Oxygen_STOX [µmol/kg] * STOX_SD [µmol/kg] * STOX_n [µmol/kg] * NO3-Suna [uM] ## **Optode Calibration.zip**  Contains all of the calibration data used to calibrate the optodes including the anoxic laboratory points, the manufacturers' calibration points, and the coefficients of the calibration model for each optode.  **Seabird 63 Optodes** Anoxic calibration data and model fit are in ***AnoxicCalibration/SBE63/2020/*** and ***/2021/***. The 2020 data was used in the final calibration. * Files are *******Tau0model.mat*** where **** is the optode serial number * Variable ***meta*** explains each variable, repeated here. Calibration model is '1./Taup.*exp(-(Etau+Etau2.*(K-283.15).^2)/R/K )*(1+Drift *(days since start) )' Variables are * Taup: 'Phase [uS]' * Etau: 'Energy is Etau+Etau2*(T-10C) [J/mol] * Drift: 'Drift coefficient in the model [1/days] * Ttau: 'Time scale of drift [days] * Drift_uSday: 'Model Drift uS/day' * Dcal: 'Robust Drift. The drift line is Dcal(2)+ Dcal(1)*(Yearday of 2021) in uMol. Drift is Dcal(1) [uMol/day] * Drms: 'RMS drift fit error [uS] * Derr: 'Uncertainty in Dcal; Drift uncertainty is Derr(1) [uMol/day]'  Calibration points from the anoxic tank are in structure ***RawS.*** Variable ***meta*** explains each variable, repeated here. * K: 'Temperature [Kelvin]' * O2phase: 'O2 phase tau [uS]' * R: 'Gas constant [J/K/mol] * dyd: 'Time since start of record [days]' * TIME: 'Time [matlab datetime] * Omodel: 'Tau computed from model with drift [uS] * OmodelND: 'Tau computed from model with drift removed [uS] **Full Calibration/** contains the oxic calibration points and calibration coefficients Calibration points from Seabird supplied with optode are in **SBE63/*FactoryCalibration/ ****_dd_mmm_yyyy.mat ***where **** is the optode serial number. The calibration date follows. Variables are * Caltime - Calibration time [matlab datum] * ID - Serial number * O2in_mll - Oxygen in tank from winklers [ml/L] * O2out_mll - Oxygen computed from Seabird calibration [ml/L] * S - Salinity [psu] * T - Temperature [deg C] * resid_mll - model residual [ml/L] * tau_us - optode phase lag [microseconds] The oxic part of the optode model calibration coefficients are in ***SBE63/Calfiles/*** Calibration model, coefficients, and check values are in ***Calfiles/_oxic_model.mat*** where **** is the optode SN Data is in structure ***Kfile*** ***Kfile.meta*** explains the variables, repeated here. Model is pO2=eta/K(T) * (1 + a(T)*eta^2.3)^q(T) ; eta= tau0(T)/tau-1.  Note that tau0(T) is computed from *******_Tau0model.mat*** coefficients above. Variables are * Check: 'Test values of T, Tau, and pO2 from SBE cal' * Lk: 'K(T)=polyval(Lk, T) - Matlab call to compute K from Lk polynomial coefficients and T [deg C] * La: 'a(T)=polyval(La,T)' * Lq: 'q(T)=polyval(Lq,T)' **Aanderaa 4330 Optodes** **Anoxic calibration** data and model fit is in ***AnoxicCalibration/AA/*** \**                  **File names and formats are the same as for SBE63 optodes **Full Calibration/AA** **/Factory Calibrations** contains the calibration information supplied with the optodes Files are *******_dd-mmm-yyyy.mat*** with the same format as for the SBE63 The relevant variables are: * Caltime - Calibration time [matlab datenum] * ID - Serial number of optode * O2in_uMol - Calibration bath oxygen [uMol/L] * S - Salinity [psu] * T - Temperature from optode [deg C] * tau_deg - optode output phase [degrees] * meta - Misc information **/Calfiles/********_M0_oxic_model.mat** contain oxic part of the optode model calibration coefficients The format is the same as for SBE63, but there is an extra variable * eta_off: Add this to eta to account for drift since calibration [uS] ## **Calibrated Oxygen.zip** contains both uncalibrated and calibrated optode data for both the ODZ and Argo floats. A README file and Matlab processing programs are included. /***SBE63/xo110**-***.mat*** contain the calibrated data for **ODZ float xo110** Format and data is identical to that in the ***optode*** structure in ***ODZ_Level2_Mat,*** but with 2 extra variables * pO2 – partial pressure of oxygen [mbar] in uncalibrated data * Cal – a structure containing calibrated data -- FINAL DATA IS HERE * pO2: partial pressure of oxygen [mbar] in calibrated data  * Tau0m: Calibration model of anoxic phase [microsecond]. Includes offset. * Tau: Measured phase [microsecond] * Tauoff: offset in Tau from in situ calibration [uS] * eta: (Tau0m+Tauoff)/Tau-1 * O2uM: oxygen concentration [micromoles/kg] * O2umol: same Note that optode(1) is the water oxygen. Optode(2) is a reference optode, which is not of scientific interest.  **/SBE63/Reprocess_SBE63.m** is a MATLAB script showing how to combine calibration data and float data to make calibrated data for SBE63 optodes **/AA/Mat/*FloatID*/*FloatID_profilenum*.mat** contains Argo float data from float FloatID, profile number profilenum. Variables are Data from Argos float archive * mtime, time - time in datetime and datenum formats * lat, lon - GPS position latitude degrees and longitude degrees * P, T, S - CTD pressure [dbar], temperature [deg C], salinity [psu] * Optode - Optode serial number * O2T - Optode temperature [deg C] * O2phase - Optode phase [degrees] * O2umol - Optode oxygen [micromole/kg] Added variables * Kfile - Structure as in Optode Calibration files. Kfile.meta also has metadata * Cal - Structure containing calibrated optode data on the same timebase * Tau - measured phase [degrees] * Tau0m - Model anoxic phase [degrees] * Tauoff - Offset from laboratory calibration [degrees]. Includes offset & drift. * Drift - Drift [degrees/year] * mtime0 - base time for drift [matlab datenum format] * eta - Tau0m/Tau-1 * pO2 - Calibrated Oxygen partial pressure [mbar] * O2umol - Calibrated Oxygen concentration [micromole/kg] * meta - similar list to this one. * SN - same as Optode * Float - FloatID **/AA/Mat/*FloatID*/*FloatID_profilenum*.xls** contains the calibrated data in Excel format ***/AA/Reprocess_3_AA.m*** is a MATLAB script showing how to combine calibration data and float data to make calibrated data for AA optodes ## ***ODZ Raw\.zip*** contains the raw data from 9 custom-built ODZ floats. Level_1 in NASAspeak. They can be read by ***MRVFloatDecode_2023.m*** included in ***ODZ Level 2 files*** ## Code/Software Processing and reading scripts in Matlab (24.1.0.2628055 (R2024a) Update 4) are provided.