Abstract

In the presented study a hyperspectral imager (400700nm) mounted on a stereo-microscope was used to separate differences in in vivo optical signatures identifying different pigment groups of bloom-forming phytoplankton and macroalgae by comparing spectral absorption, transmittance, and reflectance from 400700nm. The results show that the hyperspectral imager could be used to detect spectral characteristics on the μm level to calibrate, validate, identify, and separate objects with differences in color (optical fingerprinting). This information can be used for pigment group specific taxonomy (bio-optical taxonomy), eco-physiological information (e.g., health status), monitoring, and mapping applications.

© 2009 Optical Society of America

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    [CrossRef]
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    [CrossRef]
  7. S. Maritorena and D. A. Siegel, “Consistent merging of satellite ocean color data sets using a bio-optical model,” Remote Sens. Environ. 94, 429-440 (2005).
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  8. M. Messie and M.-H. Radenac, “Seasonal variability of the surface chlorophyll in the western tropical Pacific from SeaWiFS data,” Deep Sea Res. I 53, 1581-1600 (2006).
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  9. S. Andrefouet, C. Payri, E. J. Hochberg, L. M. Che, and M. J. Atkinson, “Airborne hyperspectral detection of microbial mat pigmentation in Rangiroa atoll (French Polynesia),” Limnol. Oceanogr. 48, (1, part 2) 426-430 (2003).
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    [CrossRef]
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    [CrossRef]
  15. M. Harwit and N. J. A. Sloan, Hadamard Transform Optics (Academic Press, 1979).
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  17. G. Johnsen, Z. Volent, F. Sigernes, and E. Sakshaug, “Ecosystem Barents Sea” in Remote sensing in the Barents Sea, E. Sakshaug, G. Johnsen, and K. Kovacs, eds. (Tapir Academic Press, 2009), Chap. 6 (to be published).
  18. G. Johnsen and E. Sakshaug, “Bio-optical characteristics of PSII and PSI in 33 species (13 pigment groups) of marine phytoplankton, and the relevance for pulse-amplitude-modulated and fast-repetition-rate fluorometry,” J. Phycol. 43, 1236-1251 (2007).
    [CrossRef]
  19. J. Grzymski, G. Johnsen, and E. Sakshaug, “The significance of intracellular self-shading on the bio-optical properties of brown, red, and green macroalgae,” J. Phycol. 33, 408-414(1997).
    [CrossRef]

2007 (5)

V. E. Brando and S. R. Phinn, “Coastal aquatic remote sensing applications for environmental monitoring and management,” J. Appl. Remote Sensing 1, 011599 (2007).
[CrossRef]

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Z. Volent, G. Johnsen, and F. Sigernes, “Kelp forest mapping by use of airborne hyperspectral imager,” J. Appl. Remote Sensing 1, 011503-011521 (2007).
[CrossRef]

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

G. Johnsen and E. Sakshaug, “Bio-optical characteristics of PSII and PSI in 33 species (13 pigment groups) of marine phytoplankton, and the relevance for pulse-amplitude-modulated and fast-repetition-rate fluorometry,” J. Phycol. 43, 1236-1251 (2007).
[CrossRef]

2006 (2)

A. M. Filippi and J. R. Jensen, “Fuzzy learning vector quantization for hyperspectral coastal vegetation classification,” Remote Sens. Environ. 100, 512-530 (2006).
[CrossRef]

M. Messie and M.-H. Radenac, “Seasonal variability of the surface chlorophyll in the western tropical Pacific from SeaWiFS data,” Deep Sea Res. I 53, 1581-1600 (2006).
[CrossRef]

2005 (1)

S. Maritorena and D. A. Siegel, “Consistent merging of satellite ocean color data sets using a bio-optical model,” Remote Sens. Environ. 94, 429-440 (2005).
[CrossRef]

2004 (1)

S. Andrefouet, C. Payri, E. J. Hochberg, C. M. Hu, M. J. Atkinson, and F. E. Muller-Karger, “Use of in situ and airborne reflectance for scaling-up spectral discrimination of coral reef macroalgae from species to communities,” Mar. Ecol. Prog. Ser. 283, 161-177 (2004).
[CrossRef]

2003 (1)

S. Andrefouet, C. Payri, E. J. Hochberg, L. M. Che, and M. J. Atkinson, “Airborne hyperspectral detection of microbial mat pigmentation in Rangiroa atoll (French Polynesia),” Limnol. Oceanogr. 48, (1, part 2) 426-430 (2003).
[CrossRef]

2000 (3)

1997 (1)

J. Grzymski, G. Johnsen, and E. Sakshaug, “The significance of intracellular self-shading on the bio-optical properties of brown, red, and green macroalgae,” J. Phycol. 33, 408-414(1997).
[CrossRef]

Andrefouet, S.

S. Andrefouet, C. Payri, E. J. Hochberg, C. M. Hu, M. J. Atkinson, and F. E. Muller-Karger, “Use of in situ and airborne reflectance for scaling-up spectral discrimination of coral reef macroalgae from species to communities,” Mar. Ecol. Prog. Ser. 283, 161-177 (2004).
[CrossRef]

S. Andrefouet, C. Payri, E. J. Hochberg, L. M. Che, and M. J. Atkinson, “Airborne hyperspectral detection of microbial mat pigmentation in Rangiroa atoll (French Polynesia),” Limnol. Oceanogr. 48, (1, part 2) 426-430 (2003).
[CrossRef]

Atkinson, M. J.

S. Andrefouet, C. Payri, E. J. Hochberg, C. M. Hu, M. J. Atkinson, and F. E. Muller-Karger, “Use of in situ and airborne reflectance for scaling-up spectral discrimination of coral reef macroalgae from species to communities,” Mar. Ecol. Prog. Ser. 283, 161-177 (2004).
[CrossRef]

S. Andrefouet, C. Payri, E. J. Hochberg, L. M. Che, and M. J. Atkinson, “Airborne hyperspectral detection of microbial mat pigmentation in Rangiroa atoll (French Polynesia),” Limnol. Oceanogr. 48, (1, part 2) 426-430 (2003).
[CrossRef]

Bach, H.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Barnes, C. A.

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

Benz, U.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Bowles, J. H.

J. H. Bowles, M. R. Corson, C. O. Davis, D. Korwan, M. J. Montes, and W. Snyder, “Hyperspectral sensor characteristics needed for coastal ocean science,” in IGARSS 2004: 2004 IEEE International Geoscience and Remote Sensing Symposium: Proceedings (IEEE, 2004), Vol. 1, pp. 461-464.
[CrossRef]

Brando, V. E.

V. E. Brando and S. R. Phinn, “Coastal aquatic remote sensing applications for environmental monitoring and management,” J. Appl. Remote Sensing 1, 011599 (2007).
[CrossRef]

Brodzik, A. K.

J. E. Murguia, T. D. Reeves, J. M. Mooney, W. S. Ewing, F. D. Shepherd, and A. K. Brodzik, “Compact visible/near-infrared hyperspectral imager,” Proc. SPIE 4028, 457-468 (2000).
[CrossRef]

Brozik, S. M.

J. A. Timlin, M. B. Sinclair, D. M. Haaland, J. Martinez, M. Manginell, S. M. Brozik, J. F. Guzowski, and M. Werner-Washburne, “Hyperspectral imaging of biological targets: the difference a high resolution spectral dimension and multivariate analysis can make,” in Biomedical Imaging: Macro to Nano, 2004. IEEE International Symposium (IEEE Computer Society, 2004), Vol. 1522, pp. 1529-1532.

Chawla, M. K.

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

Che, L. M.

S. Andrefouet, C. Payri, E. J. Hochberg, L. M. Che, and M. J. Atkinson, “Airborne hyperspectral detection of microbial mat pigmentation in Rangiroa atoll (French Polynesia),” Limnol. Oceanogr. 48, (1, part 2) 426-430 (2003).
[CrossRef]

Corson, M. R.

J. H. Bowles, M. R. Corson, C. O. Davis, D. Korwan, M. J. Montes, and W. Snyder, “Hyperspectral sensor characteristics needed for coastal ocean science,” in IGARSS 2004: 2004 IEEE International Geoscience and Remote Sensing Symposium: Proceedings (IEEE, 2004), Vol. 1, pp. 461-464.
[CrossRef]

Davis, C. O.

J. H. Bowles, M. R. Corson, C. O. Davis, D. Korwan, M. J. Montes, and W. Snyder, “Hyperspectral sensor characteristics needed for coastal ocean science,” in IGARSS 2004: 2004 IEEE International Geoscience and Remote Sensing Symposium: Proceedings (IEEE, 2004), Vol. 1, pp. 461-464.
[CrossRef]

DeVerse, R. A.

Eckardt, A.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Ewing, W. S.

J. E. Murguia, T. D. Reeves, J. M. Mooney, W. S. Ewing, F. D. Shepherd, and A. K. Brodzik, “Compact visible/near-infrared hyperspectral imager,” Proc. SPIE 4028, 457-468 (2000).
[CrossRef]

Fateley, W. G.

Filippi, A. M.

A. M. Filippi and J. R. Jensen, “Fuzzy learning vector quantization for hyperspectral coastal vegetation classification,” Remote Sens. Environ. 100, 512-530 (2006).
[CrossRef]

Forster, K. P.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Grzymski, J.

J. Grzymski, G. Johnsen, and E. Sakshaug, “The significance of intracellular self-shading on the bio-optical properties of brown, red, and green macroalgae,” J. Phycol. 33, 408-414(1997).
[CrossRef]

Guzowski, J. F.

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

J. A. Timlin, M. B. Sinclair, D. M. Haaland, J. Martinez, M. Manginell, S. M. Brozik, J. F. Guzowski, and M. Werner-Washburne, “Hyperspectral imaging of biological targets: the difference a high resolution spectral dimension and multivariate analysis can make,” in Biomedical Imaging: Macro to Nano, 2004. IEEE International Symposium (IEEE Computer Society, 2004), Vol. 1522, pp. 1529-1532.

Haaland, D. M.

J. A. Timlin, M. B. Sinclair, D. M. Haaland, J. Martinez, M. Manginell, S. M. Brozik, J. F. Guzowski, and M. Werner-Washburne, “Hyperspectral imaging of biological targets: the difference a high resolution spectral dimension and multivariate analysis can make,” in Biomedical Imaging: Macro to Nano, 2004. IEEE International Symposium (IEEE Computer Society, 2004), Vol. 1522, pp. 1529-1532.

Hammaker, R. M.

Harwit, M.

M. Harwit and N. J. A. Sloan, Hadamard Transform Optics (Academic Press, 1979).

Haydn, R.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Heia, K.

Hochberg, E. J.

S. Andrefouet, C. Payri, E. J. Hochberg, C. M. Hu, M. J. Atkinson, and F. E. Muller-Karger, “Use of in situ and airborne reflectance for scaling-up spectral discrimination of coral reef macroalgae from species to communities,” Mar. Ecol. Prog. Ser. 283, 161-177 (2004).
[CrossRef]

S. Andrefouet, C. Payri, E. J. Hochberg, L. M. Che, and M. J. Atkinson, “Airborne hyperspectral detection of microbial mat pigmentation in Rangiroa atoll (French Polynesia),” Limnol. Oceanogr. 48, (1, part 2) 426-430 (2003).
[CrossRef]

Hofer, S.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Hu, C. M.

S. Andrefouet, C. Payri, E. J. Hochberg, C. M. Hu, M. J. Atkinson, and F. E. Muller-Karger, “Use of in situ and airborne reflectance for scaling-up spectral discrimination of coral reef macroalgae from species to communities,” Mar. Ecol. Prog. Ser. 283, 161-177 (2004).
[CrossRef]

Jensen, J. R.

A. M. Filippi and J. R. Jensen, “Fuzzy learning vector quantization for hyperspectral coastal vegetation classification,” Remote Sens. Environ. 100, 512-530 (2006).
[CrossRef]

Johnsen, G.

Z. Volent, G. Johnsen, and F. Sigernes, “Kelp forest mapping by use of airborne hyperspectral imager,” J. Appl. Remote Sensing 1, 011503-011521 (2007).
[CrossRef]

G. Johnsen and E. Sakshaug, “Bio-optical characteristics of PSII and PSI in 33 species (13 pigment groups) of marine phytoplankton, and the relevance for pulse-amplitude-modulated and fast-repetition-rate fluorometry,” J. Phycol. 43, 1236-1251 (2007).
[CrossRef]

J. Grzymski, G. Johnsen, and E. Sakshaug, “The significance of intracellular self-shading on the bio-optical properties of brown, red, and green macroalgae,” J. Phycol. 33, 408-414(1997).
[CrossRef]

G. Johnsen, Z. Volent, F. Sigernes, and E. Sakshaug, “Ecosystem Barents Sea” in Remote sensing in the Barents Sea, E. Sakshaug, G. Johnsen, and K. Kovacs, eds. (Tapir Academic Press, 2009), Chap. 6 (to be published).

Kaufmann, C.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Korwan, D.

J. H. Bowles, M. R. Corson, C. O. Davis, D. Korwan, M. J. Montes, and W. Snyder, “Hyperspectral sensor characteristics needed for coastal ocean science,” in IGARSS 2004: 2004 IEEE International Geoscience and Remote Sensing Symposium: Proceedings (IEEE, 2004), Vol. 1, pp. 461-464.
[CrossRef]

Lorentzen, D. A.

Manginell, M.

J. A. Timlin, M. B. Sinclair, D. M. Haaland, J. Martinez, M. Manginell, S. M. Brozik, J. F. Guzowski, and M. Werner-Washburne, “Hyperspectral imaging of biological targets: the difference a high resolution spectral dimension and multivariate analysis can make,” in Biomedical Imaging: Macro to Nano, 2004. IEEE International Symposium (IEEE Computer Society, 2004), Vol. 1522, pp. 1529-1532.

Maritorena, S.

S. Maritorena and D. A. Siegel, “Consistent merging of satellite ocean color data sets using a bio-optical model,” Remote Sens. Environ. 94, 429-440 (2005).
[CrossRef]

Martinez, J.

J. A. Timlin, M. B. Sinclair, D. M. Haaland, J. Martinez, M. Manginell, S. M. Brozik, J. F. Guzowski, and M. Werner-Washburne, “Hyperspectral imaging of biological targets: the difference a high resolution spectral dimension and multivariate analysis can make,” in Biomedical Imaging: Macro to Nano, 2004. IEEE International Symposium (IEEE Computer Society, 2004), Vol. 1522, pp. 1529-1532.

McNaughton, B. L.

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

Messie, M.

M. Messie and M.-H. Radenac, “Seasonal variability of the surface chlorophyll in the western tropical Pacific from SeaWiFS data,” Deep Sea Res. I 53, 1581-1600 (2006).
[CrossRef]

Montes, M. J.

J. H. Bowles, M. R. Corson, C. O. Davis, D. Korwan, M. J. Montes, and W. Snyder, “Hyperspectral sensor characteristics needed for coastal ocean science,” in IGARSS 2004: 2004 IEEE International Geoscience and Remote Sensing Symposium: Proceedings (IEEE, 2004), Vol. 1, pp. 461-464.
[CrossRef]

Mooney, J. M.

J. E. Murguia, T. D. Reeves, J. M. Mooney, W. S. Ewing, F. D. Shepherd, and A. K. Brodzik, “Compact visible/near-infrared hyperspectral imager,” Proc. SPIE 4028, 457-468 (2000).
[CrossRef]

Mueller, A.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Muller-Karger, F. E.

S. Andrefouet, C. Payri, E. J. Hochberg, C. M. Hu, M. J. Atkinson, and F. E. Muller-Karger, “Use of in situ and airborne reflectance for scaling-up spectral discrimination of coral reef macroalgae from species to communities,” Mar. Ecol. Prog. Ser. 283, 161-177 (2004).
[CrossRef]

Murguia, J. E.

J. E. Murguia, T. D. Reeves, J. M. Mooney, W. S. Ewing, F. D. Shepherd, and A. K. Brodzik, “Compact visible/near-infrared hyperspectral imager,” Proc. SPIE 4028, 457-468 (2000).
[CrossRef]

Nieman, L. T.

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

Payri, C.

S. Andrefouet, C. Payri, E. J. Hochberg, C. M. Hu, M. J. Atkinson, and F. E. Muller-Karger, “Use of in situ and airborne reflectance for scaling-up spectral discrimination of coral reef macroalgae from species to communities,” Mar. Ecol. Prog. Ser. 283, 161-177 (2004).
[CrossRef]

S. Andrefouet, C. Payri, E. J. Hochberg, L. M. Che, and M. J. Atkinson, “Airborne hyperspectral detection of microbial mat pigmentation in Rangiroa atoll (French Polynesia),” Limnol. Oceanogr. 48, (1, part 2) 426-430 (2003).
[CrossRef]

Penne, B.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Phinn, S. R.

V. E. Brando and S. R. Phinn, “Coastal aquatic remote sensing applications for environmental monitoring and management,” J. Appl. Remote Sensing 1, 011599 (2007).
[CrossRef]

Radenac, M.-H.

M. Messie and M.-H. Radenac, “Seasonal variability of the surface chlorophyll in the western tropical Pacific from SeaWiFS data,” Deep Sea Res. I 53, 1581-1600 (2006).
[CrossRef]

Reeves, T. D.

J. E. Murguia, T. D. Reeves, J. M. Mooney, W. S. Ewing, F. D. Shepherd, and A. K. Brodzik, “Compact visible/near-infrared hyperspectral imager,” Proc. SPIE 4028, 457-468 (2000).
[CrossRef]

Roysam, B.

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

Sakshaug, E.

G. Johnsen and E. Sakshaug, “Bio-optical characteristics of PSII and PSI in 33 species (13 pigment groups) of marine phytoplankton, and the relevance for pulse-amplitude-modulated and fast-repetition-rate fluorometry,” J. Phycol. 43, 1236-1251 (2007).
[CrossRef]

J. Grzymski, G. Johnsen, and E. Sakshaug, “The significance of intracellular self-shading on the bio-optical properties of brown, red, and green macroalgae,” J. Phycol. 33, 408-414(1997).
[CrossRef]

G. Johnsen, Z. Volent, F. Sigernes, and E. Sakshaug, “Ecosystem Barents Sea” in Remote sensing in the Barents Sea, E. Sakshaug, G. Johnsen, and K. Kovacs, eds. (Tapir Academic Press, 2009), Chap. 6 (to be published).

Saptari, V.

V. Saptari, Fourier-Transform Spectroscopy Instrumentation Engineering (SPIE, 2004).

Schreier, G.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Shepherd, F. D.

J. E. Murguia, T. D. Reeves, J. M. Mooney, W. S. Ewing, F. D. Shepherd, and A. K. Brodzik, “Compact visible/near-infrared hyperspectral imager,” Proc. SPIE 4028, 457-468 (2000).
[CrossRef]

Siegel, D. A.

S. Maritorena and D. A. Siegel, “Consistent merging of satellite ocean color data sets using a bio-optical model,” Remote Sens. Environ. 94, 429-440 (2005).
[CrossRef]

Sigernes, F.

Z. Volent, G. Johnsen, and F. Sigernes, “Kelp forest mapping by use of airborne hyperspectral imager,” J. Appl. Remote Sensing 1, 011503-011521 (2007).
[CrossRef]

F. Sigernes, D. A. Lorentzen, K. Heia, and T. Svenoe, “Multipurpose spectral imager,” Appl. Opt. 39, 3143-3153 (2000).
[CrossRef]

G. Johnsen, Z. Volent, F. Sigernes, and E. Sakshaug, “Ecosystem Barents Sea” in Remote sensing in the Barents Sea, E. Sakshaug, G. Johnsen, and K. Kovacs, eds. (Tapir Academic Press, 2009), Chap. 6 (to be published).

Sinclair, M. B.

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

J. A. Timlin, M. B. Sinclair, D. M. Haaland, J. Martinez, M. Manginell, S. M. Brozik, J. F. Guzowski, and M. Werner-Washburne, “Hyperspectral imaging of biological targets: the difference a high resolution spectral dimension and multivariate analysis can make,” in Biomedical Imaging: Macro to Nano, 2004. IEEE International Symposium (IEEE Computer Society, 2004), Vol. 1522, pp. 1529-1532.

Sloan, N. J. A.

M. Harwit and N. J. A. Sloan, Hadamard Transform Optics (Academic Press, 1979).

Snyder, W.

J. H. Bowles, M. R. Corson, C. O. Davis, D. Korwan, M. J. Montes, and W. Snyder, “Hyperspectral sensor characteristics needed for coastal ocean science,” in IGARSS 2004: 2004 IEEE International Geoscience and Remote Sensing Symposium: Proceedings (IEEE, 2004), Vol. 1, pp. 461-464.
[CrossRef]

Stuffler, T.

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Sutherland, V. L.

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

Svenoe, T.

Timlin, J. A.

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

J. A. Timlin, M. B. Sinclair, D. M. Haaland, J. Martinez, M. Manginell, S. M. Brozik, J. F. Guzowski, and M. Werner-Washburne, “Hyperspectral imaging of biological targets: the difference a high resolution spectral dimension and multivariate analysis can make,” in Biomedical Imaging: Macro to Nano, 2004. IEEE International Symposium (IEEE Computer Society, 2004), Vol. 1522, pp. 1529-1532.

Volent, Z.

Z. Volent, G. Johnsen, and F. Sigernes, “Kelp forest mapping by use of airborne hyperspectral imager,” J. Appl. Remote Sensing 1, 011503-011521 (2007).
[CrossRef]

G. Johnsen, Z. Volent, F. Sigernes, and E. Sakshaug, “Ecosystem Barents Sea” in Remote sensing in the Barents Sea, E. Sakshaug, G. Johnsen, and K. Kovacs, eds. (Tapir Academic Press, 2009), Chap. 6 (to be published).

Werner-Washburne, M.

J. A. Timlin, M. B. Sinclair, D. M. Haaland, J. Martinez, M. Manginell, S. M. Brozik, J. F. Guzowski, and M. Werner-Washburne, “Hyperspectral imaging of biological targets: the difference a high resolution spectral dimension and multivariate analysis can make,” in Biomedical Imaging: Macro to Nano, 2004. IEEE International Symposium (IEEE Computer Society, 2004), Vol. 1522, pp. 1529-1532.

Worley, P. F.

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

Acta Astronaut. (1)

T. Stuffler, C. Kaufmann, S. Hofer, K. P. Forster, G. Schreier, A. Mueller, A. Eckardt, H. Bach, B. Penne, U. Benz, and R. Haydn, “The EnMAP hyperspectral imager--an advanced optical payload for future applications in Earth observation programmes,” Acta Astronaut. 61, 115-120 (2007).
[CrossRef]

Appl. Opt. (1)

Appl. Spectrosc. (1)

Deep Sea Res. I (1)

M. Messie and M.-H. Radenac, “Seasonal variability of the surface chlorophyll in the western tropical Pacific from SeaWiFS data,” Deep Sea Res. I 53, 1581-1600 (2006).
[CrossRef]

J. Appl. Remote Sensing (2)

V. E. Brando and S. R. Phinn, “Coastal aquatic remote sensing applications for environmental monitoring and management,” J. Appl. Remote Sensing 1, 011599 (2007).
[CrossRef]

Z. Volent, G. Johnsen, and F. Sigernes, “Kelp forest mapping by use of airborne hyperspectral imager,” J. Appl. Remote Sensing 1, 011503-011521 (2007).
[CrossRef]

J. Neurosci. Methods (1)

V. L. Sutherland, J. A. Timlin, L. T. Nieman, J. F. Guzowski, M. K. Chawla, P. F. Worley, B. Roysam, B. L. McNaughton, M. B. Sinclair, and C. A. Barnes, “Advanced imaging of multiple mRNAs in brain tissue using a custom hyperspectral imager and multivariate curve resolution,” J. Neurosci. Methods 160, 144-148 (2007).
[CrossRef]

J. Phycol. (2)

G. Johnsen and E. Sakshaug, “Bio-optical characteristics of PSII and PSI in 33 species (13 pigment groups) of marine phytoplankton, and the relevance for pulse-amplitude-modulated and fast-repetition-rate fluorometry,” J. Phycol. 43, 1236-1251 (2007).
[CrossRef]

J. Grzymski, G. Johnsen, and E. Sakshaug, “The significance of intracellular self-shading on the bio-optical properties of brown, red, and green macroalgae,” J. Phycol. 33, 408-414(1997).
[CrossRef]

Limnol. Oceanogr. (1)

S. Andrefouet, C. Payri, E. J. Hochberg, L. M. Che, and M. J. Atkinson, “Airborne hyperspectral detection of microbial mat pigmentation in Rangiroa atoll (French Polynesia),” Limnol. Oceanogr. 48, (1, part 2) 426-430 (2003).
[CrossRef]

Mar. Ecol. Prog. Ser. (1)

S. Andrefouet, C. Payri, E. J. Hochberg, C. M. Hu, M. J. Atkinson, and F. E. Muller-Karger, “Use of in situ and airborne reflectance for scaling-up spectral discrimination of coral reef macroalgae from species to communities,” Mar. Ecol. Prog. Ser. 283, 161-177 (2004).
[CrossRef]

Proc. SPIE (1)

J. E. Murguia, T. D. Reeves, J. M. Mooney, W. S. Ewing, F. D. Shepherd, and A. K. Brodzik, “Compact visible/near-infrared hyperspectral imager,” Proc. SPIE 4028, 457-468 (2000).
[CrossRef]

Remote Sens. Environ. (2)

A. M. Filippi and J. R. Jensen, “Fuzzy learning vector quantization for hyperspectral coastal vegetation classification,” Remote Sens. Environ. 100, 512-530 (2006).
[CrossRef]

S. Maritorena and D. A. Siegel, “Consistent merging of satellite ocean color data sets using a bio-optical model,” Remote Sens. Environ. 94, 429-440 (2005).
[CrossRef]

Other (5)

J. H. Bowles, M. R. Corson, C. O. Davis, D. Korwan, M. J. Montes, and W. Snyder, “Hyperspectral sensor characteristics needed for coastal ocean science,” in IGARSS 2004: 2004 IEEE International Geoscience and Remote Sensing Symposium: Proceedings (IEEE, 2004), Vol. 1, pp. 461-464.
[CrossRef]

J. A. Timlin, M. B. Sinclair, D. M. Haaland, J. Martinez, M. Manginell, S. M. Brozik, J. F. Guzowski, and M. Werner-Washburne, “Hyperspectral imaging of biological targets: the difference a high resolution spectral dimension and multivariate analysis can make,” in Biomedical Imaging: Macro to Nano, 2004. IEEE International Symposium (IEEE Computer Society, 2004), Vol. 1522, pp. 1529-1532.

M. Harwit and N. J. A. Sloan, Hadamard Transform Optics (Academic Press, 1979).

V. Saptari, Fourier-Transform Spectroscopy Instrumentation Engineering (SPIE, 2004).

G. Johnsen, Z. Volent, F. Sigernes, and E. Sakshaug, “Ecosystem Barents Sea” in Remote sensing in the Barents Sea, E. Sakshaug, G. Johnsen, and K. Kovacs, eds. (Tapir Academic Press, 2009), Chap. 6 (to be published).

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Figures (10)

Fig. 1
Fig. 1

Principle of hyperspectral imaging: Left image illustrates the capturing and stacking of the hyperspectral profiles into a spectral image cube. The configuration of the hyperspectral imager in the middle shows L 1 = front lens, S = entrance slit, L 2 = collector lens, P = grism, and L 3 = camera lens and CCD (imaging detector). Δ x is the spatial resolution in the moving direction dependent of the entrance slit width. Right image shows the configuration of the moving table, stereo-microscope, and the hyperspectral imager.

Fig. 2
Fig. 2

(a) Stepper motor and moving table assembly; (b) arrangement for measurements of transmission with the moving table assembled to the microscope, fiber bundles, and the mirror/diffuser arrangement; (c) arrangement for measurements of reflection with the fiber bundles directed 45 ° to the sample; (d) reflector and diffuser unit.

Fig. 3
Fig. 3

(a) Area for measurements of the transmitted light ( E t ( λ ) ) through Emiliania huxleyi cells concentrated on a Whatman GF/F filter and the corresponding transmitted light through the filter without algae ( E h t ( λ ) ); (b) area for measurements of the reflection spectra for Emiliania cells ( E r ( λ ) ) and the corresponding reflected light from the filter without algal cells ( E h r ( λ ) ).

Fig. 4
Fig. 4

Example of the artificial light source spectra ( E h t ( λ ) ) used for the calculation of transmittance in macroalgae ( T ( λ ) ) from the green alga Ulva, (spectra not shown). (a) Areas for measurements of E h t ( λ ) . (b)  E h t ( λ ) obtained by averaging 130 spectra. See Eq. (2).

Fig. 5
Fig. 5

In vivo reflectance, transmittance, and absorption spectra of the bloom-forming microalga Emiliania huxleyi: (a) and (c) show the configuration of the filters for measurement of reflection and transmission, respectively, and (b) and (d) indicate the areas for measurements of E r ( λ ) and E t ( λ ) , respectively, shown on a monochromatic images at 560 nm . (e) illustrates the T ( λ ) and R ( λ ) for Emiliania (dimensionless) and the in vivo Chl a -specific absorption coefficient (scale to the right). R ( λ ) for Area 1 and T ( λ ) for Area 2 were obtained by averaging 50 spectra measured within each area. The line marking 590 nm indicates the red absorption peak of Chl c 3 , typical for bloom-forming prymnesiophytes, and the corresponding decrease of reflectance and transmittance at this wavelength.

Fig. 6
Fig. 6

In vivo transmittance [ T ( λ ) ] and optical density [ OD ( λ ) ] of the red macro alga Phycodrys: (a) Sample of Phycodrys with epiphytic microphytobenthos (benthic diatoms); (b) areas of E t ( λ ) , indicated on a monochromatic image of Phycodrys at 600 nm ; (c)  OD ( λ ) and T ( λ ) for Phycodrys (dimensionless). T ( λ ) for Area 1, 2, 3, and 4 were obtained by averaging 411, 165, 365, and 90 spectra, correspondingly.

Fig. 7
Fig. 7

In vivo reflectance [ R ( λ ) ] and optical density [ OD ( λ ) ] of the red alga Phycodrys: (a) Sample of Phycodrys [same as shown in Fig. 6a]; (b) areas for measurements of E r ( λ ) , indicated on a monochromatic image of Phycodrys at 600 nm ; (c)  OD ( λ ) and R ( λ ) for Phycodrys (dimensionless). R ( λ ) for Area 1, 2, and 3 were obtained by averaging 172, 270, 35, and 47 spectra, respectively. Area 3 was measured at a thin part of the tissue and is shown to indicate how spectral reflectance characteristics can be influenced by transmission through the tissue and reflection from the bottom substrate, especially in the blue-green part of the spectrum.

Fig. 8
Fig. 8

In vivo reflectance [ R ( λ ) ] and optical density [ OD ( λ ) ] measurements of the brown macro alga Pelvetia: (a) Image of Pelvetia used for measurements of reflection; (b) area for measurements of E r ( λ ) , indicated on a monochromatic image of Pelvetia at 600 nm ; (c)  OD ( λ ) and R ( λ ) for Pelvetia (dimensionless). R ( λ ) for Area 1 was obtained by averaging 130 spectra.

Fig. 9
Fig. 9

In vivo transmittance [ T ( λ ) ], reflectance [ R ( λ ) ], and optical density [ OD ( λ ) ] of Ulva: (a) Example of Ulva used for measurements of transmission through the tissue; (b) area for measurements of E t ( λ ) , indicated on a monochromatic image of Ulva at 600 nm ; (c) area for measurements of E t ( λ ) ; (d) spectral characteristics of T ( λ ) , R ( λ ) , and OD ( λ ) for Ulva (dimensionless). T ( λ ) for Area 1 was obtained by averaging 120 spectra. R ( λ ) for Area 2 was obtained by averaging 100 spectra.

Fig. 10
Fig. 10

Comparison of In vivo (a) reflectance [ R ( λ ) ], (b) transmittance [ T ( λ ) ], and (c) optical density [ OD ( λ ) and specific absorption coefficient [ a ϕ * ( λ ) ] for Emiliania huxleyi. The R ( λ ) for Phycodrys show the average for Area 1 and 2 (Fig. 7). The T ( λ ) for Phycodrys show the average for Area 1–4 (Fig. 6). The R ( λ ) for Emiliania, Pelvetia, and Ulva are shown for the whole tissue. Also T ( λ ) for Emiliania and Ulva are shown for the whole tissue.

Tables (2)

Tables Icon

Table 1 Advantages and Drawbacks of Different Spectral Imaging Techniques

Tables Icon

Table 2 Major Pigmentation and in vivo Absorption Maxima Given for Red, Green, and Brown Macroalgae and for Microalga Emiliania Huxleyi

Equations (2)

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R ( λ ) = E r ( λ ) E h r ( λ ) 1 ,
T ( λ ) = E t ( λ ) E h t ( λ ) 1 .

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