Abstract

We describe the design, construction, and operation of a hyperspectral microarray scanner for functional genomic research. The hyperspectral instrument operates with spatial resolutions ranging from 3 to 30 μm and records the emission spectrum between 490 and 900 nm with a spectral resolution of 3 nm for each pixel of the microarray. This spectral information, when coupled with multivariate data analysis techniques, allows for identification and elimination of unwanted artifacts and greatly improves the accuracy of microarray experiments. Microarray results presented in this study clearly demonstrate the separation of fluorescent label emission from the spectrally overlapping emission due to the underlying glass substrate. We also demonstrate separation of the emission due to green fluorescent protein expressed by yeast cells from the spectrally overlapping autofluorescence of the yeast cells and the growth media.

© 2004 Optical Society of America

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2003 (3)

M. J. Martinez, A. D. Aragon, A. L. Rodriguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland, M. Werner-Washburne, “Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays,” Nucl. Acids Res. 31, e18 (2003).
[CrossRef] [PubMed]

M. S. Robbins, B. J. Hadwen, “The noise performance of electron multiplying charge coupled devices,” IEEE Trans. Electron Devices 5, 1227–1232 (2003).
[CrossRef]

K. P. Doyle, R. P. Simon, A. Snyder, M. P. Stenzel-Poore, “Working with GFP in the brain,” Biotechniques 34, 492–494 (2003).

2002 (3)

D. Bumann, “Examination of Salmonella gene expression in an infected mammalian host using the green fluorescent protein and two-colour flow cytometry,” Mol. Microbiol. 43, 1269–1283 (2002).
[CrossRef] [PubMed]

A. J. Sutherland, “Quantum dots as luminescent probes in biological systems,” Curr. Opin. Solid State Mater. Sci. 6, 365–370 (2002).
[CrossRef]

P. H. Tran, D. A. Peiffer, Y. Shin, L. M. Meek, J. P. Brody, K. W. Y. Cho, “Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals,” Nucl. Acids Res. 30, e54 (2002).
[CrossRef] [PubMed]

2001 (3)

C. S. Brown, P. C. Goodwin, P. K. Sorger, “Image metrics in the statistical analysis of DNA microarray data,” Proc. Natl. Acad. Sci. USA 98, 8944–8949 (2001).
[CrossRef] [PubMed]

R. A. Schultz, T. Nielsen, J. R. Zavaleta, R. Ruch, R. Wyatt, H. R. Garner, “Hyperspectral imaging: a novel approach for microscopic analysis,” Cytometry 43, 239–247 (2001).
[CrossRef] [PubMed]

N. Billinton, A. W. Knight, “Seeing the wood through the trees: a review of techniques for distinguishing green fluorescent protein from endogenous autofluorescence,” Anal. Biochem. 291, 175–197 (2001).
[CrossRef] [PubMed]

2000 (2)

H. Tsurui, H. Nishimura, S. Hattori, S. Hirose, K. Okumura, T. Shirai, “Seven-color fluorescence imaging of tissue samples based on Fourier spectroscopy and singular value decomposition,” J. Histochem. Cytochem. 48, 653–662 (2000).
[CrossRef] [PubMed]

N. L. W. van Hal, O. Vorst, A. M. M. L. van Houwelingen, E. J. Kok, A. Peijnenburg, A. Aharoni, A. J. van Tunen, J. Keijer, “The application of DNA microarrays in gene expression analysis,” J. Biotechnol. 78, 271–280 (2000).
[CrossRef] [PubMed]

1999 (5)

D. J. Duggan, M. Bittner, Y. Chen, P. Meltzer, J. M. Trent, “Expression profiling using cDNA microarrays,” Nat. Genet. 21(Suppl.), 10–14 (1999).
[CrossRef]

P. O. Brown, D. Botstein, “Exploring the new world of the genome with DNA microarrays,” Nat. Genet. 21(Suppl.), 33–37 (1999).
[CrossRef]

M. J. Stimson, N. Haralampus-Grynaviski, J. D. Simon, “A unique optical arrangement for obtaining spectrally resolved confocal images,” Rev. Sci. Instrum. 70, 3351–3354 (1999).
[CrossRef]

Q. S. Hanley, P. J. Verveer, T. M. Jovin, “Spectral imaging in a programmable array microscope by Hadamard transform fluorescence spectroscopy,” Appl. Spectrosc. 53, 1–10 (1999).
[CrossRef]

V. C. Cheung, M. Morley, F. Aquilar, A. Massimi, R. Kucherlapati, G. Childs, “Making and reading microarrays,” Nat. Genet. 21(Suppl.), 15–19 (1999).
[CrossRef]

1998 (1)

1997 (2)

R. Bro, S. DeJong, “A fast non-negativity-constrained least squares algorithm,” J. Chemometr. 11, 393–401 (1997).
[CrossRef]

J. L. DeRisi, V. R. Iyer, P. O. Brown, “Exploring the metabolic and genetic control of gene expression on a genomic scale,” Science 278, 680–686 (1997).
[CrossRef] [PubMed]

1996 (1)

1993 (1)

S. A. Soper, H. L. Nutter, R. A. Keller, L. M. Davei, E. B. Shera, “The photophysical constants of several fluorescent dyes pertaining to ultrasensitive fluorescence spectroscopy,” Photochem. Photobiol. 57, 972–977 (1993).
[CrossRef]

Aharoni, A.

N. L. W. van Hal, O. Vorst, A. M. M. L. van Houwelingen, E. J. Kok, A. Peijnenburg, A. Aharoni, A. J. van Tunen, J. Keijer, “The application of DNA microarrays in gene expression analysis,” J. Biotechnol. 78, 271–280 (2000).
[CrossRef] [PubMed]

Aquilar, F.

V. C. Cheung, M. Morley, F. Aquilar, A. Massimi, R. Kucherlapati, G. Childs, “Making and reading microarrays,” Nat. Genet. 21(Suppl.), 15–19 (1999).
[CrossRef]

Aragon, A. D.

M. J. Martinez, A. D. Aragon, A. L. Rodriguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland, M. Werner-Washburne, “Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays,” Nucl. Acids Res. 31, e18 (2003).
[CrossRef] [PubMed]

D. M. Haaland, J. A. Timlin, M. B. Sinclair, M. H. Van Benthem, M. J. Martinez, A. D. Aragon, M. Werner-Washburne, “Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology,” in Spectral Imaging: Instrumentation, Applications, and Analysis, R. M. Levenson, G. H. Bearman, A. Mahadevan-Jansen, eds., Proc. SPIE4959, (2003).
[CrossRef]

Bell, R.

C. D. Mackay, R. N. Tubbs, R. Bell, D. Burt, I. Moody, “Subelectron read noise at MHz pixel rates,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 289–298 (2001).
[CrossRef]

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Bewsher, A.

Billinton, N.

N. Billinton, A. W. Knight, “Seeing the wood through the trees: a review of techniques for distinguishing green fluorescent protein from endogenous autofluorescence,” Anal. Biochem. 291, 175–197 (2001).
[CrossRef] [PubMed]

Bittner, M.

D. J. Duggan, M. Bittner, Y. Chen, P. Meltzer, J. M. Trent, “Expression profiling using cDNA microarrays,” Nat. Genet. 21(Suppl.), 10–14 (1999).
[CrossRef]

Boland, W.

Botstein, D.

P. O. Brown, D. Botstein, “Exploring the new world of the genome with DNA microarrays,” Nat. Genet. 21(Suppl.), 33–37 (1999).
[CrossRef]

Bowring, S.

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Bro, R.

R. Bro, S. DeJong, “A fast non-negativity-constrained least squares algorithm,” J. Chemometr. 11, 393–401 (1997).
[CrossRef]

Brody, J. P.

P. H. Tran, D. A. Peiffer, Y. Shin, L. M. Meek, J. P. Brody, K. W. Y. Cho, “Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals,” Nucl. Acids Res. 30, e54 (2002).
[CrossRef] [PubMed]

Brown, C. S.

C. S. Brown, P. C. Goodwin, P. K. Sorger, “Image metrics in the statistical analysis of DNA microarray data,” Proc. Natl. Acad. Sci. USA 98, 8944–8949 (2001).
[CrossRef] [PubMed]

Brown, P. O.

P. O. Brown, D. Botstein, “Exploring the new world of the genome with DNA microarrays,” Nat. Genet. 21(Suppl.), 33–37 (1999).
[CrossRef]

J. L. DeRisi, V. R. Iyer, P. O. Brown, “Exploring the metabolic and genetic control of gene expression on a genomic scale,” Science 278, 680–686 (1997).
[CrossRef] [PubMed]

Bumann, D.

D. Bumann, “Examination of Salmonella gene expression in an infected mammalian host using the green fluorescent protein and two-colour flow cytometry,” Mol. Microbiol. 43, 1269–1283 (2002).
[CrossRef] [PubMed]

Burt, D.

C. D. Mackay, R. N. Tubbs, R. Bell, D. Burt, I. Moody, “Subelectron read noise at MHz pixel rates,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 289–298 (2001).
[CrossRef]

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Catlett, N.

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Chen, Y.

D. J. Duggan, M. Bittner, Y. Chen, P. Meltzer, J. M. Trent, “Expression profiling using cDNA microarrays,” Nat. Genet. 21(Suppl.), 10–14 (1999).
[CrossRef]

Cheung, V. C.

V. C. Cheung, M. Morley, F. Aquilar, A. Massimi, R. Kucherlapati, G. Childs, “Making and reading microarrays,” Nat. Genet. 21(Suppl.), 15–19 (1999).
[CrossRef]

Childs, G.

V. C. Cheung, M. Morley, F. Aquilar, A. Massimi, R. Kucherlapati, G. Childs, “Making and reading microarrays,” Nat. Genet. 21(Suppl.), 15–19 (1999).
[CrossRef]

Cho, K. W. Y.

P. H. Tran, D. A. Peiffer, Y. Shin, L. M. Meek, J. P. Brody, K. W. Y. Cho, “Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals,” Nucl. Acids Res. 30, e54 (2002).
[CrossRef] [PubMed]

Christensen, K. A.

Davei, L. M.

S. A. Soper, H. L. Nutter, R. A. Keller, L. M. Davei, E. B. Shera, “The photophysical constants of several fluorescent dyes pertaining to ultrasensitive fluorescence spectroscopy,” Photochem. Photobiol. 57, 972–977 (1993).
[CrossRef]

DeJong, S.

R. Bro, S. DeJong, “A fast non-negativity-constrained least squares algorithm,” J. Chemometr. 11, 393–401 (1997).
[CrossRef]

DeRisi, J. L.

J. L. DeRisi, V. R. Iyer, P. O. Brown, “Exploring the metabolic and genetic control of gene expression on a genomic scale,” Science 278, 680–686 (1997).
[CrossRef] [PubMed]

Doyle, K. P.

K. P. Doyle, R. P. Simon, A. Snyder, M. P. Stenzel-Poore, “Working with GFP in the brain,” Biotechniques 34, 492–494 (2003).

Duggan, D. J.

D. J. Duggan, M. Bittner, Y. Chen, P. Meltzer, J. M. Trent, “Expression profiling using cDNA microarrays,” Nat. Genet. 21(Suppl.), 10–14 (1999).
[CrossRef]

Garner, H. R.

R. A. Schultz, T. Nielsen, J. R. Zavaleta, R. Ruch, R. Wyatt, H. R. Garner, “Hyperspectral imaging: a novel approach for microscopic analysis,” Cytometry 43, 239–247 (2001).
[CrossRef] [PubMed]

Goodwin, P. C.

C. S. Brown, P. C. Goodwin, P. K. Sorger, “Image metrics in the statistical analysis of DNA microarray data,” Proc. Natl. Acad. Sci. USA 98, 8944–8949 (2001).
[CrossRef] [PubMed]

Haaland, D. M.

M. J. Martinez, A. D. Aragon, A. L. Rodriguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland, M. Werner-Washburne, “Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays,” Nucl. Acids Res. 31, e18 (2003).
[CrossRef] [PubMed]

D. M. Haaland, J. A. Timlin, M. B. Sinclair, M. H. Van Benthem, M. J. Martinez, A. D. Aragon, M. Werner-Washburne, “Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology,” in Spectral Imaging: Instrumentation, Applications, and Analysis, R. M. Levenson, G. H. Bearman, A. Mahadevan-Jansen, eds., Proc. SPIE4959, (2003).
[CrossRef]

Hadwen, B. J.

M. S. Robbins, B. J. Hadwen, “The noise performance of electron multiplying charge coupled devices,” IEEE Trans. Electron Devices 5, 1227–1232 (2003).
[CrossRef]

Hanley, Q. S.

Haralampus-Grynaviski, N.

M. J. Stimson, N. Haralampus-Grynaviski, J. D. Simon, “A unique optical arrangement for obtaining spectrally resolved confocal images,” Rev. Sci. Instrum. 70, 3351–3354 (1999).
[CrossRef]

Hattori, S.

H. Tsurui, H. Nishimura, S. Hattori, S. Hirose, K. Okumura, T. Shirai, “Seven-color fluorescence imaging of tissue samples based on Fourier spectroscopy and singular value decomposition,” J. Histochem. Cytochem. 48, 653–662 (2000).
[CrossRef] [PubMed]

Hazelwood, M.

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Heyes, P.

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Hirose, S.

H. Tsurui, H. Nishimura, S. Hattori, S. Hirose, K. Okumura, T. Shirai, “Seven-color fluorescence imaging of tissue samples based on Fourier spectroscopy and singular value decomposition,” J. Histochem. Cytochem. 48, 653–662 (2000).
[CrossRef] [PubMed]

Iyer, V. R.

J. L. DeRisi, V. R. Iyer, P. O. Brown, “Exploring the metabolic and genetic control of gene expression on a genomic scale,” Science 278, 680–686 (1997).
[CrossRef] [PubMed]

Jerram, P.

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Jovin, T. M.

Keijer, J.

N. L. W. van Hal, O. Vorst, A. M. M. L. van Houwelingen, E. J. Kok, A. Peijnenburg, A. Aharoni, A. J. van Tunen, J. Keijer, “The application of DNA microarrays in gene expression analysis,” J. Biotechnol. 78, 271–280 (2000).
[CrossRef] [PubMed]

Keller, R. A.

S. A. Soper, H. L. Nutter, R. A. Keller, L. M. Davei, E. B. Shera, “The photophysical constants of several fluorescent dyes pertaining to ultrasensitive fluorescence spectroscopy,” Photochem. Photobiol. 57, 972–977 (1993).
[CrossRef]

Knight, A. W.

N. Billinton, A. W. Knight, “Seeing the wood through the trees: a review of techniques for distinguishing green fluorescent protein from endogenous autofluorescence,” Anal. Biochem. 291, 175–197 (2001).
[CrossRef] [PubMed]

Kok, E. J.

N. L. W. van Hal, O. Vorst, A. M. M. L. van Houwelingen, E. J. Kok, A. Peijnenburg, A. Aharoni, A. J. van Tunen, J. Keijer, “The application of DNA microarrays in gene expression analysis,” J. Biotechnol. 78, 271–280 (2000).
[CrossRef] [PubMed]

Kucherlapati, R.

V. C. Cheung, M. Morley, F. Aquilar, A. Massimi, R. Kucherlapati, G. Childs, “Making and reading microarrays,” Nat. Genet. 21(Suppl.), 15–19 (1999).
[CrossRef]

Mackay, C. D.

C. D. Mackay, R. N. Tubbs, R. Bell, D. Burt, I. Moody, “Subelectron read noise at MHz pixel rates,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 289–298 (2001).
[CrossRef]

Martinez, M. J.

M. J. Martinez, A. D. Aragon, A. L. Rodriguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland, M. Werner-Washburne, “Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays,” Nucl. Acids Res. 31, e18 (2003).
[CrossRef] [PubMed]

D. M. Haaland, J. A. Timlin, M. B. Sinclair, M. H. Van Benthem, M. J. Martinez, A. D. Aragon, M. Werner-Washburne, “Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology,” in Spectral Imaging: Instrumentation, Applications, and Analysis, R. M. Levenson, G. H. Bearman, A. Mahadevan-Jansen, eds., Proc. SPIE4959, (2003).
[CrossRef]

Massimi, A.

V. C. Cheung, M. Morley, F. Aquilar, A. Massimi, R. Kucherlapati, G. Childs, “Making and reading microarrays,” Nat. Genet. 21(Suppl.), 15–19 (1999).
[CrossRef]

Meek, L. M.

P. H. Tran, D. A. Peiffer, Y. Shin, L. M. Meek, J. P. Brody, K. W. Y. Cho, “Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals,” Nucl. Acids Res. 30, e54 (2002).
[CrossRef] [PubMed]

Meltzer, P.

D. J. Duggan, M. Bittner, Y. Chen, P. Meltzer, J. M. Trent, “Expression profiling using cDNA microarrays,” Nat. Genet. 21(Suppl.), 10–14 (1999).
[CrossRef]

Moody, I.

C. D. Mackay, R. N. Tubbs, R. Bell, D. Burt, I. Moody, “Subelectron read noise at MHz pixel rates,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 289–298 (2001).
[CrossRef]

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Morley, M.

V. C. Cheung, M. Morley, F. Aquilar, A. Massimi, R. Kucherlapati, G. Childs, “Making and reading microarrays,” Nat. Genet. 21(Suppl.), 15–19 (1999).
[CrossRef]

Morris, M. D.

Nielsen, T.

R. A. Schultz, T. Nielsen, J. R. Zavaleta, R. Ruch, R. Wyatt, H. R. Garner, “Hyperspectral imaging: a novel approach for microscopic analysis,” Cytometry 43, 239–247 (2001).
[CrossRef] [PubMed]

Nishimura, H.

H. Tsurui, H. Nishimura, S. Hattori, S. Hirose, K. Okumura, T. Shirai, “Seven-color fluorescence imaging of tissue samples based on Fourier spectroscopy and singular value decomposition,” J. Histochem. Cytochem. 48, 653–662 (2000).
[CrossRef] [PubMed]

Nutter, H. L.

S. A. Soper, H. L. Nutter, R. A. Keller, L. M. Davei, E. B. Shera, “The photophysical constants of several fluorescent dyes pertaining to ultrasensitive fluorescence spectroscopy,” Photochem. Photobiol. 57, 972–977 (1993).
[CrossRef]

Okumura, K.

H. Tsurui, H. Nishimura, S. Hattori, S. Hirose, K. Okumura, T. Shirai, “Seven-color fluorescence imaging of tissue samples based on Fourier spectroscopy and singular value decomposition,” J. Histochem. Cytochem. 48, 653–662 (2000).
[CrossRef] [PubMed]

Peiffer, D. A.

P. H. Tran, D. A. Peiffer, Y. Shin, L. M. Meek, J. P. Brody, K. W. Y. Cho, “Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals,” Nucl. Acids Res. 30, e54 (2002).
[CrossRef] [PubMed]

Peijnenburg, A.

N. L. W. van Hal, O. Vorst, A. M. M. L. van Houwelingen, E. J. Kok, A. Peijnenburg, A. Aharoni, A. J. van Tunen, J. Keijer, “The application of DNA microarrays in gene expression analysis,” J. Biotechnol. 78, 271–280 (2000).
[CrossRef] [PubMed]

Pool, P.

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Powell, I.

Robbins, M. S.

M. S. Robbins, B. J. Hadwen, “The noise performance of electron multiplying charge coupled devices,” IEEE Trans. Electron Devices 5, 1227–1232 (2003).
[CrossRef]

Rodriguez, A. L.

M. J. Martinez, A. D. Aragon, A. L. Rodriguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland, M. Werner-Washburne, “Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays,” Nucl. Acids Res. 31, e18 (2003).
[CrossRef] [PubMed]

Ruch, R.

R. A. Schultz, T. Nielsen, J. R. Zavaleta, R. Ruch, R. Wyatt, H. R. Garner, “Hyperspectral imaging: a novel approach for microscopic analysis,” Cytometry 43, 239–247 (2001).
[CrossRef] [PubMed]

Schena, M.

M. Schena, Microarray Biochip Technology (Eaton, Natick, Mass., 2000).

Schultz, R. A.

R. A. Schultz, T. Nielsen, J. R. Zavaleta, R. Ruch, R. Wyatt, H. R. Garner, “Hyperspectral imaging: a novel approach for microscopic analysis,” Cytometry 43, 239–247 (2001).
[CrossRef] [PubMed]

Shera, E. B.

S. A. Soper, H. L. Nutter, R. A. Keller, L. M. Davei, E. B. Shera, “The photophysical constants of several fluorescent dyes pertaining to ultrasensitive fluorescence spectroscopy,” Photochem. Photobiol. 57, 972–977 (1993).
[CrossRef]

Shin, Y.

P. H. Tran, D. A. Peiffer, Y. Shin, L. M. Meek, J. P. Brody, K. W. Y. Cho, “Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals,” Nucl. Acids Res. 30, e54 (2002).
[CrossRef] [PubMed]

Shirai, T.

H. Tsurui, H. Nishimura, S. Hattori, S. Hirose, K. Okumura, T. Shirai, “Seven-color fluorescence imaging of tissue samples based on Fourier spectroscopy and singular value decomposition,” J. Histochem. Cytochem. 48, 653–662 (2000).
[CrossRef] [PubMed]

Simon, J. D.

M. J. Stimson, N. Haralampus-Grynaviski, J. D. Simon, “A unique optical arrangement for obtaining spectrally resolved confocal images,” Rev. Sci. Instrum. 70, 3351–3354 (1999).
[CrossRef]

Simon, R. P.

K. P. Doyle, R. P. Simon, A. Snyder, M. P. Stenzel-Poore, “Working with GFP in the brain,” Biotechniques 34, 492–494 (2003).

Sinclair, M. B.

M. J. Martinez, A. D. Aragon, A. L. Rodriguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland, M. Werner-Washburne, “Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays,” Nucl. Acids Res. 31, e18 (2003).
[CrossRef] [PubMed]

D. M. Haaland, J. A. Timlin, M. B. Sinclair, M. H. Van Benthem, M. J. Martinez, A. D. Aragon, M. Werner-Washburne, “Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology,” in Spectral Imaging: Instrumentation, Applications, and Analysis, R. M. Levenson, G. H. Bearman, A. Mahadevan-Jansen, eds., Proc. SPIE4959, (2003).
[CrossRef]

Snyder, A.

K. P. Doyle, R. P. Simon, A. Snyder, M. P. Stenzel-Poore, “Working with GFP in the brain,” Biotechniques 34, 492–494 (2003).

Soper, S. A.

S. A. Soper, H. L. Nutter, R. A. Keller, L. M. Davei, E. B. Shera, “The photophysical constants of several fluorescent dyes pertaining to ultrasensitive fluorescence spectroscopy,” Photochem. Photobiol. 57, 972–977 (1993).
[CrossRef]

Sorger, P. K.

C. S. Brown, P. C. Goodwin, P. K. Sorger, “Image metrics in the statistical analysis of DNA microarray data,” Proc. Natl. Acad. Sci. USA 98, 8944–8949 (2001).
[CrossRef] [PubMed]

Spencer, S.

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Stenzel-Poore, M. P.

K. P. Doyle, R. P. Simon, A. Snyder, M. P. Stenzel-Poore, “Working with GFP in the brain,” Biotechniques 34, 492–494 (2003).

Stimson, M. J.

M. J. Stimson, N. Haralampus-Grynaviski, J. D. Simon, “A unique optical arrangement for obtaining spectrally resolved confocal images,” Rev. Sci. Instrum. 70, 3351–3354 (1999).
[CrossRef]

Sutherland, A. J.

A. J. Sutherland, “Quantum dots as luminescent probes in biological systems,” Curr. Opin. Solid State Mater. Sci. 6, 365–370 (2002).
[CrossRef]

Timlin, J. A.

M. J. Martinez, A. D. Aragon, A. L. Rodriguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland, M. Werner-Washburne, “Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays,” Nucl. Acids Res. 31, e18 (2003).
[CrossRef] [PubMed]

D. M. Haaland, J. A. Timlin, M. B. Sinclair, M. H. Van Benthem, M. J. Martinez, A. D. Aragon, M. Werner-Washburne, “Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology,” in Spectral Imaging: Instrumentation, Applications, and Analysis, R. M. Levenson, G. H. Bearman, A. Mahadevan-Jansen, eds., Proc. SPIE4959, (2003).
[CrossRef]

Tran, P. H.

P. H. Tran, D. A. Peiffer, Y. Shin, L. M. Meek, J. P. Brody, K. W. Y. Cho, “Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals,” Nucl. Acids Res. 30, e54 (2002).
[CrossRef] [PubMed]

Trent, J. M.

D. J. Duggan, M. Bittner, Y. Chen, P. Meltzer, J. M. Trent, “Expression profiling using cDNA microarrays,” Nat. Genet. 21(Suppl.), 10–14 (1999).
[CrossRef]

Tsurui, H.

H. Tsurui, H. Nishimura, S. Hattori, S. Hirose, K. Okumura, T. Shirai, “Seven-color fluorescence imaging of tissue samples based on Fourier spectroscopy and singular value decomposition,” J. Histochem. Cytochem. 48, 653–662 (2000).
[CrossRef] [PubMed]

Tubbs, R. N.

C. D. Mackay, R. N. Tubbs, R. Bell, D. Burt, I. Moody, “Subelectron read noise at MHz pixel rates,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 289–298 (2001).
[CrossRef]

Van Benthem, M. H.

D. M. Haaland, J. A. Timlin, M. B. Sinclair, M. H. Van Benthem, M. J. Martinez, A. D. Aragon, M. Werner-Washburne, “Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology,” in Spectral Imaging: Instrumentation, Applications, and Analysis, R. M. Levenson, G. H. Bearman, A. Mahadevan-Jansen, eds., Proc. SPIE4959, (2003).
[CrossRef]

van Hal, N. L. W.

N. L. W. van Hal, O. Vorst, A. M. M. L. van Houwelingen, E. J. Kok, A. Peijnenburg, A. Aharoni, A. J. van Tunen, J. Keijer, “The application of DNA microarrays in gene expression analysis,” J. Biotechnol. 78, 271–280 (2000).
[CrossRef] [PubMed]

van Houwelingen, A. M. M. L.

N. L. W. van Hal, O. Vorst, A. M. M. L. van Houwelingen, E. J. Kok, A. Peijnenburg, A. Aharoni, A. J. van Tunen, J. Keijer, “The application of DNA microarrays in gene expression analysis,” J. Biotechnol. 78, 271–280 (2000).
[CrossRef] [PubMed]

van Tunen, A. J.

N. L. W. van Hal, O. Vorst, A. M. M. L. van Houwelingen, E. J. Kok, A. Peijnenburg, A. Aharoni, A. J. van Tunen, J. Keijer, “The application of DNA microarrays in gene expression analysis,” J. Biotechnol. 78, 271–280 (2000).
[CrossRef] [PubMed]

Verveer, P. J.

Vorst, O.

N. L. W. van Hal, O. Vorst, A. M. M. L. van Houwelingen, E. J. Kok, A. Peijnenburg, A. Aharoni, A. J. van Tunen, J. Keijer, “The application of DNA microarrays in gene expression analysis,” J. Biotechnol. 78, 271–280 (2000).
[CrossRef] [PubMed]

Weber, J. M.

M. J. Martinez, A. D. Aragon, A. L. Rodriguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland, M. Werner-Washburne, “Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays,” Nucl. Acids Res. 31, e18 (2003).
[CrossRef] [PubMed]

Werner-Washburne, M.

M. J. Martinez, A. D. Aragon, A. L. Rodriguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland, M. Werner-Washburne, “Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays,” Nucl. Acids Res. 31, e18 (2003).
[CrossRef] [PubMed]

D. M. Haaland, J. A. Timlin, M. B. Sinclair, M. H. Van Benthem, M. J. Martinez, A. D. Aragon, M. Werner-Washburne, “Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology,” in Spectral Imaging: Instrumentation, Applications, and Analysis, R. M. Levenson, G. H. Bearman, A. Mahadevan-Jansen, eds., Proc. SPIE4959, (2003).
[CrossRef]

Wyatt, R.

R. A. Schultz, T. Nielsen, J. R. Zavaleta, R. Ruch, R. Wyatt, H. R. Garner, “Hyperspectral imaging: a novel approach for microscopic analysis,” Cytometry 43, 239–247 (2001).
[CrossRef] [PubMed]

Zavaleta, J. R.

R. A. Schultz, T. Nielsen, J. R. Zavaleta, R. Ruch, R. Wyatt, H. R. Garner, “Hyperspectral imaging: a novel approach for microscopic analysis,” Cytometry 43, 239–247 (2001).
[CrossRef] [PubMed]

Anal. Biochem. (1)

N. Billinton, A. W. Knight, “Seeing the wood through the trees: a review of techniques for distinguishing green fluorescent protein from endogenous autofluorescence,” Anal. Biochem. 291, 175–197 (2001).
[CrossRef] [PubMed]

Appl. Opt. (1)

Appl. Spectrosc. (2)

Biotechniques (1)

K. P. Doyle, R. P. Simon, A. Snyder, M. P. Stenzel-Poore, “Working with GFP in the brain,” Biotechniques 34, 492–494 (2003).

Curr. Opin. Solid State Mater. Sci. (1)

A. J. Sutherland, “Quantum dots as luminescent probes in biological systems,” Curr. Opin. Solid State Mater. Sci. 6, 365–370 (2002).
[CrossRef]

Cytometry (1)

R. A. Schultz, T. Nielsen, J. R. Zavaleta, R. Ruch, R. Wyatt, H. R. Garner, “Hyperspectral imaging: a novel approach for microscopic analysis,” Cytometry 43, 239–247 (2001).
[CrossRef] [PubMed]

IEEE Trans. Electron Devices (1)

M. S. Robbins, B. J. Hadwen, “The noise performance of electron multiplying charge coupled devices,” IEEE Trans. Electron Devices 5, 1227–1232 (2003).
[CrossRef]

J. Biotechnol. (1)

N. L. W. van Hal, O. Vorst, A. M. M. L. van Houwelingen, E. J. Kok, A. Peijnenburg, A. Aharoni, A. J. van Tunen, J. Keijer, “The application of DNA microarrays in gene expression analysis,” J. Biotechnol. 78, 271–280 (2000).
[CrossRef] [PubMed]

J. Chemometr. (1)

R. Bro, S. DeJong, “A fast non-negativity-constrained least squares algorithm,” J. Chemometr. 11, 393–401 (1997).
[CrossRef]

J. Histochem. Cytochem. (1)

H. Tsurui, H. Nishimura, S. Hattori, S. Hirose, K. Okumura, T. Shirai, “Seven-color fluorescence imaging of tissue samples based on Fourier spectroscopy and singular value decomposition,” J. Histochem. Cytochem. 48, 653–662 (2000).
[CrossRef] [PubMed]

Mol. Microbiol. (1)

D. Bumann, “Examination of Salmonella gene expression in an infected mammalian host using the green fluorescent protein and two-colour flow cytometry,” Mol. Microbiol. 43, 1269–1283 (2002).
[CrossRef] [PubMed]

Nat. Genet. (3)

D. J. Duggan, M. Bittner, Y. Chen, P. Meltzer, J. M. Trent, “Expression profiling using cDNA microarrays,” Nat. Genet. 21(Suppl.), 10–14 (1999).
[CrossRef]

P. O. Brown, D. Botstein, “Exploring the new world of the genome with DNA microarrays,” Nat. Genet. 21(Suppl.), 33–37 (1999).
[CrossRef]

V. C. Cheung, M. Morley, F. Aquilar, A. Massimi, R. Kucherlapati, G. Childs, “Making and reading microarrays,” Nat. Genet. 21(Suppl.), 15–19 (1999).
[CrossRef]

Nucl. Acids Res. (2)

M. J. Martinez, A. D. Aragon, A. L. Rodriguez, J. M. Weber, J. A. Timlin, M. B. Sinclair, D. M. Haaland, M. Werner-Washburne, “Identification and removal of contaminating fluorescence from commercial and in-house printed DNA microarrays,” Nucl. Acids Res. 31, e18 (2003).
[CrossRef] [PubMed]

P. H. Tran, D. A. Peiffer, Y. Shin, L. M. Meek, J. P. Brody, K. W. Y. Cho, “Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals,” Nucl. Acids Res. 30, e54 (2002).
[CrossRef] [PubMed]

Photochem. Photobiol. (1)

S. A. Soper, H. L. Nutter, R. A. Keller, L. M. Davei, E. B. Shera, “The photophysical constants of several fluorescent dyes pertaining to ultrasensitive fluorescence spectroscopy,” Photochem. Photobiol. 57, 972–977 (1993).
[CrossRef]

Proc. Natl. Acad. Sci. USA (1)

C. S. Brown, P. C. Goodwin, P. K. Sorger, “Image metrics in the statistical analysis of DNA microarray data,” Proc. Natl. Acad. Sci. USA 98, 8944–8949 (2001).
[CrossRef] [PubMed]

Rev. Sci. Instrum. (1)

M. J. Stimson, N. Haralampus-Grynaviski, J. D. Simon, “A unique optical arrangement for obtaining spectrally resolved confocal images,” Rev. Sci. Instrum. 70, 3351–3354 (1999).
[CrossRef]

Science (1)

J. L. DeRisi, V. R. Iyer, P. O. Brown, “Exploring the metabolic and genetic control of gene expression on a genomic scale,” Science 278, 680–686 (1997).
[CrossRef] [PubMed]

Other (6)

M. Schena, Microarray Biochip Technology (Eaton, Natick, Mass., 2000).

C. D. Mackay, R. N. Tubbs, R. Bell, D. Burt, I. Moody, “Subelectron read noise at MHz pixel rates,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 289–298 (2001).
[CrossRef]

P. Jerram, P. Pool, R. Bell, D. Burt, S. Bowring, S. Spencer, M. Hazelwood, I. Moody, N. Catlett, P. Heyes, “The LLCCD: low-light imaging without the need for an intensifier,” in Sensors and Camera Systems for Scientific, Industrial, and Digital Photography Applications II, M. M. Blouke, J. Canosa, N. Sampat, eds., Proc. SPIE4306, 178–186 (2001).
[CrossRef]

Cy3 dilution slide DS3001 , Panomics Inc. , Redwood City, Calif. , http://www.panomics.com .

Photomultiplier Tubes: Basics and Applications, 2nd ed. (Hamamatsu Photonics KK, Japan, 1999).

D. M. Haaland, J. A. Timlin, M. B. Sinclair, M. H. Van Benthem, M. J. Martinez, A. D. Aragon, M. Werner-Washburne, “Multivariate curve resolution for hyperspectral image analysis: applications to microarray technology,” in Spectral Imaging: Instrumentation, Applications, and Analysis, R. M. Levenson, G. H. Bearman, A. Mahadevan-Jansen, eds., Proc. SPIE4959, (2003).
[CrossRef]

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Figures (9)

Fig. 1
Fig. 1

(Top) Diagram of the illumination and scan geometries for the hyperspectral scanner. The microarray is scanned in the x direction, whereas the y direction is parallel to the focused line of laser light as well as the spectrograph entrance slit. (Bottom) Illustration of a data cube comprising a complete emission spectrum from each spatial pixel of the 2-D image.

Fig. 2
Fig. 2

Schematic diagram of the hyperspectral scanner layout.

Fig. 3
Fig. 3

(a) and (b) Images of a U.S. Air Force resolution target and (c) and (d) a microarray taken with 10-μm resolution and 30-μm resolution. The microarray spots are still clearly resolved at the coarser resolution setting.

Fig. 4
Fig. 4

Emission spectra recorded from the Cy3 dilution standard. The emission recorded within the Cy3 spots contains emission from both the Cy3 and the substrate glass. The emission recorded in regions between the spots contains only glass emission. Subtraction of the glass emission from the spot emission yields the true Cy3 emission spectrum.

Fig. 5
Fig. 5

(a) Recorded signal counts as a function of fluorophore concentration for the Cy3 dilution standard obtained with the hyperspectral scanner. (b) The SNR calculated with Eq. (1) as a function of Cy3 concentration for both the hyperspectral scanner and a commercial microarray scanner.

Fig. 6
Fig. 6

(Left) Portion of a Cy3–Cy5 microarray image recorded with the hyperspectral scanner. Although the excitation wavelength (532 nm) used in this scan is optimized only for Cy3, residual Cy5 absorption allowed observation of Cy5 signatures from several DNA spots. (Right) The raw emission spectra obtained at various locations (labeled a-c) within the image. Spectrum a is obtained in a region between the DNA spots and contains only glass emission. Spectrum b is obtained from a DNA spot and contains both Cy3 and Cy5 emission. Spectrum c is obtained from a DNA spot containing only Cy3.

Fig. 7
Fig. 7

Results of a hyperspectral scan and multivariate analysis of a microarray containing two spectrally overlapping fluorophores. In this microarray, the top four spots contained only Cy3, the middle four spots contained only Alexa 532, and the bottom four spots contained a mixture of Cy3 and Alexa 532. (Top) The emission spectra of Cy3 (dashed curve), Alexa 532 (solid curve), and the glass substrate (dotted curve) obtained from the MCR analysis. (Bottom) The relative concentration maps obtained from the MCR analysis demonstrate the ability to separate the two overlapping fluorophores.

Fig. 8
Fig. 8

Emission spectra obtained from a hyperspectral scan and MCR analysis of yeast cells expressing GFP. An average raw emission spectrum containing contributions from the GFP and autofluorescence from the growth medium is shown, along with the primary pure-component spectra of GFP emission and the autofluorescence obtained from the MCR.

Fig. 9
Fig. 9

Relative concentration maps of the GFP and autofluorescence obtained from the MCR. The GFP emission is observed only in the region of the microfluidic channel occupied by the yeast cells whereas the autofluorescence from the growth medium is observed everywhere in the channel.

Equations (1)

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SNR=ns-nbσb,

Metrics