When preparing a submission, check to see if the data type is in the list below. Certain types of SeaBASS data submissions have special requirements. For example, some data files need conditionally required metadata headers, and some submissions require extra "checklist" documents. These requirements and several examples are listed below, sorted by data types. This list is growing and evolving and more data types will be added in the future.
Check if your submission type lists any required extra documents. These checklists are designed to standardize and preserve critical methods and analysis details that are needed for intercomparison, reprocessing, to make it easier for data users to assess the data quality and to consider them for satellite validation or inclusion in algorithm development datasets. We prefer you submit a plain text (.txt) document, but if multiple format versions are offered (e.g., rich text and plain text), pick your preference and fill out the necessary sections. Rename the file in a relevant way to make it unique (e.g., add the cruise name to the end of the file name), and add it to the other documents and calibration files that are part of your submission.
The special notes section for each data type highlights any necessary measurement-specific metadata (e.g., conditionally required headers), fields, or formatting.
This page also provides example submission sections containing model data files and documentation bundles to help you format different types of submissions. These files were picked from the archive or created to serve as references. Your files might look a bit different, but hopefully the examples are helpful as a starting place from which to further adapt or improve as needed.
Table of Contents
Absorbance values (abs_ag) must be submitted without any null correction applied. Null correction may be applied to the absorbance values when calculating absorption coefficients (e.g., ag). However, besides preserving the null_correction value as a metadata header, do not include the intermediate absorbance values in the SeaBASS files.
Please do NOT apply smoothing algorithms. Smoothing must not be applied to absorbance / optical density (e.g., abs_ag), and should not be applied to absorption coefficients (e.g., ag).
If your instrument collects data below 400nm, we required optical densities (abs_ag) to be submitted. However, calculated absorption coefficients below 400nm are optional and missing values (e.g., –9999) can be used to mask ag if the PI desires not to include them.
Data replicates are submitted separately (one per file). Multiple scans must be averaged; and if so, standard deviation or standard error should be reported (e.g., abs_ag_sd, abs_ag_se). The number of measurements (n) averaged into the reported value should be included in the header “/bincount”. See examples below.
Data must be submitted at native wavelength resolution (do not bin data together over intervals of wavelegths).
"Conditionally Required" metadata headers:
/s_ag may be used to report calculated spectral slope (e.g., /s_ag=s_ag_300nmmin_600nmmax:0.023197)
/null_correction If applicable, report the null correction (normally via values in units of absorbance) used while calculating the ag absorption coefficient. Example:
/null_correction=abs_ag:0.005)
/bincount if multiple scans were average, please indicate the number of measurements (n) averaged. List them by pairing the field name, including blank scans (abs_blank) with the bincount value, separated by commas. (e.g., /bincount=ag:3
Data fields in each file should nominally include:
example submission, ag
The following bundle contains an excerpt example of a CDOM submission. The download bundle (.zip) includes two example data files, each from a different type of spectrophotometer, and several example documents and a completed CDOM Checklist file.
Download example CDOM submission ( .zip )
Absorbance, also known as optical density values (e.g., abs_ap, abs_ad) must be submitted without any null correction applied. Null correction can be applied to the optical densities when calculating absorption coefficients, however besides preserving the null_correction value as a metadata header, the intermediate absorbance values should not be included in the SeaBASS files.
Please do NOT apply smoothing algorithms. Smoothing must not be applied to absorbances / optical densities (e.g., abs_ap, abs_ad), and should not be applied to absorption coefficients (e.g., ap, ad).
If your instrument collects data below 400nm, we require absorbance values (abs_ap, abs_ad) to be submitted. However, calculated absorption coefficients below 400nm are optional and –9999 can be used if the PI desires not to include them.
Data from replicate filters are submitted individually (one per file). Multiple scans must be averaged; and if so, standard error/deviation should be reported (e.g., abs_ap_sd). The number of measurements (n) averaged into the reported value should be included in the header “/bincount”. See examples below.
Data must be submitted at native wavelength resolution (do not bin data together over intervals of wavelegths).
"Conditionally Required" metadata headers:
/volfilt (L) volume filtered. Example:
/volfilt=10
/area (m2) for filter pads, the area over which particles are collected onto the filter. Example:
/area=0.05
/null_correction If applicable, report the null correction used when calculating absorption coefficients. Normally the null correction is performed using absorbance values. List a null correction by pairing a field name with its null correction value separated by a colon. To report multiple null corrections, separate them by commas. Units are assumed to be the same as the fields used for null correction. Example:
/null_correction=abs_ap:0.002,abs_ad:0.001)
/bincount if multiple scans were averaged, please indicate the number of measurements (n) averaged. List them by pairing the field name, including blank scans (abs_blank) with the bincount value, separated by commas. Example:
/bincount=abs_ap:3,abs_ad:3,abs_blank:2
Data fields in each file should nominally include:
**See Chapter 5.3.4 the Absorption Coefficient protocol document1
1Neeley, A.R., Mannino, A., Reynolds, R.A., Roesler, C., Rottgers, R., Stramski, D., Twardowski, M. and Zaneveld, J.R.V., 2018. Ocean Optics & Biogeochemistry Protocols for Satellite Ocean Colour Sensor Validation: Absorption Coefficient. http://dx.doi.org/10.25607/OBP-119
N/A
Data fields in each file should nominally include:
1. POC / PON values (nominally adsorption blank corrected)
2. volfilt
3. bincount and standard deviations ("_sd"), or another uncertainty metric to quantify replicates
Other notes:
DOC/DON adsorption ("filtrate") blank correction should be measured and applied to POC/PON.
Moran, S. B., M. A. A. Charette, S. M. Pike, C. A. Wicklund, M. S. Bradley, M. A. A. Charette, S. M. Pike, and C. A. Wicklund. 1999. Differences in seawater particulate organic carbon concentration in samples collected using small- and large-volume methods: the importance of DOC adsorption to the filter blank S.B. Mar. Chem. 67: 33–42.
"Conditionally Required" metadata headers:
N/A
Data fields in each file should nominally include:
1. DOC_L (umol/L)
2. bincount (as a data field or field suffix, i.e., doc_l_bincount) and standard deviations ("_sd"), or another uncertainty metric to quantify replicate uncertainty
Other notes:
Please use the recommended SeaBASS unit for DOC (DOC_L, umol/L). Even though it is customary for chemical oceanography data to be reported in mass per kg, for the purposes of remote sensing calibration, the recommended units must be normalized by volume.
Data fields in each file should nominally include:
1. Individual and summed pigments (based on SeaBASS fields/SeaHARRE reports)
2. Separate columns for any size-fractionated measurements (e.g., Tot_Chl_a_20umprefilt goes in a separate column from Tot_Chl_a)
3. Include "hplc_gsfc_id" as a column if your data were analyzed at the NASA GSFC lab to preserve the lab's sample ID
Other notes:
Data fields in each file should include:
1. Depth
2. Tilt, Roll, and/or Pitch
3. Time
Data fields that are optional but recommended include:
1. cond (i.e., conductivity)
2. wt (i.e., water temperature
Other notes
* If data from multiple sensors are expressed at common depths in the same data matrix, any offsets from the depth sensor must be described
This section describes data management and submission of above-water radiometry (AWR), e.g., shipborne, or tower-mounted radiometers in automated or manual configurations. SeaBASS field names for these types of submissions of AOPs usually include Rrs and Es, and often include Lt, Lsky, Lw, Lwn, and Lwnex. Data submissions from handheld instruments should include Es, Lt, Lsky, Lw, and Rrs at a minimum.
Some estimate of uncertainties should be provided. Ideally, these would include all sources of uncertainty from the instrument characterizations, data processing (e.g., glint correction), and environmental variability. At a minimum, variability (e.g., standard deviation) across multiple measurements for a single, averaged and submitted spectrum submitted should be reported (e.g., Rrs_unc or Rrs_std).
New data submissions should be collected and processed in compliance with the most recent NASA / IOCCG protocols.
AWR data acquisition systems typically include between one and three radiometers. Configurations with three radiometers are deployed above the sea surface and comprise two radiometers measuring skylight (Lsky) and total upwelling radiance (Lt) simultaneously with surface irradiance (Es) measured by a third radiometer equipped with a cosine collector. Fully above water systems with two radiometers typically measure Es with one and tilt the other to measure Lt and Lsky alternately. A two-radiometer system can also be configured in a skylight blocked approach (SBA) directly at the sea surface with no need to measure Lsky. Single radiometer systems typically measure Lt and Lsky alternately (by tilting) and estimate Es by measuring reflectance from a Lambertian plaque. Systems can be manually operated or fully autonomous (i.e., using a robotic platform to adjust/measure sensor geometries and a data logger to merge multiple ancillary datasets such as GPS time and position and tilt).
Three-radiometer AWR systems using Sea-Bird Scientific HyperOCRs or TriOS RAMSES radiometers are supported in the HyperInSPACE Community Processor (HyperCP). This software allows for protocol-driven, standardized processing of AWR with rigorous quality controls and is encouraged for the submission of validation-quality radiometry. Full radiometric characterization of radiometers for stray light, thermal response, polarization sensitivity, angular response (cosine collectors), and absolute radiometric calibration uncertainty, as described in the protocols, is strongly encouraged and used by HyperCP to deliver fully Fiducial Reference Measurement compliant, validation-quality radiometry with end-to-end uncertainty estimation. The information gathered by HyperCP and automatically formatted for SeaBASS submission simplifies the submission and review process for everyone.
An extensive description of measurement procedures for AWR can be found in the D-6 document prepared by the Fiducial Reference Measurements for Satellite Ocean Colour (FRM4SOC) initiative. It is written specifically for TriOS triplets, but also largely applicable to similar systems such as the Sea-Bird HyperSAS.
Files may be submitted as a single set of spectra (i.e., at one time stamp) with wavelength as a column, or as multiple spectra per file as rows with wavelength denoted in field names and a column for date/time.
For continuously sampling radiometer systems with inherent sampling rates on the order of 1 Hz, data should generally be binned to 300 s (see Ensemble_Interval metadata below).
AWR submissions require supplemental documentation to preserve critical methods information. Download the following checklist, fill it out, and submit it along with your other documentation and calibration information.
When using HyperCP to process AWR, many of the headers and fields below will be supplied automatically in the SeaBASS file, provided the data are included in the processing (i.e., see HyperCP README on Ancillary data inputs here). A field log template is also provided for AWR collections here.
"Optional but recommended" metadata headers (if not included as fields):
Metadata header comments (preceded by “!”):
Data fields in each file should include (if not included as headers):
Data fields that are optional but recommended include:
"Optional (but recommended)” metadata headers:
/wind_speed (m/s)
/cloud_percent (%)
/wave_height (m)
/instrument_manufacturer
/instrument_model
/calibration_date
Data fields in each file should include:
/instrument_model
/instrument_manufacturer
/PSD_bin_size_method=specify method used to select the nominal bin size such as arithmetic_mean or geometric_mean
/PSD_bin_size_boundaries=please provide a comma-separated list with the bin size boundaries in increasing order, e.g., 5,9.5,15,20 ...
Data fields in each file should include:
1. PSD_DNSD_###umsize=Differential number size distribution. Units: number/m^3/um
Data fields that are optional but recommended include:
N/ASeaBASS provides a mechanism to accept and ingest measurements of plankton and particles collected by flow cytometry and imaging-in-flow methods (e.g., IFCB, FlowCAM, UV-P, etc.). For flow cytometry data, Level 2 is defined as sums of the total abundances of each phytoplankton or bacterial group.
For imaging-in-flow data, Level 1b for plankton and other particle observations is defined as individual level counts with automatic (including interpretation of class scores or probabilities) and manual classifications, and biovolume and size parameters for each region of interest (ROI). An ROI is defined as a rectangular subset of pixels in a given image. The submission of a Level 1b data table for plankton and other particle observations to SeaBASS must include morphological information for each ROI and must be accompanied by documents that include relevant metadata and processing information.
Submissions of both types of data must be accompanied by documents that include relevant metadata and processing information.