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Virtual Journal for Biomedical Optics

Virtual Journal for Biomedical Optics


  • Editor: Gregory W. Faris
  • Vol. 4, Iss. 9 — Sep. 4, 2009

Microscopic hyperspectral imaging used as a bio-optical taxonomic tool for micro- and macroalgae

Zsolt Volent, Geir Johnsen, and Fred Sigernes  »View Author Affiliations

Applied Optics, Vol. 48, Issue 21, pp. 4170-4176 (2009)

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In the presented study a hyperspectral imager ( 400 700 nm ) 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 400 700 nm . 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

OCIS Codes
(110.0180) Imaging systems : Microscopy
(110.4234) Imaging systems : Multispectral and hyperspectral imaging

ToC Category:
Imaging Systems

Original Manuscript: January 22, 2009
Revised Manuscript: June 26, 2009
Manuscript Accepted: June 26, 2009
Published: July 14, 2009

Virtual Issues
Vol. 4, Iss. 9 Virtual Journal for Biomedical Optics

Zsolt Volent, Geir Johnsen, and Fred Sigernes, "Microscopic hyperspectral imaging used as a bio-optical taxonomic tool for micro- and macroalgae," Appl. Opt. 48, 4170-4176 (2009)

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  1. F. Sigernes, D. A. Lorentzen, K. Heia, and T. Svenoe, “Multipurpose spectral imager,” Appl. Opt. 39, 3143-3153 (2000). [CrossRef]
  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]
  3. 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]
  4. 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]
  5. 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]
  6. A. M. Filippi and J. R. Jensen, “Fuzzy learning vector quantization for hyperspectral coastal vegetation classification,” Remote Sens. Environ. 100, 512-530 (2006). [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). [CrossRef]
  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). [CrossRef]
  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). [CrossRef]
  10. 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]
  11. 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]
  12. 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.
  13. 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]
  14. R. A. DeVerse, R. M. Hammaker, and W. G. Fateley, “Realization of the Hadamard multiplex advantage using a programmable optical mask in a dispersive flat-field near-infrared spectrometer,” Appl. Spectrosc. 54, 1751-1758 (2000). [CrossRef]
  15. M. Harwit and N. J. A. Sloan, Hadamard Transform Optics (Academic Press, 1979).
  16. V. Saptari, Fourier-Transform Spectroscopy Instrumentation Engineering (SPIE, 2004).
  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]

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