Software Used to Process Ocean-Colour Data

SeaDAS (SeaWiFS Data Analysis System) is a comprehensive image analysis package developed by NASA’s Ocean Biology Processing Group (OBPG) for the processing, display, analysis, and quality control of all SeaWiFS data products. It is freely available for download.

BEAM Software: The Basic ERS & Envisat (A)ATSR and Meris Toolbox (BEAM) is a collection of executable tools and an application programming interface (API) which has been developed to facilitate the utilisation, viewing and processing of ESA MERIS, (A)ATSR and ASAR data. It can be downloaded fee of charge.

ODESA provides users with a complete Level 2 processing environment for the MERIS instrument: It includes MEGS_8.1 and associated Auxiliary Data Files (ADF) used for the MERIS 3rd reprocessing in line with the current version of the IPF (6.0). Within this environment, users have several possibilities:

  • Access to MERIS data from remote processing facility,
  • Download MERIS level 2 processor (MEGS®, source code available) and its operational environment,
  • Download the ODESA analysis tools,
  • Access to the MERMAID algorithm validation facilities, and
  • Access to the ODESA and MERIS forum.

WASI (Water Colour Simulator) (.zip 55MB) is a tool for the simulation of optical properties and light field parameters of deep and shallow waters, and for data analysis of instruments disposed above the water surface and submerged in the water. Examples of supported measurements are downwelling irradiance, upwelling radiance, irradiance reflectance, remote sensing reflectance, attenuation, and absorption. Data analysis is done by inverse modeling. The provided database, which covers the spectral range from 350 to 1000 nm in 1 nm intervals, can be exchanged easily to represent the studied area. The module WASI-2D extends the functionality towards image processing of atmospherically corrected data from airborne sensors and satellite instruments. WASI is free of charge. It has been developed for Windows, but can be operated also under Linux, BSD, Solaris and Mac OS X using the wine emulator (www.winehq.org). For further information contact Peter Gege at peter.gege@dlr.de.

SeaBatch – If you work with ocean colour data and utilize SeaDAS (see above), you likely need a way to batch process multiple files. SeaBatch can help. SeaBatch is a group of Unix shell scripts that batch process ocean colour data derived from NASA’s MODIS (Aqua and Terra) and SeaWiFS sensors. With SeaBatch you can:

  • Process MODIS Level-0 files (utilize high-resolution bands)
  • Process Level-1 files to Level-2
  • Spatially bin Level-2 files (.5, 1, 2, 4, 9, and 36 km)
  • Temporally bin Level-2 files (day, 7day, 8day, and month)
  • Output Level-3 files as ascii, flat, hdf, png, etc.

SeaBatch is a powerful tool that will greatly assist you with your research. It is free, as are SeaDAS and Unix. If using runtime SeaDAS, an IDL license is not required.

ArcGIS & satellite data – Importing satellite data into ArcGIS just got easier! There is now an ArcGIS extension that allows users to browse THREDDS catalogs and connect directly to OPeNDAP servers to access large amounts of scientific data and ingest the data into ArcGIS desktop 9.3. This extension, called the Environmental Data Connector (EDC), uses a Java-based browser and leverages existing components from Unidata and NOAA/PMEL libraries so that users can filter large amounts of data in space and time. The user has a choice of importing the data into ArcGIS in either raster or feature format. The time stamped data can then be animated using a TimeSlider extension which is built into the EDC. A stand-alone version is also available, which provides a GUI to browse THREDDS catalogs or OPeNDAP directories, to subset the selected data in space and time, and to download the data as a netcdf file. The EDC was developed for NOAA Fisheries by Applied Science Associates, Inc. with funding from NOAA’s Satellite Research and Operation (R&O) project, and is freely available at www.pfeg.noaa.gov/products/EDC/. A patch that affects the handling of files within ArcGIS (not necessary for use with the standalone version of EDC) is available from the same website. For further information contact Cara Wilson at cara.wilson@noaa.gov.

Calculation of Photosynthetically Available Radiation (PAR)

WIM (Windows Image Manager) is a general-purpose image display and analysis programme for various satellite images, including those from ocean colour sensors (see http://wimsoft.com). This is commercial software, but it is available for free evaluation. A major addition to the tools is the WIM Automation Module (WAM), which allows automating repetitive tasks by writing simple programs using WIM functions e.g. calculating primary production according to Behrenfeld-Falkowski model.

Algorithm Software (used in IOCCG Report 5)

The software for the various algorithms discussed in IOCCG Report 5 can be found below. Please remember to check the relevant weblinks, or contact the authors for algorithm updates.

  • Inversion of IOP based on Rrs and Remotely Retrieved Kd (Chapter 5: Inversion of IOP based on Rrs and Remotely Retrieved Kd by Hubert Loisel and Antoine Poteau). The Fortran program for the IOP inversion algorithm, as well as three look-up tables can be downloaded below.Fortran Program: IOP_inversion.f [Posted 26 February 2007]
    Look-up tables: LUT_AWLUT_KD and LUT_RRS [Posted 26 February 2007]
  • Over Constrained Linear Matrix Inversion (Chapter 8: Over Constrained Linear Matrix Inversion with Statistical Selection by Emmanuel Boss and Collin Roesler). The updated code files can be found on the University of Maine, In-situ Sound & Color Lab website, or they can be downloaded below:
    In situ data inversion [Posted 31 October 2006]
    Synthetic data inversion [Posted 31 October 2006]
  • Quasi-Analytical Algorithm (Chapter 10: Quasi-Analytical Algorithm by ZhongPing Lee, Kendall Carder and Robert Arnone)
    This IOP algorithm was updated in March 2009 and November 2014. See QAA_v5.pdf and  QAA_v6.pdf for a full description of updates.
    Quasi-Analytical Algorithm (QAA) Excel file [Version 6: updated 4 May 2015].
  • Garver, Siegel, Maritorena Model (GSM-01) (Chapter 11: The GSM Semi-Analytical Bio-Optical Model by Stéphane Maritorena and Dave Siegel). The updated IDL code files for this model can be downloaded at GSM 01 IDL code files [Posted 25 October 2006]
  • PML algorithm by Smyth, Moore, Hirata and Aiken (2006).The PML algorithm is an IOP algorithm developed by Smyth et al. (2006) at the Plymouth Marine Laboratory, which was not available for evaluation when the IOCCG working group was convened. PML algorithm software . [Posted 23 February 2007]
    The PML IOP model is an analytical approach for determining the spectral inherent optical properties of the ocean which uses spectral slopes, derived from field measurements, at the central wavelengths of 490 and 510 nm (or 531 for MODIS). Once the absorption and backscatter are known at these wavelengths, based on the assertion of Morel (1980), then the absorption and backscatter across the spectrum can be determined if you assume a spectral shape for backscatter.

Once the primary inherent optical properties of total absorption and backscatter have been determined the bio-geochemical parameters can be determined using standard relationships and slopes for CDOM and phytoplankton. The reference for the model, together with its validation using the NOMAD dataset can be found in:

Smyth T. J., G. F. Moore, T. Hirata and J. Aiken (2006) Semianalytical model for the derivation of ocean color inherent optical properties: description, implementation, and performance assessment. Applied Optics, 45, 8116-8131.

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