Dataset: Inlet particle speeds in Oikopleura dioica at 3 temperature treatments

Name: Inlet particle speeds from 5 high-speed video frames at 3 temperature treatments from Oikopleura dioica particle tracking experiments 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.897682.1

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

Inlet particle speeds from 5 high-speed video frames at 3 temperature treatments from Oikopleura dioica particle tracking experiments 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 data were collected from high-speed video frames. The experiments comprised 3 temperature treatments. This dataset includes measurements of particle movement. Manual particle tracking was used to estimate flow speeds across the inlet filter as driven by tail beating in O. dioica. Data were used to describe how flow and particle movement across food concentrating filters 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.897682.1	2023-06-30

Description

The primary data file for this dataset, "897682_particle_speed.csv", contains the raw data. The supplemental file, "897682_particle_speed_averages_and_maximums.csv", contains the maximum speed and average speed for each video, as well as the population mean maximum speeds. 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:
Particle tracking to estimate inlet flow speeds were measured in ImageJ. Flow speeds were determined by manual particle tracking, with distance over time obtained from the first and last of 10 frames. An average and maximum of 5 particle speeds were recorded for all individuals.

BCO-DMO Processing:
- separated the original data file into two resources: one with the averages and maximums (summary statistics) and one with the raw data;
- 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
897682_particle_speed.csv (Comma Separated Values (.csv), 126.79 KB) MD5:e73cac013d6431814f61e9404ca72f05 Primary data file for dataset ID 897682.

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.
897682_particle_speed_averages_and_maximums.csv (Comma Separated Values (.csv), 9.15 KB) MD5:8a723728bac0b144bf8a14c9a699c0ce Supplemental file for dataset ID 897682. This file contains the maximum speed and average speed for each video, as well as the population mean maximum speeds. Column descriptions: (column_name, definition, units, type) Temperature,Temperature treatment,degrees Celsius,Float Video,Video identifier,unitless,String Max_Speed,Maximum particle speed of the video,millimeters per second (mm/s),Float Avg_Speed,Average particle speed of the video,millimeters per second (mm/s),Float Pop_Mean_Max_Speed,Maximum particle speed for all particles in one video,millimeters per second (mm/s),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	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 population of particles and the letter denotes each of 5 particles measured in that population. For example, "75974-1A" is the identifier for population 1, particle A 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
Frame	Video frame number	unitless	file_name
Time	Time between frames	seconds	time_elapsed
X	Particle x position	millimeters (mm)	xpos
Y	Particle y position	millimeters (mm)	ypos
Distance	Particle distance traveled (calculated)	millimeters (mm)	length
Speed	Particle speed (calculated)	millimeters per second (mm/s)	speed

Database

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Dataset: Inlet particle speeds in Oikopleura dioica at 3 temperature treatments