Abstract

It was demonstrated that statistical analysis of bacteria colonies Fresnel patterns recorded in the optical system with converging spherical wave illumination is suitable for highly effective bacteria species classification. The proposed method includes Fresnel patterns recording followed by image processing and the statistical analysis based on feature extraction, feature selection, classification and classification performance methods. Examination performed on various bacteria species (Salmonella enteritidis, Staphylococcus aureus, Staphylococcus intermedius, Escherichia coli, Proteus mirabilis, Pseudomonas aeruginosa and Citrobacter freundii) revealed that the proposed method achieved very high accuracy of over 98%.

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2012 (3)

S. E. Gould, “Underground Network,” Sci. Am. 307(4), 28–28 (2012).
[CrossRef]

E. Bae, V. Patsekin, B. Rajwa, A. K. Bhunia, C. Holdman, V. J. Davisson, E. D. Hirleman, and J. P. Robinson, “Development of a microbial high-throughput screening instrument based on elastic light scatter patterns,” Rev. Sci. Instrum. 83(4), 044304 (2012).
[CrossRef] [PubMed]

A. Suchwalko, I. Buzalewicz, and H. Podbielska, “Computer-based classification of bacteria species by analysis of their colonies Fresnel diffraction patterns,” Proc. SPIE 11, 82120R, 82120R-13 (2012).
[CrossRef]

2011 (3)

E. Bae, A. Aroonnual, A. K. Bhunia, and E. D. Hirleman, “On the sensitivity of forward scattering patterns from bacterial colonies to media composition,” J Biophoton. 4(4), 236–243 (2011).
[CrossRef] [PubMed]

I. Buzalewicz, A. Wieliczko, and H. Podbielska, “Influence of various growth conditions on Fresnel diffraction patterns of bacteria colonies examined in the optical system with converging spherical wave illumination,” Opt. Express 19(22), 21768–21785 (2011).
[CrossRef] [PubMed]

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

2010 (3)

E. Bae, N. Bai, A. Aroonnual, J. P. Robinson, A. K. Bhunia, and E. D. Hirleman, “Modeling light propagation through bacterial colonies and its correlation with forward scattering patterns,” J. Biomed. Opt. 15(4), 045001 (2010).
[CrossRef] [PubMed]

I. Buzalewicz, K. Wysocka-Król, and H. Podbielska, “Image processing guided analysis for estimation of bacteria colonies number by means of optical transforms,” Opt. Express 18(12), 12992–13005 (2010).
[CrossRef] [PubMed]

I. Buzalewicz, K. Wysocka-Król, K. Kowal, and H. Podbielska, “Evaluation of antibacterial agents efficiency,” IEEE Trans. Inf. Technol. Biomed. 2, 341–351 (2010).
[CrossRef]

2009 (2)

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

A. C. Samuels, A. P. Snyder, D. K. Emge, D. S. T. Amant, J. Minter, M. Campbell, and A. Tripathi, “Classification of select category A and B bacteria by Fourier transform infrared spectroscopy,” Appl. Spectrosc. 63(1), 14–24 (2009).
[CrossRef] [PubMed]

2008 (4)

A. Manninen, M. Putkiranta, A. Rostedt, J. Saarela, T. Laurila, M. Marjamäki, J. Keskinen, and R. Hernberg, “Instrumentation for measuring fluorescence cross sections from airborne microsized particles,” Appl. Opt. 47(2), 110–115 (2008).
[CrossRef] [PubMed]

A. M. Nicol, C. Hurrell, W. McDowall, K. Bartlett, and N. Elmieh, “Communicating the risks of a new, emerging pathogen: the case of Cryptococcus gattii,” Risk Anal. 28(2), 373–386 (2008).
[CrossRef] [PubMed]

M. Venkatapathi, B. Rajwa, K. Ragheb, P. P. Banada, T. Lary, J. P. Robinson, and E. D. Hirleman, “High speed classification of individual bacterial cells using a model-based light scatter system and multivariate statistics,” Appl. Opt. 47(5), 678–686 (2008).
[CrossRef] [PubMed]

E. Bae, P. P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Analysis of time-resolved scattering from macroscale bacterial colonies,” J. Biomed. Opt. 13(1), 014010 (2008).
[CrossRef] [PubMed]

2007 (3)

2006 (4)

G. E. Fernandes, Y. L. Pan, R. K. Chang, K. Aptowicz, and R. G. Pinnick, “Simultaneous forward- and backward-hemisphere elastic-light-scattering patterns of respirable-size aerosols,” Opt. Lett. 31(20), 3034–3036 (2006).
[CrossRef] [PubMed]

A. Alimova, A. Katz, P. Gottlieb, and R. R. Alfano, “Proteins and dipicolinic acid released during heat shock activation of Bacillus subtilis spores probed by optical spectroscopy,” Appl. Opt. 45(3), 445–450 (2006).
[CrossRef] [PubMed]

S. J. Mechery, X. J. Zhao, L. Wang, L. R. Hilliard, A. Munteanu, and W. Tan, “Using bioconjugated nanoparticles to monitor E. coli in a flow channel,” Chem. Asian J. 1(3), 384–390 (2006).
[CrossRef] [PubMed]

A. Subramanian, J. Irudayaraj, and T. Ryan, “A mixed self-assembled monolayer-based surface plasmon immunosensor for detection of E. coli O157: H7,” Biosens. Bioelectron. 21(7), 998–1006 (2006).
[CrossRef] [PubMed]

2005 (1)

R. T. Noble and S. B. Weisberg, “A review of technologies for rapid detection of bacteria in recreational waters,” J. Water Health 3(4), 381–392 (2005).
[PubMed]

2004 (3)

M. D. Abràmoff, P. J. Magalhães, and S. J. Ram, “Image processing with ImageJ,” Biophoton. Inter. 11, 36–42 (2004).

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

S. B. S. B. Levy and B. Marshall, “Antibacterial resistance worldwide: causes, challenges and responses,” Nat. Med. 10(12S), S122–S129 (2004).
[CrossRef] [PubMed]

2003 (1)

2002 (1)

J. Homola, J. Dostálek, S. Chen, A. Rasooly, S. Jiang, and S. S. Yee, “Spectral surface plasmon resonance biosensor for detection of staphylococcal enterotoxin B in milk,” Int. J. Food Microbiol. 75(1-2), 61–69 (2002).
[CrossRef] [PubMed]

2001 (2)

K. Christen, “Bioterrorism and waterborne pathogens: how big is the threat?” Environ. Sci. Technol. 35(19), 396A–397A (2001).
[CrossRef] [PubMed]

C. Dennis, “The bugs of war,” Nature 411(6835), 232–235 (2001).
[CrossRef] [PubMed]

2000 (1)

S. G. Amyes, “The rise in bacterial resistance,” BMJ 320(7229), 199–200 (2000).
[CrossRef] [PubMed]

1998 (1)

A. S. S. Colsky, R. S. S. Kirsner, and F. A. A. Kerdel, “Analysis of antibiotic susceptibilities of skin wound flora in hospitalized dermatology patients. The crisis of antibiotic resistance has come to the surface,” Arch. Dermatol. 134(8), 1006–1009 (1998).
[CrossRef] [PubMed]

1997 (1)

Abràmoff, M. D.

M. D. Abràmoff, P. J. Magalhães, and S. J. Ram, “Image processing with ImageJ,” Biophoton. Inter. 11, 36–42 (2004).

Adam, P.

Adil, A.

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

Alfano, R. R.

Alimova, A.

Amant, D. S. T.

Amouroux, J.

Amyes, S. G.

S. G. Amyes, “The rise in bacterial resistance,” BMJ 320(7229), 199–200 (2000).
[CrossRef] [PubMed]

Aptowicz, K.

Aptowicz, K. B.

Aroonnual, A.

E. Bae, A. Aroonnual, A. K. Bhunia, and E. D. Hirleman, “On the sensitivity of forward scattering patterns from bacterial colonies to media composition,” J Biophoton. 4(4), 236–243 (2011).
[CrossRef] [PubMed]

E. Bae, N. Bai, A. Aroonnual, J. P. Robinson, A. K. Bhunia, and E. D. Hirleman, “Modeling light propagation through bacterial colonies and its correlation with forward scattering patterns,” J. Biomed. Opt. 15(4), 045001 (2010).
[CrossRef] [PubMed]

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

Auger, J. C.

Badrane, H.

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

Bae, E.

E. Bae, V. Patsekin, B. Rajwa, A. K. Bhunia, C. Holdman, V. J. Davisson, E. D. Hirleman, and J. P. Robinson, “Development of a microbial high-throughput screening instrument based on elastic light scatter patterns,” Rev. Sci. Instrum. 83(4), 044304 (2012).
[CrossRef] [PubMed]

E. Bae, A. Aroonnual, A. K. Bhunia, and E. D. Hirleman, “On the sensitivity of forward scattering patterns from bacterial colonies to media composition,” J Biophoton. 4(4), 236–243 (2011).
[CrossRef] [PubMed]

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

E. Bae, N. Bai, A. Aroonnual, J. P. Robinson, A. K. Bhunia, and E. D. Hirleman, “Modeling light propagation through bacterial colonies and its correlation with forward scattering patterns,” J. Biomed. Opt. 15(4), 045001 (2010).
[CrossRef] [PubMed]

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

E. Bae, P. P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Analysis of time-resolved scattering from macroscale bacterial colonies,” J. Biomed. Opt. 13(1), 014010 (2008).
[CrossRef] [PubMed]

P. P. Banada, S. Guo, B. Bayraktar, E. Bae, B. Rajwa, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species,” Biosens. Bioelectron. 22(8), 1664–1671 (2007).
[CrossRef] [PubMed]

E. Bae, P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Biophysical modeling of forward scattering from bacterial colonies using scalar diffraction theory,” Appl. Opt. 46(17), 3639–3648 (2007).
[CrossRef] [PubMed]

Bai, N.

E. Bae, N. Bai, A. Aroonnual, J. P. Robinson, A. K. Bhunia, and E. D. Hirleman, “Modeling light propagation through bacterial colonies and its correlation with forward scattering patterns,” J. Biomed. Opt. 15(4), 045001 (2010).
[CrossRef] [PubMed]

Baker, H. V.

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

Banada, P. P.

Banada, P. P. P.

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

E. Bae, P. P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Analysis of time-resolved scattering from macroscale bacterial colonies,” J. Biomed. Opt. 13(1), 014010 (2008).
[CrossRef] [PubMed]

Bartlett, K.

A. M. Nicol, C. Hurrell, W. McDowall, K. Bartlett, and N. Elmieh, “Communicating the risks of a new, emerging pathogen: the case of Cryptococcus gattii,” Risk Anal. 28(2), 373–386 (2008).
[CrossRef] [PubMed]

Bayraktar, B.

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

P. P. Banada, S. Guo, B. Bayraktar, E. Bae, B. Rajwa, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species,” Biosens. Bioelectron. 22(8), 1664–1671 (2007).
[CrossRef] [PubMed]

Bhunia, A.

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

Bhunia, A. K.

E. Bae, V. Patsekin, B. Rajwa, A. K. Bhunia, C. Holdman, V. J. Davisson, E. D. Hirleman, and J. P. Robinson, “Development of a microbial high-throughput screening instrument based on elastic light scatter patterns,” Rev. Sci. Instrum. 83(4), 044304 (2012).
[CrossRef] [PubMed]

E. Bae, A. Aroonnual, A. K. Bhunia, and E. D. Hirleman, “On the sensitivity of forward scattering patterns from bacterial colonies to media composition,” J Biophoton. 4(4), 236–243 (2011).
[CrossRef] [PubMed]

E. Bae, N. Bai, A. Aroonnual, J. P. Robinson, A. K. Bhunia, and E. D. Hirleman, “Modeling light propagation through bacterial colonies and its correlation with forward scattering patterns,” J. Biomed. Opt. 15(4), 045001 (2010).
[CrossRef] [PubMed]

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

E. Bae, P. P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Analysis of time-resolved scattering from macroscale bacterial colonies,” J. Biomed. Opt. 13(1), 014010 (2008).
[CrossRef] [PubMed]

P. P. Banada, S. Guo, B. Bayraktar, E. Bae, B. Rajwa, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species,” Biosens. Bioelectron. 22(8), 1664–1671 (2007).
[CrossRef] [PubMed]

E. Bae, P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Biophysical modeling of forward scattering from bacterial colonies using scalar diffraction theory,” Appl. Opt. 46(17), 3639–3648 (2007).
[CrossRef] [PubMed]

Bronk, B. V.

Buzalewicz, I.

A. Suchwalko, I. Buzalewicz, and H. Podbielska, “Computer-based classification of bacteria species by analysis of their colonies Fresnel diffraction patterns,” Proc. SPIE 11, 82120R, 82120R-13 (2012).
[CrossRef]

I. Buzalewicz, A. Wieliczko, and H. Podbielska, “Influence of various growth conditions on Fresnel diffraction patterns of bacteria colonies examined in the optical system with converging spherical wave illumination,” Opt. Express 19(22), 21768–21785 (2011).
[CrossRef] [PubMed]

I. Buzalewicz, K. Wysocka-Król, and H. Podbielska, “Image processing guided analysis for estimation of bacteria colonies number by means of optical transforms,” Opt. Express 18(12), 12992–13005 (2010).
[CrossRef] [PubMed]

I. Buzalewicz, K. Wysocka-Król, K. Kowal, and H. Podbielska, “Evaluation of antibacterial agents efficiency,” IEEE Trans. Inf. Technol. Biomed. 2, 341–351 (2010).
[CrossRef]

Campbell, M.

Chang, R. K.

Chen, S.

J. Homola, J. Dostálek, S. Chen, A. Rasooly, S. Jiang, and S. S. Yee, “Spectral surface plasmon resonance biosensor for detection of staphylococcal enterotoxin B in milk,” Int. J. Food Microbiol. 75(1-2), 61–69 (2002).
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Christen, K.

K. Christen, “Bioterrorism and waterborne pathogens: how big is the threat?” Environ. Sci. Technol. 35(19), 396A–397A (2001).
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Colsky, A. S. S.

A. S. S. Colsky, R. S. S. Kirsner, and F. A. A. Kerdel, “Analysis of antibiotic susceptibilities of skin wound flora in hospitalized dermatology patients. The crisis of antibiotic resistance has come to the surface,” Arch. Dermatol. 134(8), 1006–1009 (1998).
[CrossRef] [PubMed]

Copeland, R. A.

Davisson, V.

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

Davisson, V. J.

E. Bae, V. Patsekin, B. Rajwa, A. K. Bhunia, C. Holdman, V. J. Davisson, E. D. Hirleman, and J. P. Robinson, “Development of a microbial high-throughput screening instrument based on elastic light scatter patterns,” Rev. Sci. Instrum. 83(4), 044304 (2012).
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Dennis, C.

C. Dennis, “The bugs of war,” Nature 411(6835), 232–235 (2001).
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Dietz, J.

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

Dostálek, J.

J. Homola, J. Dostálek, S. Chen, A. Rasooly, S. Jiang, and S. S. Yee, “Spectral surface plasmon resonance biosensor for detection of staphylococcal enterotoxin B in milk,” Int. J. Food Microbiol. 75(1-2), 61–69 (2002).
[CrossRef] [PubMed]

Dundar, M. M.

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

Elmieh, N.

A. M. Nicol, C. Hurrell, W. McDowall, K. Bartlett, and N. Elmieh, “Communicating the risks of a new, emerging pathogen: the case of Cryptococcus gattii,” Risk Anal. 28(2), 373–386 (2008).
[CrossRef] [PubMed]

Emge, D. K.

Faris, G. W.

Fernandes, G. E.

Gottlieb, P.

Gould, S. E.

S. E. Gould, “Underground Network,” Sci. Am. 307(4), 28–28 (2012).
[CrossRef]

Gulig, P. A.

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

Guo, S.

P. P. Banada, S. Guo, B. Bayraktar, E. Bae, B. Rajwa, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species,” Biosens. Bioelectron. 22(8), 1664–1671 (2007).
[CrossRef] [PubMed]

Hernberg, R.

Hilliard, L. R.

S. J. Mechery, X. J. Zhao, L. Wang, L. R. Hilliard, A. Munteanu, and W. Tan, “Using bioconjugated nanoparticles to monitor E. coli in a flow channel,” Chem. Asian J. 1(3), 384–390 (2006).
[CrossRef] [PubMed]

Hirleman, E. D.

E. Bae, V. Patsekin, B. Rajwa, A. K. Bhunia, C. Holdman, V. J. Davisson, E. D. Hirleman, and J. P. Robinson, “Development of a microbial high-throughput screening instrument based on elastic light scatter patterns,” Rev. Sci. Instrum. 83(4), 044304 (2012).
[CrossRef] [PubMed]

E. Bae, A. Aroonnual, A. K. Bhunia, and E. D. Hirleman, “On the sensitivity of forward scattering patterns from bacterial colonies to media composition,” J Biophoton. 4(4), 236–243 (2011).
[CrossRef] [PubMed]

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

E. Bae, N. Bai, A. Aroonnual, J. P. Robinson, A. K. Bhunia, and E. D. Hirleman, “Modeling light propagation through bacterial colonies and its correlation with forward scattering patterns,” J. Biomed. Opt. 15(4), 045001 (2010).
[CrossRef] [PubMed]

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

E. Bae, P. P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Analysis of time-resolved scattering from macroscale bacterial colonies,” J. Biomed. Opt. 13(1), 014010 (2008).
[CrossRef] [PubMed]

M. Venkatapathi, B. Rajwa, K. Ragheb, P. P. Banada, T. Lary, J. P. Robinson, and E. D. Hirleman, “High speed classification of individual bacterial cells using a model-based light scatter system and multivariate statistics,” Appl. Opt. 47(5), 678–686 (2008).
[CrossRef] [PubMed]

P. P. Banada, S. Guo, B. Bayraktar, E. Bae, B. Rajwa, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species,” Biosens. Bioelectron. 22(8), 1664–1671 (2007).
[CrossRef] [PubMed]

E. Bae, P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Biophysical modeling of forward scattering from bacterial colonies using scalar diffraction theory,” Appl. Opt. 46(17), 3639–3648 (2007).
[CrossRef] [PubMed]

Holdman, C.

E. Bae, V. Patsekin, B. Rajwa, A. K. Bhunia, C. Holdman, V. J. Davisson, E. D. Hirleman, and J. P. Robinson, “Development of a microbial high-throughput screening instrument based on elastic light scatter patterns,” Rev. Sci. Instrum. 83(4), 044304 (2012).
[CrossRef] [PubMed]

Homola, J.

J. Homola, J. Dostálek, S. Chen, A. Rasooly, S. Jiang, and S. S. Yee, “Spectral surface plasmon resonance biosensor for detection of staphylococcal enterotoxin B in milk,” Int. J. Food Microbiol. 75(1-2), 61–69 (2002).
[CrossRef] [PubMed]

Huff, K.

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

E. Bae, P. P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Analysis of time-resolved scattering from macroscale bacterial colonies,” J. Biomed. Opt. 13(1), 014010 (2008).
[CrossRef] [PubMed]

E. Bae, P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Biophysical modeling of forward scattering from bacterial colonies using scalar diffraction theory,” Appl. Opt. 46(17), 3639–3648 (2007).
[CrossRef] [PubMed]

Hurrell, C.

A. M. Nicol, C. Hurrell, W. McDowall, K. Bartlett, and N. Elmieh, “Communicating the risks of a new, emerging pathogen: the case of Cryptococcus gattii,” Risk Anal. 28(2), 373–386 (2008).
[CrossRef] [PubMed]

Irudayaraj, J.

A. Subramanian, J. Irudayaraj, and T. Ryan, “A mixed self-assembled monolayer-based surface plasmon immunosensor for detection of E. coli O157: H7,” Biosens. Bioelectron. 21(7), 998–1006 (2006).
[CrossRef] [PubMed]

Jiang, S.

J. Homola, J. Dostálek, S. Chen, A. Rasooly, S. Jiang, and S. S. Yee, “Spectral surface plasmon resonance biosensor for detection of staphylococcal enterotoxin B in milk,” Int. J. Food Microbiol. 75(1-2), 61–69 (2002).
[CrossRef] [PubMed]

Jin, S.

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

Katz, A.

Kerdel, F. A. A.

A. S. S. Colsky, R. S. S. Kirsner, and F. A. A. Kerdel, “Analysis of antibiotic susceptibilities of skin wound flora in hospitalized dermatology patients. The crisis of antibiotic resistance has come to the surface,” Arch. Dermatol. 134(8), 1006–1009 (1998).
[CrossRef] [PubMed]

Keskinen, J.

Kirsner, R. S. S.

A. S. S. Colsky, R. S. S. Kirsner, and F. A. A. Kerdel, “Analysis of antibiotic susceptibilities of skin wound flora in hospitalized dermatology patients. The crisis of antibiotic resistance has come to the surface,” Arch. Dermatol. 134(8), 1006–1009 (1998).
[CrossRef] [PubMed]

Kowal, K.

I. Buzalewicz, K. Wysocka-Król, K. Kowal, and H. Podbielska, “Evaluation of antibacterial agents efficiency,” IEEE Trans. Inf. Technol. Biomed. 2, 341–351 (2010).
[CrossRef]

Lary, T.

Laurila, T.

Leone, N.

Levy, S. B. S. B.

S. B. S. B. Levy and B. Marshall, “Antibacterial resistance worldwide: causes, challenges and responses,” Nat. Med. 10(12S), S122–S129 (2004).
[CrossRef] [PubMed]

Lian, W.

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

Lim, D. V.

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

Litherland, S. A.

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

Magalhães, P. J.

M. D. Abràmoff, P. J. Magalhães, and S. J. Ram, “Image processing with ImageJ,” Biophoton. Inter. 11, 36–42 (2004).

Manninen, A.

Marjamäki, M.

Marshall, B.

S. B. S. B. Levy and B. Marshall, “Antibacterial resistance worldwide: causes, challenges and responses,” Nat. Med. 10(12S), S122–S129 (2004).
[CrossRef] [PubMed]

McDowall, W.

A. M. Nicol, C. Hurrell, W. McDowall, K. Bartlett, and N. Elmieh, “Communicating the risks of a new, emerging pathogen: the case of Cryptococcus gattii,” Risk Anal. 28(2), 373–386 (2008).
[CrossRef] [PubMed]

Mechery, S. J.

S. J. Mechery, X. J. Zhao, L. Wang, L. R. Hilliard, A. Munteanu, and W. Tan, “Using bioconjugated nanoparticles to monitor E. coli in a flow channel,” Chem. Asian J. 1(3), 384–390 (2006).
[CrossRef] [PubMed]

Minter, J.

Morel, S.

Mortelmans, K.

Munteanu, A.

S. J. Mechery, X. J. Zhao, L. Wang, L. R. Hilliard, A. Munteanu, and W. Tan, “Using bioconjugated nanoparticles to monitor E. coli in a flow channel,” Chem. Asian J. 1(3), 384–390 (2006).
[CrossRef] [PubMed]

Nicol, A. M.

A. M. Nicol, C. Hurrell, W. McDowall, K. Bartlett, and N. Elmieh, “Communicating the risks of a new, emerging pathogen: the case of Cryptococcus gattii,” Risk Anal. 28(2), 373–386 (2008).
[CrossRef] [PubMed]

Noble, R. T.

R. T. Noble and S. B. Weisberg, “A review of technologies for rapid detection of bacteria in recreational waters,” J. Water Health 3(4), 381–392 (2005).
[PubMed]

Pan, Y. L.

Patsekin, V.

E. Bae, V. Patsekin, B. Rajwa, A. K. Bhunia, C. Holdman, V. J. Davisson, E. D. Hirleman, and J. P. Robinson, “Development of a microbial high-throughput screening instrument based on elastic light scatter patterns,” Rev. Sci. Instrum. 83(4), 044304 (2012).
[CrossRef] [PubMed]

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

Pinnick, R. G.

Podbielska, H.

A. Suchwalko, I. Buzalewicz, and H. Podbielska, “Computer-based classification of bacteria species by analysis of their colonies Fresnel diffraction patterns,” Proc. SPIE 11, 82120R, 82120R-13 (2012).
[CrossRef]

I. Buzalewicz, A. Wieliczko, and H. Podbielska, “Influence of various growth conditions on Fresnel diffraction patterns of bacteria colonies examined in the optical system with converging spherical wave illumination,” Opt. Express 19(22), 21768–21785 (2011).
[CrossRef] [PubMed]

I. Buzalewicz, K. Wysocka-Król, and H. Podbielska, “Image processing guided analysis for estimation of bacteria colonies number by means of optical transforms,” Opt. Express 18(12), 12992–13005 (2010).
[CrossRef] [PubMed]

I. Buzalewicz, K. Wysocka-Król, K. Kowal, and H. Podbielska, “Evaluation of antibacterial agents efficiency,” IEEE Trans. Inf. Technol. Biomed. 2, 341–351 (2010).
[CrossRef]

Putkiranta, M.

Ragheb, K.

Rajwa, B.

E. Bae, V. Patsekin, B. Rajwa, A. K. Bhunia, C. Holdman, V. J. Davisson, E. D. Hirleman, and J. P. Robinson, “Development of a microbial high-throughput screening instrument based on elastic light scatter patterns,” Rev. Sci. Instrum. 83(4), 044304 (2012).
[CrossRef] [PubMed]

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

M. Venkatapathi, B. Rajwa, K. Ragheb, P. P. Banada, T. Lary, J. P. Robinson, and E. D. Hirleman, “High speed classification of individual bacterial cells using a model-based light scatter system and multivariate statistics,” Appl. Opt. 47(5), 678–686 (2008).
[CrossRef] [PubMed]

P. P. Banada, S. Guo, B. Bayraktar, E. Bae, B. Rajwa, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species,” Biosens. Bioelectron. 22(8), 1664–1671 (2007).
[CrossRef] [PubMed]

Ram, S. J.

M. D. Abràmoff, P. J. Magalhães, and S. J. Ram, “Image processing with ImageJ,” Biophoton. Inter. 11, 36–42 (2004).

Rasooly, A.

J. Homola, J. Dostálek, S. Chen, A. Rasooly, S. Jiang, and S. S. Yee, “Spectral surface plasmon resonance biosensor for detection of staphylococcal enterotoxin B in milk,” Int. J. Food Microbiol. 75(1-2), 61–69 (2002).
[CrossRef] [PubMed]

Robinson, J.

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

Robinson, J. P.

E. Bae, V. Patsekin, B. Rajwa, A. K. Bhunia, C. Holdman, V. J. Davisson, E. D. Hirleman, and J. P. Robinson, “Development of a microbial high-throughput screening instrument based on elastic light scatter patterns,” Rev. Sci. Instrum. 83(4), 044304 (2012).
[CrossRef] [PubMed]

E. Bae, N. Bai, A. Aroonnual, J. P. Robinson, A. K. Bhunia, and E. D. Hirleman, “Modeling light propagation through bacterial colonies and its correlation with forward scattering patterns,” J. Biomed. Opt. 15(4), 045001 (2010).
[CrossRef] [PubMed]

P. P. P. Banada, K. Huff, E. Bae, B. Rajwa, A. Aroonnual, B. Bayraktar, A. Adil, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Label-free detection of multiple bacterial pathogens using light-scattering sensor,” Biosens. Bioelectron. 24(6), 1685–1692 (2009).
[CrossRef] [PubMed]

E. Bae, P. P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Analysis of time-resolved scattering from macroscale bacterial colonies,” J. Biomed. Opt. 13(1), 014010 (2008).
[CrossRef] [PubMed]

M. Venkatapathi, B. Rajwa, K. Ragheb, P. P. Banada, T. Lary, J. P. Robinson, and E. D. Hirleman, “High speed classification of individual bacterial cells using a model-based light scatter system and multivariate statistics,” Appl. Opt. 47(5), 678–686 (2008).
[CrossRef] [PubMed]

E. Bae, P. P. Banada, K. Huff, A. K. Bhunia, J. P. Robinson, and E. D. Hirleman, “Biophysical modeling of forward scattering from bacterial colonies using scalar diffraction theory,” Appl. Opt. 46(17), 3639–3648 (2007).
[CrossRef] [PubMed]

P. P. Banada, S. Guo, B. Bayraktar, E. Bae, B. Rajwa, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species,” Biosens. Bioelectron. 22(8), 1664–1671 (2007).
[CrossRef] [PubMed]

Rostedt, A.

Roumani, A.

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

Ryan, T.

A. Subramanian, J. Irudayaraj, and T. Ryan, “A mixed self-assembled monolayer-based surface plasmon immunosensor for detection of E. coli O157: H7,” Biosens. Bioelectron. 21(7), 998–1006 (2006).
[CrossRef] [PubMed]

Saarela, J.

Samuels, A. C.

Snyder, A. P.

Subramanian, A.

A. Subramanian, J. Irudayaraj, and T. Ryan, “A mixed self-assembled monolayer-based surface plasmon immunosensor for detection of E. coli O157: H7,” Biosens. Bioelectron. 21(7), 998–1006 (2006).
[CrossRef] [PubMed]

Suchwalko, A.

A. Suchwalko, I. Buzalewicz, and H. Podbielska, “Computer-based classification of bacteria species by analysis of their colonies Fresnel diffraction patterns,” Proc. SPIE 11, 82120R, 82120R-13 (2012).
[CrossRef]

Tan, W.

S. J. Mechery, X. J. Zhao, L. Wang, L. R. Hilliard, A. Munteanu, and W. Tan, “Using bioconjugated nanoparticles to monitor E. coli in a flow channel,” Chem. Asian J. 1(3), 384–390 (2006).
[CrossRef] [PubMed]

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

Thomas, J.

J. Robinson, B. Rajwa, E. Bae, V. Patsekin, A. Roumani, A. Bhunia, J. Dietz, V. Davisson, M. M. Dundar, J. Thomas, and E. D. Hirleman, “Using Scattering to Identify Bacterial Pathogens,” Opt. Photon. News 22(10), 20–27 (2011).
[CrossRef]

Tripathi, A.

Venkatapathi, M.

Wang, L.

S. J. Mechery, X. J. Zhao, L. Wang, L. R. Hilliard, A. Munteanu, and W. Tan, “Using bioconjugated nanoparticles to monitor E. coli in a flow channel,” Chem. Asian J. 1(3), 384–390 (2006).
[CrossRef] [PubMed]

Weisberg, S. B.

R. T. Noble and S. B. Weisberg, “A review of technologies for rapid detection of bacteria in recreational waters,” J. Water Health 3(4), 381–392 (2005).
[PubMed]

Wieliczko, A.

Wu, D.

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

Wysocka-Król, K.

I. Buzalewicz, K. Wysocka-Król, K. Kowal, and H. Podbielska, “Evaluation of antibacterial agents efficiency,” IEEE Trans. Inf. Technol. Biomed. 2, 341–351 (2010).
[CrossRef]

I. Buzalewicz, K. Wysocka-Król, and H. Podbielska, “Image processing guided analysis for estimation of bacteria colonies number by means of optical transforms,” Opt. Express 18(12), 12992–13005 (2010).
[CrossRef] [PubMed]

Yee, S. S.

J. Homola, J. Dostálek, S. Chen, A. Rasooly, S. Jiang, and S. S. Yee, “Spectral surface plasmon resonance biosensor for detection of staphylococcal enterotoxin B in milk,” Int. J. Food Microbiol. 75(1-2), 61–69 (2002).
[CrossRef] [PubMed]

Zhao, X. J.

S. J. Mechery, X. J. Zhao, L. Wang, L. R. Hilliard, A. Munteanu, and W. Tan, “Using bioconjugated nanoparticles to monitor E. coli in a flow channel,” Chem. Asian J. 1(3), 384–390 (2006).
[CrossRef] [PubMed]

Anal. Biochem. (1)

W. Lian, S. A. Litherland, H. Badrane, W. Tan, D. Wu, H. V. Baker, P. A. Gulig, D. V. Lim, and S. Jin, “Ultrasensitive detection of biomolecules with fluorescent dye-doped nanoparticles.,” Anal. Biochem. 334(1), 135–144 (2004).
[CrossRef] [PubMed]

Appl. Opt. (6)

Appl. Spectrosc. (1)

Arch. Dermatol. (1)

A. S. S. Colsky, R. S. S. Kirsner, and F. A. A. Kerdel, “Analysis of antibiotic susceptibilities of skin wound flora in hospitalized dermatology patients. The crisis of antibiotic resistance has come to the surface,” Arch. Dermatol. 134(8), 1006–1009 (1998).
[CrossRef] [PubMed]

Biophoton. Inter. (1)

M. D. Abràmoff, P. J. Magalhães, and S. J. Ram, “Image processing with ImageJ,” Biophoton. Inter. 11, 36–42 (2004).

Biosens. Bioelectron. (3)

P. P. Banada, S. Guo, B. Bayraktar, E. Bae, B. Rajwa, J. P. Robinson, E. D. Hirleman, and A. K. Bhunia, “Optical forward-scattering for detection of Listeria monocytogenes and other Listeria species,” Biosens. Bioelectron. 22(8), 1664–1671 (2007).
[CrossRef] [PubMed]

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Figures (9)

Fig. 1
Fig. 1

The configuration of the optical system for bacteria species classification based on Fresnel diffraction patterns

Fig. 2
Fig. 2

Exemplary Fresnel patterns of bacterial colonies of various bacteria species

Fig. 3
Fig. 3

Workflow of the performed studies of the bacteria species Fresnel diffraction patterns, with split into two statistical analysis workflows. Workflow contain normalization as an optional step.

Fig. 4
Fig. 4

Examples of 10 rings partitioning of various Fresnel patterns.

Fig. 5
Fig. 5

Exemplary Fresenl patterns after normalization

Fig. 6
Fig. 6

ANOVA (F value) feature selection results for non-normalized data. The features are ordered from best to worst.

Fig. 7
Fig. 7

ANOVA (F value) feature selection results for normalized data. The features are ordered from best to worst.

Fig. 8
Fig. 8

Boxplot chart of sd.4 feature of normalized data for examined bacteria species.

Fig. 9
Fig. 9

Boxplot chart of sd.10 feature of normalized data for examined bacteria species.

Tables (6)

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Table 1 Number of patterns analyzed for various bacteria species.

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Table 2 Sensitivity, specificity and cross-validation error for full model for proposed diffraction pattern partitioning into 3, 5 and 10 rings with and without normalization.

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Table 3 Results (accuracy of identification) of exemplary, single run of identification analysis with data split into learning and test sets.

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Table 4 Cross-validation errors, sensitivity and specificity measures for three classifiers and data set with and without normalization

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Table 5 CV error estimation, sensitivity and specificity for best fitted classification models after ANOVA feature selection for non-normalized data

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Table 6 CV error estimation, sensitivity and specificity for best fitted classification models after ANOVA feature selection for normalized data.

Equations (1)

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new.pixel.value= old.pixel.valuemin(original)  max( oryginal )min(oryginal) *( max( new )min( new ) )+min(new),

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