http://lod.bco-dmo.org/id/dataset/1003447
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2026-08-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Vertical profiles of low and high-optical-density particles (LODP and HODP) and CTD hydrographic data from Focused Shadowgraph Imaging (FoSI) in the NE Atlantic, Jan-Mar 2023 (DESAFÍO)
2026-08-04
publication
2026-08-04
revision
Woods Hole Oceanographic Institution (WHOI BCO-DMO)
2026-08-08
publication
https://doi.org/10.26008/1912/bco-dmo.1003447.1
Alexander Boris Bochdansky
Old Dominion University
principalInvestigator
Santiago Hernández-León
Universidad de Las Palmas de Gran Canaria
principalInvestigator
Maria Couret
Universidad de Las Palmas de Gran Canaria
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Huang, H., Bochdansky, A. B., Couret, M., Hernández-León, S. (2026) Vertical profiles of low and high-optical-density particles (LODP and HODP) and CTD hydrographic data from Focused Shadowgraph Imaging (FoSI) in the NE Atlantic, Jan-Mar 2023 (DESAFÍO). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-08-04 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.1003447.1 [access date]
Dataset Description: <p>See the "Related Datasets" section for other datasets from the same profiles.<br />
<br />
Acronyms:&nbsp;<br />
<br />
DESAFÍO = DisEntangling Seasonality of Active Flux in the Ocean (expedition name)<br />
FoSI = Focused Shadowgraph Imaging<br />
LODP = Low Optical-Density Particles<br />
HODP = High Optical-Density Particles<br />
OD = Optical Density<br />
ESD =&nbsp;equivalent spherical diameter<br />
AZ = Azores<br />
CI = Canary Islands<br />
OO = Open Ocean<br />
RGF = Relative Gel Fraction<br />
ART ANOVA = Aligned Rank Transform (ART)&nbsp;Analysis of Variance (ANOVA)<br />
ANCOVA = Analysis of Covariance</p> Methods and Sampling: <p>Particle and hydrographic profile data were collected during the DESAFÍO expedition (DisEntangling Seasonality of Active Flux in the Ocean; PID2020-118118RB-100) in the Northeastern subtropical Atlantic Ocean, from 31 January to 2 March 2023, along a transect between the Azores (AZ; 41°5'32.39"N, 24°58'41.00"W) and the Canary Islands (CI; 28°41'00.00"N, 13°12'2.40"W). Twenty-two CTD casts were grouped into three geographic regions — CI (casts 1–6), the open-ocean station OO (casts 7–14, west of CI and south of the Azores), and AZ (casts 15–22) — and profiles were further partitioned into three depth strata: epipelagic (≤200 m), mesopelagic (200–1,000 m), and bathypelagic (&gt;1,000 m). Because the particle imaging system was mounted directly on the CTD rosette, particle and hydrographic data were collected simultaneously on the same vertical casts, allowing direct depth-matching between the two profile types. Four casts (5, 6, 18, and 20) have incomplete particle profiles due to unexpected camera shutdowns, likely from low battery voltage.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2128438 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2128438
completed
Alexander Boris Bochdansky
Old Dominion University
757-683-4933
Ocean, Earth and Atmospheric Sciences 4600 Elkhorn Ave.
Norfolk
VA
23529
USA
ABochdan@odu.edu
pointOfContact
Santiago Hernández-León
Universidad de Las Palmas de Gran Canaria
shernandezleon@ulpgc.es
pointOfContact
Maria Couret
Universidad de Las Palmas de Gran Canaria
maria.couret101@alu.ulpgc.es
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Depth
Part_No
TotalParticleArea
TotalParticleVolume
Date
Conductivity
Density
Fluorescence
Oxygen
PotentialTemperature
SalinityPractical
Turbidity
PAR
Latitude
Longitude
ParticlePool
Focused Shadowgraph Imaging (FoSI) System
Sea-Bird SBE911 Plus CTD
Sea-Bird SBE43 dissolved-oxygen
Wet Labs ECO-NTU-RTD fluorometer/turbidimeter
theme
None, User defined
depth
abundance
area
No BCO-DMO term
date
conductivity
density
fluorescence
dissolved Oxygen
potential temperature
practical salinity
turbidity
PAR
latitude
longitude
sample description
featureType
BCO-DMO Standard Parameters
Camera
CTD Sea-Bird SBE 911plus
Sea-Bird SBE 43 Dissolved Oxygen Sensor
Sea-Bird WETLabs ECO FLNTU(RT)D combined fluorometer and turbidity sensor
instrument
BCO-DMO Standard Instruments
PID2020-118118RB-100
service
Deployment Activity
Northeast Atlantic
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Linking optical characteristics of small particles (50 - 500 micrometer) with their sinking velocities in the mesopelagic environment
https://osprey.bco-dmo.org/project/882082
Linking optical characteristics of small particles (50 - 500 micrometer) with their sinking velocities in the mesopelagic environment
<p>NSF Award Abstract</p>
<p>Globally, the ocean removes more carbon dioxide than it releases into the atmosphere storing a portion of the excess carbon in the deep sea. Sinking particles, both living plankton and non-living detritus, are major contributors to this flux of carbon. Modern camera systems and image analysis techniques have made it possible to count, measure and classify these particles, thus providing oceanographers with a tool to estimate carbon transfers to the deep ocean at high resolution in space and time. Unfortunately, it is not enough to know the sizes of particles to estimate how fast these particles sink because shape and particle density also influence the sinking velocity. This project examines the velocities of individual particles as they sink into the deep ocean using a camera attached to a particle trap. For each of these particles, classification criteria, such as size, shape factors, optical density, and in the case of plankton, taxonomic identification, is determined and compared to their individual sinking velocities. This information serves to calculate overall sinking velocities from surveys of particles in the water column and thereby produce more reliable estimates of carbon fluxes from camera images. This project supports technology development in underwater imaging systems, graduate and undergraduate student education, and science literacy initiatives for middle-school students and their mentors through public outreach programs.</p>
<p>Shipboard and autonomous vehicle surveys of oceanic particle inventories hold great promise for estimating carbon fluxes at high temporal and spatial resolutions. However, while the sinking velocities of larger particles such as foraminifera shells and fecal pellets of salps, krill, and larger copepods are relatively well constrained, the dynamics of the smaller particle size pool (50–500 micrometers) remain more elusive. Despite their size and presumed slow sinking velocities, small particles occur in large numbers in the mesopelagic layer and sediment-trap material. Their abundance in the mesopelagic could be the result of deep mixing, or small particles could be remnants of digested larger particles, particles with a high excess density such as lithogenic dust particles, minipellets egested by protists, protist spores, or the result of fragmentation at depth due to the activity of flux feeders, among other possibilities. This project addresses some unanswered questions about the small particle pool by linking individually-resolved optical features with sinking velocities. Using Stokes’ law, excess density is being estimated from size and sinking velocity and then assigned to particles from optical surveys. A horizontally installed camera system records sinking velocities, sizes, and features of particles in a sediment trap attached to the Oceanic Flux Program mooring array. The recorded particles are being characterized using 1) classic image analysis, taking various shape factors into account; 2) opacity of individual particles; and 3) image classification with supervised and unsupervised deep learning using convolutional neural networks. A second identical camera surveys the particle inventory at the same station and time in the water column to integrate flux estimates over the existing and undisturbed particle pool. Niskin bottle samples and microscopic examination of particles augment the interpretation of image data. The results of this project contribute to the overarching goal of achieving higher predictive power for carbon flux models based on optical particle surveys.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Mesopelagic particles
largerWorkCitation
project
eng; USA
oceans
Northeast Atlantic
-25.147
-13.2007
28.7
41.0923
2023-01-31
2023-03-02
North Atlantic
0
BCO-DMO catalogue of parameters from Vertical profiles of low and high-optical-density particles (LODP and HODP) and CTD hydrographic data from Focused Shadowgraph Imaging (FoSI) in the NE Atlantic, Jan-Mar 2023 (DESAFÍO)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/1004163.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth at which particles were imaged</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004165.rdf
Name: Part_No
Units: particles per liter (#/L)
Description: <p>Particle abundance. Particle number per liter of water sample derived from FoSI image data.</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004166.rdf
Name: TotalParticleArea
Units: pix/frame
Description: <p>Particle area per image frame derived from FoSI image data</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004167.rdf
Name: TotalParticleVolume
Units: parts per million (ppm)
Description: <p>Total particle volume concentration in part per million (ppm) derived from FoSI image data</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004168.rdf
Name: Date
Units: unitless
Description: <p>Date when particles were imaged (ISO format).</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004169.rdf
Name: Conductivity
Units: Siemens per meter (S/m)
Description: <p>Shows how well the water carries electricity measured by CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004170.rdf
Name: Density
Units: kilograms per cubic meter (kg/m^3)
Description: <p>Shows how dense the water was, measured by CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004171.rdf
Name: Fluorescence
Units: milligrams per cubic meter (mg/m^3)
Description: <p>An indicator of Chlorophyll concentration measured by CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004172.rdf
Name: Oxygen
Units: milliliters per liter (mL/L)
Description: <p>Oxygen concentration in water measured by CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004173.rdf
Name: PotentialTemperature
Units: degrees Celsius
Description: <p>The temperature a water parcel would have if moved adiabatically to the surface, eliminating pressure effects measured by CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004174.rdf
Name: SalinityPractical
Units: practical salinity units (PSU)
Description: <p>Determined by measuring electrical conductivity, in-situ temperature, and pressure (depth) measured by CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004175.rdf
Name: Turbidity
Units: nephelometric turbidity units (NTU)
Description: <p>An indicator of water clarity measured by CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004176.rdf
Name: PAR
Units: micromoles of photons per square meter per second (umol photons/m^2/sec)
Description: <p>Photosynthetically Active Radiation measured by CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004177.rdf
Name: Latitude
Units: decimal degrees
Description: <p>The latitude of the sampling cast. North-south position from the equator</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004179.rdf
Name: Longitude
Units: decimal degrees
Description: <p>The longitude of the sampling cast. East-west position from the prime meridian</p>
http://lod.bco-dmo.org/id/dataset-parameter/1004181.rdf
Name: ParticlePool
Units: unitless
Description: <p>Indicate which particle pool the data belong to. LODP represent low-optical density particles, HODP represent high-optical density particles.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
https://doi.org/10.26008/1912/bco-dmo.1003447.1
download
onLine
dataset
<p>Particle and hydrographic profile data were collected during the DESAFÍO expedition (DisEntangling Seasonality of Active Flux in the Ocean; PID2020-118118RB-100) in the Northeastern subtropical Atlantic Ocean, from 31 January to 2 March 2023, along a transect between the Azores (AZ; 41°5'32.39"N, 24°58'41.00"W) and the Canary Islands (CI; 28°41'00.00"N, 13°12'2.40"W). Twenty-two CTD casts were grouped into three geographic regions — CI (casts 1–6), the open-ocean station OO (casts 7–14, west of CI and south of the Azores), and AZ (casts 15–22) — and profiles were further partitioned into three depth strata: epipelagic (≤200 m), mesopelagic (200–1,000 m), and bathypelagic (&gt;1,000 m). Because the particle imaging system was mounted directly on the CTD rosette, particle and hydrographic data were collected simultaneously on the same vertical casts, allowing direct depth-matching between the two profile types. Four casts (5, 6, 18, and 20) have incomplete particle profiles due to unexpected camera shutdowns, likely from low battery voltage.</p>
Specified by the Principal Investigator(s)
<p>CTD-derived temperature, salinity, dissolved oxygen, fluorescence, and turbidity profiles were binned to 1 dbar. Particle images were processed following the pipeline of Huang and Bochdansky, restricting analysis to particles ≥23.5 μm to exclude single-pixel noise, and classifying particles by optical density into low-OD (LODP; threshold 11, OD = 0.1466) and high-OD (HODP; threshold 29, OD = 0.2246) pools. Particle abundance and total particle volume (TPV) were resolved to 1-m depth bins to match the vertical resolution of the CTD data, and the Relative Gel Fraction (RGF) was calculated at each depth bin from the ratio of LODP to HODP abundance. Depth-resolved trends in particle metrics were evaluated using the Theil–Sen estimator with Mann–Kendall significance testing.</p>
<p>&nbsp;</p>
<p><em>Huang H and Bochdansky AB (2025) Optimizing an image analysis protocol for ocean particles in focused shadowgraph imaging systems. Front. Mar. Sci. 12:1539828. doi: 10.3389/fmars.2025.1539828</em></p>
Specified by the Principal Investigator(s)
- Loaded sum_allcasts_twopools.csv from source submission files, naming resulting table 1003447_v1_fosi-particle-profiles
- Configured CSV parsing with comma delimiter, header row 1, and treated empty string, "NaT", and "NA" as missing values
- Retained blank-header columns and empty rows were removed as part of load
- Updated column metadata with BCO-DMO standard name IDs, descriptions, and supplied units for Conductivity, Date, Density, Depth, Fluorescence, Latitude, Longitude, Oxygen, PAR, Part_No, ParticlePool, PotentialTemperature, SalinityPractical, TotalParticleArea, TotalParticleVolume, and Turbidity columns
- Flagged Depth, Latitude, and Longitude columns as primary parameters
- Converted Date column from string format %m/%d/%Y to date type with output format %Y-%m-%d, preserving column metadata
- Set column data types: Conductivity, Density, Fluorescence, Latitude, Longitude, Oxygen, PAR, PotentialTemperature, SalinityPractical, and Turbidity set to number type; Depth set to integer type; Date set to date type with format %Y-%m-%d; Part_No, TotalParticleArea, and TotalParticleVolume set to numeric float, ParticlePool to string.
- Dumped final table to CSV output as 1003447_v1_fosi-particle-profiles.csv, including generation of a unique latitude/longitude file and saving of the pipeline specification
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Focused Shadowgraph Imaging (FoSI) System
Focused Shadowgraph Imaging (FoSI) System
PI Supplied Instrument Name: Focused Shadowgraph Imaging (FoSI) System PI Supplied Instrument Description:Vertical profiles of conductivity, temperature, dissolved oxygen, fluorescence, and turbidity were measured from the surface to 4,000 m using a Sea-Bird SBE911 Plus CTD fitted with a Sea-Bird SBE43 dissolved-oxygen sensor and a Wet Labs ECO-NTU-RTD fluorometer/turbidimeter, all mounted on the rosette sampler; these profiles were binned to 1 dbar. Particle imagery was collected concurrently using a Focused Shadowgraph Imaging (FoSI) System attached to the base of the CTD rosette, providing particle data co-located in space and time with the CTD sensor suite. The configuration of FoSI was described by Bochdansky et al. (2022) and Huang and Bochdansky (2025). The FoSI imaged particles at a resolution of 11.75 μm/pixel. Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
Sea-Bird SBE911 Plus CTD
Sea-Bird SBE911 Plus CTD
PI Supplied Instrument Name: Sea-Bird SBE911 Plus CTD PI Supplied Instrument Description:Vertical profiles of conductivity, temperature, dissolved oxygen, fluorescence, and turbidity were measured from the surface to 4,000 m using a Sea-Bird SBE911 Plus CTD fitted with a Sea-Bird SBE43 dissolved-oxygen sensor and a Wet Labs ECO-NTU-RTD fluorometer/turbidimeter, all mounted on the rosette sampler; these profiles were binned to 1 dbar. Particle imagery was collected concurrently using a Focused Shadowgraph Imaging (FoSI) System attached to the base of the CTD rosette, providing particle data co-located in space and time with the CTD sensor suite. The configuration of FoSI was described by Bochdansky et al. (2022) and Huang and Bochdansky (2025). The FoSI imaged particles at a resolution of 11.75 μm/pixel. Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
Sea-Bird SBE43 dissolved-oxygen
Sea-Bird SBE43 dissolved-oxygen
PI Supplied Instrument Name: Sea-Bird SBE43 dissolved-oxygen Instrument Name: Sea-Bird SBE 43 Dissolved Oxygen Sensor Instrument Short Name:SBE-43 DO Instrument Description: The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. More information from the manufacturer: https://www.seabird.com/products/sbe-43-dissolved-oxygen-sensor Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0036/
Wet Labs ECO-NTU-RTD fluorometer/turbidimeter
Wet Labs ECO-NTU-RTD fluorometer/turbidimeter
PI Supplied Instrument Name: Wet Labs ECO-NTU-RTD fluorometer/turbidimeter Instrument Name: Sea-Bird WETLabs ECO FLNTU(RT)D combined fluorometer and turbidity sensor Instrument Short Name:WET Labs ECO FLNTU(RT)D Instrument Description: This optical sensor is available in combinations of backscattering, turbidity, and fluorescence measurements. It records in real-time and does not store data. ECOs feature optional active anti-fouling and internal batteries for long-term deployments. This instrument has a user-selectable sample rate up to 8 Hz The fluorometer can typically measure pigment concentrations in the range 0-75 ug/l, with a sensitivity of 0.037 ug/l, at wavelengths of 470 or 695 nm. The turbidity sensor can measure within the range 0-200 NTU, with a sensitivity of 0.098 NTU, at a wavelength of 700 nm. The instrument is stable over a temperature range of 0-30 degC and is rated to a depth of 6000 m.
Cruise: PID2020-118118RB-100
PID2020-118118RB-100
R/V Sarmiento de Gamboa
vessel
PID2020-118118RB-100
Santiago Hernández-León
Universidad de Las Palmas de Gran Canaria
R/V Sarmiento de Gamboa
vessel