Dataset: Antarctic krill schooling: Coordinates for speed and nearest neighbor distances

Name: 3D coordinates to calculate speed and nearest neighbor distances in each trial of Antarctic krill in lab experiments at Palmer Station, Antarctica in November 2022.
Published: 2024-03-26
Keywords: antarctic krill, schooling, kreisel tank, flow characterization, southern ocean ecology, collective behavior, stereophotogrammetry, oceans

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Palmer Station, Antarctica

Project:

Collaborative Research: Individual Based Approaches to Understanding Krill Distributions and Aggregations (Krill Aggregation)

Principal Investigator:

David Murphy (University of South Florida, USF)

Student:

Kuvvat Garayev (University of South Florida, USF)

Contact:

Kuvvat Garayev (University of South Florida, USF)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-03-26

Restricted:

Validated:

Current State:

Data not available

3D coordinates to calculate speed and nearest neighbor distances in each trial of Antarctic krill in lab experiments at Palmer Station, Antarctica in November 2022.

Abstract:

Laboratory experiments were conducted on schools of Antarctic krill in the novel annular flume at Palmer Station, Antarctica, in November 2022. Using overhead camera along with stereophotogrammetry system the swimming trajectories of krill were recorded while altering flow and light levels in the tank. The purpose of the study is to understand how Antarctic krill schooling structure changes under environmental cues such as flow and light, with the hope that distribution of these important species can be predicted through knowledge of the environment in the wild. Southern Ocean ecologists, biologists, and oceanographers in general could benefit from this work. Kuvvat Garayev and David Murphy from University of South Florida were responsible for the collection and interpretation of data.

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Description

The dataset was modified for marchine readbility reasons. The original 4 datasets are added as supplemental files to the landing page.

Methods & Sampling

We deployed on the R/V Laurence M. Gould to Palmer Station, Antarctica in October - December 2022. On the way, we collected krill using an Isaac-Kidd Midwater Trawl net at the following locations: 63°06.5′ S, 61°46.6′ W (on October 5th, 2022) and 64°37.9′ S, 62°14.5′ W (on October 6th, 2022). Krill were kept in two tanks with a continuous seawater supply on the boat until being transferred to holding tanks at the Station. Additional krill were collected from Wilhelmina Bay (64°42.0′ S, 62°16.6′ W) on November 12th by the R/V Nathaniel B. Palmer, transported to Palmer Station, and added to the same holding tanks filled with filtered seawater (100 µm).

Data Processing Description

These files are to calculate speed and nearest neighbor distances of krill in the field of view of 3 high-magnification cameras (i.e., cam2, cam5, and cam4). “speed and nnd” contains 4 folders: “trial 4”, “trial 31”, “trial 43”, and “trial 46”. For speed and nearest neighbor distance (NND) calculations, DLTdv8 app in MATLAB was used (Hedrick, T. L. (2008))

These raw 3D coordinates are organized in bursts consisting of 3 consecutive frames (time points). The idea is to get one speed in each burst by using the difference between third frame and first frame positions divided by 2*1/20 sec. NND is also each krill’s nearest neighbor.

The original .csv file called *_data.csv (see supplemental files) has several bursts consisting of 3 consecutive frames (rows) separated by NaN rows. Columns, except Column 1 which is NaN, sequentially correspond to X, Y, and Z coordinates of krill in meters. For example, rows 2, 3, and 4 correspond to 3 consecutive time points that make up one burst. Columns 2 to 4 correspond to X, Y, and Z coordinates of one krill, and 5 to 7 correspond to X, Y, and Z coordinates of another krill, etc.

BCO-DMO Processing

* merged files
* converted merged files to long format

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Office of Polar Programs (formerly NSF PLR)	OPP-1840941

Deployments

None available yet

Instruments

Machine Vision Camera System

Supplied Name:

Supplied Description:

Four 4 cameras (5 MP AVT Mako) were time synchronized using StreamPix software and recorded to a system at 20 Hz frame rate (Norpix, Canada). Overhead camera (Camera 1) is equipped with a 8 mm focal length lens (M0824-MPW2, Computar) whereas stereo cameras (Cameras 2-4) are equipped with 25 mm focal length lenses (M3520-MPW2, Computar).

Instrument Type

Generic Name: Machine Vision Camera System

Generic Description:

A machine vision camera captures images or videos of a scene, which are then processed and analyzed using machine vision algorithms.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
trial	Trial number (4, 31, 43 or 46)	exp_id	sample_descrip
burst	Burst identification, each burts sonsists of 3 consecutive frames (see next column).	unitless	sample_descrip
consecutive_time_point	Consecutive frame	unitless	sample_descrip
krill_count	krill number	unitless	sample_descrip
x	x coordinate of krill	pixel units	pixel_coordinate
y	y coordinate of krill	pixel units	pixel_coordinate
z	z coordinate of kirll	pixel units	pixel_coordinate

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Dataset: Antarctic krill schooling: Coordinates for speed and nearest neighbor distances