http://lod.bco-dmo.org/id/dataset/860725
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
2021-09-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Images and associated metadata of individually classified particles imaged and quantified in sediment trap gel layers collected on four research cruises conducted between 2015 and 2018
2021-09-14
publication
2021-09-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-09-15
publication
https://doi.org/10.26008/1912/bco-dmo.860725.1
Colleen Durkin
Moss Landing Marine Laboratories
principalInvestigator
Margaret L. Estapa
Skidmore College
principalInvestigator
Melissa Omand
University of Rhode Island
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: Durkin, C., Estapa, M. L., Omand, M. (2021) Images and associated metadata of individually classified particles imaged and quantified in sediment trap gel layers collected on four research cruises conducted between 2015 and 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-09-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.860725.1 [access date]
Images and associated metadata of individually classified particles imaged and quantified in sediment trap gel layers Dataset Description: Methods and Sampling: <p>The classified particle images described in this dataset are extracted from gel micrograph images available as dataset 749412 (<a href="https://www.bco-dmo.org/dataset/749412" target="_blank">https://www.bco-dmo.org/dataset/749412</a>) and further classified into categories. Refer to dataset 749412 for additional details on methodologies. In short:</p>
<p>Samples were collected on four research cruises:<br />
-&nbsp; at the New England shelf break aboard the R/V Endeavor on 3-7 November 2017 (EN572) and 13-18 June 2016 (EN581);<br />
-&nbsp;on a transit between Honolulu, Hawaii and Portland, Oregon aboard the R/V Falkor between 24 January-20 February 2017 (FK170124);<br />
- in the Subarctic North Pacific aboard the&nbsp;R/V Roger Revelle between 10 August and 12 September 2018.</p>
<p>Sediment trap collector tubes were deployed on various platform designs, including a neutrally-buoyant sediment trap (NBST), a surface tethered sediment trap (STST), and a Wire Walker (WW) trap.</p>
<p>Upon recovery, collection tubes were allowed to settle for at least 1 hour before the overlying water was siphoned off. Jars containing polyacrylamide gel were removed from trap tubes and the remaining overlying water was carefully pipetted off the gel. Gels were stored at 4 degrees C and imaged within the following 2 days before being stored at -80 degrees C. Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) with either a Luminera Infinity 2 or an Allied Vision Technologies StingRay camera attachment. Particles collected in gel layers during EN572 and EN581 were imaged under brightfield illumination. Particles collected in gel layers during FK170124 were imaged under both brightfield and oblique illumination, producing two separate sets of images for each sample.</p>
<p>Particles detected in gel image micrographs were manually sorted into distinct classes. Images are attached as two .tar.gz files.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1703664 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1703664
completed
Colleen Durkin
Moss Landing Marine Laboratories
831-771-4431
8272 Moss Landing Road
Moss Landing
CA
95039-9647
USA
cdurkin@mbari.org
pointOfContact
Margaret L. Estapa
Skidmore College
207-581-5176
193 Clarks Cove Road
Walpole
ME
04573
United States
margaret.estapa@maine.edu
pointOfContact
Melissa Omand
University of Rhode Island
401-874-6610
215 S Ferry Rd
Narrangsett
RI
02882-1197
USA
momand@uri.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Type
Area
ESD
ID
Number
bounding_box
file_name
particle_image_name
Luminera Infinity 2 microscope camera (FK170124 and EXPORTS "RR" images)
Allied Vision Technologies StingRay camera (EN572 and EN582)
Olympus SZX16 Stereomicroscope
theme
None, User defined
sampling_method
area_measured
ESD (Equivalent spherical diameter)
sample type
sample identification
No BCO-DMO term
file_name
featureType
BCO-DMO Standard Parameters
Camera
Camera
Microscope - Optical
instrument
BCO-DMO Standard Instruments
EN572
EN581
FK170124
RR1813
service
Deployment Activity
North Pacific Ocean
Subarctic North Pacific near Station PAPA (50 N, 144.8 W)
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.
Collaborative Research: EAGER: Particle-specific DNA sequencing to directly observe ecological mechanisms of the biological pump
https://osprey.bco-dmo.org/project/675296
Collaborative Research: EAGER: Particle-specific DNA sequencing to directly observe ecological mechanisms of the biological pump
<p><em>NSF Award Abstract:</em><br />
Carbon is fixed into organic matter by phytoplankton growing in the surface ocean, and is naturally sequestered in the ocean interior when particles and organisms sink: a process called the "biological pump." Because of its recognized influence on the global carbon cycle, ocean scientists have studied the biological pump for decades. However, we still do not have a sufficient understanding of the underlying processes to accurately quantify and predict carbon cycling. Much of this uncertainty stems from an inability to directly link specific plankton in the surface ocean with the types of particles sinking out of the surface ocean. To address this missing link in biological pump research, this work will directly observe how plankton are transported out of the surface ocean using novel, particle-specific observational approaches embedded within an interdisciplinary field program that will finely resolve upper ocean plankton groups and the resulting amount of sinking carbon across space and in time. The genetic identity of organisms within different types of sinking particles will be determined by sequencing the genetic contents of individually collected particles. This new application of a molecular method will definitively link surface plankton with sinking particles at five locations across the Pacific Ocean. This work has the potential to transform our understanding of the biological pump by identifying previously unknown links between surface ecosystems and sinking carbon particles. Because this work is embedded within an interdisciplinary field program, including biogeochemical modelers and remote sensing scientists, these data will feed directly into new models of the biological pump, improving our ability to quantify and predict carbon uptake by the ocean. This project will train 1 graduate student and at least 2 undergraduate researchers. Findings will be communicated to the non-scientific public through blogs, videos, and the public communication channels of participating institutions.</p>
<p>Accurate prediction of the global carbon cycle requires an understanding of the specific processes that link surface plankton communities and sinking particulate carbon flux (export) out of the surface ocean, but current methodological paradigms in biological pump research do not directly observe these processes. This project will comprehensively determine who is exported from the surface ocean and how using new, particle-resolving optical and molecular techniques embedded within a sampling scheme that characterizes export events at high time and space resolution. The investigation suggests that different plankton types in the surface waters are transported out of the surface ocean by distinct export pathways, and that an understanding of these connections is critical knowledge for global carbon cycle modeling. If successful, this work has the potential to transform our conceptual understanding of the biological pump by directly identifying mechanisms that link surface plankton with particle export, without relying on bulk sampling schemes and large-scale correlation analysis. Particle export environments will be studied at five open ocean locations during a cruise from Hawaii to Seattle in January-February 2017. The surface plankton communities will be characterized by a combination of satellite observations, sensors attached to a free-drifting, continuously profiling WireWalker, an in situ holographic camera, microscopy, and by sequencing 18S and 16S rRNA gene fragments. Exported particles will simultaneously be captured by various specialized sediment traps and their characteristics will be directly related to their sources in the surface community by identifying the genetic contents of individual particle types. Individual particles will be isolated from gel layers and the 16S and 18S rRNA gene fragments will be amplified and sequenced. This work would, for the first time, combine molecular approaches with particle-specific observations to enable simultaneous identification of both which organisms are exported and the processes responsible for their export.</p>
EAGER DNA BioPump
largerWorkCitation
project
eng; USA
oceans
North Pacific Ocean; Subarctic North Pacific near Station PAPA (50 N, 144.8 W)
-157.8749
-70.9367
20.99
50.5113
2015-11-03
2018-09-12
Eastern Pacific
0
BCO-DMO catalogue of parameters from Images and associated metadata of individually classified particles imaged and quantified in sediment trap gel layers collected on four research cruises conducted between 2015 and 2018
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/860743.rdf
Name: Type
Units: unitless
Description: <p>Illumination type (Oblique or Brightfield)</p>
http://lod.bco-dmo.org/id/dataset-parameter/860744.rdf
Name: Area
Units: square micrometers (um^2)
Description: <p>particle 2-dimensional area</p>
http://lod.bco-dmo.org/id/dataset-parameter/860745.rdf
Name: ESD
Units: micrometers (um)
Description: <p>equivalent spherical diameter</p>
http://lod.bco-dmo.org/id/dataset-parameter/860746.rdf
Name: ID
Units: unitless
Description: <p>particle identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/860747.rdf
Name: Number
Units: unitless
Description: <p>particle identifier number</p>
http://lod.bco-dmo.org/id/dataset-parameter/860748.rdf
Name: bounding_box
Units: unitless
Description: <p>pixel coordinates of particle bounding box in main image; format: [minimum row; minimum column; maximum row; maximum column]</p>
http://lod.bco-dmo.org/id/dataset-parameter/860749.rdf
Name: file_name
Units: unitless
Description: <p>name of main micrograph image from which particle was detected</p>
http://lod.bco-dmo.org/id/dataset-parameter/860750.rdf
Name: particle_image_name
Units: unitless
Description: <p>name of particle image associated with this metadata</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
79893679
https://darchive.mblwhoilibrary.org/bitstream/1912/27552/1/Durkin_geltrap_oblique_particles.tar.gz
download
31866824
https://darchive.mblwhoilibrary.org/bitstream/1912/27552/2/Durkin_geltrap_brightfield_particles.tar.gz
download
18278081
https://darchive.mblwhoilibrary.org/bitstream/1912/27552/3/dataset-860725_classified-particle-images__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.860725.1
download
onLine
dataset
<p>The classified particle images described in this dataset are extracted from gel micrograph images available as dataset 749412 (<a href="https://www.bco-dmo.org/dataset/749412" target="_blank">https://www.bco-dmo.org/dataset/749412</a>) and further classified into categories. Refer to dataset 749412 for additional details on methodologies. In short:</p>
<p>Samples were collected on four research cruises:<br />
-&nbsp; at the New England shelf break aboard the R/V Endeavor on 3-7 November 2017 (EN572) and 13-18 June 2016 (EN581);<br />
-&nbsp;on a transit between Honolulu, Hawaii and Portland, Oregon aboard the R/V Falkor between 24 January-20 February 2017 (FK170124);<br />
- in the Subarctic North Pacific aboard the&nbsp;R/V Roger Revelle between 10 August and 12 September 2018.</p>
<p>Sediment trap collector tubes were deployed on various platform designs, including a neutrally-buoyant sediment trap (NBST), a surface tethered sediment trap (STST), and a Wire Walker (WW) trap.</p>
<p>Upon recovery, collection tubes were allowed to settle for at least 1 hour before the overlying water was siphoned off. Jars containing polyacrylamide gel were removed from trap tubes and the remaining overlying water was carefully pipetted off the gel. Gels were stored at 4 degrees C and imaged within the following 2 days before being stored at -80 degrees C. Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) with either a Luminera Infinity 2 or an Allied Vision Technologies StingRay camera attachment. Particles collected in gel layers during EN572 and EN581 were imaged under brightfield illumination. Particles collected in gel layers during FK170124 were imaged under both brightfield and oblique illumination, producing two separate sets of images for each sample.</p>
<p>Particles detected in gel image micrographs were manually sorted into distinct classes. Images are attached as two .tar.gz files.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- concatenated two separate.csv files into a single dataset, creating the new column "Type";<br />
- replaced commas in the bounding_box field with semi-colons.</p>
Specified by the Principal Investigator(s)
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
Luminera Infinity 2 microscope camera (FK170124 and EXPORTS "RR" images)
Luminera Infinity 2 microscope camera (FK170124 and EXPORTS "RR" images)
PI Supplied Instrument Name: Luminera Infinity 2 microscope camera (FK170124 and EXPORTS "RR" images) 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/
Allied Vision Technologies StingRay camera (EN572 and EN582)
Allied Vision Technologies StingRay camera (EN572 and EN582)
PI Supplied Instrument Name: Allied Vision Technologies StingRay camera (EN572 and EN582) 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/
Olympus SZX16 Stereomicroscope
Olympus SZX16 Stereomicroscope
PI Supplied Instrument Name: Olympus SZX16 Stereomicroscope Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Cruise: EN572
EN572
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN572
Melissa Omand
University of Rhode Island
Cruise: EN581
EN581
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN581
Susanne Menden-Deuer
University of Rhode Island
Cruise: FK170124
FK170124
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK170124
Ivona Cetinic
National Aeronautics and Space Administration
https://datadocs.bco-dmo.org/docs/302/EAGER_DNA_BioPump/data_docs/DurkinOmandEstapa_Cruise_report.pdf
Report describing FK170124
Cruise: RR1813
RR1813
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
RR1813
Deborah K. Steinberg
Virginia Institute of Marine Science
https://datadocs.bco-dmo.org/docs/EXPORTS/data_docs/RR1813_Cruise_Report.pdf
Report describing RR1813
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel