PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
Tytuł artykułu

Methods of Classification of the Genera and Species of Bacteria Using Decision Tree

Autorzy
Treść / Zawartość
Identyfikatory
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
This paper presents a computer-based method for recognizing digital images of bacterial cells. It covers automatic recognition of twenty genera and species of bacteria chosen by the author whose original contribution to the work consisted in the decision to conduct the process of recognizing bacteria using the simultaneous analysis of the following physical features of bacterial cells: color, size, shape, number of clusters, cluster shape, as well as density and distribution of the cells. The proposed method may be also used to recognize the microorganisms other than bacteria. In addition, it does not require the use of any specialized equipment. The lack of demand for high infrastructural standards and complementarity with the hardware and software widens the scope of the method’s application in diagnostics, including microbiological diagnostics. The proposed method may be used to identify new genera and species of bacteria, but also other microorganisms that exhibit similar morphological characteristics.
Rocznik
Tom
Strony
74--82
Opis fizyczny
Bibliogr. 50 poz., rys., tab.
Twórcy
autor
  • Faculty of Computer Science and Telecommunications Department of Computer Science, Cracow University of Technology, Warszawska 24, 31-155 Kraków, Poland
Bibliografia
  • [1] P. Lutomski et al., „Wykorzystanie informatyki medycznej w Polsce i na świecie" (An Application of the medical computer sciences in Poland and worldwide), Przedsiębiorczość i Zarządzanie, vol. 3, no. 15, pp. 83-92, 2014 [Online]. Available: http://piz.san.edu.pl/docs/e-XV-12-3.pdf [in Polish].
  • [2] R. Rudowski, Informatyka Medyczna. Wydawnictwo Naukowe PWN, 2003 (ISBN: 9788301140564) [in Polish].
  • [3] R. Tadeusiewicz and W. Wajs, Informatyka Medyczna. Uczelniane Wyd. Naukowo-Dydaktyczne Akademii Górniczo-Hutniczej, 1999 [in Polish].
  • [4] F. Sahba and H. R. Tizhoosh, „Filter fusion for image enhancement using reinforcement learning", in Proc. Canadian Conf. on Elec. and Comp. Engin. CCECE 2003, Montreal, Quebec, Kanada, 2003, vol. 2, pp. 847-850 (doi: 10.1109/CCECE.2003.1226027).
  • [5] M. Sonka, V. Hlavac, and R. Boyle, Image Processing, Analysis, and Machine Vision. Cengage Learning, 2014 (ISBN: 9781133593690).
  • [6] Ch. Hau, Handbook of Pattern Recognition and Computer Vision. World Scientific, 2015 (ISBN: 9789814656535).
  • [7] P. R. Murray, K. S. Rosenthal and M. A. Pfaller, Medical Microbiology. Elsevier Health Sciences, pp. 16-348, 2015 (ISBN: 9780323299565).
  • [8] H. J. Busse, E. B. M. Denner, and W. Lubitz, „Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics", J. of Biotechnol., vol. 47, no. 1, pp. 3-38, 1996 (doi: 10.1016/0168-1656(96)01379-X).
  • [9] A. R. Hall, D. C. Angst, K. T. Schiessl, and M. Ackermann, „Costs of antibiotic resistance separating trait effects and selective effects", Evol. Appl., vol. 8, no. 3, pp. 261-272, 2015 (doi: 10.1111/eva.12187).
  • [10] J. Penterman et al., „Rapid evolution of culture-impaired bacteria during adaptation to biofilm growth", Cell Reports, vol. 6, no. 2, pp. 293-300, 2014 (doi: 10.1016/j.celrep.2013.12.019).
  • [11] G. G. Perron, R. F. Inglis, P. S. Pennings, and S. Cobey, „Fighting microbial drug resistance: a primer on the role of evolutionary biology in public health", Evol. Appl., vol. 8, no. 3, pp. 211-222, 2015 (doi: 10.1111/eva.12254).
  • [12] S. H. Gillespie, Medical Microbiology Illustrated. Butterworth-Heinemann Ltd., 2014, pp. 1-12 and 146-159 (ISBN: 978-1483177823).
  • [13] E. Goldman and L. H. Green, Practical Handbook of Microbiology. CRC Press, 2015, pp. 19-77 and 135-153 (ISBN: 9780429168932).
  • [14] F. J. Baker, R. E. Silverton, and E. D. Luckcock An Introduction to Medical Laboratory Technology. Butterworth-Heinemann, 2014, pp. 441-451 (ISBN 978-1483179605).
  • [15] J. Wójkowska-Mach, A. Ró»a«ska, T. Gosiewski, M. Brzychczy-Włoch, and A. Chmielarczyk, Mikrobiologia z parazytologi¡: skrypt dla studentów II roku Wydziału Lekarskiego Uniwersytetu Jagiellońskiego Collegium Medicum. Krakowska Oficyna Naukowa Tekst, 2015 (ISBN: 9788394273019).
  • [16] M. R. Arabestani, H. Fazzeli, and B. N. Esfahani, „Identification of the most common pathogenic bacteria in patients with suspected sepsis by multiplex PCR", The J. of Infection in Develop. Countries, vol. 8, no. 4, pp. 461-468, 2014 (doi: 10.3855/jidc.3856).
  • [17] M. Ford, Medical Microbiology, 3rd ed. Oxford University Press, 2014, pp. 1-32 (ISBN: 9780198818144).
  • [18] J. R. Jamison, Man Meets Microbes: An Introduction to Medical Microbiology. Butterworth-Heinemann, 2014, pp. 1-65 (ISBN: 9781483141626).
  • [19] W. M. Ahmed et al., „Classification of bacterial contamination using image processing and distributed computing", IEEE J. of Biomed. and Health Inform., vol. 17, no. 1, pp. 232-239, 2013 (doi: 10.1109/TITB.2012.2222654).
  • [20] S. Trattner, H. Greenspan, G. Tepper, and S. Abboud, „Automatic identification of bacterial types using statistical imaging methods", IEEE Trans. on Medi. Imag., vol. 23, pp. 807-820, 2004 (doi: 10.1109/TMI.2004.827481).
  • [21] N. Blackburn et al., „Rapid determination of bacterial abundance, biovolume, morphology, and growth by neural network based image analysis", Appl. and Environmen. Microbiol., vol. 64, no. 9, pp. 3246-3255, 1998 [Online]. Available: https://aem.asm.org/content/aem/64/9/3246.full.pdf
  • [22] P. Perner, „Classification of he-2 cells using uorescent image analysis and data mining", in Medical Data Analysis Second International Symposium, ISMDA 2001, Madrid, Spain, October 8-9, 2001. Proceedings, J. Crespo, V. Maojo, and F. Martin, Eds. LNCS, vol. 2199, pp. 219-224 Springer, 2001 (doi: 10.1007/3-540-45497-7 33).
  • [23] P. S. Hiremath and P. Bannigidad, „Automated Gram-staining characterization of digital bacterial cell images", in Proc. 6th Int. Conf.on Sig. and Image Process. ICSIP 2009, Amsterdam, The Netherlands, 2009, pp. 209-211.
  • [24] B. K. De Bruyne et al., „Bacterial species identification from malditof mass spectra through data analysis and machine learning", System. and Appl. Microbiol., vol. 34, no. 1, pp. 20-29, 2011 (doi: 10.1016/j.syapm.2010.11.003).
  • [25] M. G. Forero, G. Cristªbal, and M. Desco, „Automatic identification of mycobacterium tuberculosis by Gaussian mixture models", J. of Microscopy, vol. 223, pp. 120-132, 2006 (doi: 10.1111/j.1365-2818.2006l.01610.x).
  • [26] J. Liu, F. B. Dazzo, O. Glagoleva, B. Yu, and A. K. Jain, „Cmeias: a computer-aided system for the image analysis of bacterial morphotypes in microbial communities", Microbial Ecol., vol. 41, no. 3, pp. 173-194, 2001 (doi:10.1007/s002480000004).
  • [27] C. Cortes and V. Vapnik, „Support-vector networks"', J. Machine Learn., vol. 20, pp. 273-297, 1995 (doi: 10.1023/A:1022627411411).
  • [28] M. Holmberg et al., „Bacteria classification based on feature extraction from sensor data", Biotechnol. Tech., vol. 12, no. 4, pp. 319-324, 1998 (doi: 10.1023/A:1008862617082).
  • [29] H. Ates and O. N. Gerek, „An image-processing based automated bacteria colony counter", in Proc. Int. Symp. on Comp. and Inform. Sci. ISCIS 2009, Guzelyurt, Cyprus, 2009, pp. 18-23 (doi: 10.1109/ISCIS.2009.5291926).
  • [30] Ch. Sommer and D. W. Gerlich, „Machine learning in cell biologyteaching computers to recognize phenotypes", J. of Cell Sci., vol. 126, pp. 1-11, 2011 (doi: 10.1242/jcs.123604).
  • [31] M. Cimpoi, S. Maji, I. Kokkinos, and A. Vedaldi, „Deep filter banks for texture recognition, description, and segmentation", Int. J. of Comp. Vision, vol. 118, no. 1, pp. 65-94, 2016 (doi: 10.1007/s11263-015-0872-3).
  • [32] A. Signorini et al., „Combining the use of CNN classification and strength-driven compression for the robust identification of bacterial species on hyperspectral culture plate images", IET Comp. Vision, vol. 12, no. 7, pp. 941-949, 2018 (doi: 10.1049/iet-cvi.2018.5237).
  • [33] K. Simonyan and A. Zisserman, „Very deep convolutional networks for large-scale image recognition", 2014 [Online]. Available: https://arxiv.org/abs/1409.1556.
  • [34] O. Russakovsky et al., „Imagenet large scale visual recognition challenge", Int. J. of Comp. Vision, vol. 115, no. 3, pp. 211-252, 2015 (doi: 10.1007/s11263-015-0816-y).
  • [35] A. Buetti-Dinh et al., „Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition", Biotechnol. Rep., vol. 22, 2019 (doi: 10.1016/j.btre.2019.e00321).
  • [36] B. Liu, S. Wang, R. Long, and K.-Ch. Chou, „iRSpot-EL: identify recombination spots with an ensemble learning approach", Bioinformatics, vol. 33, no. 1, pp. 35-41, 2016 (doi: 10.1093/bioinformatics/btw539).
  • [37] O. Garner et al., „Multi-centre evaluation of mass spectrometric identification of anaerobic bacteria using the VITEK MS system", Clinical Microbiol. and Infection, vol. 20, no. 4, pp. 335-339, 2014 (doi: 10.1111/1469-0691.12317).
  • [38] J. A. Branda et al., „Multicenter validation of the VITEK MS v2.0 MALDI-TOF mass spectrometry system for the identification of fastidious Gram-negative bacteria", Diag. Microbiol. and Infect. Disease, vol. 78, no. 2, pp. 129-131, 2014 (doi: 10.1016/j.diagmicrobio.2013.08.013).
  • [39] G. C. Green, A. D. C. Chan, and M. Lin, „Robust identification of bacteria based on repeated odor measurements from individual bacteria colonies", Sensors and Actuators B.: Chemical, vol. 190, pp. 16-24, 2014 (doi: 10.1016/j.snb.2013.08.001).
  • [40] A. Alvarez-Ordonez, D. J. M. Mouwen, M. Lopez, and M. Prieto, „Fourier transform infrared spectroscopy as a tool to characterize molecular composition and stress response in foodborne pathogenic bacteria", J. of Microbiol. Methods, vol. 84, no. 3, pp. 369-378, 2011 (doi: 10.1016/j.mimet.2011.01.009).
  • [41] X. D. Wang and O. S. Wolfbeis, „Fiber-optic chemical sensors and biosensors (2008-2012)", Anal. Chemistry, vol. 85, no. 2, pp. 487-508, 2012 (doi: 10.1021/ac303159b).
  • [42] A. A. Abdullah et al., „Rapid identification method of aerobic bacteria in diabetic foot ulcers using electronic nose", Adv. Sci. Lett., vol. 20, no. 1, pp. 37-41, 2014 (doi: 10.1166/asl.2014.5306).
  • [43] N. Yusuf et al., „Comparison of various pattern recognition techniques based on e-nose for identifying bacterial species in diabetic wound infections", Trans. on Inform. and Commun. Technol., vol. 53, pp. 43-59, 2014 (doi: 10.2495/Intelsys130061).
  • [44] A. Suchwałko, I. Buzalewicz, and H. Podbielska, „Computer-based classification of bacteria species by analysis of their colonies Fresnel diffraction patterns", in Proc. of SPIE - The Int. Soc. of Opt. Engin., San Francisco, CA, USA, 2012, vol. 8212, pp. 82120R-82120R13 (doi: 10.1117/12.907420).
  • [45] H. Podbielska, I. Buzalewicz, A. Suchwaªko, and A. Wieliczko, „Bacteria classification by means of the statistical analysis of fresnel diffraction patterns of bacteria colonies", in Proc. of Conf. Biomed. Optics, Miami, FL, USA, 2012, pp. 1-3 (doi: 10.1364/BIOMED.2012.BSu5A.5).
  • [46] H. Kim, I. J. Doh, A. K. Bhunia, G. B. King, and E. Bae, „Scalar diffraction modeling of multispectral forward scatter patterns from bacterial colonies", Opt. Express, vol. 23, no. 7, pp. 8545-8554, 2015 (doi: 10.1364/OE.23.008545).
  • [47] J. R. Carey et al., „Rapid identification of bacteria with a disposable colorimetric sensing array", J. of the American Chemical Soc., vol. 133, no. 19, pp. 7571-7576, 2011 (doi: 10.1021/ja201634d).
  • [48] A. Suchwałko, I. Buzalewicz, and H. Podbielska, „Bacteria identification in an optical system with optimized diffraction pattern registration condition supported by enhanced statistical analysis", Opt. Express, vol. 22, no. 21, pp. 26312-26327, 2014 (doi: 10.1364/O.E.22.026312).
  • [49] E. Baee et al., „Portable bacterial identification system based on elastic light scatter patterns", J. of Biological Engin., vol. 6, no. 1, pp. 1-11, 2012 (doi: 10.1186/1754-1611-6-12).
  • [50] A. Suchwałko, I. Buzalewicz, A. Wieliczko, and H. Podbielska, „Bacteria species identification by the statistical analysis of bacterial colonies fresnel patterns", Opt. Express, vol. 21, no. 9, pp. 11322-11337, 2013 (doi: 10.1364/OE.21.011322).
Uwagi
Opracowanie rekordu ze środków MNiSW, umowa Nr 461252 w ramach programu "Społeczna odpowiedzialność nauki" - moduł: Popularyzacja nauki i promocja sportu (2020).
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-ac88d438-f2fa-484e-896e-43628824b304
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.