http://lod.bco-dmo.org/id/dataset/683038
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
2017-02-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Phaeocystis colony counts from raw Digital Holographic Microscope images from casts on RVIB Nathaniel B. Palmer NBP1302, March 2013 (TRACERS project)
2017-02-28
publication
2017-02-28
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-02-18
publication
https://doi.org/10.26008/1912/bco-dmo.683038.1
Alexander Boris Bochdansky
Old Dominion University
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: Bochdansky, A. B. (2021) Phaeocystis colony counts from raw Digital Holographic Microscope images from casts on RVIB Nathaniel B. Palmer NBP1302, March 2013 (TRACERS project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2017-02-28 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.683038.1 [access date]
Phaeocystis counts Dataset Description: Methods and Sampling: <p>Digital inline holographic microscopy (DIHM): (from Bochdansky,et al (2017) JMS)</p>
<p>Details of the DIHM were published in Bochdansky et al. (2013). Briefly, a laser beam is focused on a 9 um single-mode optical fiber that serves as a small but intense point source of light. The expanding beam intercepts particles that create interfering shadow images on the adjacent screen of a high-resolution (4.2 megapixel) charge-coupled device (CCD) camera without a lens. The camera was connected to an eBOX530-820-FL1.6G-RC computer (Axiomtek) with a Gb LAN cable; images were recorded on a 750 GB hard disk at a frame rate of ~7-12 images per second. When the laser beam intercepts a structure, a portion of the image beam scatters and interferes with the light of the primary beam in a predictable pattern. This raw image represents a hologram that can then be reconstructed by applying the Kirchhoff–Helmholtz transform (Xu et al., 2001) in commercially available reconstruction software (Octopus, 4-Deep Inwater Imaging, formerly Resolution Optics). Being lens-less, the advantage of this method is that anything in the 7-cm long image beam can be reconstructed without having to adjust the focus on the object. The entirety of the image beam volume (i.e., 1.8 ml in this configuration) can be reconstructed in this fashion, and thus explores orders of magnitude more volume than any lens-based system would at the same resolution. Reconstruction of the images and analysis (particle quantities, sizes, and type) were performed manually as no reliable image reconstruction and analysis system currently exists for this custom-built DIHM. The DIHM is well suited to detect hard structures (e.g., silica, chitin, calcium carbonate, strontium sulfate) to a resolution as small as 5 um, and reliably images particles of any composition from 50 um to ~8 um in the image volume (Bochdansky et al., 2013). The DIHM does not "see" transparent exopolymers (TEP), which can only be inferred from the distribution of finer particles suspended in that matrix. Even at speeds of 1.5 m s-1 through the water, our instrument yields sharp images (Bochdansky et al., 2013, 2017).</p>
<p>NOTE: Phaeocystis colonies, because of their dense structure, did not reconstruct well (Fig. 3); however, they have a very characteristic shape and texture even in the unreconstructed holograms (Fig. 1) that we were able to verify in tests with laboratory cultures of P. antarctica. Consequently, we were able to perform a detailed analysis on Phaeocystis colonies on all casts through all depths (including the surface mixed layer).</p>
<p>Fig. 1. Four Phaeocystis antarctica colonies in a single unreconstructed hologram (a), and after reconstruction of one colony (b). The image volume of an individual hologram is 1.8 ml, but the reconstruction can only visualize a specific image plane within that volume. We concluded that Phaeocystis colonies were sufficiently distinguishable and unique that unreconstructed images could be used for quantification. Poor reconstruction of Phaeocystis colonies makes exact size determination unreliable but colony diameters in field collections in the Ross Sea range from approximately 10 to 400 um (Mathot et al., 2000). DOI: 10.4319/lom.2013.11.28</p>
Funding provided by NSF Division of Polar Programs (NSF PLR) Award Number: PLR-1142097 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1142097
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
asNeeded
Dataset Version: 1
Unknown
station
julian_day
lat
lon
press
depth
Phaeocystis_L
DIHM
theme
None, User defined
station number
Julian day as a decimal (time elapsed in days from 00:00 on January 1st 4713 BC)
latitude
longitude
water pressure
depth
abundance
featureType
BCO-DMO Standard Parameters
Digital inline holographic microscope
instrument
BCO-DMO Standard Instruments
NBP1302
service
Deployment Activity
Ross Sea
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.
TRacing the fate of Algal Carbon Export in the Ross Sea
https://osprey.bco-dmo.org/project/547771
TRacing the fate of Algal Carbon Export in the Ross Sea
<p>Sinking particles are a major element of the biological pump and they are commonly assigned to two fates: mineralization in the water column and accumulation at the seafloor. However, there is another fate of export hidden within the vertical decline of carbon, the transformation of sinking organic matter to fine suspended and/or dissolved organic fractions. This process has been suggested but has rarely been observed or quantified. As a result, it is presumed that the solubilized fraction is largely mineralized over short time scales. However, global ocean surveys of dissolved organic carbon are demonstrating a significant water column accumulation of organic matter under high productivity environments. This proposal will investigate the transformation of organic particles from sinking to solubilized phases of the export flux in the Ross Sea. The Ross Sea experiences high export particle production, low dissolved organic carbon export with overturning circulation, and the area has a predictable succession of production and export events. In addition, the basin is shallow (< 1000 m) so the products the PIs will target are relatively concentrated. To address the proposed hypothesis, the PIs will use both well-established and novel biochemical and optical measures of export production and its fate. The outcomes of this work will help researchers close the carbon budget in the Ross Sea.</p>
TRACERS
largerWorkCitation
project
eng; USA
biota
oceans
Ross Sea
164
-135
-78.59056
-66.66096
2013-03-01
2013-03-01
Ross Sea
0
BCO-DMO catalogue of parameters from Phaeocystis colony counts from raw Digital Holographic Microscope images from casts on RVIB Nathaniel B. Palmer NBP1302, March 2013 (TRACERS 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
http://lod.bco-dmo.org/id/dataset-parameter/683044.rdf
Name: station
Units: unitless
Description: <p>station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/683045.rdf
Name: julian_day
Units: unitless
Description: <p>Julian Day in 2013</p>
http://lod.bco-dmo.org/id/dataset-parameter/683046.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/683047.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/683048.rdf
Name: press
Units: decibars
Description: <p>pressure</p>
http://lod.bco-dmo.org/id/dataset-parameter/683049.rdf
Name: depth
Units: meters
Description: <p>depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/683050.rdf
Name: Phaeocystis_L
Units: colonies/liter
Description: <p>Phaeocystis colonies</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
1725084
https://darchive.mblwhoilibrary.org/bitstream/1912/26700/1/dataset-683038_phaeocystis-counts__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.683038.1
download
onLine
dataset
<p>Digital inline holographic microscopy (DIHM): (from Bochdansky,et al (2017) JMS)</p>
<p>Details of the DIHM were published in Bochdansky et al. (2013). Briefly, a laser beam is focused on a 9 um single-mode optical fiber that serves as a small but intense point source of light. The expanding beam intercepts particles that create interfering shadow images on the adjacent screen of a high-resolution (4.2 megapixel) charge-coupled device (CCD) camera without a lens. The camera was connected to an eBOX530-820-FL1.6G-RC computer (Axiomtek) with a Gb LAN cable; images were recorded on a 750 GB hard disk at a frame rate of ~7-12 images per second. When the laser beam intercepts a structure, a portion of the image beam scatters and interferes with the light of the primary beam in a predictable pattern. This raw image represents a hologram that can then be reconstructed by applying the Kirchhoff–Helmholtz transform (Xu et al., 2001) in commercially available reconstruction software (Octopus, 4-Deep Inwater Imaging, formerly Resolution Optics). Being lens-less, the advantage of this method is that anything in the 7-cm long image beam can be reconstructed without having to adjust the focus on the object. The entirety of the image beam volume (i.e., 1.8 ml in this configuration) can be reconstructed in this fashion, and thus explores orders of magnitude more volume than any lens-based system would at the same resolution. Reconstruction of the images and analysis (particle quantities, sizes, and type) were performed manually as no reliable image reconstruction and analysis system currently exists for this custom-built DIHM. The DIHM is well suited to detect hard structures (e.g., silica, chitin, calcium carbonate, strontium sulfate) to a resolution as small as 5 um, and reliably images particles of any composition from 50 um to ~8 um in the image volume (Bochdansky et al., 2013). The DIHM does not "see" transparent exopolymers (TEP), which can only be inferred from the distribution of finer particles suspended in that matrix. Even at speeds of 1.5 m s-1 through the water, our instrument yields sharp images (Bochdansky et al., 2013, 2017).</p>
<p>NOTE: Phaeocystis colonies, because of their dense structure, did not reconstruct well (Fig. 3); however, they have a very characteristic shape and texture even in the unreconstructed holograms (Fig. 1) that we were able to verify in tests with laboratory cultures of P. antarctica. Consequently, we were able to perform a detailed analysis on Phaeocystis colonies on all casts through all depths (including the surface mixed layer).</p>
<p>Fig. 1. Four Phaeocystis antarctica colonies in a single unreconstructed hologram (a), and after reconstruction of one colony (b). The image volume of an individual hologram is 1.8 ml, but the reconstruction can only visualize a specific image plane within that volume. We concluded that Phaeocystis colonies were sufficiently distinguishable and unique that unreconstructed images could be used for quantification. Poor reconstruction of Phaeocystis colonies makes exact size determination unreliable but colony diameters in field collections in the Ross Sea range from approximately 10 to 400 um (Mathot et al., 2000). DOI: 10.4319/lom.2013.11.28</p>
Specified by the Principal Investigator(s)
<p>The field of view of each image represents 1.8 ml. The number of observed colonies in each meter bin was divided by the number of images and by 1.8 to yield the number of Phaeocystis colonies per liter for each meter.</p>
<p><strong>BCO-DMO Processing notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- reduced number of digits to right of decimal of cell counts from 7 to 1 due to sampling precision methods</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
DIHM
DIHM
PI Supplied Instrument Name: DIHM PI Supplied Instrument Description:Used to count Phaeocystis colonies in situ. Instrument Name: Digital inline holographic microscope Instrument Short Name:DIHM Instrument Description: A Digital Inline Holographic Microscope (DIHM) uses coherent (laser) light and a digital camera to image objects with micrometer scale resolution. A portion of the light scattered by illuminated objects interferes with incident light in a predictable manner. The resulting interference patterns projected onto a two-dimensional plane (i.e. digital camera sensor) are recorded as holograms. These digital holograms are then numerically reconstructed to produce an in-focus image at a given distance from the recording plane. A relatively large illuminated volume (>100 mL) can be reconstructed in this manner to produce a single image with an extended depth of field.
Cruise: NBP1302
NBP1302
Community Standard Description
International Council for the Exploration of the Sea
RVIB Nathaniel B. Palmer
vessel
NBP1302
Dennis Hansell
University of Miami Rosenstiel School of Marine and Atmospheric Science
http://dmoserv3.whoi.edu/data_docs/TRACERS/NBP1302_data_report.pdf
Report describing NBP1302
Community Standard Description
International Council for the Exploration of the Sea
RVIB Nathaniel B. Palmer
vessel