http://lod.bco-dmo.org/id/dataset/928222
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
2024-05-21
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
In Situ Amphipod and Copepod Video Output Captured by the Hoodsport ORCA Profiling Mooring Mounted SPC-2 Zoocam in the Hood Canal, Puget Sound, Washington from August to September 2018 (Zooplankton Swimming project)
2024-05-21
publication
2024-05-21
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-06-24
publication
https://doi.org/10.26008/1912/bco-dmo.928222.1
Julie E. Keister
University of Washington
principalInvestigator
Daniel Grunbaum
University of Washington
principalInvestigator
Paul Roberts
University of California-San Diego
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., Roberts, P. (2024) In Situ Amphipod and Copepod Video Output Captured by the Hoodsport ORCA Profiling Mooring Mounted SPC-2 Zoocam in the Hood Canal, Puget Sound, Washington from August to September 2018 (Zooplankton Swimming project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-05-21 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.928222.1 [access date]
In situ zooplankton ZooCam video captured in the Puget Sound during summer 2018 Dataset Description: <p>The primary file of this dataset is a tabular file of data containing an overview of each in situ video included in this analysis, the nearest CTD cast to the recording location of that vide, and selected environemntal data from the nearest CTD cast.</p> Methods and Sampling: <p>Videos were recorded only under low-flow (&lt; 1 cm/s) conditions, using infrared lighting to avoid modifying zooplankton behavior. The video camera recorded swimming in the X (left, right) and Z (up, down) directions, observing true vertical motion and projected horizontal motion. Videos were recorded at an average frame rate of 20 frames per second. The frame rate varied slightly during videos due to data throughput limitations of the onboard, single-board computer. However, each video frame was precisely timestamped, and the exact difference in time between frames was used when converting speeds from pixels per frames to mm per second. Each frame was 650 x 876 pixels, and each pixel was 0.088 mm2, corresponding to a 57.2 x 77.1 mm field of view.</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
completed
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
Paul Roberts
University of California-San Diego
proberts@mbari.org
pointOfContact
asNeeded
Dataset Version: 1
Unknown
vid_id
datetime_utc
total_frames
avg_frm_rate
nearest_ctd_cast
nearest_ctd_offset
depth
oxygen
temperature
SPC-UW-Zoocam
theme
None, User defined
time begin
image_analysis
cast
depth
dissolved Oxygen
water temperature at measurement depth
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
2018-08-01
2018-09-30
Puget Sound, WA
0
BCO-DMO catalogue of parameters from In Situ Amphipod and Copepod Video Output Captured by the Hoodsport ORCA Profiling Mooring Mounted SPC-2 Zoocam in the Hood Canal, Puget Sound, Washington from August 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/929110.rdf
Name: vid_id
Units: unitless
Description: <p>Video identifier, also the timestamp of when the recording started in Unix epoch time</p>
http://lod.bco-dmo.org/id/dataset-parameter/929111.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/929112.rdf
Name: total_frames
Units: frames
Description: <p>The total number of frames in the video, a way to measure the video length</p>
http://lod.bco-dmo.org/id/dataset-parameter/929113.rdf
Name: avg_frm_rate
Units: frames per second
Description: <p>The average frame rate of the video (frame rates varied slightly during videos)</p>
http://lod.bco-dmo.org/id/dataset-parameter/929114.rdf
Name: nearest_ctd_cast
Units: unitless
Description: <p>Date and time of the nearest completed CTD cast to the recorded video</p>
http://lod.bco-dmo.org/id/dataset-parameter/929115.rdf
Name: nearest_ctd_offset
Units: unitless
Description: <p>Time difference between the nearest completed CTD cast and the video recording</p>
http://lod.bco-dmo.org/id/dataset-parameter/929116.rdf
Name: depth
Units: meters (m)
Description: <p>The depth the camera was parked when the video was recorded</p>
http://lod.bco-dmo.org/id/dataset-parameter/929117.rdf
Name: oxygen
Units: milligrams per liter (mg/L)
Description: <p>Oxygen concentration from the nearest CTD cast at the depth the video was recorded</p>
http://lod.bco-dmo.org/id/dataset-parameter/929118.rdf
Name: temperature
Units: degrees Celcius
Description: <p>Temperature from the nearest CTD cast at the depth the video was recorded</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
22055
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/6e6213e7-dba8-434c-ab7f-e428440252a7/content
download
https://doi.org/10.26008/1912/bco-dmo.928222.1
download
onLine
dataset
<p>Videos were recorded only under low-flow (&lt; 1 cm/s) conditions, using infrared lighting to avoid modifying zooplankton behavior. The video camera recorded swimming in the X (left, right) and Z (up, down) directions, observing true vertical motion and projected horizontal motion. Videos were recorded at an average frame rate of 20 frames per second. The frame rate varied slightly during videos due to data throughput limitations of the onboard, single-board computer. However, each video frame was precisely timestamped, and the exact difference in time between frames was used when converting speeds from pixels per frames to mm per second. Each frame was 650 x 876 pixels, and each pixel was 0.088 mm2, corresponding to a 57.2 x 77.1 mm field of view.</p>
Specified by the Principal Investigator(s)
<p dir="ltr">Zooplankton and other particles appeared in videos as grayscale images against a dark background. Regions of Interest (ROIs) from each frame were identified using the Python package OpenCV (version 4.7.0) (Bradski 2000). OpenCV-fitted contours and rotated bounding boxes were used to calculate width, height, and area metrics for each ROI. The nominal “length” of each ROI was defined as the longer of its width and height measurements. Position, defined as the optical centroid of the zooplankter outline, and size metrics were saved for each ROI that were potentially zooplankton (areas larger than 30 pixels) within each frame.</p>
<p dir="ltr">Zooplankton positions were assembled into swimming trajectories using the Matlab software Tracker3D (Chan and Grünbaum 2010). Small particles in videos were used to reconstruct a background flow field with Particle Image Velocimetry (PIV), using the Python package OpenPIV (version 0.23.9) (Liberzon et al. 2021).</p>
<p>Each zooplankton ROI was assigned a taxonomic identification using a Machine Learning (ML) image classification algorithm. The algorithm was generated using a pre-trained convolutional neural network 50 layers deep (ResNet-50) with PyTorch, an open-source, Python-based machine learning framework.</p>
Specified by the Principal Investigator(s)
- Changed column name of video column to "vid_id" to match the "vid_id" columns of the supplemental files
- Changed date time format in nearest_ctd_cast from %m/%d/%y %H:%M to %Y-%m-%d %H:%M
- A human readable datetime column was created from the unix_datetimestamp value present in the filename, this column is named "datetime_utc"
- All video data has been compressed and uploaded to this data package in a zip folder called "fps_20.zip" the contents of this zip are represented in the primary tabular data file associated with this dataset
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 with a 500-mL imaged area that captured still images while profiling using lighting in the visible wavelength range (images submitted as a separate dataset) and videos of zooplankton using IR lighting (while stationary and under low-flow conditions. 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