Dataset: IVARS Phaeocystis
Deployment: IVARS_cruises

Profile of the abundance and size distribution of abandoned (ghost) Phaeocystis colonines

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/768570

Principal Investigator:

Vernon L. Asper (University of Southern Mississippi, USM)

Co-Principal Investigator:

Walker O. Smith (Virginia Institute of Marine Science, VIMS)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Interannual Variability in the Antarctic-Ross Sea (IVARS): Nutrients and Seasonal Production (IVARS)

Version:

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Description

Abundance and size distribution of abandoned (ghost) Phaeocystis colonies from profiles conducted during R/V Polar Star cruises in the Ross Sea, Antarctica between 2001 and 2005.

Related dataset (collected during the same profiles):
IVARS Marine Snow Profiles: https://www.bco-dmo.org/dataset/719478

Methods & Sampling

Dataset acquisition description

Methodology:

A marine snow imaging system was lowered through the water column to acquire photographs of aggregates but these images also included abandoned (ghost) Phaeocystis colonies that are enumerated in this data set. The imaging system consisted of a collimated strobe system and either a 35-mm film camera (Lobsiger Deepslope 6000; Years 1 - 3) or a digital camera (Insite Pacific Scorpio; Year 4) mounted on an aluminum frame. The system was lowered at a rate of 10 m min-1 through the water column, acquiring ca. six images min-1 at an interval of ca. 1.7 m throughout the entire water column. Illumination was provided by a pair of strobe lights (Deep Sea Power and Light) positioned to produce an 8.4-cm deep beam of uniform, collimated light 66 or 79 cm from the camera lens. Aggregates larger than 0.5 mm within this volume (3 - 15 L, depending on the camera, lens and resultant geometry) are quantified from images taken by a camera that is mounted perpendicular to the long axis of the light beam, which can subsequently be distinguished and quantified by digital analysis. Ambient light illuminates particles in front of and behind this light beam and invalidates the calculation of illuminated volume. Thus, profiles were obtained near local midnight whenever possible (24-h photoperiods occurred throughout all cruises) to minimize this interference; images with the frame visible, due to ambient light, were discarded. The depth of first aggregate counts ranged from 30 - 88 m (a function of water clarity and solar angle). A Sea-Bird SeaCat CTD and 25-cm SeaTech transmissometer mounted on the camera frame provided continuous measurements of temperature, salinity and optical transmission. These data were used to calculate the depth at which each image was acquired. All film (Tmax 400) and images were returned to the laboratory for processing except for short sections viewed at sea to assess camera operation. The films were developed and then digitized to JPG format either in house, using a Nikon camera and macro lens (3767 x 2368), or commercially (3544 x 2341).

Data Processing Description

Dataset Processing Description

The images were analyzed with Image Pro Plus, with a final resolution of the digitized images (2048 x 1536 pixels) of 4.2 pixels mm-1. Digital images were analyzed directly with a final resolution of 4.2 Pixels mm-1. To insure that the same portion of each image was analyzed, an area of Interest (AOI) was created within the region of maximum illumination. This AOI was positioned to the same location within each image before particles were counted. Within this AOI, Phaeocystis were identified by the analyst and counted separately from the much more abundant marine snow aggregates.

BCO-DMO Data Manager Processing Notes:
* station information added to marine snow data from separate Excel spreadsheet.
* various date formats in the date column changed to ISO 8601 (yyyy-mm-dd)
* longitude was decimal degrees with directional (W E), corrected so longitude negative for W, positive for E.
* replaced comma in station comment with ; to better support export as csv format
* removed padded whitespaces
From originally submitted profiles in individual Excel sheets:
* copied and pasted contests of sheets (contained data by profile) into two separate tables to concatenate all the profiles together. Split into two "datasets" for marine snow and Phaeocystis ghost colonies.
* Some sheets in the original file had two separate tables in each of the sheets (for profiles that didn't have canister letter). Separate datasets made for particles per liter and ghost colonies.
* Changed column names so they could be imported into BCO-DMO data system (column names can't start with number or contain > or - characters. e.g. column named "0.0 - 0.5" changed to "bin_0_0_to_0_5" and "> 2.5 - 3.0" changed to "bin_gt_2_5_to_3_0"

version 2 (2019-06-12) replaces version 1 (2019-05-28):
* The latitude and longitude maximum and minimum bounds updated. The latitude changed to negative values. The latitude and longitude in the dataset itself remain unchanged as they were accurate.

More information about this dataset deployment

Funding

Award Number	Funding Source
PLR-0087401	NSF Division of Polar Programs

Instruments

Camera

Supplied Name: We used a custom-built marine snow imaging system

Supplied Description:

See methodology

Instrument Type

Generic Name: Camera

Acronym: camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/311/

Generic Description:

All types of photographic equipment including stills, video, film and digital systems.

CTD Sea-Bird SEACAT

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD Sea-Bird SEACAT

Acronym: CTD SEACAT

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/350/

Generic Description:

The CTD SEACAT recorder is an instrument package manufactured by Sea-Bird Electronics. The first Sea-Bird SEACAT Recorder was the original SBE 16 SEACAT developed in 1987. There are several model numbers including the SBE 16plus (SEACAT C-T Recorder (P optional))and the SBE 19 (SBE 19plus SEACAT Profiler measures conductivity, temperature, and pressure (depth)). M ore information from Sea-Bird Electronics.

Sea Tech Transmissometer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Sea Tech Transmissometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0003/

Generic Description:

The Sea Tech Transmissometer can be deployed in either moored or profiling mode to estimate the concentration of suspended or particulate matter in seawater. The transmissometer measures the beam attenuation coefficient in the red spectral band (660 nm) of the laser lightsource over the instrument's path-length (e.g. 20 or 25 cm). This instrument designation is used when specific make and model are not known. The Sea Tech Transmissometer was manufactured by Sea Tech, Inc. (Corvalis, OR, USA).

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
bin_0_0_to_0_5	Number of particles per liter number/liter between 0 and 0.5mm in size	count	no_bcodmo_term
bin_gt_0_5_to_1_0	Number of particles per liter number/liter between 0.5 and 1.0mm in size	count	no_bcodmo_term
bin_gt_1_0_to_1_5	Number of particles per liter number/liter between 1.0 and 1.5mm in size	count	no_bcodmo_term
bin_gt_1_5_to_2_0	Number of particles per liter number/liter between 1.5 and 2.0mm in size	count	no_bcodmo_term
bin_gt_2_0_to_2_5	Number of particles per liter number/liter between 2.0 and 2.5mm in size	count	no_bcodmo_term
bin_gt_2_5_to_3_0	Number of particles per liter number/liter between 2.5 and 3.0mm in size	count	no_bcodmo_term
bin_gt_3_0_to_3_5	Number of particles per liter number/liter between 3.0 and 3.5mm in size	count	no_bcodmo_term
bin_gt_3_5_to_4_0	Number of particles per liter number/liter between 3.5 and 4.0mm in size	count	no_bcodmo_term
bin_gt_4_0_to_4_5	Number of particles per liter number/liter between 4.0 and 4.5mm in size	count	no_bcodmo_term
bin_gt_4_5	Number of particles per liter number/liter larger than 4.5mm in size	count	no_bcodmo_term
Canister	An internal reference to the film canister, if applicable. This is included to enable future resarchers to positively identify the correct film	unitless	sample_descrip
cruise_name	Name of the cruise which includes the year number and sequence number (For example, IVARS 1-1 is the first year and the first of two cruise)	unitless	cruise_id
date_local	Calendar Date in local (Christchurch, NZ) (NZST/NZDT)	unitless	date_local
depth	Depth	meters (m)	depth
In_water_DateTime_UTC	Timestamp (UTC) when the camera lowering began in standard ISO 8601:2004(E) format YYYY-mm-ddTHH:MM:SSZ	yyyy-MM-dd'T'HH:mm'Z'	ISO_DateTime_UTC
In_water_time_local	Local time (HH:MM:SS) when the camera lowering began. Local time (Christchurch, NZ) (NZST/NZDT)	unitless	time_local
Latitude	Latitude. Negative = South	decimal degrees (DD)	lat
Longitude	Longitude. Negative = West	decimal degrees (DD)	lon
particles_per_L	Total number of particles larger than 0.5mm in diameter per liter number/liter	count	no_bcodmo_term
Station	Station number as assigned during the cruise. Many are at the same location but individual numbers are used to allow separation based on time	unitless	station

Database

Contribute Data

Dataset: IVARS Phaeocystis
Deployment: IVARS_cruises

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: IVARS PhaeocystisDeployment: IVARS_cruises

Dataset acquisition description

Dataset Processing Description

Dataset: IVARS Phaeocystis
Deployment: IVARS_cruises