http://lod.bco-dmo.org/id/dataset/925893
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
2024-04-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Movies of mysid aggregations in Damariscotta Estuary, Maine obtained during the summer of 2023
2024-04-25
publication
2024-04-25
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-08-19
publication
https://doi.org/10.26008/1912/bco-dmo.925893.1
Aditya Nayak
Florida Atlantic University
principalInvestigator
Sumit Dass
Florida Atlantic 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: Nayak, A., Dass, S. (2024) Movies of mysid aggregations in Damariscotta Estuary, Maine obtained during the summer of 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-04-25 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.925893.1 [access date]
Dataset Description: <p>This dataset contains image files and a metadata table in the "Data Files" section and additional "Supplemental Files" including processing code and a file inventory.</p> Methods and Sampling: <p>For in situ mysid behavioral observations, we have&nbsp;developed and deployed a custom-built stereoimaging system capable of capturing synchronized high-quality images at a high frame rate (up to 21 fps). Our current setup features Teledyne Blackfly S GigE cameras with 5 MP resolution, IEEE1588 clock synchronization, and PoE support.&nbsp;Navitar&nbsp;lenses, with focal lengths of&nbsp;12 mm&nbsp;or&nbsp;25 mm, are attached via C-type lens mounts to ensure compatibility. Lighting is provided by a&nbsp;TrustFire&nbsp;DF50 scuba diving light with white and red LED modes. The stereo housing, designed in-house,&nbsp;comprises&nbsp;galvanized aluminum structures and acrylic end caps housing optical-grade glass lenses. It offers flexibility in inter-camera distance and angle. Custom-made underwater&nbsp;DragonFish&nbsp;Ethernet cables&nbsp;facilitate&nbsp;power and data transfer, enabling live feed monitoring, and synchronized camera frame storage, while also simplifying power management, thus extending deployment time.&nbsp;</p>
<p>The stereo housing and lighting system are affixed to an aluminum bar frame, which is lowered into the water using a crane. Initially, the frame is positioned at a shallow depth for calibration purposes. An 8x9 checkboard pattern with a&nbsp;10 mm&nbsp;square size, printed on an aluminum composite panel, is submerged for calibration. Synchronized images are captured by both cameras as the checkerboard is moved to cover the common field of view and focused depth. Once calibration images are&nbsp;recorded, the camera rig is lowered to the desired recording depth. Live feed monitoring ensures proper lighting and clear visibility before recording synchronized images&nbsp;commences. After sufficient images are captured, recording&nbsp;is stopped, and the stored data undergoes quality and synchronization analysis.&nbsp;Finally, details such as the data recording location, folder identification, camera synchronization status, and the number of recorded images&nbsp;are&nbsp;documented in our field notes before&nbsp;proceeding&nbsp;to the next data recording session. Calibration is typically&nbsp;required&nbsp;only once at each location.&nbsp; File naming conventions: Maine2023_Pxx or Maine2023_Sxx as the naming protocol (for primary and secondary cameras, where xx represents the number of the dataset, e.g., P80, S80).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2138465 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2138465
completed
Aditya Nayak
Florida Atlantic University
772-242-6427
Florida Atlantic University - Harbor Branch Oceanographic Institute 5600 US 1 North
Fort Pierce
FL
34946
USA
anayak@fau.edu
pointOfContact
Sumit Dass
Florida Atlantic University
dasss@fau.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Date_Local
Start_Time_Local
End_Time_Local
Location
Latitude
Longitude
Primary_Folder
Primary_Movie
Secondary_Folder
Secondary_Movie
Camera_FPS
Strobe_Light_Color
Image_Numbers
Camera_Orientation
Start_DateTime_UTC
End_DateTime_UTC
Image_Storage_GB
Video_Storage_GB
In-house custom-developed stereoimaging system for zooplankton observations: Teledyne Blackfly S GigE cameras
theme
None, User defined
date_local
time_local
site
latitude
longitude
sample description
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
Camera
instrument
BCO-DMO Standard Instruments
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: Characterizing benthic mysid ecology and animal-fluid interactions in response to background flow, food, and light conditions
https://osprey.bco-dmo.org/project/867464
Collaborative Research: Characterizing benthic mysid ecology and animal-fluid interactions in response to background flow, food, and light conditions
<p><em>NSF Award Abstract:</em><br />
Mysid shrimp are a group of zooplankton that are distributed in diverse aquatic environments – freshwater, marine and estuarine – in both shallow and deep waters throughout the world. Due to their ubiquitous presence, mysids form a critical link in marine food webs, yet little is known about their ecology and interactions with their local surroundings. An interdisciplinary team of investigators will develop and deploy a novel in situ imaging system in coastal Maine over the span of two summers, conducting a comprehensive investigation of mysid behavior in their natural environment, including their interactions and distribution under varying local flow, food, and light conditions. The investigators will train two graduate students at the interface of fluid mechanics, instrumentation, and ecology. In addition, ten students from Florida Atlantic University and the University of Southern Maine will be invited to participate in annual workshops on ecological fluid mechanics, with first-generation college students or those from other underrepresented communities encouraged to apply. The cutting-edge instrumentation suite, including the imaging system being developed as part of this project, can be used to address different questions associated with spatial patterns and zooplankton or fish behavior in the future. Image datasets will be openly accessible to the scientific community and the public. Project results will be disseminated through public outreach lectures at the Harbor Branch Oceanographic Institute, Darling Marine Center, and the Woods Hole Oceanographic Institution.</p>
<p>Mysids have been historically understudied compared to other zooplankton groups (e.g., copepods, krill), despite their ubiquitous presence and importance to marine food webs. This project will investigate mysid behavior, feeding ecology, and swarm distributions in relation to prey availability, light levels, and background flow conditions, focusing on a single mysid species – Neomysis americana. The investigators will use a state-of-the-art suite of instruments in the field, including two separate imaging systems and a high resolution Acoustic Doppler Profiler, to conduct field experiments at the Damariscotta River Estuary. This instrumentation suite will collect data to analyze mysid distributions and animal-fluid interactions in their natural environment, as well as ancillary data on benthic particle/plankton community composition and physical parameters (including currents, waves, temperature and depth). Multi-spectral analysis will find correlation patterns with water turbidity, flow conditions, bottom topography, mysid abundance, and food source concentrations. Mysid samples will be collected several times a week throughout the summer months to monitor changes in the mysid population abundance, sex ratio, and stage structure. The investigators will determine how seasonal changes in environmental variables and Neomysis population structure affect distribution within the estuary, as well as small-scale swimming and aggregation behavior. They will answer questions related to how swarm organization, aggregation, and swimming behavior differ under conditions of varying zooplankton abundance and swarm composition. Results will ultimately improve our understanding of marine ecosystem dynamics.</p>
<p>This project is jointly funded by the Biological Oceanography Program and the Established Program to Stimulate Competitive Research (EPSCoR).</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>
Mysid ecology
largerWorkCitation
project
eng; USA
oceans
-69.57958
-69.57958
43.93419
43.93419
2023-07-26
2023-08-04
Damariscotta River Estuary, Maine, USA
0
BCO-DMO catalogue of parameters from Movies of mysid aggregations in Damariscotta Estuary, Maine obtained during the summer of 2023
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/929742.rdf
Name: Date_Local
Units: unitless
Description: <p>The date on which the field data is recorded (time zone EST/EDT).</p>
http://lod.bco-dmo.org/id/dataset-parameter/929743.rdf
Name: Start_Time_Local
Units: unitless
Description: <p>The start time of field data recording.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929744.rdf
Name: End_Time_Local
Units: unitless
Description: <p>The end time of field data recording.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929745.rdf
Name: Location
Units: decimal degrees
Description: <p>The location at which the data is recorded. The datas are recorded at two docks of the Darling Marine Center. DMC Pedestrian dock: Darling Marine Center Pedestrian dock; DMC Main dock: Darling Marine Center Mine Dock.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929746.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of the data recording location</p>
http://lod.bco-dmo.org/id/dataset-parameter/929747.rdf
Name: Longitude
Units: unitless
Description: <p>Longitude of the data recording location.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929748.rdf
Name: Primary_Folder
Units: unitless
Description: <p>Reference folder name of the camera which initiates the trigger for camera synchronization.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929749.rdf
Name: Primary_Movie
Units: unitless
Description: <p>Filename of the movie for the primary Primary_Folder images</p>
http://lod.bco-dmo.org/id/dataset-parameter/929750.rdf
Name: Secondary_Folder
Units: unitless
Description: <p>Reference folder name of the camera which receives the trigger for camera synchronization.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929751.rdf
Name: Secondary_Movie
Units: unitless
Description: <p>Filename of the movie for the Secondary_Folder images</p>
http://lod.bco-dmo.org/id/dataset-parameter/929752.rdf
Name: Camera_FPS
Units: unitless
Description: <p>Camera frame per second (FPS) set for the data recording. For all the recordings the same FPS is maintained for both cameras.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929753.rdf
Name: Strobe_Light_Color
Units: unitless
Description: <p>Strobe light color. The used strobe light is a battery-powered LED tourch which has four modes: Bright White/White/Red/UV.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929754.rdf
Name: Image_Numbers
Units: unitless
Description: <p>Image Numbers (Primary Camera/Secondary Camera ). Number of images captured by primary and secondary camera. Similar image numbers indicate that the cameras capture images in a synchronized manner.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929755.rdf
Name: Camera_Orientation
Units: unitless
Description: <p>Camera orientation description. Two different camera orientations are used: one parallel to the waterbed looking horizontally and the other vertical to the waterbed looking downwards.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929756.rdf
Name: Start_DateTime_UTC
Units: unitless
Description: <p>The start timestamp with timezone (UTC) of field data recording. Datetime format is ISO 8601.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929757.rdf
Name: End_DateTime_UTC
Units: unitless
Description: <p>The end timestamp with timezone (UTC) of field data recording. Datetime format is ISO 8601.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929758.rdf
Name: Image_Storage_GB
Units: Gigabytes (GB)
Description: <p>Storage volume (Video). Camera captures 8-bit monochrome images saved in '.tiff' format. These values show the total hard drive space requied to save both the primary and secondary image folders.</p>
http://lod.bco-dmo.org/id/dataset-parameter/929759.rdf
Name: Video_Storage_GB
Units: Gigabytes (GB)
Description: <p>Storage volume (Video). We employed a Python script to create a video file (.mp4 format) from a designated folder containing the raw image files (.tiff format). The column values indicate the cumulative hard drive space necessary to store the videos from both the primary and secondary folders.</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
29107041700
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/85efadb1-65c5-48ec-adc8-94e01fc3f369/content
download
29357026736
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/726a8095-2f9a-4968-9089-6e28f773a869/content
download
9209
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/f7afc619-da46-4686-8924-973e0b513adc/content
download
https://doi.org/10.26008/1912/bco-dmo.925893.1
download
onLine
dataset
<p>For in situ mysid behavioral observations, we have&nbsp;developed and deployed a custom-built stereoimaging system capable of capturing synchronized high-quality images at a high frame rate (up to 21 fps). Our current setup features Teledyne Blackfly S GigE cameras with 5 MP resolution, IEEE1588 clock synchronization, and PoE support.&nbsp;Navitar&nbsp;lenses, with focal lengths of&nbsp;12 mm&nbsp;or&nbsp;25 mm, are attached via C-type lens mounts to ensure compatibility. Lighting is provided by a&nbsp;TrustFire&nbsp;DF50 scuba diving light with white and red LED modes. The stereo housing, designed in-house,&nbsp;comprises&nbsp;galvanized aluminum structures and acrylic end caps housing optical-grade glass lenses. It offers flexibility in inter-camera distance and angle. Custom-made underwater&nbsp;DragonFish&nbsp;Ethernet cables&nbsp;facilitate&nbsp;power and data transfer, enabling live feed monitoring, and synchronized camera frame storage, while also simplifying power management, thus extending deployment time.&nbsp;</p>
<p>The stereo housing and lighting system are affixed to an aluminum bar frame, which is lowered into the water using a crane. Initially, the frame is positioned at a shallow depth for calibration purposes. An 8x9 checkboard pattern with a&nbsp;10 mm&nbsp;square size, printed on an aluminum composite panel, is submerged for calibration. Synchronized images are captured by both cameras as the checkerboard is moved to cover the common field of view and focused depth. Once calibration images are&nbsp;recorded, the camera rig is lowered to the desired recording depth. Live feed monitoring ensures proper lighting and clear visibility before recording synchronized images&nbsp;commences. After sufficient images are captured, recording&nbsp;is stopped, and the stored data undergoes quality and synchronization analysis.&nbsp;Finally, details such as the data recording location, folder identification, camera synchronization status, and the number of recorded images&nbsp;are&nbsp;documented in our field notes before&nbsp;proceeding&nbsp;to the next data recording session. Calibration is typically&nbsp;required&nbsp;only once at each location.&nbsp; File naming conventions: Maine2023_Pxx or Maine2023_Sxx as the naming protocol (for primary and secondary cameras, where xx represents the number of the dataset, e.g., P80, S80).</p>
Specified by the Principal Investigator(s)
<p>The original field data comprises 8-bit monochrome TIFF or BMP image files recorded synchronously by two cameras. The uploaded data consists of movies (MP4 video format) of the raw images, i.e., each movie is a compilation of all the raw images in a single dataset.&nbsp;<br />
<br />
A Python script was used to process a sequence of image files from a specified folder (a single dataset) and generate an output video using the 'mp4v' codec. The video's frame rate matches that of the image recording rate. You can find the Python script code we used within a python notebook for this purpose within the supplemental file 'video_from_imgs.txt</p>
Specified by the Principal Investigator(s)
Mysid videos were bundled up into two zip packages with zip64 support using 7z. These two zip files were added to the "Data File" section (Mysid_movies_summer2023_Maine_P.zip, Mysid_movies_summer2023_Maine_S.zip).
* File inventory was created containing the imagename, filesize and checksums. Added columns to contain identifiers within the image name: image set id (primary or secondary folder), and Primary_or_Secondary indicating if it was the primary or secondary camera. (file_inventory.csv)
Sheet "Metadata" within file Maine_dataset_report_5.xlsx was imported into the BCO-DMO data system. With additional added columns with the associated primary and secondary movie name. Metadata table added as a supplemental file.
* Date converted to ISO 8601 format, ISO timestamps with timezone added (UTC) in addition to local times.
* Lat lon converted to decimal degrees
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]
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
In-house custom-developed stereoimaging system for zooplankton observations: Teledyne Blackfly S GigE cameras
In-house custom-developed stereoimaging system for zooplankton observations: Teledyne Blackfly S GigE cameras
PI Supplied Instrument Name: In-house custom-developed stereoimaging system for zooplankton observations: Teledyne Blackfly S GigE cameras PI Supplied Instrument Description:A custom-built stereoimaging system capable of capturing synchronized high-quality images at a high frame rate (up to 21 fps). Our current setup features Teledyne Blackfly S GigE cameras with 5 MP resolution, IEEE1588 clock synchronization, and PoE support. Navitar lenses, with focal lengths of 12 mm or 25 mm, are attached via C-type lens mounts to ensure compatibility. Lighting is provided by a TrustFire DF50 scuba diving light with white and red LED modes. 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/