Abstract

We present a statistical analysis of a large set of absorption spectra of phytoplankton, measured in natural samples collected from ocean water, in conjunction with detailed pigment concentrations. We processed the absorption spectra with a sophisticated neural network method suitable for classifying complex phenomena, the so-called self-organizing maps (SOM) proposed by Kohonen [Kohonen, Self Organizing Maps (Springer-Verlag, 1984)]. The aim was to compress the information embedded in the data set into a reduced number of classes characterizing the data set, which facilitates the analysis. By processing the absorption spectra, we were able to retrieve well-known relationships among pigment concentrations and to display them on maps to facilitate their interpretation. We then showed that the SOM enabled us to extract pertinent information about pigment concentrations normalized to chlorophyll a. We were able to propose new relationships between the fucoxanthin∕Tchl-a ratio and the derivative of the absorption spectrum at 510  nm and between the Tchl-b∕Tchl-a ratio and the derivative at 640   nm. Finally, we demonstrate the possibility of inverting the absorption spectrum to retrieve the pigment concentrations with better accuracy than a regression analysis using the Tchl-a concentration derived from the absorption at 440   nm. We also discuss the data coding used to build the self-organizing map. This methodology is very general and can be used to analyze a large class of complex data.

© 2006 Optical Society of America

Full Article  |  PDF Article

References

  • View by:
  • |
  • |
  • |

  1. C. S. Roesler and M. J. Perry, "In situ phytoplankton absorption, fluorescence emission, and particulate backscattering spectra determined from reflectance," J. Geophys. Res 100, 22767-22767 (1995).
    [CrossRef]
  2. Z. Lee, K. L. Carder, C. D. Mobley, R. G. Steward, and J. S. Patch, "Hyperspectral remote sensing for shallow waters: I. A semianalytical model," Appl. Opt. 37, 6329-6338 (1998).
    [CrossRef]
  3. A. M. Ciotti and A. Bricaud, "Retrievals of a size parameter for phytoplankton and spectral light absorption by colored detrital matter from water-leaving radiances at SeaWiFS channels in a continental shelf region off Brazil" Limnol. Oceanogr. Methods 4, 237-253 (2006).
    [CrossRef]
  4. N. Hoepffner and S. Sathyendranath, "Determination of the major groups of phytoplankton pigments from the absorption spectra of total particulate matter," J. Geophys. Res. 98, 22789-22803 (1993).
    [CrossRef]
  5. V. Stuart, S. Sathyendranath, T. Platt, H. Mass, and B. D. Irwin, "Pigments and species composition of natural phytoplankton populations: effect on the absorption spectra," J. Plankton Res. 20, 187-217 (1998).
    [CrossRef]
  6. S. Alvain, C. Moulin, Y. Dandonneau, and F. M. Bréon, "Remote sensing of phytoplankton groups in case 1 waters from global SeaWiFS Imagery," Deep-Sea Res . Part I 52, 1989-2004 (2005).
    [CrossRef]
  7. A. Morel and A. Bricaud, "Theoretical results concerning light absorption in a discretet medium, and application to specific absorption of phytoplankton," Deep-Sea Res. Part A 28, 1375-1393 (1981).
    [CrossRef]
  8. A. Bricaud, H. Claustre, J. Ras, and K. Oubelkheir, "Natural variability of phytoplankton absorption in oceanic waters: influence of the size structure of algal population," J. Geophys. Res. 109, C11010, doi: (2004).
    [CrossRef]
  9. T. Kohonen, Self-Organizing Maps (Springer-Verlag, 1984).
  10. K. Allali, A. Bricaud, M. Babin, A. Morel, and P. Chang, "A new method for measuring spectral absorption coefficients of marine particles," Limnol. Oceanogr. 40, 1526-1532 (1995).
    [CrossRef]
  11. K. Allali, A. Bricaud, and H. Claustre, "Spatial variations in the chlorophyll-specific absorption coefficients of phytoplankton and photosynthetically active pigments in the equatorial Pacific," J. Geophys. Res. 102, 12413-12423 (1997).
    [CrossRef]
  12. A. Bricaud and D. Stramski, "Spectral absorption coefficients of living phytoplankton and non-algal biogenous matter: a comparison between the Peru upwelling area and the Sargasso Sea," Limnol. Oceanogr. 35, 562-582 (1990).
    [CrossRef]
  13. M. Kishino, M. Takahashi, N. Okami, and S. Ichimura, "Estimation of the spectral absorption coefficients of phytoplankton in the sea," Bull. Mar. Sci. 37, 634-642 (1985).
  14. F. Vidussi, H. Claustre, J. Bustillos-Guzman, C. Cailliau, and J. C. Marty, "Rapid HPLC method for determination of phytoplankton chemotaxonomic pigments: separation of chlorophyll a from divinyl-chlorophyll-a, and zeaxanthin from lutein," J. Plankton Res. 18, 2377-2382 (1996).
    [CrossRef]
  15. A. Morel and S. Maritorena, "Bio-optical properties of oceanic waters: a reappraisal," J. Geophys. Res. 106, 7763-7780 (2001).
    [CrossRef]
  16. A. Niang, F. Badran, C. Moulin, M. Crepon, and S. Thiria, "Retrieval of aerosol type and optical thickness over the Mediterranean from SeaWiFS images using an automatic neural classification method," Remote Sens. Environ. 100, 82-94 (2006).
    [CrossRef]
  17. R. R. Bidigare, J. H. Morrow, and D. A. Kiefer, "Derivative analysis of spectral absorption by photosynthetic pigments in the western Sargasso Sea," J. Mar. Res. 47, 323-341 (1989).
    [CrossRef]
  18. M. A. Faust and K. H. Norris, "Rapid in vivo spectrophotometric analysis of chlorophyll pigments in intact phytoplankton cultures," Br. Phycol. J. 17, 351-361 (1982).
    [CrossRef]
  19. M. A. Faust and K. H. Norris, "In vivo spectrophotometric analysis of photosynthetic pigments in natural populations of phytoplankton," Limnol. Oceanogr. 30, 1316-1322 (1985).
    [CrossRef]
  20. A. Niang, S. Thiria, F. Badran, and C. Moulin, "Automatic neural classification of ocean colour reflectance spectra at the top of the atmosphere with introduction of expert knowledge," Remote Sens. Environ. 86, 257-271 (2003).
    [CrossRef]
  21. S. A. Garver, D. A. Siegel, and B. G. Mitchell, "Variability in near surface particulate absorption spectra : what can a satellite ocean color image see?" Limnol. Oceanogr. 39, 1349-1367 (1994).
    [CrossRef]
  22. A. Bricaud, M. Babin, A. Morel, and H. Claustre, "Variability in the chlorophyll-specific absorption coefficients of natural phytoplankton: analysis and parameterization," J. Geophys. Res. 100, 13331-13332 (1995).
    [CrossRef]
  23. F. Vidussi, H. Claustre, B. B. Manca, A. Luchetta, and J. C. Marty, "Phytoplankton pigment distribution in relation to upper thermocline circulation in the eastern Mediterranean Sea during winter," J. Geophys. Res. 106, 19939-19956 (2001).
    [CrossRef]
  24. L. B. Eisner, M. S. Twardowski, and T. J. Cowles, "Resolving phytoplankton photoprotective:photosynthetic carotenoid ratios on fine scales using in situ spectral absorption measurements," Limnol. Oceanogr. 48, 632-646 (2003).
    [CrossRef]
  25. E. N. Lorenz, "Atmospheric predictabilty as revealed by naturally occurring analogues," J. Atmos. Sci. 26, 636-646 (1969).
    [CrossRef]
  26. R. T. Clark and M. Déqué, "Conditional probability seasonal predictions of precipitation," Q. J. R. Meteorol. Soc. 129, 1-15 (2003).
    [CrossRef]
  27. S. Thiria, C. Mejia, F. Badran, and M. Crepon, "A neural network approach for modelling nonlinear transfer function: application for dealiasing spaceborne scatterometer data," J. Geophys. Res. 98, 827-841 (1993).
    [CrossRef]

2006 (2)

A. M. Ciotti and A. Bricaud, "Retrievals of a size parameter for phytoplankton and spectral light absorption by colored detrital matter from water-leaving radiances at SeaWiFS channels in a continental shelf region off Brazil" Limnol. Oceanogr. Methods 4, 237-253 (2006).
[CrossRef]

A. Niang, F. Badran, C. Moulin, M. Crepon, and S. Thiria, "Retrieval of aerosol type and optical thickness over the Mediterranean from SeaWiFS images using an automatic neural classification method," Remote Sens. Environ. 100, 82-94 (2006).
[CrossRef]

2005 (1)

S. Alvain, C. Moulin, Y. Dandonneau, and F. M. Bréon, "Remote sensing of phytoplankton groups in case 1 waters from global SeaWiFS Imagery," Deep-Sea Res . Part I 52, 1989-2004 (2005).
[CrossRef]

2004 (1)

A. Bricaud, H. Claustre, J. Ras, and K. Oubelkheir, "Natural variability of phytoplankton absorption in oceanic waters: influence of the size structure of algal population," J. Geophys. Res. 109, C11010, doi: (2004).
[CrossRef]

2003 (3)

A. Niang, S. Thiria, F. Badran, and C. Moulin, "Automatic neural classification of ocean colour reflectance spectra at the top of the atmosphere with introduction of expert knowledge," Remote Sens. Environ. 86, 257-271 (2003).
[CrossRef]

L. B. Eisner, M. S. Twardowski, and T. J. Cowles, "Resolving phytoplankton photoprotective:photosynthetic carotenoid ratios on fine scales using in situ spectral absorption measurements," Limnol. Oceanogr. 48, 632-646 (2003).
[CrossRef]

R. T. Clark and M. Déqué, "Conditional probability seasonal predictions of precipitation," Q. J. R. Meteorol. Soc. 129, 1-15 (2003).
[CrossRef]

2001 (2)

F. Vidussi, H. Claustre, B. B. Manca, A. Luchetta, and J. C. Marty, "Phytoplankton pigment distribution in relation to upper thermocline circulation in the eastern Mediterranean Sea during winter," J. Geophys. Res. 106, 19939-19956 (2001).
[CrossRef]

A. Morel and S. Maritorena, "Bio-optical properties of oceanic waters: a reappraisal," J. Geophys. Res. 106, 7763-7780 (2001).
[CrossRef]

1998 (2)

V. Stuart, S. Sathyendranath, T. Platt, H. Mass, and B. D. Irwin, "Pigments and species composition of natural phytoplankton populations: effect on the absorption spectra," J. Plankton Res. 20, 187-217 (1998).
[CrossRef]

Z. Lee, K. L. Carder, C. D. Mobley, R. G. Steward, and J. S. Patch, "Hyperspectral remote sensing for shallow waters: I. A semianalytical model," Appl. Opt. 37, 6329-6338 (1998).
[CrossRef]

1997 (1)

K. Allali, A. Bricaud, and H. Claustre, "Spatial variations in the chlorophyll-specific absorption coefficients of phytoplankton and photosynthetically active pigments in the equatorial Pacific," J. Geophys. Res. 102, 12413-12423 (1997).
[CrossRef]

1996 (1)

F. Vidussi, H. Claustre, J. Bustillos-Guzman, C. Cailliau, and J. C. Marty, "Rapid HPLC method for determination of phytoplankton chemotaxonomic pigments: separation of chlorophyll a from divinyl-chlorophyll-a, and zeaxanthin from lutein," J. Plankton Res. 18, 2377-2382 (1996).
[CrossRef]

1995 (3)

K. Allali, A. Bricaud, M. Babin, A. Morel, and P. Chang, "A new method for measuring spectral absorption coefficients of marine particles," Limnol. Oceanogr. 40, 1526-1532 (1995).
[CrossRef]

C. S. Roesler and M. J. Perry, "In situ phytoplankton absorption, fluorescence emission, and particulate backscattering spectra determined from reflectance," J. Geophys. Res 100, 22767-22767 (1995).
[CrossRef]

A. Bricaud, M. Babin, A. Morel, and H. Claustre, "Variability in the chlorophyll-specific absorption coefficients of natural phytoplankton: analysis and parameterization," J. Geophys. Res. 100, 13331-13332 (1995).
[CrossRef]

1994 (1)

S. A. Garver, D. A. Siegel, and B. G. Mitchell, "Variability in near surface particulate absorption spectra : what can a satellite ocean color image see?" Limnol. Oceanogr. 39, 1349-1367 (1994).
[CrossRef]

1993 (2)

N. Hoepffner and S. Sathyendranath, "Determination of the major groups of phytoplankton pigments from the absorption spectra of total particulate matter," J. Geophys. Res. 98, 22789-22803 (1993).
[CrossRef]

S. Thiria, C. Mejia, F. Badran, and M. Crepon, "A neural network approach for modelling nonlinear transfer function: application for dealiasing spaceborne scatterometer data," J. Geophys. Res. 98, 827-841 (1993).
[CrossRef]

1990 (1)

A. Bricaud and D. Stramski, "Spectral absorption coefficients of living phytoplankton and non-algal biogenous matter: a comparison between the Peru upwelling area and the Sargasso Sea," Limnol. Oceanogr. 35, 562-582 (1990).
[CrossRef]

1989 (1)

R. R. Bidigare, J. H. Morrow, and D. A. Kiefer, "Derivative analysis of spectral absorption by photosynthetic pigments in the western Sargasso Sea," J. Mar. Res. 47, 323-341 (1989).
[CrossRef]

1985 (2)

M. A. Faust and K. H. Norris, "In vivo spectrophotometric analysis of photosynthetic pigments in natural populations of phytoplankton," Limnol. Oceanogr. 30, 1316-1322 (1985).
[CrossRef]

M. Kishino, M. Takahashi, N. Okami, and S. Ichimura, "Estimation of the spectral absorption coefficients of phytoplankton in the sea," Bull. Mar. Sci. 37, 634-642 (1985).

1982 (1)

M. A. Faust and K. H. Norris, "Rapid in vivo spectrophotometric analysis of chlorophyll pigments in intact phytoplankton cultures," Br. Phycol. J. 17, 351-361 (1982).
[CrossRef]

1981 (1)

A. Morel and A. Bricaud, "Theoretical results concerning light absorption in a discretet medium, and application to specific absorption of phytoplankton," Deep-Sea Res. Part A 28, 1375-1393 (1981).
[CrossRef]

1969 (1)

E. N. Lorenz, "Atmospheric predictabilty as revealed by naturally occurring analogues," J. Atmos. Sci. 26, 636-646 (1969).
[CrossRef]

Allali, K.

K. Allali, A. Bricaud, and H. Claustre, "Spatial variations in the chlorophyll-specific absorption coefficients of phytoplankton and photosynthetically active pigments in the equatorial Pacific," J. Geophys. Res. 102, 12413-12423 (1997).
[CrossRef]

K. Allali, A. Bricaud, M. Babin, A. Morel, and P. Chang, "A new method for measuring spectral absorption coefficients of marine particles," Limnol. Oceanogr. 40, 1526-1532 (1995).
[CrossRef]

Alvain, S.

S. Alvain, C. Moulin, Y. Dandonneau, and F. M. Bréon, "Remote sensing of phytoplankton groups in case 1 waters from global SeaWiFS Imagery," Deep-Sea Res . Part I 52, 1989-2004 (2005).
[CrossRef]

Babin, M.

K. Allali, A. Bricaud, M. Babin, A. Morel, and P. Chang, "A new method for measuring spectral absorption coefficients of marine particles," Limnol. Oceanogr. 40, 1526-1532 (1995).
[CrossRef]

A. Bricaud, M. Babin, A. Morel, and H. Claustre, "Variability in the chlorophyll-specific absorption coefficients of natural phytoplankton: analysis and parameterization," J. Geophys. Res. 100, 13331-13332 (1995).
[CrossRef]

Badran, F.

A. Niang, F. Badran, C. Moulin, M. Crepon, and S. Thiria, "Retrieval of aerosol type and optical thickness over the Mediterranean from SeaWiFS images using an automatic neural classification method," Remote Sens. Environ. 100, 82-94 (2006).
[CrossRef]

A. Niang, S. Thiria, F. Badran, and C. Moulin, "Automatic neural classification of ocean colour reflectance spectra at the top of the atmosphere with introduction of expert knowledge," Remote Sens. Environ. 86, 257-271 (2003).
[CrossRef]

S. Thiria, C. Mejia, F. Badran, and M. Crepon, "A neural network approach for modelling nonlinear transfer function: application for dealiasing spaceborne scatterometer data," J. Geophys. Res. 98, 827-841 (1993).
[CrossRef]

Bidigare, R. R.

R. R. Bidigare, J. H. Morrow, and D. A. Kiefer, "Derivative analysis of spectral absorption by photosynthetic pigments in the western Sargasso Sea," J. Mar. Res. 47, 323-341 (1989).
[CrossRef]

Bréon, F. M.

S. Alvain, C. Moulin, Y. Dandonneau, and F. M. Bréon, "Remote sensing of phytoplankton groups in case 1 waters from global SeaWiFS Imagery," Deep-Sea Res . Part I 52, 1989-2004 (2005).
[CrossRef]

Bricaud, A.

A. M. Ciotti and A. Bricaud, "Retrievals of a size parameter for phytoplankton and spectral light absorption by colored detrital matter from water-leaving radiances at SeaWiFS channels in a continental shelf region off Brazil" Limnol. Oceanogr. Methods 4, 237-253 (2006).
[CrossRef]

A. Bricaud, H. Claustre, J. Ras, and K. Oubelkheir, "Natural variability of phytoplankton absorption in oceanic waters: influence of the size structure of algal population," J. Geophys. Res. 109, C11010, doi: (2004).
[CrossRef]

K. Allali, A. Bricaud, and H. Claustre, "Spatial variations in the chlorophyll-specific absorption coefficients of phytoplankton and photosynthetically active pigments in the equatorial Pacific," J. Geophys. Res. 102, 12413-12423 (1997).
[CrossRef]

A. Bricaud, M. Babin, A. Morel, and H. Claustre, "Variability in the chlorophyll-specific absorption coefficients of natural phytoplankton: analysis and parameterization," J. Geophys. Res. 100, 13331-13332 (1995).
[CrossRef]

K. Allali, A. Bricaud, M. Babin, A. Morel, and P. Chang, "A new method for measuring spectral absorption coefficients of marine particles," Limnol. Oceanogr. 40, 1526-1532 (1995).
[CrossRef]

A. Bricaud and D. Stramski, "Spectral absorption coefficients of living phytoplankton and non-algal biogenous matter: a comparison between the Peru upwelling area and the Sargasso Sea," Limnol. Oceanogr. 35, 562-582 (1990).
[CrossRef]

A. Morel and A. Bricaud, "Theoretical results concerning light absorption in a discretet medium, and application to specific absorption of phytoplankton," Deep-Sea Res. Part A 28, 1375-1393 (1981).
[CrossRef]

Bustillos-Guzman, J.

F. Vidussi, H. Claustre, J. Bustillos-Guzman, C. Cailliau, and J. C. Marty, "Rapid HPLC method for determination of phytoplankton chemotaxonomic pigments: separation of chlorophyll a from divinyl-chlorophyll-a, and zeaxanthin from lutein," J. Plankton Res. 18, 2377-2382 (1996).
[CrossRef]

Cailliau, C.

F. Vidussi, H. Claustre, J. Bustillos-Guzman, C. Cailliau, and J. C. Marty, "Rapid HPLC method for determination of phytoplankton chemotaxonomic pigments: separation of chlorophyll a from divinyl-chlorophyll-a, and zeaxanthin from lutein," J. Plankton Res. 18, 2377-2382 (1996).
[CrossRef]

Carder, K. L.

Chang, P.

K. Allali, A. Bricaud, M. Babin, A. Morel, and P. Chang, "A new method for measuring spectral absorption coefficients of marine particles," Limnol. Oceanogr. 40, 1526-1532 (1995).
[CrossRef]

Ciotti, A. M.

A. M. Ciotti and A. Bricaud, "Retrievals of a size parameter for phytoplankton and spectral light absorption by colored detrital matter from water-leaving radiances at SeaWiFS channels in a continental shelf region off Brazil" Limnol. Oceanogr. Methods 4, 237-253 (2006).
[CrossRef]

Clark, R. T.

R. T. Clark and M. Déqué, "Conditional probability seasonal predictions of precipitation," Q. J. R. Meteorol. Soc. 129, 1-15 (2003).
[CrossRef]

Claustre, H.

A. Bricaud, H. Claustre, J. Ras, and K. Oubelkheir, "Natural variability of phytoplankton absorption in oceanic waters: influence of the size structure of algal population," J. Geophys. Res. 109, C11010, doi: (2004).
[CrossRef]

F. Vidussi, H. Claustre, B. B. Manca, A. Luchetta, and J. C. Marty, "Phytoplankton pigment distribution in relation to upper thermocline circulation in the eastern Mediterranean Sea during winter," J. Geophys. Res. 106, 19939-19956 (2001).
[CrossRef]

K. Allali, A. Bricaud, and H. Claustre, "Spatial variations in the chlorophyll-specific absorption coefficients of phytoplankton and photosynthetically active pigments in the equatorial Pacific," J. Geophys. Res. 102, 12413-12423 (1997).
[CrossRef]

F. Vidussi, H. Claustre, J. Bustillos-Guzman, C. Cailliau, and J. C. Marty, "Rapid HPLC method for determination of phytoplankton chemotaxonomic pigments: separation of chlorophyll a from divinyl-chlorophyll-a, and zeaxanthin from lutein," J. Plankton Res. 18, 2377-2382 (1996).
[CrossRef]

A. Bricaud, M. Babin, A. Morel, and H. Claustre, "Variability in the chlorophyll-specific absorption coefficients of natural phytoplankton: analysis and parameterization," J. Geophys. Res. 100, 13331-13332 (1995).
[CrossRef]

Cowles, T. J.

L. B. Eisner, M. S. Twardowski, and T. J. Cowles, "Resolving phytoplankton photoprotective:photosynthetic carotenoid ratios on fine scales using in situ spectral absorption measurements," Limnol. Oceanogr. 48, 632-646 (2003).
[CrossRef]

Crepon, M.

A. Niang, F. Badran, C. Moulin, M. Crepon, and S. Thiria, "Retrieval of aerosol type and optical thickness over the Mediterranean from SeaWiFS images using an automatic neural classification method," Remote Sens. Environ. 100, 82-94 (2006).
[CrossRef]

S. Thiria, C. Mejia, F. Badran, and M. Crepon, "A neural network approach for modelling nonlinear transfer function: application for dealiasing spaceborne scatterometer data," J. Geophys. Res. 98, 827-841 (1993).
[CrossRef]

Dandonneau, Y.

S. Alvain, C. Moulin, Y. Dandonneau, and F. M. Bréon, "Remote sensing of phytoplankton groups in case 1 waters from global SeaWiFS Imagery," Deep-Sea Res . Part I 52, 1989-2004 (2005).
[CrossRef]

Déqué, M.

R. T. Clark and M. Déqué, "Conditional probability seasonal predictions of precipitation," Q. J. R. Meteorol. Soc. 129, 1-15 (2003).
[CrossRef]

Eisner, L. B.

L. B. Eisner, M. S. Twardowski, and T. J. Cowles, "Resolving phytoplankton photoprotective:photosynthetic carotenoid ratios on fine scales using in situ spectral absorption measurements," Limnol. Oceanogr. 48, 632-646 (2003).
[CrossRef]

Faust, M. A.

M. A. Faust and K. H. Norris, "In vivo spectrophotometric analysis of photosynthetic pigments in natural populations of phytoplankton," Limnol. Oceanogr. 30, 1316-1322 (1985).
[CrossRef]

M. A. Faust and K. H. Norris, "Rapid in vivo spectrophotometric analysis of chlorophyll pigments in intact phytoplankton cultures," Br. Phycol. J. 17, 351-361 (1982).
[CrossRef]

Garver, S. A.

S. A. Garver, D. A. Siegel, and B. G. Mitchell, "Variability in near surface particulate absorption spectra : what can a satellite ocean color image see?" Limnol. Oceanogr. 39, 1349-1367 (1994).
[CrossRef]

Hoepffner, N.

N. Hoepffner and S. Sathyendranath, "Determination of the major groups of phytoplankton pigments from the absorption spectra of total particulate matter," J. Geophys. Res. 98, 22789-22803 (1993).
[CrossRef]

Ichimura, S.

M. Kishino, M. Takahashi, N. Okami, and S. Ichimura, "Estimation of the spectral absorption coefficients of phytoplankton in the sea," Bull. Mar. Sci. 37, 634-642 (1985).

Irwin, B. D.

V. Stuart, S. Sathyendranath, T. Platt, H. Mass, and B. D. Irwin, "Pigments and species composition of natural phytoplankton populations: effect on the absorption spectra," J. Plankton Res. 20, 187-217 (1998).
[CrossRef]

Kiefer, D. A.

R. R. Bidigare, J. H. Morrow, and D. A. Kiefer, "Derivative analysis of spectral absorption by photosynthetic pigments in the western Sargasso Sea," J. Mar. Res. 47, 323-341 (1989).
[CrossRef]

Kishino, M.

M. Kishino, M. Takahashi, N. Okami, and S. Ichimura, "Estimation of the spectral absorption coefficients of phytoplankton in the sea," Bull. Mar. Sci. 37, 634-642 (1985).

Kohonen, T.

T. Kohonen, Self-Organizing Maps (Springer-Verlag, 1984).

Lee, Z.

Lorenz, E. N.

E. N. Lorenz, "Atmospheric predictabilty as revealed by naturally occurring analogues," J. Atmos. Sci. 26, 636-646 (1969).
[CrossRef]

Luchetta, A.

F. Vidussi, H. Claustre, B. B. Manca, A. Luchetta, and J. C. Marty, "Phytoplankton pigment distribution in relation to upper thermocline circulation in the eastern Mediterranean Sea during winter," J. Geophys. Res. 106, 19939-19956 (2001).
[CrossRef]

Manca, B. B.

F. Vidussi, H. Claustre, B. B. Manca, A. Luchetta, and J. C. Marty, "Phytoplankton pigment distribution in relation to upper thermocline circulation in the eastern Mediterranean Sea during winter," J. Geophys. Res. 106, 19939-19956 (2001).
[CrossRef]

Maritorena, S.

A. Morel and S. Maritorena, "Bio-optical properties of oceanic waters: a reappraisal," J. Geophys. Res. 106, 7763-7780 (2001).
[CrossRef]

Marty, J. C.

F. Vidussi, H. Claustre, B. B. Manca, A. Luchetta, and J. C. Marty, "Phytoplankton pigment distribution in relation to upper thermocline circulation in the eastern Mediterranean Sea during winter," J. Geophys. Res. 106, 19939-19956 (2001).
[CrossRef]

F. Vidussi, H. Claustre, J. Bustillos-Guzman, C. Cailliau, and J. C. Marty, "Rapid HPLC method for determination of phytoplankton chemotaxonomic pigments: separation of chlorophyll a from divinyl-chlorophyll-a, and zeaxanthin from lutein," J. Plankton Res. 18, 2377-2382 (1996).
[CrossRef]

Mass, H.

V. Stuart, S. Sathyendranath, T. Platt, H. Mass, and B. D. Irwin, "Pigments and species composition of natural phytoplankton populations: effect on the absorption spectra," J. Plankton Res. 20, 187-217 (1998).
[CrossRef]

Mejia, C.

S. Thiria, C. Mejia, F. Badran, and M. Crepon, "A neural network approach for modelling nonlinear transfer function: application for dealiasing spaceborne scatterometer data," J. Geophys. Res. 98, 827-841 (1993).
[CrossRef]

Mitchell, B. G.

S. A. Garver, D. A. Siegel, and B. G. Mitchell, "Variability in near surface particulate absorption spectra : what can a satellite ocean color image see?" Limnol. Oceanogr. 39, 1349-1367 (1994).
[CrossRef]

Mobley, C. D.

Morel, A.

A. Morel and S. Maritorena, "Bio-optical properties of oceanic waters: a reappraisal," J. Geophys. Res. 106, 7763-7780 (2001).
[CrossRef]

A. Bricaud, M. Babin, A. Morel, and H. Claustre, "Variability in the chlorophyll-specific absorption coefficients of natural phytoplankton: analysis and parameterization," J. Geophys. Res. 100, 13331-13332 (1995).
[CrossRef]

K. Allali, A. Bricaud, M. Babin, A. Morel, and P. Chang, "A new method for measuring spectral absorption coefficients of marine particles," Limnol. Oceanogr. 40, 1526-1532 (1995).
[CrossRef]

A. Morel and A. Bricaud, "Theoretical results concerning light absorption in a discretet medium, and application to specific absorption of phytoplankton," Deep-Sea Res. Part A 28, 1375-1393 (1981).
[CrossRef]

Morrow, J. H.

R. R. Bidigare, J. H. Morrow, and D. A. Kiefer, "Derivative analysis of spectral absorption by photosynthetic pigments in the western Sargasso Sea," J. Mar. Res. 47, 323-341 (1989).
[CrossRef]

Moulin, C.

A. Niang, F. Badran, C. Moulin, M. Crepon, and S. Thiria, "Retrieval of aerosol type and optical thickness over the Mediterranean from SeaWiFS images using an automatic neural classification method," Remote Sens. Environ. 100, 82-94 (2006).
[CrossRef]

S. Alvain, C. Moulin, Y. Dandonneau, and F. M. Bréon, "Remote sensing of phytoplankton groups in case 1 waters from global SeaWiFS Imagery," Deep-Sea Res . Part I 52, 1989-2004 (2005).
[CrossRef]

A. Niang, S. Thiria, F. Badran, and C. Moulin, "Automatic neural classification of ocean colour reflectance spectra at the top of the atmosphere with introduction of expert knowledge," Remote Sens. Environ. 86, 257-271 (2003).
[CrossRef]

Niang, A.

A. Niang, F. Badran, C. Moulin, M. Crepon, and S. Thiria, "Retrieval of aerosol type and optical thickness over the Mediterranean from SeaWiFS images using an automatic neural classification method," Remote Sens. Environ. 100, 82-94 (2006).
[CrossRef]

A. Niang, S. Thiria, F. Badran, and C. Moulin, "Automatic neural classification of ocean colour reflectance spectra at the top of the atmosphere with introduction of expert knowledge," Remote Sens. Environ. 86, 257-271 (2003).
[CrossRef]

Norris, K. H.

M. A. Faust and K. H. Norris, "In vivo spectrophotometric analysis of photosynthetic pigments in natural populations of phytoplankton," Limnol. Oceanogr. 30, 1316-1322 (1985).
[CrossRef]

M. A. Faust and K. H. Norris, "Rapid in vivo spectrophotometric analysis of chlorophyll pigments in intact phytoplankton cultures," Br. Phycol. J. 17, 351-361 (1982).
[CrossRef]

Okami, N.

M. Kishino, M. Takahashi, N. Okami, and S. Ichimura, "Estimation of the spectral absorption coefficients of phytoplankton in the sea," Bull. Mar. Sci. 37, 634-642 (1985).

Oubelkheir, K.

A. Bricaud, H. Claustre, J. Ras, and K. Oubelkheir, "Natural variability of phytoplankton absorption in oceanic waters: influence of the size structure of algal population," J. Geophys. Res. 109, C11010, doi: (2004).
[CrossRef]

Patch, J. S.

Perry, M. J.

C. S. Roesler and M. J. Perry, "In situ phytoplankton absorption, fluorescence emission, and particulate backscattering spectra determined from reflectance," J. Geophys. Res 100, 22767-22767 (1995).
[CrossRef]

Platt, T.

V. Stuart, S. Sathyendranath, T. Platt, H. Mass, and B. D. Irwin, "Pigments and species composition of natural phytoplankton populations: effect on the absorption spectra," J. Plankton Res. 20, 187-217 (1998).
[CrossRef]

Ras, J.

A. Bricaud, H. Claustre, J. Ras, and K. Oubelkheir, "Natural variability of phytoplankton absorption in oceanic waters: influence of the size structure of algal population," J. Geophys. Res. 109, C11010, doi: (2004).
[CrossRef]

Roesler, C. S.

C. S. Roesler and M. J. Perry, "In situ phytoplankton absorption, fluorescence emission, and particulate backscattering spectra determined from reflectance," J. Geophys. Res 100, 22767-22767 (1995).
[CrossRef]

Sathyendranath, S.

V. Stuart, S. Sathyendranath, T. Platt, H. Mass, and B. D. Irwin, "Pigments and species composition of natural phytoplankton populations: effect on the absorption spectra," J. Plankton Res. 20, 187-217 (1998).
[CrossRef]

N. Hoepffner and S. Sathyendranath, "Determination of the major groups of phytoplankton pigments from the absorption spectra of total particulate matter," J. Geophys. Res. 98, 22789-22803 (1993).
[CrossRef]

Siegel, D. A.

S. A. Garver, D. A. Siegel, and B. G. Mitchell, "Variability in near surface particulate absorption spectra : what can a satellite ocean color image see?" Limnol. Oceanogr. 39, 1349-1367 (1994).
[CrossRef]

Steward, R. G.

Stramski, D.

A. Bricaud and D. Stramski, "Spectral absorption coefficients of living phytoplankton and non-algal biogenous matter: a comparison between the Peru upwelling area and the Sargasso Sea," Limnol. Oceanogr. 35, 562-582 (1990).
[CrossRef]

Stuart, V.

V. Stuart, S. Sathyendranath, T. Platt, H. Mass, and B. D. Irwin, "Pigments and species composition of natural phytoplankton populations: effect on the absorption spectra," J. Plankton Res. 20, 187-217 (1998).
[CrossRef]

Takahashi, M.

M. Kishino, M. Takahashi, N. Okami, and S. Ichimura, "Estimation of the spectral absorption coefficients of phytoplankton in the sea," Bull. Mar. Sci. 37, 634-642 (1985).

Thiria, S.

A. Niang, F. Badran, C. Moulin, M. Crepon, and S. Thiria, "Retrieval of aerosol type and optical thickness over the Mediterranean from SeaWiFS images using an automatic neural classification method," Remote Sens. Environ. 100, 82-94 (2006).
[CrossRef]

A. Niang, S. Thiria, F. Badran, and C. Moulin, "Automatic neural classification of ocean colour reflectance spectra at the top of the atmosphere with introduction of expert knowledge," Remote Sens. Environ. 86, 257-271 (2003).
[CrossRef]

S. Thiria, C. Mejia, F. Badran, and M. Crepon, "A neural network approach for modelling nonlinear transfer function: application for dealiasing spaceborne scatterometer data," J. Geophys. Res. 98, 827-841 (1993).
[CrossRef]

Twardowski, M. S.

L. B. Eisner, M. S. Twardowski, and T. J. Cowles, "Resolving phytoplankton photoprotective:photosynthetic carotenoid ratios on fine scales using in situ spectral absorption measurements," Limnol. Oceanogr. 48, 632-646 (2003).
[CrossRef]

Vidussi, F.

F. Vidussi, H. Claustre, B. B. Manca, A. Luchetta, and J. C. Marty, "Phytoplankton pigment distribution in relation to upper thermocline circulation in the eastern Mediterranean Sea during winter," J. Geophys. Res. 106, 19939-19956 (2001).
[CrossRef]

F. Vidussi, H. Claustre, J. Bustillos-Guzman, C. Cailliau, and J. C. Marty, "Rapid HPLC method for determination of phytoplankton chemotaxonomic pigments: separation of chlorophyll a from divinyl-chlorophyll-a, and zeaxanthin from lutein," J. Plankton Res. 18, 2377-2382 (1996).
[CrossRef]

Appl. Opt. (1)

Br. Phycol. J. (1)

M. A. Faust and K. H. Norris, "Rapid in vivo spectrophotometric analysis of chlorophyll pigments in intact phytoplankton cultures," Br. Phycol. J. 17, 351-361 (1982).
[CrossRef]

Bull. Mar. Sci. (1)

M. Kishino, M. Takahashi, N. Okami, and S. Ichimura, "Estimation of the spectral absorption coefficients of phytoplankton in the sea," Bull. Mar. Sci. 37, 634-642 (1985).

Deep-Sea Res (1)

S. Alvain, C. Moulin, Y. Dandonneau, and F. M. Bréon, "Remote sensing of phytoplankton groups in case 1 waters from global SeaWiFS Imagery," Deep-Sea Res . Part I 52, 1989-2004 (2005).
[CrossRef]

Deep-Sea Res. (1)

A. Morel and A. Bricaud, "Theoretical results concerning light absorption in a discretet medium, and application to specific absorption of phytoplankton," Deep-Sea Res. Part A 28, 1375-1393 (1981).
[CrossRef]

J. Atmos. Sci. (1)

E. N. Lorenz, "Atmospheric predictabilty as revealed by naturally occurring analogues," J. Atmos. Sci. 26, 636-646 (1969).
[CrossRef]

J. Geophys. Res (1)

C. S. Roesler and M. J. Perry, "In situ phytoplankton absorption, fluorescence emission, and particulate backscattering spectra determined from reflectance," J. Geophys. Res 100, 22767-22767 (1995).
[CrossRef]

J. Geophys. Res. (7)

S. Thiria, C. Mejia, F. Badran, and M. Crepon, "A neural network approach for modelling nonlinear transfer function: application for dealiasing spaceborne scatterometer data," J. Geophys. Res. 98, 827-841 (1993).
[CrossRef]

A. Bricaud, M. Babin, A. Morel, and H. Claustre, "Variability in the chlorophyll-specific absorption coefficients of natural phytoplankton: analysis and parameterization," J. Geophys. Res. 100, 13331-13332 (1995).
[CrossRef]

F. Vidussi, H. Claustre, B. B. Manca, A. Luchetta, and J. C. Marty, "Phytoplankton pigment distribution in relation to upper thermocline circulation in the eastern Mediterranean Sea during winter," J. Geophys. Res. 106, 19939-19956 (2001).
[CrossRef]

A. Bricaud, H. Claustre, J. Ras, and K. Oubelkheir, "Natural variability of phytoplankton absorption in oceanic waters: influence of the size structure of algal population," J. Geophys. Res. 109, C11010, doi: (2004).
[CrossRef]

N. Hoepffner and S. Sathyendranath, "Determination of the major groups of phytoplankton pigments from the absorption spectra of total particulate matter," J. Geophys. Res. 98, 22789-22803 (1993).
[CrossRef]

K. Allali, A. Bricaud, and H. Claustre, "Spatial variations in the chlorophyll-specific absorption coefficients of phytoplankton and photosynthetically active pigments in the equatorial Pacific," J. Geophys. Res. 102, 12413-12423 (1997).
[CrossRef]

A. Morel and S. Maritorena, "Bio-optical properties of oceanic waters: a reappraisal," J. Geophys. Res. 106, 7763-7780 (2001).
[CrossRef]

J. Mar. Res. (1)

R. R. Bidigare, J. H. Morrow, and D. A. Kiefer, "Derivative analysis of spectral absorption by photosynthetic pigments in the western Sargasso Sea," J. Mar. Res. 47, 323-341 (1989).
[CrossRef]

J. Plankton Res. (2)

F. Vidussi, H. Claustre, J. Bustillos-Guzman, C. Cailliau, and J. C. Marty, "Rapid HPLC method for determination of phytoplankton chemotaxonomic pigments: separation of chlorophyll a from divinyl-chlorophyll-a, and zeaxanthin from lutein," J. Plankton Res. 18, 2377-2382 (1996).
[CrossRef]

V. Stuart, S. Sathyendranath, T. Platt, H. Mass, and B. D. Irwin, "Pigments and species composition of natural phytoplankton populations: effect on the absorption spectra," J. Plankton Res. 20, 187-217 (1998).
[CrossRef]

Limnol. Oceanogr. (5)

K. Allali, A. Bricaud, M. Babin, A. Morel, and P. Chang, "A new method for measuring spectral absorption coefficients of marine particles," Limnol. Oceanogr. 40, 1526-1532 (1995).
[CrossRef]

A. Bricaud and D. Stramski, "Spectral absorption coefficients of living phytoplankton and non-algal biogenous matter: a comparison between the Peru upwelling area and the Sargasso Sea," Limnol. Oceanogr. 35, 562-582 (1990).
[CrossRef]

M. A. Faust and K. H. Norris, "In vivo spectrophotometric analysis of photosynthetic pigments in natural populations of phytoplankton," Limnol. Oceanogr. 30, 1316-1322 (1985).
[CrossRef]

S. A. Garver, D. A. Siegel, and B. G. Mitchell, "Variability in near surface particulate absorption spectra : what can a satellite ocean color image see?" Limnol. Oceanogr. 39, 1349-1367 (1994).
[CrossRef]

L. B. Eisner, M. S. Twardowski, and T. J. Cowles, "Resolving phytoplankton photoprotective:photosynthetic carotenoid ratios on fine scales using in situ spectral absorption measurements," Limnol. Oceanogr. 48, 632-646 (2003).
[CrossRef]

Limnol. Oceanogr. Methods (1)

A. M. Ciotti and A. Bricaud, "Retrievals of a size parameter for phytoplankton and spectral light absorption by colored detrital matter from water-leaving radiances at SeaWiFS channels in a continental shelf region off Brazil" Limnol. Oceanogr. Methods 4, 237-253 (2006).
[CrossRef]

Q. J. R. Meteorol. Soc. (1)

R. T. Clark and M. Déqué, "Conditional probability seasonal predictions of precipitation," Q. J. R. Meteorol. Soc. 129, 1-15 (2003).
[CrossRef]

Remote Sens. Environ. (2)

A. Niang, S. Thiria, F. Badran, and C. Moulin, "Automatic neural classification of ocean colour reflectance spectra at the top of the atmosphere with introduction of expert knowledge," Remote Sens. Environ. 86, 257-271 (2003).
[CrossRef]

A. Niang, F. Badran, C. Moulin, M. Crepon, and S. Thiria, "Retrieval of aerosol type and optical thickness over the Mediterranean from SeaWiFS images using an automatic neural classification method," Remote Sens. Environ. 100, 82-94 (2006).
[CrossRef]

Other (1)

T. Kohonen, Self-Organizing Maps (Springer-Verlag, 1984).

Cited By

OSA participates in CrossRef's Cited-By Linking service. Citing articles from OSA journals and other participating publishers are listed here.

Alert me when this article is cited.


Figures (13)

Fig. 1
Fig. 1

(Color online) Assumed in vivo weight-specific absorption spectra of the main pigments, asol, i * ( λ ) ( in   m 2 mg 1 ) , as derived from absorption spectra of individual pigments in solvent. [This figure is taken from Bricaud et al. (Ref. 8).]

Fig. 2
Fig. 2

Structure of the SOM. The network comprises two layers: an input layer used to present observations and an adaptation layer ( n × p neurons) for which a neighborhood system (square surrounding neuron i) is defined (distance δ between neurons and neighborhood function). Each neuron i is associated with a reference vector rv i and is fully connected to the input layer. At each step of the learning all the input vectors (x) are attributed to the closest neuron. Then each neuron rv i is computed according to its attributed data and its neighbor's attributed data. We proceed until convergence or a fixed number of iterations is reached.

Fig. 3
Fig. 3

Representation of the reference vectors rv corresponding to log-transformed phytoplankton absorption spectra of the SOM. The neuron number goes from top to bottom and left to right. The arrow shows the spectrum amplitude gradient. The number displayed on each spectrum is the amount of data captured by the neuron. (All the plots have the same axis scale.)

Fig. 4
Fig. 4

Mean absorption spectrum ( m 1 ) (rv spectrum) versus wavelength for some neurons of the SOM. The thick full curves represent the mean spectrum (rv spectrum) and the thick dotted curves represent the mean plus or minus two standard deviations; the thin curves in between represent the spectra captured by the neuron.

Fig. 5
Fig. 5

(Color online) (a)–(e) Mean of the pigment concentrations (on a logarithmic scale) of the neurons of the SOM for the five pigment classes. The color scale is different for each pigment. (f) Mean maximum amplitude for each neuron. Panels (a)–(e) show the strong link between accessory pigments (TPSC, TPPC) and Tchl-a concentrations.

Fig. 6
Fig. 6

(Color online) (a)–(e) Ratios of the concentrations of the four pigment classes to the Tchl-a concentration for all the neurons of the SOM. The color scale is different for each pigment class. The ellipses enclose clear patterns for each of the pigment ratios. The neurons above the gray line roughly correspond to neurons associated with deep samples. The neurons below the gray line roughly correspond to neurons associated with samples in the “first optical depth.” (b) Tchl-b∕Tchl-a ratios for neurons of the first optical depth.

Fig. 7
Fig. 7

(Color online) Thirty maps of the thirty and one maps of the rvs. We have the 30 derivatives. Only the amplitude maximum is missing (shown in Fig. 5).

Fig. 8
Fig. 8

(Color online) (a) Fucoxanthin∕Tchl-a concentration ratios for the neurons of the SOM. (b) Derivative at 510   nm of the log 10 absorption spectra. The correspondence between the patterns displayed by the two maps suggests a strong link between the two values.

Fig. 9
Fig. 9

Fucoxanthin∕Tchl-a ratio as a function of the derivative of the log 10 of the absorption spectrum of phytoplankton at 510   nm . The water sample data are represented by dots (⋅). The reference vector data (provided by the SOM map) are represented by crosses (+). The regression line linking the two quantities is shown as a solid line (—). Two estimators of the quality of the regression are provided ( s = 0.284 , R 2 = 0.591 ) .

Fig. 10
Fig. 10

(Color online) (a) Values of log 10 (TPPC∕TPSC) for the SOM neurons. (b) Absorption spectrum slope computed as ( a 490 a 530 ) / [ a 680 ( 490 530 ) ] . A correspondence between the patterns displayed by the two maps suggests a strong link between the two quantities.

Fig. 11
Fig. 11

Absorption ratio of Eisner et al.[24] ( a 490 a 530 ) / [ a 680 ( 490 530 ) ] as a function of the log 10 of the TPPC∕TPSC ratio, for the samples collected in the first optical depth. The water sample data are represented by dots (⋅). The reference vector data (provided by the SOM map) are represented by crosses (+). The log-linear regression line linking the two quantities is shown as a solid line (—). Two estimators of the quality of the regression are displayed ( s = 0.011 , R 2 = 0.515 ).

Fig. 12
Fig. 12

(Color online) (a) Tchl-b∕Tchl-a concentration ratios for the SOM neurons. (b) Derivative of the log 10 of the absorption spectra at 650   nm . A correspondence between the patterns displayed by the two maps suggests a strong link between the two quantities.

Fig. 13
Fig. 13

Tchl-b∕Tchl-a ratio as a function of the slope of the log 10 of the absorption spectrum at 510   nm . The water sample data are represented by dots (⋅). The reference vector data (provided by the SOM map) are represented by crosses (+). Log-linear regression linking the two values is shown by a solid line (—). s and R 2 , two estimators of the quality of the regression are displayed. In (a) all the data are processed ( s = 0.842 , R 2 = 0.277 ). In (b) the outliers are removed, which greatly improves the quality of the regression ( s = 0.246 , R 2 = 0.531 ).

Tables (4)

Tables Icon

Table 1 Cruises Where Absorption and HPLC Data Were Simultaneously Collected

Tables Icon

Table 2 Characteristics of Three Outliers Neurons

Tables Icon

Table 3 Error Performances on Pigment Retrieving

Tables Icon

Table 4 Error Performances for Various Codings

Equations (10)

Equations on this page are rendered with MathJax. Learn more.

log 10 ( a j ) log 10 ( a j 10 ) = log 10 ( a j / a j 10 ) , where   j = ( 400 + 10 i )   and   i = 1 , 2 , 3 , , 30.
fucoxanthin / Tchl - a = 1.311 ( a 510 / a 500 ) 8.19
( a 490 a 530 ) / [ a 680 ( 490 530 ) ] = 0.0416 0.0262 × log 10 ( TPPC / TPSC ) .
Tchl- b / Tchl- a = 0.019 ( a 650 / a 640 ) 13.33 with   ( R 2 = 0.28 , s = 0.84 ) .
Tchl- b / Tchl- a = 0.090 ( a 650 / a 640 ) 6.838 ,
R 2 = ( y i estimated y ¯ ) 2 ( y i observed y ¯ ) 2 ,
s = ( ( y i observed y i estimated ) 2 n 2 ) 1 / 2 .
RMSE = [ 1 N i = 1 N ( x i estimated x i observed ) 2 ] 1 / 2 .
RRMSE = [ 1 N i = 1 N ( x i estimated x i observed ) 2 ( x i observed ) 2 ] 1 / 2 ,
VRRMSE = 1 N j = 1 N [ 1 M i = 1 M ( x j , i estimated x j , i observed ) 2 ( x j , i observed ) 2 ] 1 / 2 .

Metrics