Chapter 8 Satellite Data of Ocean Color Remote Sensing of Ocean Color Instructor: Dr. Cheng-Chien LiuCheng-Chien Liu Department of Earth Sciences National Cheng-Kung University Last updated: 27 April 2003

8.1 Introduction  Outline Level Type Format Parameters Name convention Access

8.1 Introduction (cont.)  Links CZCS  Getting Started with Coastal Zone Color Scanner (CZCS) Data kit.html kit.html SeaWiFS  Summary and Samples of SeaWiFS Operational Data Products TS.html TS.html  SeaWiFS Archive Product Specifications - version updated October

8.1 Introduction (cont.)  Links (cont.) MODIS  An overview of the MODIS Ocean Data products  Ocean product information bin/whom/infoscript.pl?cfg=MODIS/ocean/info.cfg bin/whom/infoscript.pl?cfg=MODIS/ocean/info.cfg

8.2 Data Level  Raw data Data in their original packets, as received from the observer  Level 0 Raw instrument data at original resolution, time ordered, with duplicate packets removed

8.2 Data Level (cont.)  Level 1A Reconstructed unprocessed instrument/payload data at full resolution; any and all communications artifacts (e.g. synchronization frames, communications headers) removed Primary output of the L1A process contains  Unconverted radiances for all detectors at all sources;  Decommutated instrument engineering and memory information;  Spacecraft ancillary data;  EOS standard metadata;  Granule-specific metadata;  Data quality information.

8.2 Data Level (cont.)  Level 1B Level 1A data that have been processed to sensor units and radiometrically corrected and geolocated  Only Channels 1 and 2 (primary use is land/cloud boundaries) have 250-m resolution, Channels 3-7 (primary use is land/cloud properties) have 500-m resolution, and the rest have 1-km resolution. This MODIS data product consists of:  250 m bands calibrated data aggregated to 1 km resolution and their uncertainties  500 m bands calibrated data aggregated to 1 km resolution and their uncertainties  1 km bands calibrated data and their uncertainties  Subset of geolocation data  Quality Assurance and Instrument Status Metadata.

8.2 Data Level (cont.)  Level 2 Derived geophysical variables at the same resolution and location as the Level 1 source data.  Level 3 Variables mapped on uniform space-time grid scales, usually with some completeness and consistency.

Fig An example of MODIS MODOCL2 Browse Image and Coordinates for APR-21 03:25:00 to 2003-APR-21 03:30:00 Source: Fig 8.2.1

8.2 Data Level (cont.)  Level 4 Model output or results from analyses of lower level data (i.e., variables derived from multiple measurements).

8.3 Data Type  GAC (Global area coverage)  LAC (Local area coverage)  Browse

8.4 Data Format: HDF  HDF A self-describing data format  All of the information necessary to examine the data in an HDF file is contained within the file Developed by the National Center for Supercomputing Applications (NCSA) at the University of Illinois To help scientists reduce the time they were spending trying to convert data sets to familiar formats and instead have more time available for actually analyzing data

8.4 Data Format: HDF (cont.)  Advantages portability to multiple machines (i.e. platform independent) self documented files efficient storage of and access to large data sets capability of storing multiple data structures or types within the same file extensibility for future enhancements

8.4 Data Format: HDF (cont.)  Example of HDF format:

8.5 Parameters  Introduction Three categories  Ocean color  36 parameters, six sub-groups Optical properties (12=5+7) Aerosol models (2) Fluorescence (3) Concentrations (8) Chlorophyll (3) Absorption coefficients (8=3+5)  Sea surface temperature (SST)  4 parameters SST bulk or skin temperature of the ocean during the day or at night (4)  Ocean productivity

8.5 Parameters (cont.)  Introduction (cont.) Resolution  Each of the forty (40) ocean color and SST parameters is associated with Products that have several time and spatial resolutions Temporal resolution  Level 2 data are 5-minute granules  level 3 data are associated with daily, 8-daily and monthly data Spatial resolution (4)  1 km, 4.6-km, 36-km or 1-degree  Ocean productivity consists of two Level 4 products: weekly and yearly ocean primary productivity at 5-km spatial resolution

8.5 Parameters (cont.)  Optical properties 12 parameters  Tau Aerosol (at 865 microns)  Epsilon (765/865)  Epsilon for Clear Water (at 531 microns)  Instantaneous PAR  Diffuse Attenuation (K 490)  Normalized Water-leaving Radiances (in seven bands from 412 to 678 microns)

8.5 Parameters (cont.)  Optical properties (cont.) Tau aerosol,  865   865  atmospheric correction  L WN  Dimensionless  Only provided for cloud-free pixels (with Sun glitter below a threshold)  All valid pixels are outside a distance threshold from land

8.5 Parameters (cont.)  Optical properties (cont.) Epsilon  78 (  765 /  865 )   78   765 /  865  Dimensionless (0 ~ 1.5)

8.5 Parameters (cont.)  Optical properties (cont.) Epsilon for clear water  clearwater   clearwater  L WN (531)/ L WN (667)  Dimensionless  Objectives  Estimate aerosol iron content  Flag suspicious L WN retrievals  Check on the Angstrom exponent

8.5 Parameters (cont.)  Optical properties (cont.) Instantaneous PAR, E d,PAR  Photosynthetically Available Radiation (PAR)  The total downwelling flux of photons (0 -, nm)  mW cm -2 micron -1 sr -1  Objectives of E d,PAR  photosynthetic rate of growth of phytoplankton  primary ocean production.  L WN  R rs  Chl-a

8.5 Parameters (cont.)  Optical properties (cont.) Diffuse attenuation K 490  Unit: m -1  AOP  K 490 = K 490 (,z)

8.5 Parameters (cont.)  Optical properties (cont.) Normalized water-leaving radiances L WN  7 bands (412, 443, 490, 531, 551, 667, 678 nm)  Unit: mW cm -2 micron -1 sr -1  L WN  R rs  Chl-a  primary productivity  The fundamental parameters for recovering most of the MODIS ocean products

8.5 Parameters (cont.)  Aerosol Models Two models  atmospheric correction  removal of aerosols (difficult)  A set of candidate aerosol models.  aerosol size distribution, aerosol index of refraction, assumption of spherical particle…  Two models from 16 candidate models

8.5 Parameters (cont.)  Fluorescence Mechanism of light reaction Application  Estimate chlorophyll concentrations and primary productivity

8.5 Parameters (cont.)  Fluorescence (cont.) Fluorescence baseline  Unit: mW cm -2 micron -1 sr -1  linear  Places on either side of the fluorescence peak. Created from Channel 13: L WN (667) and Channel 15: L WN (748)

8.5 Parameters (cont.)  Fluorescence (cont.) Fluorescence line height (FLH)  The intensity of Channel 14: L WN (678) above the baseline  Unit: mW cm -2 micron -1 sr -1  Solar-stimulated chlorophyll fluorescence  current photophysiology of phytoplankton  estimate primary productivity

8.5 Parameters (cont.)  Fluorescence (cont.) Fluorescence efficiency (FE)  Dimensionless  Quantifies the level of photosynthesis by phytoplankton

8.5 Parameters (cont.)  Application of FLH and FE FLH  Chl  FE  photosynthesis   levels of nutrient availability  Fig  Top vortex  spinning counterclockwise  draw nutrient- rich water upward  Bottom vortex  spinning clockwise  force water downward

Fig FLH and FE from the northwestern portion of the Arabian Sea, collected by MODIS on Dec. 2, Source: Image credit: MODIS Ocean Team/Ocean Fluorescence Product, Mark Abbott, Principal Investigator, Oregon State University. Fig

8.5 Parameters (cont.)  Concentrations 8 parameters  CZCS pigment  Total pigment - case 1  Suspended Solids Concentration  Pigment concentration in coccolith blooms  Coccolith concentration  Calcite concentration  Phycoerythrobilin (PEB)  Phycourobilin (PUB)

8.5 Parameters (cont.)  Concentrations (cont.) CZCS pigment  CZCS pigment concentration  The sum of chlorophyll-a and associated degradation products.  Unit: mg m -3  Based primarily on methods and algorithms developed for the CZCS program and refined and adapted to the MODIS bands

8.5 Parameters (cont.)  Concentrations (cont.) Total pigment - case 1  The sum of chlorophyll a and phaeopigment concentration  Case 1 waters: optical properties are dominated by chlorophyll and associated covarying detrital pigments  Case 2 waters: optical properties which may not covary with chlorophyll. Other substance, such as gelbstoff, suspended sediments, coccolithophores, detritus and bacteria, change optical properties as well  Unit: mg m -3

8.5 Parameters (cont.)  Concentrations (cont.) Suspended Solids Concentration  Ocean suspended sediments  analysis of complex bio- optical properties of coastal and estuarine regions/environments  Unit: mg m -3  Ocean substance concentrations  productivity  global biogeochemical models  global climate models

8.5 Parameters (cont.)  Concentrations (cont.) Pigment concentration in coccolith blooms  Unit: mg m -3  Coccolithophores  Small marine phytoplankton  Form external calcium carbonate scales having diameters of a few microns and a thickness of 250 to 750 nm  The main source of calcium carbonate on Earth  An important part of the biogenic carbon cycle

Fig Two side-views of coccoliths. Source: Fig

Fig Coccoliths in the Celtic Sea Source: Fig

8.5 Parameters (cont.)  Concentrations (cont.) Coccolith concentration  This is the detached coccolith concentration  Unit: 1/m 3

8.5 Parameters (cont.)  Concentrations (cont.) Calcite concentration  This is the estimated calcite concentration due to coccoliths  Unit: mg m -3 of calcium carbonate

8.5 Parameters (cont.)  Concentrations (cont.) Phycoerythrobilin (PEB)  Unit: mg m -3  Phycoerythrins ( 藻紅素 )  phycourobilin-rich (PUB) phycoerythrins  phycoerythrobilin-rich (PEB) phycoerythrins  The PUB and PEB parameters are retrieved by a sequential-convergent-iteration method, which uses five independent bands

8.5 Parameters (cont.)  Concentrations (cont.) Phycourobilin (PUB)  Unit: mg m -3

8.5 Parameters (cont.)  Chlorophyll Significance  A key input to the primary ocean production product  To trace oceanographic currents, jets, and plumes

Fig Eddies off the Queen Charlotte Islands Source: QueenCharlotte_S jpghttp://earthobservatory.nasa.gov/Newsroom/NewImages/Images/ QueenCharlotte_S jpg Fig

8.5 Parameters (cont.)  Chlorophyll (cont.) Chlorophyll MODIS  Unit: mg m -3  The concentration of Case 1 chlorophyll in sea water  Derived using the Clark 3 or 4-band algorithm

8.5 Parameters (cont.)  Chlorophyll (cont.) Chlorophyll-a (SeaWiFS)  Using the standard SeaWiFS "OC2" algorithm  It contains ocean chlorophyll a pigment concentration for Case 1 waters and Case 2 waters  Unit: mg m -3

8.5 Parameters (cont.)  Chlorophyll (cont.) Chlorophyll-a (semi-analytic)  Using multiple bands in an analytic model  It contains ocean chlorophyll a pigment concentration for Case 1 waters and Case 2 waters  Unit: mg m -3

8.5 Parameters (cont.)  Absorption Absorbed radiation by phytoplankton (ARP)  Averaged over the first optical depth  Unit: mW cm -2 micron -1 sr -1  Critical for calculation of fluorescence efficiency (FE)

8.5 Parameters (cont.)  Absorption Gelbstoff absorption coefficient  a g  Unit: m -1  It is operationally defined as a of the material that can fit through a 0.2 micron filter  It is also known as yellow substance or colored dissolved organic material (CDOM) absorption

8.5 Parameters (cont.)  Absorption Chlorophyll-a absorption  a c  Unit: m -1

8.5 Parameters (cont.)  Absorption Total absorption  Total absorption includes absorption due to water, phytoplankton, detritus and gelbstoff  Wavelengths: 412, 433, 488, 531 and 551 nm  Valid data exist only for ocean cloud-free pixels  Unit: m -1

8.5 Parameters (cont.)  Sea Surface Temperature (SST) IR radiometers 11-micron bands and the 4 micron bands  SST for day data, 11 microns (D1)  SST for day data, 4 microns (D2)  contamination by sun glitter during the day  SST for night data, 11 microns (N1)  SST for night data, 4 microns (N2)

8.6 Name convention  L1B and L2 files.A....hdf

8.6 Name convention (cont.)  L3 and L4 files..ADD...hdf  where  is the Earth Science Data Type (see below)  is the starting data day in the form yyyyddd  is the collection version, using three digits (e.g., 004)  is the production time in the form yyyydddhhmmss  is the parameter name (see Table 11 : MODIS Ocean Parameters)  yyyy = year  ddd = day of year  hh = hour  mm = minute  ss = seconds

8.6 Name convention (cont.)  MODIS Ocean ESDT Definitions L1b ESDT: MOD021KM L2 Ocean Color ESDT's:  MODOCL2 MODOCL2A MODOCL2B MODOCQC L2 Sea Surface Temperature (SST) ESDT's:  MOD28L2 MOD28QC

8.6 Name convention (cont.)  MODIS Ocean ESDT Definitions (cont.) L3 and L4 ESDT's:  binned files (ISEAG projection)  MOD  represents: OC: Ocean Color (L3) 27: Primary Production (L4) 28: SST (L3) OQ: Ocean Color QC products (L3) SQ: SST QC products (L3)  represents the file type: D: daily W: weekly M: monthly N: yearly (L3 only) Y: yearly (L4 only) HV: annual carbon, export carbon, and new nitrogen production (L4 only)  is the parameter number (01-36) for Ocean Color only and null otherwise

8.6 Name convention (cont.)  MODIS Ocean ESDT Definitions (cont.) L3 and L4 ESDT's (cont.):  L3 map files (carte platte projection)  MO  is the resolution: 1D = one degree 04 = 4.88 km 36 = 39 km  is the statistic that was mapped: M: mean N: number of pixels summed S: standard deviation F: common flags Q: quality 1: flag byte 1 2: flag byte 2 3: flag byte 3  and see definition for L3 binned files (above)

8.6 Name convention (cont.)  MODIS Ocean ESDT Definitions (cont.) L3 and L4 ESDT's (cont.):  L4 map files (carte platte projection)  MO  is the model class: AP: semi-analytical primary production model SP: statistical primary production model  is the temporal resolution: W: weekly (AP & SP) Y: yearly (SP only)  is the spatial resolution: A: 5 km B: 39 km 1: one degree

8.6 Name convention (cont.)  MODIS Ocean ESDT Definitions (cont.) L3 and L4 ESDT's (cont.):  MO (cont.)  is the field type: M: mean S: standard deviation (SP chl only) W: number of weeks N: number of observations F: quality map  is the field identifier: 1: Behrenfeld/Falkowski productivity index (AP only) 2: Howard/Yoder/Ryan productivity index (AP only) E: photosynthetically available radiation (AP only) D: mixed-layer depth (AP only) P: annual empirical primary production (SP only) N: annual empirical new production (SP only) X: annual empirical export production (SP only) C: running annual chlorophyll mean (SP only)

8.6 Name convention (cont.)  MODIS Ocean ESDT Definitions (cont.) L3 and L4 ESDT's (cont.):  Only the following 78 combinations are possible for L4 maps:  MOAPW M1, MOAPW M2, MOAPW ME, MOAPW MD, MOAPW N1, MOAPW N2, MOAPW F1, MOAPW F2, MOAPY M1, MOAPY M2, MOAPY ME, MOAPY MD, MOAPY N1, MOAPY N2, MOAPY F1, MOAPY F2, MOSPY MP, MOSPY MN, MOSPY MX, MOSPY MC, MOSPY FP, MOSPY FN, MOSPY FX, MOSPY FC, MOSPY NC, MOSPY SC. metadata  filename.met  where filename is the corresponding level 2, 3, or 4 filename, as above.

8.7 Data access  GSFC Earth Sciences Distributed Active Archive Center (DAAC) Ocean color  CZCS   OCTS   SeaWiFS   MODIS  