http://lod.bco-dmo.org/id/dataset/927518
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
2024-05-14
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Classified Zooplankton ZooCam Images Captured by the Hoodsport ORCA Profiling Mooring Mounted SPC-2 Zoocam in the Hood Canal, Puget Sound, Washington from July to September 2018 (Zooplankton Swimming project)
2024-05-14
publication
2024-05-14
revision
BCO-DMO Linked Data URI
2024-05-14
creation
http://lod.bco-dmo.org/id/dataset/927518
Julie E. Keister
University of Washington
principalInvestigator
Daniel Grunbaum
University of Washington
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: Keister, J. E., Grunbaum, D. (2024) Classified Zooplankton ZooCam Images Captured by the Hoodsport ORCA Profiling Mooring Mounted SPC-2 Zoocam in the Hood Canal, Puget Sound, Washington from July to September 2018 (Zooplankton Swimming project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-14 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/927518 [access date]
Classified zooplankton ZooCam images captured in the Puget Sound during summer 2018 Dataset Description: <p><strong>Image Directory Category Descriptions</strong></p>
<ul>
<li>ClusteredSnow - Non-symmetrical "aggregated" clusters of marine snow</li>
<li>Filament_Filaments - singular and/or multiple, slender filament/threadlike objects</li>
<li>MarineSnow - Non-symmetrical "scattered" snow (smaller and numerous vs ClusteredSnow)</li>
<li>Unknown - Images that are too blurry to confidently classify or are "unknown"</li>
</ul>
<p><u>Gelatinous:</u></p>
<ul>
<li>Anthomedusae - (Euphysa tentaculata)</li>
<li>Cydippida - (Euplokamis dunlapae)</li>
<li>Cydippida - (Pleurobrachia bachei)&nbsp;</li>
<li>Cydippida - (Unknown)</li>
</ul>
<p><u>Lobata:</u></p>
<ul>
<li>Siphonophore - Calycophorae (Muggiaea atlantica)</li>
<li>Trachymedusae - (Aglantha digitale)</li>
<li>Trachymedusae - (Pantachogon haeckeli)</li>
<li>Trachymedusae - (young)</li>
</ul>
<p><u>Copepoda:</u></p>
<ul>
<li>Calanoida - (Acartia spp.)</li>
<li>Calanoida - (Calanus sp.)</li>
<li>Calanoida - (Centropages abdominalis)</li>
<li>Calanoida - (Metridia spp.)</li>
<li>Calanoida - (Psudo Micro Para) - includes pseudocalanus, microcalanus, and paracalanus</li>
<li>Copepoda - (nauplii)</li>
<li>Cyclopoida - (Oithona spp.)</li>
<li>Harpacticoida - (Microsetella rosea)</li>
<li>Poecilostomatoida - (Ditrichocoryceaus anglicus)</li>
<li>Poecilostomatoida - (Triconia spp.)</li>
</ul>
<p><u>Amphipoda:</u></p>
<ul>
<li>Cyphocariadae - (Cyphocaris challengeri)</li>
<li>Hyperiidea - (Themisto pacifica_Hyperoche sp.)&nbsp;</li>
<li>Gammeridea - (possibly Calliopius sp.)</li>
</ul>
<p><u>Phytoplankton:</u></p>
<ul>
<li>Dinoflagellata - (Noctiluca)</li>
<li>(Diatoms)</li>
</ul>
<p><u>Other:</u></p>
<ul>
<li>Chaetognatha</li>
<li>Decapoda - Caridea (Shrimp)</li>
<li>Euphausiacea - Euphausiidae (Krill)</li>
<li>Ostracoda - (Halocyprididae)</li>
<li>Fish_larvae</li>
<li>Larvacea - (Oikopleaura dioica)</li>
<li>Pteropoda - (Clione limacina)</li>
<li>Ptreropoda - (Limacina helicina)</li>
</ul> Methods and Sampling: <p>These images were collected by the SPC-UW-Zoocam, which is an underwater imaging system that was mounted on a profiling mooring. Images were collected during profiling of the mooring at depths between&nbsp;<span style="background-color:rgb(255, 255, 221); font-family:verdana,sans-serif; font-size:12px">5 - 110 meters</span>.</p>
<p>Image data processing (Region of Interest (ROI) selection) was conducted internally, with processed and compressed images streamed to shore over cellular networks.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1657992 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1657992
onGoing
Julie E. Keister
University of Washington
206-543-7620
School of Oceanography Box 357940
Seattle
WA
98195
United States
jkeister@uw.edu
pointOfContact
Daniel Grunbaum
University of Washington
206-221-6594
School of Oceanography Box 357940
Seattle
WA
98195
USA
random@uw.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
filename
relative_filepath
filesize_bytes
md5sum
latitude
longitude
augmented_image_flag
datetime_utc
roi_x
roi_y
roi_w
roi_h
roi_image_size
SPC-UW-Zoocam
theme
None, User defined
file_name
file_size
No BCO-DMO term
latitude
longitude
flag
Date and time
featureType
BCO-DMO Standard Parameters
Underwater Camera
instrument
BCO-DMO Standard Instruments
UW_SPC-2_Zoocam
service
Deployment Activity
Hoodsport, Hood Canal, Puget Sound, WA
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.
Causes and consequences of hypoxia and pH impacts on zooplankton: Linking movement behavior to vertical distribution.
https://osprey.bco-dmo.org/project/709640
Causes and consequences of hypoxia and pH impacts on zooplankton: Linking movement behavior to vertical distribution.
<p><em>NSF Award Abstract:</em><br />
Low oxygen (hypoxia) and low pH are known to have profound physiological effects on zooplankton, the microscopic animals of the sea. It is likely that many individual zooplankton change vertical mirgration behaviors to reduce or avoid these stresses. However, avoidance responses and their consequences for zooplankton distributions, and for interactions of zooplankton with their predators and prey, are poorly understood. This study will provide information on small-scale behavioral responses of zooplankton to oxygen and pH using video systems deployed in the field in a seasonally hypoxic estuary. The results will deepen our understanding of how zooplankton respond to low oxygen and pH conditions in ways that could profoundly affect marine ecosystems and fisheries through changes in their populations and distributions. This project will train graduate students and will engage K-12 students and teachers in under-served coastal communities by developing ocean technology-based citizen-scientist activities and curricular materials in plankton ecology, ocean change, construction and use of biological sensors, and quantitative analysis of environmental data.</p>
<p>Individual directional motility is a primary mechanism underlying spatio-temporal patterns in zooplankton population distributions. Motility is used by most zooplankton species to select among water column positions that differ in biotic and abiotic variables such as prey, predators, light, oxygen concentration, and pH. Species-specific movement responses to de-oxygenation and acidification are likely mechanisms through which short-term, localized impacts of these stressful conditions on individual zooplankton will be magnified or suppressed as they propagate up to population, community, and ecosystem-level dynamics. This study will quantify responses by key zooplankton species to oxygen and pH using in situ video systems to measure changes in individual behavior in hypoxic, low- pH versus well-oxygenated, high-pH regions of a seasonally hypoxic estuary. Distributions and movements of zooplankton will be quantified using three approaches: 1) an imaging system deployed in situ on a profiling mooring over two summers in a hypoxic region, 2) imagers deployed on Lagrangian drifters to sample simultaneously throughout the water column, and 3) vertically-stratified pumps and net tows to verify species identification and video-based abundance estimates. These field observations will be combined with laboratory analysis of zooplankton movements in oxygen and pH gradients, and with spatially-explicit models to predict how behavioral mechanisms lead to large-scale impacts of environmental stresses.</p>
<p>The following deployments were conducted in 2017 and 2018:<br />
CB1077: <a href="https://www.bco-dmo.org/deployment/735746" target="_blank">https://www.bco-dmo.org/deployment/735746</a><br />
CB1072: <a href="https://www.bco-dmo.org/deployment/735748" target="_blank">https://www.bco-dmo.org/deployment/735748</a><br />
Zoocam_ORCA_Twanoh_2017: <a href="https://www.bco-dmo.org/deployment/735762" target="_blank">https://www.bco-dmo.org/deployment/735762</a><br />
RC0008: <a href="https://www.bco-dmo.org/deployment/775288" target="_blank">https://www.bco-dmo.org/deployment/775288</a><br />
Mooring ORCA_Hoodsport; NANOOS-APL4: <a href="https://www.bco-dmo.org/deployment/775291" target="_blank">https://www.bco-dmo.org/deployment/775291</a></p>
Zooplankton Swimming
largerWorkCitation
project
eng; USA
oceans
Hoodsport, Hood Canal, Puget Sound, WA
-123.112583
-123.112583
47.421817
47.421817
2018-07-09
2018-09-22
Puget Sound, WA
0
BCO-DMO catalogue of parameters from Classified Zooplankton ZooCam Images Captured by the Hoodsport ORCA Profiling Mooring Mounted SPC-2 Zoocam in the Hood Canal, Puget Sound, Washington from July to September 2018 (Zooplankton Swimming 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/928207.rdf
Name: filename
Units: unitless
Description: <p>Filename of an individual zooplankton image, i.e., region of interest (ROI)</p>
http://lod.bco-dmo.org/id/dataset-parameter/928208.rdf
Name: relative_filepath
Units: unitless
Description: <p>Relative directory path where the "filename" image is stored within the zip file, SPC-UW-ZooCam_Training_Photos.zip</p>
http://lod.bco-dmo.org/id/dataset-parameter/928209.rdf
Name: filesize_bytes
Units: bytes
Description: <p>Image file size</p>
http://lod.bco-dmo.org/id/dataset-parameter/928210.rdf
Name: md5sum
Units: unitless
Description: <p>Image file md5sum value</p>
http://lod.bco-dmo.org/id/dataset-parameter/928211.rdf
Name: latitude
Units: decimal degrees
Description: <p>Latitude of mooring location where the ZooCam camera was deployed and the image file was collected in decimal degrees; a positive value indicates a Northern coordinate</p>
http://lod.bco-dmo.org/id/dataset-parameter/928212.rdf
Name: longitude
Units: decimal degrees
Description: <p>Longitude of mooring location where the ZooCam camera was deployed and the image file was collected in decimal degrees; a negative value indicates a Western coordinate</p>
http://lod.bco-dmo.org/id/dataset-parameter/928213.rdf
Name: augmented_image_flag
Units: unitless
Description: <p>A "augmented_image" value indicates that an image was duplicated and rotated to create an augmented dataset; blank data values in this column indicate that an image was not augmented</p>
http://lod.bco-dmo.org/id/dataset-parameter/928214.rdf
Name: datetime_utc
Units: unitless
Description: <p>Datetime value derived from the unix timestamp represented in the image filename. </p>
http://lod.bco-dmo.org/id/dataset-parameter/928215.rdf
Name: roi_x
Units: image_analysis
Description: <p>ROI (region of interest) x value of image file</p>
http://lod.bco-dmo.org/id/dataset-parameter/928216.rdf
Name: roi_y
Units: image_analysis
Description: <p>ROI (region of interest) y value of image file</p>
http://lod.bco-dmo.org/id/dataset-parameter/928217.rdf
Name: roi_w
Units: image_analysis
Description: <p>ROI (region of interest) w value of image file</p>
http://lod.bco-dmo.org/id/dataset-parameter/928218.rdf
Name: roi_h
Units: image_analysis
Description: <p>ROI (region of interest) h value of image file</p>
http://lod.bco-dmo.org/id/dataset-parameter/928219.rdf
Name: roi_image_size
Units: pixels
Description: <p>ROI (region of interest) image size</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://osprey.bco-dmo.org/dataset/927518/data/download
download
onLine
dataset
<p>These images were collected by the SPC-UW-Zoocam, which is an underwater imaging system that was mounted on a profiling mooring. Images were collected during profiling of the mooring at depths between&nbsp;<span style="background-color:rgb(255, 255, 221); font-family:verdana,sans-serif; font-size:12px">5 - 110 meters</span>.</p>
<p>Image data processing (Region of Interest (ROI) selection) was conducted internally, with processed and compressed images streamed to shore over cellular networks.</p>
Specified by the Principal Investigator(s)
<p><strong>Image processing</strong></p>
<p>Images were visually (manually) identified for taxonomy and sorted into folders. In this dataset, some images were duplicated and rotated to create an augmented dataset to train a Machine Learning algorithm (labeled as “augmented” in each file name).</p>
<p>Images that are too blurry to confidently classify are stored within the "Unknown" folder in the zipped image directory file.</p>
<p><strong>Image File Naming Convention</strong></p>
<p>File name example:&nbsp;SPC-UW-1534792542343244-337276376507-004392-154-2546-848-756-780.png</p>
<p class="rteindent1">SPC: Scripps Plankton Camera</p>
<p class="rteindent1">UW: University of Washington</p>
<p class="rteindent1">1534792542343244: Unix Date/Timestamp [To convert to UTC, use (X / 86400) + 25569.]</p>
<p class="rteindent1">337276376507: Directory and subdirectory extension specific to this directory organization system.</p>
<p class="rteindent1">154-2546-848-756-780: ROI (Region of Interest) details (x, y, w, h, image size)</p>
<p><strong>Processing for Reuse</strong></p>
<p>This dataset needs to undergo pre-processing steps (i.e., image augmentation and balancing) before it should be used to train an algorithm for best results.</p>
<p class="rteindent1">&nbsp;</p>
Specified by the Principal Investigator(s)
- Latitude and longitude values added to the data file
- augmented_image_flag column added to indicate if an image file has gone through augmentation
- A human readable datetime column was created from the unix_datetimestamp value present in the filename
- roi_x, roi_y, roi_h, and roi_image_size columns added from the image file name; this was parsed from the image file name
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
SPC-UW-Zoocam
SPC-UW-Zoocam
PI Supplied Instrument Name: SPC-UW-Zoocam PI Supplied Instrument Description:The SPC-UW-Zoocam designed and built specifically for this project. The Zoocam was custom-built by Paul Roberts in the Jaffe Imaging Laboratory at the University of California San Diego. It is an underwater camera system that captured still images of zooplankton within a 500-mL imaged area using lighting in the visible wavelength range. Instrument Name: Underwater Camera Instrument Short Name: Instrument Description: All types of photographic equipment that may be deployed underwater including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/180/
Deployment: UW_SPC-2_Zoocam
UW_SPC-2_Zoocam
ORCA-UW-Hoodsport
ORCA-UW-Hoodsport
mooring
UW_SPC-2_Zoocam
Julie E. Keister
University of Washington
ORCA-UW-Hoodsport
ORCA-UW-Hoodsport
mooring