Dataset: Carbon Flux Explorer CCE_LTER P1706 - Imagery

Name: Original transmitted-light imagery and processed attenuance images of sinking particles observed by autonomous Carbon Flux Explorers deployed 100-500m in the California Current Regime, during the CCE-LTER process study (P1706) between June 2 and July 1, 2
Published: 2020-09-17
Keywords: marine snow, Aggregates, Twilight Zone, California Current Ecosystem, Autonomous Carbon Flux Explorer, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.825076.1

Spatial Extent: N:35.2 E:-120.8 S:33.5 W:-123.5

Temporal Extent: 2017-06-10 - 2017-06-26

Project:

California Current Ecosystem Long Term Ecological Research site (CCE LTER)

Carbon Flux Explorer Development (C-SNOW Development)

Carbon Sedimentation In the Ocean Watercolumn (C-SNOW): Calibration (C-SNOW)

Program:

Ocean Carbon and Biogeochemistry (OCB)

Long Term Ecological Research network (LTER)

Principal Investigator:

James K.B. Bishop (University of California-Berkeley, UC Berkeley)

Contact:

James K.B. Bishop (University of California-Berkeley, UC Berkeley)

BCO-DMO Data Manager:

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

Version:

Version Date:

2020-09-17

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Original transmitted-light imagery and processed attenuance images of sinking particles observed by autonomous Carbon Flux Explorers deployed 100-500m in the California Current Regime, during the CCE-LTER process study (P1706) between June 2 and July 1, 2

Abstract:

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2020-09-17	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.825076.1	2020-09-30

Description

These data are submitted with this manuscript: Bourne et al., 2020

Methods & Sampling

The expedition followed a newly formed filament of upwelled water in a region bounded by 33.5N, 123.5W and 35.2N, 120.8W.

Sample attenuance calculation. Transmitted light color images were normalized by an in-situ composite image of the clean sample stage following Bishop et al., 2016 yielding a map of fractional transmission corrected for inhomogeneities of the light source. Attenuance (ATN) values were then calculated by taking the -log10 of the normalized image. Results were saved as bmp formatted images in attenuance units where counts in each 8- bit (red, green, blue) color plane are scaled so that 100 counts = 1 attenuance unit.

The Carbon Flux Explorer is built on a standard ARGO style float, called the Sounding Oceanographic Lagrangian Explorer (SOLO and SOLO-II). The float is the buoyancy engine for the CFE and also manages all satellite communication of data from the CFE. The top of the float has an integrated Seabird CTD system. Temperature, pressure, and salinity data are read in bursts at 10 minute intervals as the CFE is monitoring flux at depth. These data are merged with the imagery meta data.

Data Processing Description

The software package ImageJ 1.52 (IJ, National Institutes of Health) was used for particle size analysis. Fortran codes were written for secondary data processing.

Data Files

File
csnow_imagery.csv (Comma Separated Values (.csv), 432.00 KB) MD5:ff387f2896a41fbf8883ad0c6e2ce114 Primary data file for dataset ID 825076
Jim_Bishop_CFE001_20170610_ATN.tgz (Octet Stream, 353.53 MB) MD5:039da382a5a6ae3bc79f605d24f180d2 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 001 during the CCE-LTER process study (P1706) on 2017-06-10
Jim_Bishop_CFE001_20170610_BCK.tgz (Octet Stream, 615.28 MB) MD5:e7354e57678a20e2662172c9b1062ce3 Transmitted light color images acquired by carbon flux explorer 001 during the CCE-LTER study P1706 on 2017-06-10.
Jim_Bishop_CFE001_20170613_ATN.tgz (Octet Stream, 381.69 MB) MD5:7ae4a2268f3f5bed2e275bbbe43fe304 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 001 during the CCE-LTER process study (P1706) on 2017-06-13.
Jim_Bishop_CFE001_20170613_BCK.tgz (Octet Stream, 1.27 GB) MD5:51edd59887e383cf6e134ab4fac53a2e Transmitted light color images acquired by autonomous Carbon Flux Explorer 001 during the CCE-LTER study P1706 on 2017-06-13.
Jim_Bishop_CFE001_20170619_ATN.tgz (Octet Stream, 77.61 MB) MD5:7094d1f4ec81061a1914cc0ffc29c309 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 001 during the CCE-LTER process study (P1706) on 2017-06-19
Jim_Bishop_CFE001_20170619_BCK.tgz (Octet Stream, 306.18 MB) MD5:e1241bff09335ad4f2388d199597c16c Transmitted light color images acquired by autonomous Carbon Flux Explorer 001 during the CCE-LTER study P1706 on 2017-06-19
Jim_Bishop_CFE001_20170621_ATN.tgz (Octet Stream, 131.30 MB) MD5:910e1b774f95467bf996fdaded1ab8ba Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 001 during the CCE-LTER process study (P1706) on 2017-06-21.
Jim_Bishop_CFE001_20170621_BCK.tgz (Octet Stream, 531.97 MB) MD5:5d7093e7364b263f3a250dc985fbc48a Transmitted light color images acquired by autonomous Carbon Flux Explorer 001 during the CCE-LTER study P1706 on 2017-06-21.
Jim_Bishop_CFE001_20170623_ATN.tgz (Octet Stream, 317.29 MB) MD5:7ba713619ce3b66385f113620ccdf56c Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 001 during the CCE-LTER process study (P1706) on 2017-06-23
Jim_Bishop_CFE002_20170609_ATN.tgz (Octet Stream, 116.53 MB) MD5:c0371d0a1c07f01ac076f290eab4bf08 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER process study (P1706) on 2017-06-09.
Jim_Bishop_CFE002_20170611_ATN.tgz (Octet Stream, 76.92 MB) MD5:2cc5b8d095830123ab82caa4c07dec37 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER process study (P1706) on 2017-06-11
Jim_Bishop_CFE002_20170611_BCK.tgz (Octet Stream, 266.29 MB) MD5:bee7d2cddc5d0cf68001dad558dcb478 Transmitted light color images acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER study P1706 on 2017-06-11.
Jim_Bishop_CFE002_20170614_ATN.tgz (Octet Stream, 117.29 MB) MD5:6d4a8389afb5d599a10c8a90e80035d3 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER process study (P1706) on 2017-06-14
Jim_Bishop_CFE002_20170614_BCK.tgz (Octet Stream, 429.71 MB) MD5:81c367a44256c53dbf33842f4553144d Transmitted light color images acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER study P1706 on 2017-06-14
Jim_Bishop_CFE002_20170616_ATN.tgz (Octet Stream, 124.91 MB) MD5:3715becca65f62a702202815b474f1e5 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER process study (P1706) on 2017-06-16
Jim_Bishop_CFE002_20170616_BCK.tgz (Octet Stream, 517.81 MB) MD5:c2bb12a76eece2d779af39be9c00b7dd Transmitted light color images acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER study P1706 on 2017-06-16
Jim_Bishop_CFE002_20170619_ATN.tgz (Octet Stream, 93.30 MB) MD5:33db8994658e8afb556858ec12a4309e Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER process study (P1706) on 2017-06-19
Jim_Bishop_CFE002_20170619_BCK.tgz (Octet Stream, 383.89 MB) MD5:c61eeea75debb3dc5beaf2e9841faad6 Transmitted light color images acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER study P1706 on 2017-06-19
Jim_Bishop_CFE002_20170621_ATN.tgz (Octet Stream, 89.61 MB) MD5:4110262d7df1cc4f96233093971b893c Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER process study (P1706) on 2017-06-21.
Jim_Bishop_CFE002_20170621_BCK.tgz (Octet Stream, 394.05 MB) MD5:9360a2c574cc8aa750a3f39188531e2f Transmitted light color images acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER study P1706 on 2017-06-21.
Jim_Bishop_CFE002_20170623_BCK.tgz (Octet Stream, 318.03 MB) MD5:d873e407b4e35a97fbe72b4de189a62b Transmitted light color images acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER study P1706 on 2017-06-23
Jim_Bishop_CFE002_20170625_BCK.tgz (Octet Stream, 802.94 MB) MD5:319cd0a57590dd7174f51862a29034b4 Transmitted light color images acquired by autonomous Carbon Flux Explorer 002 during the CCE-LTER study P1706 on 2017-06-25
Jim_Bishop_CFE003_20170610_ATN.tgz (Octet Stream, 185.51 MB) MD5:381c7ecca3c9a60a1cac6252a55e5322 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 003 during the CCE-LTER process study (P1706) on 2017-06-10
Jim_Bishop_CFE003_20170610_BCK.tgz (Octet Stream, 401.31 MB) MD5:848d80052b50f102bf11574c570933bb Transmitted light color images acquired by autonomous Carbon Flux Explorer 003 during the CCE-LTER study P1706 on 2017-06-10
Jim_Bishop_CFE003_20170613_ATN.tgz (Octet Stream, 424.76 MB) MD5:b0f64a6ebbb9f039fce2280ebaf49726 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 003 during the CCE-LTER process study (P1706) on 2017-06-13
Jim_Bishop_CFE003_20170613_BCK.tgz (Octet Stream, 1.15 GB) MD5:62627140e693a82285d2361d4a3428d3 Transmitted light color images acquired by autonomous Carbon Flux Explorer 003 during the CCE-LTER study P1706 on 2017-06-13
Jim_Bishop_CFE004_20170613_ATN.tgz (Octet Stream, 45 bytes) MD5:cf597f32713e23b8cb165e4d2d6c2a30 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER process study (P1706) on 2017-06-13
Jim_Bishop_CFE004_20170614_ATN.tgz (Octet Stream, 110.99 MB) MD5:a2b684e282b5aa77060f72d2d3e59a2e Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER process study (P1706) on 2017-06-14.
Jim_Bishop_CFE004_20170614_BCK.tgz (Octet Stream, 380.83 MB) MD5:a0ba323a38768cdf109bf6eaaee7dd81 Transmitted light color images acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER study P1706 on 2017-06-14
Jim_Bishop_CFE004_20170616_ATN.tgz (Octet Stream, 114.04 MB) MD5:4973be85f6cd992be9e6d1cf8a7d83fe Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER process study (P1706) on 2017-06-16
Jim_Bishop_CFE004_20170616_BCK.tgz (Octet Stream, 389.28 MB) MD5:965bc96c39204c40c69605e47db11108 Transmitted light color images acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER study P1706 on 2017-06-16
Jim_Bishop_CFE004_20170621_ATN.tgz (Octet Stream, 74.59 MB) MD5:1398923666c920ef7a0fea70191e6c7e Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER process study (P1706) on 2017-06-21
Jim_Bishop_CFE004_20170621_BCK.tgz (Octet Stream, 298.75 MB) MD5:46fe6612528f8a4213c1cf8a0bfac090 Transmitted light color images acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER study P1706 on 2017-06-21
Jim_Bishop_CFE004_20170623_ATN.tgz (Octet Stream, 122.83 MB) MD5:080c5cfb43b04c888b47fb7b6efadd05 Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER process study (P1706) on 2017-06-23
Jim_Bishop_CFE004_20170623_BCK.tgz (Octet Stream, 362.68 MB) MD5:b4d33de9b6356a71264acd7afeb0d572 Transmitted light color images acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER study P1706 on 2017-06-23
Jim_Bishop_CFE004_20170625_ATN.tgz (Octet Stream, 208.81 MB) MD5:11380ad4bc6cc5d31e85175955e1b0db Imagery in attenuance units acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER process study (P1706) on 2017-06-25.
Jim_Bishop_CFE004_20170625_BCK.tgz (Octet Stream, 671.18 MB) MD5:5aa443249020e7c27bcba2b4f27f76da Transmitted light color images acquired by autonomous Carbon Flux Explorer 004 during the CCE-LTER study P1706 on 2017-06-25

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1538686

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
RR1710	LTER CCE-P1706 CCE-P1706 CCE LTER P1706 P1706	2017-06-01	R/V Roger Revelle	Mark D. Ohman (Chief Scientist)	data info

Instruments

Carbon Flux Explorer

Supplied Description:

The CFE and the operation of its particle flux sensing Optical Sedimentation Recorder (OSR) have been discussed in detail in Bishop et al. (2016). CFE has a design mission capability of 8 months of hourly operations (16 months @ 2 hours …) and has been demonstrated by deployments of 40 days; CFE design depth is 1500m and it has been proven to 1000 m. The system has demonstrated operations in high sea states.

Briefly, once deployed, the CFE dives below the surface make particle flux observations at target depths as it drifts with currents. The OSR wakes once the CFE has reached the target depth. On first wake-up of a given CFE dive, the sample stage is flushed with water and images of the particle-free stage are obtained. Particles settle through a 1-cm opening hexagonal celled light baffle into a high-aspect ratio funnel assembly before landing on a 2.54 cm diameter glass sample stage. At 25-minute intervals, particles are imaged at 13 µm pixel resolution in three lighting modes: dark field, transmitted and transmitted-cross polarized.

Instrument Type

Generic Name: Carbon Flux Explorer

Acronym: CFE

Generic Description:

The Carbon Flux Explorer (CFE) is designed to perform sustained high-frequency observations of POC and PIC sedimentation within the upper kilometer (or twilight zone) of the ocean for seasons to years and to operate in an observational context not dependent on ships. The CFE melds the concept of current-following, sample-collecting neutrally buoyant sediment traps with photographic imaging of the particles as they are deposited in a sediment trap.

The CFE and the operation of its particle flux sensing Optical Sedimentation Recorder (OSR) have been discussed in detail in Bishop et al. (2016). CFE has a design mission capability of 8 months of hourly operations (16 months @ 2 hours) and has been demonstrated by deployments of 40 days; CFE design depth is 1500m and it has been proven to 1000 m. The system has demonstrated operations in high sea states.

Diagram: https://datadocs.bco-dmo.org/docs/302/C-SNOW/data_docs/CFE_CFE-Cal.png

Bishop, J. K. B., Fong, M. B., and Wood, T. J.: Robotic observations of high wintertime carbon export in California coastal waters, Biogeosciences, 13, 3109–3129, https://doi.org/10.5194/bg-13-3109-2016, 2016.

Bourne, H. L., Bishop, J. K. B., Wood, T. J., Loew, T. J., and Liu, Y.: Carbon Flux Explorer optical assessment of C, N and P fluxes, Biogeosciences, 16, 1249–1264, https://doi.org/10.5194/bg-16-1249-2019, 2019

CTD Sea-Bird 41

Supplied Name: SBE 41 CTD

Supplied Description:

The CTD used with the SOLO floats is the Seabird SBE 41 CTD.

Salinity ± 0.0035 psu
Pressure Initial Accuracy: ± 2 dbar
Temperature Accuracy: ± 0.002 °C

Instrument Type

Generic Name: CTD Sea-Bird 41

Acronym: CTD SBE 41

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Sea-Bird SBE 41 CTD module was originally developed in 1997 for integration with sub-surface oceanographic floats. It uses MicroCAT Temperature, Conductivity, and Pressure sensors.

Sounding Oceanographic Lagrangian Observer

Supplied Name: SOLO

Supplied Description:

Instrument Type

Generic Name: Sounding Oceanographic Lagrangian Observer

Acronym: SOLO

Generic Description:

A standard ARGO style float, called the Sounding Oceanographic Lagrangian Explorer (SOLO and SOLO-II).

SOLO floats are drifting instruments and have the ability to change their own buoyancy. After deployment it moves with the ocean currents and can, therefore, travel long distances on their own without the need of a ship or a person to handle them. They are programmed to come to the ocean surface at regular intervals to transmit their data and position to orbiting satellites. The float then sinks again, continuing the process.

To control the buoyancy of the float, a small amount of oil is contained within the float. When the float is submerged, all of the oil is kept entirely within the hull. When it is time to rise to the surface, the oil is pumped into an external rubber bladder that expands. Since the weight of the float does not change but its volume increases when the bladder expands, the float becomes more buoyant and floats to the surface. Similarly, when the float is on the surface and it is time to submerge, the oil is withdrawn from the bladder into the hull of the float and the buoyancy decreases.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cycle	CCE cycle number = our location number (range 1 to 4)	unitless	sample_descrip
cfeid	Carbon Flux Explorer Identity (CFE00X) where X is serial number (1 through 4)	unitless	inst_model
cfeno	Carbon Flux Explorer (CFE) serial number (1 through 4)	unitless	inst_model
dive	CFE dive number	unitless	sample_descrip
ISO_DateTime_UTC	Datetime of image acquisition in ISO format (yyyy-mm-ddThh:mm:ssZ) in UTC zone	yyyy-MM-dd'T'HH:mm:ss	date_utc
jday	Day: Jan 1 = 1, use to correlate with satellite imagery	unitless	days
ddays	decimal days since Jan 1 2017 at 0000 UTC, ddays = 0.5 on Jan 1 2017 at 1200UTC, ADCP data use same time	unitless	days
driftdays	CTD obs decimal days since Jan 1 2017 at 0000 UTC, ddays = 0.5 on Jan 1 2017 at 1200UTC, ADCP data use same time	unitless	days
lon	Decimal Longitude (negative for west)	decimal degrees	lon
lat	Decimal Latitude (negative for south)	decimal degrees	lat
press	SOLO CTD pressure	dbar	press
pressflag	SOLO Data (0 - profiling or unstable; 1 during flux measurement; 4 single value for dive; 5 SOLO at surface)	unitless	sample_descrip
temp	SOLO CTD insitu temperature	degrees Celcius	temperature
sal	SOLO CTD salinity	PSU	sal
cm_sec	SOLO Rate of depth change over 10 minute intervals	cm s-1	sample_descrip
diveimage_seq	dive image number	unitless	sample_descrip
cleanflag	1 = means taken seconds after a cleaning cycle; 0 = images after cleaning; -1 means failed clean; -2 image taken at start of dive before first stage cleaning	unitless	sample_descrip
class_ATN	UPPER CASE 'ATN' if useful OR lowercase 'bck' if non useful.	unitless	sample_descrip
class_BCK	UPPER CASE 'BCK' if useful OR lowercase 'bck' if non useful.	unitless	sample_descrip
illum	illumination mode (bck=transmitted light, led=darkfield illumnation, pol crosspolarized transmission, pl2=pol at longer exposure time)	unitless	sample_descrip
sensor	CFE enginnering information: SUMIX imager serial number	unitless	inst_model
exp_msec	Imager exposure time in milli seconds	s*10^-3	sample_descrip
b_gain	Imager gain settinng blue channnel	unitless	sample_descrip
g_gain	imager gain settinng green channnel	unitless	sample_descrip
r_gain	imager gain setting red channel	unitless	sample_descrip
therm	instrument temperature (C) NOT CALIBRATED	unitless	sample_descrip
iqual	flag (1 = image is useful for flux information ; 4 = image is not useful since the CFE was profiling or was stuck at the surface)	unitless	sample_descrip
flatflag_bck_images	flag (1 = image has been corrected for non uniformity of illumimation; 0 = no corection)	unitless	sample_descrip
flatflag_atn_images	flag (1 = image has been corrected for non uniformity of illumimation; 0 = no corection)	unitless	sample_descrip
filename_bck	Filename of BCK images	unitless	file_name
filename_atn_images	Filename of ATN image	unitless	file_name

Database

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Dataset: Carbon Flux Explorer CCE_LTER P1706 - Imagery