Dataset: Tail beat frequency in Oikopleura dioica at 3 temperature treatments

Name: Tail beat frequency in the appendicularian Oikopleura dioica during particle tracking experiments comprised of three temperature treatments conducted in December 2015
Published: 2023-06-15
Keywords: Oikopleura dioica, temperature, filter feeding, plankton, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.897617.1

Temporal Extent: 2015-12-05 - 2015-12-10

Project:

Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey (Gelatinous Grazer Feeding)

Principal Investigator:

Brad J. Gemmell (University of South Florida, USF)

Kelly Rakow Sutherland (University of Oregon)

Scientist:

Keats R. Conley (University of Oregon)

Terra C. Hiebert (University of Oregon)

George von Dassow (University of Oregon)

Contact:

Kelly Rakow Sutherland (University of Oregon)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-06-15

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Tail beat frequency in the appendicularian Oikopleura dioica during particle tracking experiments comprised of three temperature treatments conducted in December 2015

Abstract:

These data include tail beat kinematics measurements and particle tracking from the appendicularian Oikopleura dioica during experiments conducted in December 2015 at the Sars Centre for Marine Molecular Biology in Bergen, Norway. The experiments comprised three temperature treatments. The data were collected from high-speed video frames. This dataset includes measurements of tail beat frequency. Tail beat kinematic measurements were used to describe how O. dioica drives flow across food concentrating filters and how it is affected by temperature.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2023-06-15	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.897617.1	2023-06-30

Description

The primary data file for this dataset, "897617_tailbeat_counts.csv", contains data on all replicates for each video. The supplemental file, "897617_tailbeat_averages_and_frequency.csv", contains the averages for each video including the average tail beat frequency for each video. The videos are attached as Supplemental Files (there is one .zip folder for each temperature treatment).

Methods & Sampling

All experimental animals were obtained from the appendicularian culture facility at the Sars Centre for Marine Molecular Biology in Bergen, Norway in December 2015. Oikopleura dioica were filmed individually following Gemmell et al. (2014). Images were recorded using an Edgertronic high-speed camera (1280 × 1024-pixel resolution, 500 frames per second) with brightfield illumination from a fiber optic light source, or a Photron FastCam Mini Ux100 (1280x1024, 125-1000 frames per second) with darkfield illumination from a tilting mirror base. The filming vessel was positioned on a manually adjustable stage between the light source and the camera. A long working-distance microscope objective (4x or 40x) was mounted to an adjustable-height optics clamp positioned between the filming vessel and the camera. Videos were converted to image stacks in QuickTime Pro. Day 1 animals were filmed in a 50-milliliter glass cuvette in treatments comprising 3 temperatures: 5° Celsius, 15° Celsius, and 25° Celsius.

Data Processing Description

Data Processing:
Tail beat kinematics were measured in ImageJ. Five tail beats were recorded per individual, with a single tail beat measured as one complete wave cycle.

BCO-DMO Processing:
- removed "-" as a missing data value (missing/null values are blank/empty in the final .csv files);
- rounded the Frames, Time, and Frequency columns to 3 decimal places;
- separated the original data file into two resources: one with the averages and frequencies and one with the counts;
- renamed fields for both resources to comply with BCO-DMO naming conventions;
- bundled the videos into 3 .zip files (see Supplemental Files).

Data Files

File
897617_tailbeat_counts.csv (Comma Separated Values (.csv), 5.24 KB) MD5:68dc5af742bdaaacdd51034ecb6f9120 Primary data file for dataset ID 897617.

Supplemental Files

File
15C.zip (ZIP Archive (ZIP), 1.94 GB) MD5:5ee628c77dd3b5079923bb2d4004a5dc This .zip contains 17 .mov video files from the 15 degrees Celsius treatments. See the file inventory (Appendicularian_Video_Inventory.csv) for a description of each file.
25C.zip (ZIP Archive (ZIP), 2.01 GB) MD5:02928e5f9fd97b1f5f73cd4dc8f5e6c4 This .zip contains 16 .mov video files from the 25 degrees Celsius treatments. See the file inventory (Appendicularian_Video_Inventory.csv) for a description of each file.
5C.zip (ZIP Archive (ZIP), 2.49 GB) MD5:6888cc317e68626484f97c5fd5a53df6 This .zip contains 20 .mov video files from the 5 degrees Celsius treatments. See the file inventory (Appendicularian_Video_Inventory.csv) for a description of each file.
897617_tailbeat_averages_and_frequency.csv (Comma Separated Values (.csv), 1.40 KB) MD5:c628f83fc1c752a5f14a1c44cc196070 Supplemental file for dataset ID 897617. This file contains the average frame number and time for each video, as well as tail beat frequency. Column descriptions: (column_name,definition,units,type) Temperature,"Temperature treatment (5°C, 15°C, or 25°C)",degrees Celsius,Float Video,Video identifier,unitless,String Frames_Avg,Average frame number of all replicates for the video,unitless,Float Time_Avg,Average time of all replicates for the video,seconds per beat,Float Frequency,Tail beat frequency calculated as 500/(Frames_Avg),beats per second,Float
Appendicularian_Video_Inventory.csv (Comma Separated Values (.csv), 2.77 KB) MD5:3984ad11c2e6a3e4373883742f6988ad Inventory/description of video files contained in the three .zip files - one for each temperature treatment. This inventory was originally provided as an Excel file and was converted to .csv by BCO-DMO.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851537

Deployments

None available yet

Instruments

Camera

Supplied Name: Edgertronic high-speed camera

Supplied Description:

Instrument Type

Generic Name: Camera

Acronym: camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/311/

Generic Description:

All types of photographic equipment including stills, video, film and digital systems.

Camera

Supplied Name: Photron FastCam Mini Ux100

Supplied Description:

Instrument Type

Generic Name: Camera

Acronym: camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/311/

Generic Description:

All types of photographic equipment including stills, video, film and digital systems.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Temperature	Temperature treatment (5°C, 15°C, or 25°C)	degrees Celsius	treatment
Video	Video identifier. This number is the last 5 digits of the .mov file names. The .mov files are provided in the attached .zip folders as Supplemental Files. The number following the dash represents the animal number. For example, "75974-1" is the identifier for animal 1 in the .mov file ending in 75974, which is in the 5C.zip folder (5C contains movies from the 5 degrees C temperature treatment.)	unitless	file_name
Tailbeat	Tailbeat replicate number	unitless	replicate
Frames	Video frame number for replicate tail beat	unitless	number
Time	Time for replicate tail beat	seconds per beat	duration

Database

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Dataset: Tail beat frequency in Oikopleura dioica at 3 temperature treatments