Dataset: SPC-UW-ZooCam classified zooplankton images
Deployment: UW_SPC-2_Zoocam

Classified zooplankton ZooCam images captured in the Puget Sound during summer 2018

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/927518

Principal Investigator:

Julie E. Keister (University of Washington, UW)

Co-Principal Investigator:

Daniel Grunbaum (University of Washington, UW)

Student:

Deana Crouser (National Oceanic and Atmospheric Administration - Alaska Fisheries Science Center, NOAA-AFSC)

Amy Wyeth (University of Washington, UW)

Contact:

Julie E. Keister (University of Washington, UW)

BCO-DMO Data Manager:

Sawyer Newman (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Causes and consequences of hypoxia and pH impacts on zooplankton: Linking movement behavior to vertical distribution. (Zooplankton Swimming)

Version:

Coordinated Deployments:

RC008

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Description

Image Directory Category Descriptions

ClusteredSnow - Non-symmetrical "aggregated" clusters of marine snow
Filament_Filaments - singular and/or multiple, slender filament/threadlike objects
MarineSnow - Non-symmetrical "scattered" snow (smaller and numerous vs ClusteredSnow)
Unknown - Images that are too blurry to confidently classify or are "unknown"

Gelatinous:

Anthomedusae - (Euphysa tentaculata)
Cydippida - (Euplokamis dunlapae)
Cydippida - (Pleurobrachia bachei)
Cydippida - (Unknown)

Lobata:

Siphonophore - Calycophorae (Muggiaea atlantica)
Trachymedusae - (Aglantha digitale)
Trachymedusae - (Pantachogon haeckeli)
Trachymedusae - (young)

Copepoda:

Calanoida - (Acartia spp.)
Calanoida - (Calanus sp.)
Calanoida - (Centropages abdominalis)
Calanoida - (Metridia spp.)
Calanoida - (Psudo Micro Para) - includes pseudocalanus, microcalanus, and paracalanus
Copepoda - (nauplii)
Cyclopoida - (Oithona spp.)
Harpacticoida - (Microsetella rosea)
Poecilostomatoida - (Ditrichocoryceaus anglicus)
Poecilostomatoida - (Triconia spp.)

Amphipoda:

Cyphocariadae - (Cyphocaris challengeri)
Hyperiidea - (Themisto pacifica_Hyperoche sp.)
Gammeridea - (possibly Calliopius sp.)

Phytoplankton:

Dinoflagellata - (Noctiluca)
(Diatoms)

Other:

Chaetognatha
Decapoda - Caridea (Shrimp)
Euphausiacea - Euphausiidae (Krill)
Ostracoda - (Halocyprididae)
Fish_larvae
Larvacea - (Oikopleaura dioica)
Pteropoda - (Clione limacina)
Ptreropoda - (Limacina helicina)

Methods & Sampling

Dataset acquisition description

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 5 - 110 meters.

Image data processing (Region of Interest (ROI) selection) was conducted internally, with processed and compressed images streamed to shore over cellular networks.

Data Processing Description

Dataset Processing Description

Image processing

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).

Images that are too blurry to confidently classify are stored within the "Unknown" folder in the zipped image directory file.

Image File Naming Convention

File name example: SPC-UW-1534792542343244-337276376507-004392-154-2546-848-756-780.png

SPC: Scripps Plankton Camera

UW: University of Washington

1534792542343244: Unix Date/Timestamp [To convert to UTC, use (X / 86400) + 25569.]

337276376507: Directory and subdirectory extension specific to this directory organization system.

154-2546-848-756-780: ROI (Region of Interest) details (x, y, w, h, image size)

Processing for Reuse

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.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1657992	NSF Division of Ocean Sciences

Instruments

Underwater Camera

Supplied Name: SPC-UW-Zoocam

Supplied 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 Type

Generic Name: Underwater Camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/180/

Generic Description:

All types of photographic equipment that may be deployed underwater including stills, video, film and digital systems.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
filename	Filename of an individual zooplankton image, i.e., region of interest (ROI)	unitless	file_name
relative_filepath	Relative directory path where the "filename" image is stored within the zip file, SPC-UW-ZooCam_Training_Photos.zip	unitless	file_name
filesize_bytes	Image file size	bytes	file_size
md5sum	Image file md5sum value	unitless	no_bcodmo_term
latitude	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	decimal degrees	lat
longitude	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	decimal degrees	lon
augmented_image_flag	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	unitless	flag
datetime_utc	Datetime value derived from the unix timestamp represented in the image filename.	unitless	DateTime
roi_x	ROI (region of interest) x value of image file	image_analysis	no_bcodmo_term
roi_y	ROI (region of interest) y value of image file	image_analysis	no_bcodmo_term
roi_w	ROI (region of interest) w value of image file	image_analysis	no_bcodmo_term
roi_h	ROI (region of interest) h value of image file	image_analysis	no_bcodmo_term
roi_image_size	ROI (region of interest) image size	pixels	no_bcodmo_term

Database

Contribute Data

Dataset: SPC-UW-ZooCam classified zooplankton images
Deployment: UW_SPC-2_Zoocam

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: SPC-UW-ZooCam classified zooplankton imagesDeployment: UW_SPC-2_Zoocam

Dataset acquisition description

Dataset Processing Description

Dataset: SPC-UW-ZooCam classified zooplankton images
Deployment: UW_SPC-2_Zoocam