OSA's Digital Library

Biomedical Optics Express

Biomedical Optics Express

  • Editor: Joseph A. Izatt
  • Vol. 3, Iss. 6 — Jun. 1, 2012
  • pp: 1291–1299

Designing microarray phantoms for hyperspectral imaging validation

Matthew L. Clarke, Ji Youn Lee, Daniel V. Samarov, David W. Allen, Maritoni Litorja, Ralph Nossal, and Jeeseong Hwang  »View Author Affiliations


Biomedical Optics Express, Vol. 3, Issue 6, pp. 1291-1299 (2012)
http://dx.doi.org/10.1364/BOE.3.001291


View Full Text Article

Enhanced HTML    Acrobat PDF (1136 KB)





Browse Journals / Lookup Meetings

Browse by Journal and Year


   


Lookup Conference Papers

Close Browse Journals / Lookup Meetings

Article Tools

Share
Citations

Abstract

The design and fabrication of custom-tailored microarrays for use as phantoms in the characterization of hyperspectral imaging systems is described. Corresponding analysis methods for biologically relevant samples are also discussed. An image-based phantom design was used to program a microarrayer robot to print prescribed mixtures of dyes onto microscope slides. The resulting arrays were imaged by a hyperspectral imaging microscope. The shape of the spots results in significant scattering signals, which can be used to test image analysis algorithms. Separation of the scattering signals allowed elucidation of individual dye spectra. In addition, spectral fitting of the absorbance spectra of complex dye mixtures was performed in order to determine local dye concentrations. Such microarray phantoms provide a robust testing platform for comparisons of hyperspectral imaging acquisition and analysis methods.

© 2012 OSA

OCIS Codes
(120.0120) Instrumentation, measurement, and metrology : Instrumentation, measurement, and metrology
(170.0170) Medical optics and biotechnology : Medical optics and biotechnology
(170.0180) Medical optics and biotechnology : Microscopy
(170.3880) Medical optics and biotechnology : Medical and biological imaging
(350.4800) Other areas of optics : Optical standards and testing
(110.4234) Imaging systems : Multispectral and hyperspectral imaging

ToC Category:
Calibration, Validation and Phantom Studies

History
Original Manuscript: March 2, 2012
Revised Manuscript: April 13, 2012
Manuscript Accepted: April 15, 2012
Published: May 9, 2012

Virtual Issues
Phantoms for the Performance Evaluation and Validation of Optical Medical Imaging Devices (2012) Biomedical Optics Express

Citation
Matthew L. Clarke, Ji Youn Lee, Daniel V. Samarov, David W. Allen, Maritoni Litorja, Ralph Nossal, and Jeeseong Hwang, "Designing microarray phantoms for hyperspectral imaging validation," Biomed. Opt. Express 3, 1291-1299 (2012)
http://www.opticsinfobase.org/boe/abstract.cfm?URI=boe-3-6-1291


Sort:  Author  |  Year  |  Journal  |  Reset  

References

  1. M. B. Sinclair, J. A. Timlin, D. M. Haaland, and M. Werner-Washburne, “Design, construction, characterization, and application of a hyperspectral microarray scanner,” Appl. Opt.43(10), 2079–2088 (2004). [CrossRef] [PubMed]
  2. C. Glasenapp, W. Mönch, H. Krause, and H. Zappe, “Biochip reader with dynamic holographic excitation and hyperspectral fluorescence detection,” J. Biomed. Opt.12(1), 014038 (2007). [CrossRef] [PubMed]
  3. M. L. Huebschman, R. A. Schultz, and H. R. Garner, “Characteristics and capabilities of the hyperspectral imaging microscope,” IEEE Eng. Med. Biol. Mag.21(4), 104–117 (2002). [CrossRef] [PubMed]
  4. F. Erfurth, A. Tretyakov, B. Nyuyki, G. Mrotzek, W. D. Schmidt, D. Fassler, and H. P. Saluz, “Two-laser, large-field hyperspectral microarray scanner for the analysis of multicolor microarrays,” Anal. Chem.80(20), 7706–7713 (2008). [CrossRef] [PubMed]
  5. J. Y. Lee, M. L. Clarke, F. Tokumasu, J. F. Lesoine, D. W. Allen, R. Chang, M. Litorja, and J. Hwang, “Absorption-based hyperspectral imaging and analysis of single erythrocytes,” IEEE J. Sel. Topics Quantum Electron.17(6) 1801–1840 (2011).
  6. R. Richards-Kortum and E. Sevick-Muraca, “Quantitative optical spectroscopy for tissue diagnosis,” Annu. Rev. Phys. Chem.47(1), 555–606 (1996). [CrossRef] [PubMed]
  7. I. Itzkan, L. Qiu, H. Fang, M. M. Zaman, E. Vitkin, I. C. Ghiran, S. Salahuddin, M. Modell, C. Andersson, L. M. Kimerer, P. B. Cipolloni, K. H. Lim, S. D. Freedman, I. Bigio, B. P. Sachs, E. B. Hanlon, and L. T. Perelman, “Confocal light absorption and scattering spectroscopic microscopy monitors organelles in live cells with no exogenous labels,” Proc. Natl. Acad. Sci. U.S.A.104(44), 17255–17260 (2007). [CrossRef] [PubMed]
  8. M. E. Martin, M. B. Wabuyele, K. Chen, P. Kasili, M. Panjehpour, M. Phan, B. Overholt, G. Cunningham, D. Wilson, R. C. Denovo, and T. Vo-Dinh, “Development of an advanced hyperspectral imaging (HSI) system with applications for cancer detection,” Ann. Biomed. Eng.34(6), 1061–1068 (2006). [CrossRef] [PubMed]
  9. B. S. Sorg, B. J. Moeller, O. Donovan, Y. T. Cao, and M. W. Dewhirst, “Hyperspectral imaging of hemoglobin saturation in tumor microvasculature and tumor hypoxia development,” J. Biomed. Opt.10(4), 044004 (2005). [CrossRef] [PubMed]
  10. K. J. Zuzak, M. T. Gladwin, R. O. Cannon, and I. W. Levin, “Imaging hemoglobin oxygen saturation in sickle cell disease patients using noninvasive visible reflectance hyperspectral techniques: effects of nitric oxide,” Am. J. Physiol. Heart Circ. Physiol.285(3), H1183–H1189 (2003). [PubMed]
  11. R. L. Greenman, S. Panasyuk, X. Wang, T. E. Lyons, T. Dinh, L. Longoria, J. M. Giurini, J. Freeman, L. Khaodhiar, and A. Veves, “Early changes in the skin microcirculation and muscle metabolism of the diabetic foot,” Lancet366(9498), 1711–1717 (2005). [CrossRef] [PubMed]
  12. W. R. Johnson, D. W. Wilson, W. Fink, M. Humayun, and G. Bearman, “Snapshot hyperspectral imaging in ophthalmology,” J. Biomed. Opt.12(1), 014036 (2007). [CrossRef] [PubMed]
  13. Y. Hirohara, Y. Okawa, T. Mihashi, T. Yamaguchi, N. Nakazawa, Y. Tsuruga, H. Aoki, N. Maeda, I. Uchida, and T. Fujikado, “Validity of retinal oxygen saturation analysis: Hyperspectral imaging in visible wavelength with fundus camera and liquid crystal wavelength tunable filter,” Opt. Rev.14(3), 151–158 (2007). [CrossRef]
  14. M. L. Clarke, M. Litorja, D. W. Allen, D. V. Samarov, and J. Hwang, “Characterization of hyperspectral imaging and analysis via microarray printing of dyes,” Proc. SPIE7891, 78910W (2011). [CrossRef]
  15. P. Geladi, J. Burger, and T. Lestander, “Hyperspectral imaging: calibration problems and solutions,” Chemom. Intell. Lab. Syst.72(2), 209–217 (2004). [CrossRef]
  16. D. V. Samarov, M. L. Clarke, J. Y. Lee, D. W. Allen, M. Litorja, and J. Hwang, “Validating the LASSO algorithm by unmixing spectral signatures in multicolor phantoms,” Proc. SPIE8229, 82290Z (2012). [CrossRef]
  17. A. Bricaud, C. Mejia, D. Blondeau-Patissier, H. Claustre, M. Crepon, and S. Thiria, “Retrieval of pigment concentrations and size structure of algal populations from their absorption spectra using multilayered perceptrons,” Appl. Opt.46(8), 1251–1260 (2007). [CrossRef] [PubMed]
  18. G. Zonios, A. Dimou, I. Bassukas, D. Galaris, A. Tsolakidis, and E. Kaxiras, “Melanin absorption spectroscopy: new method for noninvasive skin investigation and melanoma detection,” J. Biomed. Opt.13(1), 014017 (2008). [CrossRef] [PubMed]
  19. J. W. Qin and R. F. Lu, “Measurement of the optical properties of fruits and vegetables using spatially resolved hyperspectral diffuse reflectance imaging technique,” Postharvest Biol. Technol.49(3), 355–365 (2008). [CrossRef]
  20. W. Jun, M. Kim, K. Lee, P. Millner, and K. Chao, “Assessment of bacterial biofilm on stainless steel by hyperspectral fluorescence imaging,” Sens. Instrum. Food Qual. Saf.3(1), 41–48 (2009). [CrossRef]

Cited By

Alert me when this paper is cited

OSA is able to provide readers links to articles that cite this paper by participating in CrossRef's Cited-By Linking service. CrossRef includes content from more than 3000 publishers and societies. In addition to listing OSA journal articles that cite this paper, citing articles from other participating publishers will also be listed.

Figures

Fig. 1 Fig. 2 Fig. 3
 
Fig. 4 Fig. 5
 

Supplementary Material


» Media 1: PDF (26 KB)     

« Previous Article  |  Next Article »

OSA is a member of CrossRef.

CrossCheck Deposited