Dataset: Images of sinking particles in BATS microbial communities
Deployment: AE1809

View Data: For data, See Dataset Metadata Page: https://www.bco-dmo.org/dataset/855320

Principal Investigator:

Susanne Neuer (Arizona State University, ASU)

Contact:

Bianca N. Cruz (Arizona State University, ASU)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Aggregation of Marine Picoplankton (Marine Plankton Aggregation)

Version:

Deployment Synonyms:

BATS20345

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Description

Methods & Sampling

Dataset acquisition description

Methodology:
Particles to be subjected to prokaryotic and eukaryotic microbial community analyses were imaged whilst embedded within polyacrylamide gels. Images were taken at various magnifications and calibrated using a 1.0 mm object micrometer slide. Particles were subsequently picked, pooled, and subjected to DNA extraction and microbial community analyses as outlined in the Methods text in Neuer et al. (2021).

Although 8 particles were pooled per sample, a limited number of particles were imaged. Magnification metadata is not available for sample PA_150m_Fall.

Data Processing Description

Dataset Processing Description

Images were taken using ToupView (version released 2020-12-21), as well as cropped and calibrated with the addition of a scale bar using ImageJ (version 153).

BCO-DMO data manager processing notes:
* converted lat and lon from degrees north and east to decimal degrees.
* replaced line returns separating image names within values for "media" column to semicolons. Replacement made to support interoperable file formats.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1658527	NSF Division of Ocean Sciences

Instruments

Camera

Supplied Name: Microscope color camera: OMAX Microscopy 3.2MP

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.

Microscope - Optical

Supplied Name: Stereomicroscope: Zeiss Stemi 2000-C (Carl Zeiss Microscopy, LLC)

Supplied Description:

Instrument Type

Generic Name: Microscope - Optical

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/

Generic Description:

Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope".

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
media	Media. List of imagenames for the sample. List delimiter is a semicolon.	unitless	file_name
sample_name	Sample name	unitless	sample
depth	Sample depth	meters (m)	depth
latitude	latitude	decimal degrees	lat
longitude	longitude	decimal degrees	lon
particle_trap_deployment_date	Particle trap deployment date (ISO 8601 format YYYY-MM-DD)	unitless	date
particle_trap_recovery_date	Particle trap recovery date (ISO 8601 format YYYY-MM-DD)	unitless	date

Database

Contribute Data

Dataset: Images of sinking particles in BATS microbial communities
Deployment: AE1809

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Images of sinking particles in BATS microbial communitiesDeployment: AE1809

Dataset acquisition description

Dataset Processing Description

Dataset: Images of sinking particles in BATS microbial communities
Deployment: AE1809