Dataset: FlowCAM imaging cytometer data from EN616 cruise

Name: FlowCAM enumeration of phytoplankton classes from samples taken during R/V Endeavor cruise EN616 in July 2018
Published: 2023-01-27
Keywords: phytoplankton enumeration, FlowCAM, phytoplankton biomass, particle size distribution function, biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.887787.1

Spatial Extent: N:43.71835 E:-66.51748 S:36.98572 W:-72.92708

Temporal Extent: 2018-07-05 - 2018-07-13

Project:

Coccolithophore Mixotrophy (Cocco-Mix)

Principal Investigator:

William M. Balch (Bigelow Laboratory for Ocean Sciences)

Co-Principal Investigator:

Stephen D. Archer (Bigelow Laboratory for Ocean Sciences)

David T. Drapeau (Bigelow Laboratory for Ocean Sciences)

Jelena Godrijan (Bigelow Laboratory for Ocean Sciences)

BCO-DMO Data Manager:

Dana Stuart Gerlach (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-01-27

Restricted:

Validated:

Yes

Current State:

Final no updates expected

FlowCAM enumeration of phytoplankton classes from samples taken during R/V Endeavor cruise EN616 in July 2018

Abstract:

This dataset presents imaging cytometer data from water samples collected during R/V Endeavor cruise EN616. Niskin bottle samples were taken at nine stations and eight depths in the northwest Atlantic in July 2018. A Yokogawa FlowCAM imaging cytometer was used to enumerate the major microalgal classes, and the particle size distribution function was estimated.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2023-01-27	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.887787.1	2023-03-09

Description

This dataset is part of a larger study with the following goals:

Goal #1: measure the mixotrophic uptake and assimilation of 14C-acetate, 14C-mannitol and 14C-glycerol as a carbon source by natural assemblages of coccolithophores and compare it to their autotrophic uptake and assimilation of DIC. These three organics were chosen due to their high potential for significant osmotrophy by coccolithophores as seen in previous culture studies (Godrijan et al. (2020) and BCO-DMO dataset: https://www.bco-dmo.org/dataset/858771). The design of these experiments used radiochemical and single cell/flow cytometer methods to distinguish osmotrophy of coccolithophores from that by other naturally-occurring microalgae.
Goal #2: test for the fixation of 14C-labeled organics into both POC and PIC fractions in natural populations of coccolithophores, in order to examine the potential role of coccolithophore osmotrophy in the biological carbon pump and alkalinity carbon pump paradigms.

Methods & Sampling

At sea collections
Nine stations were visited during R/V Endeavor EN616 cruise in the northwest Atlantic.
At eight depths, three 10L Niskin samples were taken for discrete measurements of:

1. Chlorophyll, nutrients including nitrate, nitrite, ammonium, phosphate, and silicate
2. Particulate organic carbon (POC) plus particulate organic nitrogen (PON)
3. Particulate inorganic carbon (PIC)
4. Biogenic silica
5. Birefringence counts of coccolithophores (done ashore)
6. Shipboard Yokogawa Fluid Imaging Technologies FlowCam imaging cytometer, in order to enumerate the major microalgal classes and estimate the particle size distribution function

Measurements 1 to 4 are part of BCO-DMO dataset 837074 (See https://www.bco-dmo.org/dataset/837074, and the Related Datasets section below).
Measurement 5 of birefringence counts data is BCO-DMO dataset 887863 (See https://www.bco-dmo.org/dataset/887863, and the Related Datasets section below).
Measurement 6 is flow cytometer data presented in this dataset.

FlowCAM enumeration of various phytoplankton classes
A Yokogowa FlowCAM imaging cytometer was used to enumerate different classes of phytoplankton. The instrument was keyed on particle backscattering and fluorescence properties. Samples were first filtered through 100um Nitex mesh to make sure the 100um diameter flow chamber did not clog. The instrument was run with a 10X objective in order to reliably count particles bigger than 4-5um diameter. Samples were processed according to Poulton and Martin (2010).

Concentrations (per mL), percent contribution with respect to total particles, and biomass are presented. Carbon biomass was determined based on the Menden-Deuer & Lessard (2000) method.

Data Processing Description

BCO-DMO processing
- Data is from columns P through AT on the original source file titled "EN616_master_datasheet_bottle_and_discrete_organics_updated_ccc_BCODMO.csv"
- FlowCAM cytometry data extracted from combined "master datasheet" into a separate file called "Flow_cytometer_EN616.csv"
- Modified parameter (column) names to conform with BCO-DMO naming conventions.
- Converted date format to ISO Date 8601 format
- Missing data identifier of -999 was removed to keep value from being mistaken for true data

Data Files

File
flow_cytometer_en616.csv (Comma Separated Values (.csv), 23.40 KB) MD5:a5c5a16b1679ac208f39487b1cb86bfe FlowCAM imaging cytometer data enumerating phytoplankton classes from samples taken during R/V Endeavor cruise EN616 in July 2018

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1635748

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
EN616	Cocco-Mix	2018-07-03	R/V Endeavor	William M. Balch (Chief Scientist)	data info

Instruments

Yokogawa Fluid Imaging Technologies FlowCam VS particle imaging system

Supplied Name: Yokogowa FlowCAM imaging cytometer

Supplied Description:

Particles were measured by Yokogowa FlowCAM imaging cytometer. Imaging cytometers are automated instruments that quantify properties of single cells, one cell at a time. They combine some aspects of flow cytometry with particle imaging capabilities in an automated device to classify small particles, including phytoplankton and protozoa. They can measure a variety of properties: cell size, cell granularity, cell aspect ratio, equivalent spherical diameter (ESD) and area-based diameter (ABD) [to estimate bio-volume, which is used to estimate cell carbon biomass]. Particle images are digitally recorded and sorted into different classes according to training libraries using a support vector machine (supervised learning methods). The instruments particle-size is calibrated using different sizes of latex beads.

Instrument Type

Generic Name: Yokogawa Fluid Imaging Technologies FlowCam VS particle imaging system

Acronym: FlowCAM

Generic Description:

Imaging cytometers are automated instruments that quantify properties of single cells, one cell at a time. They combine some aspects of flow cytometry with particle imaging capabilities in an automated device to classify small particles, including phytoplankton and protozoa. They can measure a variety of properties: cell size, cell granularity, cell aspect ratio, equivalent spherical diameter (ESD) and area-based diameter (ABD) [to estimate bio-volume, which is used to estimate cell carbon biomass]. Particle images are digitally recorded and sorted into different classes according to training libraries using a support vector machine (supervised learning methods). The instruments particle-size is calibrated using different sizes of latex beads.

The FlowCam VS series are automated imaging-in-flow instruments that generate high-resolution digital images for measuring size and shape of microscopic particles. The sample introduced in the system is attracted by a peristaltic or a syringe pump into a flow cell (or flow chamber) with known dimensions, located in front of a microscope objective which is connected to a camera video. The benchtop model is ideally suited to a typical laboratory environment with applications in oceanographic research, municipal water, biopharmaceutical formulations, chemicals, oil and gas, biofuels, and many other markets. FlowCam VS is available in four models, from the imaging-only VS-I (i.e. without excitation wavelength or fluorescence emission wavelengths) to the top-of-the-line VS-IV with two channels of fluorescence measurement and scatter triggering capabilities. The instrument can measure particles between 2µm and 2mm; can analyse in vivo or fixed samples; has a flow rate between 0.005 ml/minute and 250 ml/minute (dependant upon magnification, flow cell depth, camera frame rate, efficiency desired, etc.). It can produce either 8-bit Grayscale (Monochrome Camera) or 24-bit Colour (Colour Camera) images, depending on the model.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Cruise identification	unitless	cruise_id
Station	Station number for EN616 cruise for water sample collection	unitless	station
Type	Type of sample. B = discrete bottle sample	unitless	sample_type
Longitude	Longitude of water sample collection	decimal degrees	lon
Latitude	Latitude of water sample collection	decimal degrees	lat
Depth	Depth of water sample	meters	depth
ISO_DateTime_UTC	Date and time of sample collection Format: %Y-%m-%dT%H:%M:%SZ	unitless	ISO_DateTime_UTC
Gear	Gear used to collect the water and coccolithophore samples	unitless	sampling_method
Balch_Sample_num	Consecutive unique numbers assigned to each water sample for all analyses done for a given station	unitless	sample
ParticleSizeDistFunc_Slope_5um	PDF Slope logABD>0.75 (only particles >5um); Particle size Distribution Function slope of the plot of log cell abundance (particles per mL) versus Area Based Diameter (micrometers) calculated for particles of >= 5 micrometers diameter using a Yokogowa FlowCAM. Area Based Diameter (ABD) is defined as the diameter measured by the number of grey scale pixels of the binary image converted to a circle with the same number of pixels.	unitless	no_bcodmo_term
StdErr_of_PDFslope	Std Err of PDF Slope logABD>0.75 (for particles >5um); Standard error of the above particle size distribution slope for only particles of 5 micrometers diameter or larger using a Yokogowa FlowCAM	unitless	std_err
Y_int_of_PDFslope	Y-int of PDF Slope logABD>0.75 (only particles >5um); the Y intercept of above PDF for only particles of 5um diameter or larger using a Yokogowa FlowCAM	unitless	no_bcodmo_term
R2_of_PDFslope	R2of PDF Slope logABD>0.75; squared correlation coefficient of above PDF for only particles of >= 5um diameter or larger using a Yokogowa FlowCAM	unitless	corr_coeff
F_statistic_of_PDFslope	F-statistic of PDF Slope logABD>0.75 (only particles >5um); the F statistic of the above PDF for only particles of >=5um diameter or larger using a Yokogowa FlowCAM	unitless	F_stat
Total	Concentration of total particles measured by Yokogowa measured by Yokogowa FlowCAM imaging cytometer	cells per milliliter (cells/mL)	cell_concentration
Small_0_to_4um	Concentration of small particles with diameters of 0 to 4 micrometers measured by Yokogowa FlowCAM imaging cytometer	cells per milliliter (cells/mL)	cell_concentration
Round_4_to_12um	Concentration of round particles with diameters of 4 to 12 micrometers measured by Yokogowa FlowCAM imaging cytometer	cells per milliliter (cells/mL)	cell_concentration
Ovoid_4_to_12um	Concentration of ovoid particles with long axis of 4 to 12 micrometers measured by Yokogowa FlowCAM imaging cytometer	cells per milliliter (cells/mL)	cell_concentration
Dinoflagellates	Concentration of dinoflagellates measured by Yokogowa FlowCAM imaging cytometer	cells per milliliter (cells/mL)	cell_concentration
Ciliates	Concentration of ciliates measured by Yokogowa FlowCAM imaging cytometer	cells per milliliter (cells/mL)	cell_concentration
Diatoms	Concentration of pennate and centric diatoms measured by Yokogowa FlowCAM imaging cytometer	cells per milliliter (cells/mL)	cell_concentration
Silicoflagellates	Concentration of silicoflagellates measured by Yokogowa FlowCAM imaging cytometer	cells per milliliter (cells/mL)	cell_concentration
Other_Cells	Concentration of unidentified other particles measured by Yokogowa FlowCAM imaging cytometer	cells per milliliter (cells/mL)	cell_concentration
Pct_Small_0_to_4um	Percent of total particles contributed by small (0-4 um) particles as measured by Yokogowa FlowCAM imaging cytometer	percent	relative_abund
Pct_Round_4_to_12um	Percent of total particles contributed by round (4-12 um diameters) particles as measured by Yokogowa FlowCAM imaging cytometer	percent	relative_abund
Pct_Ovoid_4_to_12um	Percent of total particles contributed by ovoid (long axis 4-12 um) particles as measured by Yokogowa FlowCAM imaging cytometer	percent	relative_abund
Pct_Dinoflagellates	Percent of total particles contributed by dinoflagellates as measured by Yokogowa FlowCAM imaging cytometer	percent	relative_abund
Pct_Ciliates	Percent of total particles contributed by ciliates as measured by Yokogowa FlowCAM imaging cytometer	percent	relative_abund
Pct_Diatoms	Percent of total particles contributed by diatoms as measured by Yokogowa FlowCAM imaging cytometer	percent	relative_abund
Pct_Silicoflagellates	Percent of total particles contributed by silicoflagellates as measured by Yokogowa FlowCAM imaging cytometer	percent	relative_abund
Pct_Other_Cells	Percent of total particles contributed by unidentified other particles as measured by Yokogowa FlowCAM imaging cytometer	percent	relative_abund
Total_C_biomass	Total carbon biomass (based on Menden-Deuer and Lessard, 2000) for total particles measured by Yokogowa FlowCAM imaging cytometer	micrograms per liter (ug/L)	biomass_C
Small_C_biomass	Carbon biomass (based on Menden-Deuer and Lessard, 2000) for small (0-4 um) particles measured by Yokogowa FlowCAM imaging cytometer	micrograms per liter (ug/L)	biomass_C
Round_C_biomass	Carbon biomass (based on Menden-Deuer and Lessard, 2000) for round-(4-12 um) particles measured by Yokogowa FlowCAM imaging cytometer	micrograms per liter (ug/L)	biomass_C
Ovoid_C_biomass	Carbon biomass (based on Menden-Deuer and Lessard, 2000) for ovoid (4-12 um long axis) particles measured by Yokogowa FlowCAM imaging cytometer	micrograms per liter (ug/L)	biomass_C
Dinoflagellates_C_biomass	Carbon biomass (based on Menden-Deuer and Lessard, 2000) for dinoflagellates measured by Yokogowa FlowCAM imaging cytometer	micrograms per liter (ug/L)	biomass_C
Ciliates_C_biomass	Carbon biomass (based on Menden-Deuer and Lessard, 2000) for ciliates measured by Yokogowa FlowCAM imaging cytometer	micrograms per liter (ug/L)	biomass_C
Diatoms_C_biomass	Carbon biomass (based on Menden-Deuer and Lessard, 2000) for the sum of pennate and centric diatoms measured by Yokogowa FlowCAM imaging cytometer	micrograms per liter (ug/L)	biomass_C
Silicoflagellates_C_biomass	Carbon biomass (based on Menden-Deuer and Lessard, 2000) for silicoflagellates measured by Yokogowa FlowCAM imaging cytometer	micrograms per liter (ug/L)	biomass_C
Other_Cells_C_biomass	Carbon biomass (based on Menden-Deuer and Lessard, 2000) for unidentified other particles measured by Yokogowa FlowCAM imaging cytometer	micrograms per liter (ug/L)	biomass_C

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Dataset: FlowCAM imaging cytometer data from EN616 cruise