Profiles of visible light absorption and attenuation coefficients were measured in the upper 100m of the water column. Data Acquisition: The Wetlabs ACS spectral absorption and attenuation meter was mounted on a deployment frame together with a Seabird pump, a Wetlabs DH-4 data logger and two battery packs. This set-up was as recommended in the Wetlabs manual. The logger was set to control the ACS once the on/off magnet had been inserted. The data acquisition program comprised 2 minutes delay time to allow the instrument to be deployed over the stern; 30 seconds warm-up time; 30 seconds flush time during which the pump was activated, and finally 12 minutes of data acquisition. Physically, the instrument was attached to the winch, the magnet was inserted as soon as permission to deploy had been obtained from the bridge, the instrument was lowered directly to 20m, until 1.5 minutes since insertion of the magnet. The instrument was then brought to just below the surface and lowered at 0.5m per second to a depth of 100m, then retrieved at the same speed. Once the instrument was back on deck the magnet was removed to prevent dry operation of the pump. The data logger received an instrument-specific binary format data file for each deployment, with automatic sequential file numbering. These files were uploaded after each deployment. Data Processing: The Wetlabs software program WAP was used to extract ascii data from the binary files. This procedure included corrections for internal instrument temperature and the latest manufacturer's calibration for wavelength. Note that although daily calibrations were performed during the cruise, the manufacturer advised against using these calibrations as conditions were suboptimal (milli-Q water not fresh, environment not totally dry or well temperature-controlled). A matlab script, acs.m, written by the principal investigator, continues the data processing. Data recorded in air are discarded, remaining data are binned to 2m depth intervals, occasional spurious data with a discontinuity in absorption or attenuation spectra are removed, and a correction is applied to account for differences in ocean water temperature and salinity compared to the calibration conditions. This final step uses first-cut CTD data courtesy of the oceanography team (Bindoff et al). Not yet complete (as of 2006-03-10): Remaining spurious data need to be weeded out by hand. These include non-systematic quirks such as occurrence of bubbles or larger particles in the optical path. The depth needs to be corrected for an offset of some 4m plus the difference between the pressure sensor location and the ACS-inlet location. Dataset Format: For each 100m profile, a single ascii file is available, comprising instrument calibration data and a time sequence of attenuation and absorption spectra. By placing each of the profile files from one cruise transect in a single directory, the acs.m routine can be applied to one leg at a time, yielding matlab fields of [station, depth (0:2m:100m), wavelength (87 wavelengths)]. The acs.m script includes details of which CTD station number refers to which ACS file number. This information is also supplied in the station log file jill_brokew_stations.xls. Acronyms Used: ACS - Absorption (a) Attenuation (c) Spectral meter, produced by Wetlabs CTD - Conductivity, Temperature, Pressure. This work was completed as part of ASAC projects 2655 and 2679 (ASAC_2655, ASAC_2679).

Bio-optical measurements (radiometry, spectral backscatter, attenuation, absorption) for particle and phytoplankton characterisation acquired during Australian Marine National Facility RV Investigator voyage IN2016_V01. The biooptical package consisted of SeaBird 19plus CTD, Satlantic HyperOCR upwelling radiance and downwelling irradiance sensors, WetLabs ac-9, HobiLabs Hydroscat-6. At selected stations the bio-optical package was lowered to the depth of 240 m (or 20 m above the sea bottom if the depth was lower than 260 m) at 20 m/minute. The radiometric measurements were taken only during the day. Parameters measured: SeaBird CTD (4 Hz frequency): - Temperature - Salinity - Pressure - PAR - Fluorescence - Oxygen Satlantic HyperOCR: - Upwelling radiance (Lu) - spectral - Downwelling irradiance (Ed) – spectral - Pressure HobiLabs Hydroscat: - Backscattering coefficient at 6 wavelengths (442, 488, 550, 589, 676, 850 nm) - Fluorescence (550, 676 nm) - Pressure WetLabs ac-9 (2 Hz frequency) - Light absorption coefficient at 9 wavelengths (412, 440, 488, 510, 532, 555, 650, 676, 715 nm) - Light attenuation coefficient at 9 wavelengths (412, 440, 488, 510, 532, 555, 650, 676, 715 nm) At some stations transmissometer data at 650 nm using the Wetlabs c-Star were collected. Data type product(s) created: raw and calibrated data files were created on board, processed and quality controlled files (.dat and/or .csv) will be available by the end of 2016. Owner of instrument: CSIRO Units: CTD data: units given in the header Hydroscat data: bbp_HEOBI_all: all bbp in m^-1, slope unitless Calibrated: depth in m, all bb in m^-1,all betabb sr^-1 m^-1 Radiometers: all Ed uW/cm^2/nm All Lu uW/cm^2/nm/sr Depth is always given in meters. See the metadata file in the download for more information.

Particulates in the water were concentrated onto 25mm glass fibre filters. Light transmission and reflection through the filters was measured using a spectrophotometer to yield spectral absorption coefficients. Data Acquisition: Water samples were taken from Niskin bottles mounted on the CTD rosette. Two or three depths were selected at each station, using the CTD fluorometer profile to identify the depth of maximum fluorescence and below the fluorescence maximum. One sample was always taken at 10m, provided water was available, as a reference depth for comparisons with satellite data (remote sensing international standard). Water sampling was carried out after other groups, leading to a considerable time delay of between half an hour and 3 hours, during which particulates are likely to have sedimented within the Niskin bottle, and algae photoadapted to the dark. In order to minimise problems of sedimentation, as large a sample as practical was taken. Often so little water remained in the Niskin bottle that the entire remnant was taken. Where less than one litre remained, leftover sample water was taken from the HPLC group. Water samples were filtered through 25mm diameter GF/F filters under a low vacuum (less than 5mmHg), in the dark. Filters were stored in tissue capsules in liquid nitrogen and transported to the lab for analysis after the cruise. Three water samples were filtered through GF/F filters under gravity, with 2 30ml pre-rinses to remove organic substances from the filter, and brought to the laboratory for further filtration through 0.2micron membrane filters. Filters were analysed in batches of 3 to 7, with all depths at each station being analysed within the same batch to ensure comparability. Filters were removed one batch at a time and place on ice in the dark. Once defrosted, the filters were placed upon a drop of filtered seawater in a clean petri dish and returned to cold, dark conditions. One by one, the filters were placed on a clean glass plate and scanned from 200 to 900nm in a spectrophotometer equipped with an integrating sphere. A fresh baseline was taken with each new batch using 2 blank filters from the same batch as the sample filters, soaked in filtered seawater. After scanning, the filters were placed on a filtration manifold, soaked in methanol for between 1 and 2 hours to extract pigments, and rinsed with filtered seawater. They were then scanned again against blanks soaked in methanol and rinsed in filtered seawater. Data Processing: The initial scan of total particulate matter, ap, and the second scan of non-pigmented particles, anp, were corrected for baseline wandering by setting the near-infrared absorption to zero. This technique requires correction for enhanced scattering within the filter, which has been reported to vary with species. One dilution series was carried out at station 118 to allow calculation of the correction (beta-factor). Since it is debatable whether this factor will be applicable to all samples, no correction has been applied to the dataset. Potential users should contact JSchwarz for advice on this matter when using the data quantitatively. Not yet complete: Comparison of the beta-factor calculated for station 118 with the literature values. Comparison of phytoplankton populations from station 118 with those found at other stations to evaluate the applicability of the beta-factor. Dataset Format: Two files: phyto_absorp_brokew.txt and phyto_absorp_brokew_2.txt: covering stations 4 to 90 and 91 to 118, respectively. Note that not every station was sampled. File format: Matlab-readable ascii text with 3 'header' lines: Row 1: col.1=-999, col.2 to end = ctd number Row 2: col.1=-999, col.2 to end = sample depth in metres Row 3: col.1=-999, col.2 to end = 1 for total absorption by particulates, 2 for absorption by non-pigmented particles Row 4 to end: col.1=wavelength in nanometres, col.2 to end = absorption coefficient corresponding to station, depth and type given in rows 1 to 3 of the same column. This work was completed as part of ASAC projects 2655 and 2679 (ASAC_2655, ASAC_2679).