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Biomedical Imaging Informatics for Diagnostic Imaging Marker Selection

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Health Informatics Data Analysis

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Abstract

With the advent of digital imaging, thousands of medical images are captured and stored for future reference. In addition to recording medical history of a patient, these images are a rich source of information about disease-related markers. To extract robust and informative imaging markers, we need to regulate image quality, extract image features, select useful features, and validate them. Research and development of these computational methods fall under the science of biomedical imaging informatics. In this chapter, we discuss challenges and techniques of biomedical imaging informatics in the context of imaging marker extraction.

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References

  1. M.Y. Gabril, G.M. Yousef, Informatics for practicing anatomical pathologists: marking a new era in pathology practice. Mod. Pathol. 23, 349–358 (2010)

    Article  Google Scholar 

  2. S. Kothari, J.H. Phan, T.H. Stokes, M.D. Wang, Pathology imaging informatics for quantitative analysis of whole-slide images. J. Am. Med. Inform. Assoc. 20, 1099–1108 (2013)

    Article  Google Scholar 

  3. J.R. Swedlow, I.G. Goldberg, K.W. Eliceiri, Bioimage informatics for experimental biology. Ann. Rev. Biophys. 38, 327–346 (2009)

    Article  Google Scholar 

  4. H. Peng, Bioimage informatics: a new area of engineering biology. Bioinformatics 24, 1827–1836 (2008)

    Article  Google Scholar 

  5. K.W. Eliceiri, M.R. Berthold, I.G. Goldberg, L. Ibáñez, B.S. Manjunath, M.E. Martone et al., Biological imaging software tools. Nat. Methods 9, 697–710 (2012)

    Article  Google Scholar 

  6. Z. Xiaobo, S.T.C. Wong, Informatics challenges of high-throughput microscopy. IEEE Signal Process. Mag. 23, 63–72 (2006)

    Article  Google Scholar 

  7. L.R. Long, S. Antani, T.M. Deserno, G.R. Thoma, Content-based image retrieval in medicine: retrospective assessment, state of the art, and future directions. Int. j healthc. inform. syst. inform. official publ. Inf. Res. Manag. Assoc. 4, 1–16 (2009)

    Article  Google Scholar 

  8. U. Sinha, A. Bui, R. Taira, J. Dionisio, C. Morioka, D. Johnson et al., A review of medical imaging informatics. Ann. N. Y. Acad. Sci. 980, 168–197 (2002)

    Article  Google Scholar 

  9. T. Liu, H. Peng, X. Zhou, Imaging informatics for personalised medicine: applications and challenges. Int. J. Funct. Inf. Personalised med. 2, 125–135 (2009)

    Article  Google Scholar 

  10. A. Wetzel, computational aspects of pathology image classification and retrieval. J. Supercomputing 11, 279–293 (1997)

    Article  Google Scholar 

  11. T.J. Fuchs, J.M. Buhmann, Computational pathology: challenges and promises for tissue analysis. Comput. Med. Imaging Graph. 35, 515–530 (2011)

    Article  Google Scholar 

  12. W. Amin, U. Chandran, V. Parwani Anil, J. Becich Michael, in Essentials of Anatomic Pathology, ed. by L. Cheng, D. G. Bostwick. Biomedical Informatics for Anatomic Pathology, (Springer, New York, 2011), pp. 469–480

    Google Scholar 

  13. M.N. Gurcan, L. Boucheron, A. Can, A. Madabhushi, N. Rajpoot, B. Yener, Histopathological image analysis: a review. IEEE Rev. Biomed. Eng. 2, 147–171 (2009)

    Article  Google Scholar 

  14. E.T. Sadimin, D.J. Foran, Pathology imaging informatics for clinical practice and investigative and translational research. North Am. J. Med. Sci. (Boston) 5, 103–109 (2012)

    Article  Google Scholar 

  15. L. Pantanowitz, P.N. Valenstein, A.J. Evans, K.J. Kaplan, J.D. Pfeifer, D.C. Wilbur et al., Review of the current state of whole slide imaging in pathology. J. Pathol. Inform. 2, 36 (2011)

    Article  Google Scholar 

  16. R. McLendon, A. Friedman, D. Bigner, E.G. Van Meir, D.J. Brat, G.M. Mastrogianakis et al., Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008)

    Article  Google Scholar 

  17. S. Kothari, J. Phan, T. Stokes, A. Osunkoya, A. Young, M. Wang, Removing batch effects from histopathological images for enhanced cancer diagnosis. IEEE J. Biomed. Health Inform. 18, 765–772 (2014)

    Article  Google Scholar 

  18. S. Kothari, J. Phan, M. Wang, Eliminating tissue-fold artifacts in histopathological whole-slide images for improved image-based prediction of cancer grade. J. Pathol. Inf. 4, 22 (2013)

    Article  Google Scholar 

  19. Y. Saeys, I. Inza, P. Larrañaga, A review of feature selection techniques in bioinformatics. Bioinformatics 23, 2507–2517 (2007)

    Article  Google Scholar 

  20. S. Palokangas, J. Selinummi, O. Yli-Harja, in 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society Segmentation of folds in tissue section images, (2007), pp. 5642–5645

    Google Scholar 

  21. P. A. Bautista, Y. Yagi, in Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Detection of tissue folds in whole slide images, (2009), pp. 3669–3672

    Google Scholar 

  22. F.W. Leong, M. Brady, J.O.D. McGee, Correction of uneven illumination (vignetting) in digital microscopy images. J. Clin. Pathol. 56, 619–621 (2003)

    Article  Google Scholar 

  23. S. Kothari, J. H. Phan, R. A. Moffitt, T. H. Stokes, S. E. Hassberger, Q. Chaudry, et al., in IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Automatic batch-invariant color segmentation of histological cancer images, (2011), pp. 657–660

    Google Scholar 

  24. M. Macenko, M. Niethammer, J. S. Marron, D. Borland, J. T. Woosley, G. Xiaojun, et al., in 6th IEEE international conference on Symposium on Biomedical Imaging: From Nano to Macro, A method for normalizing histology slides for quantitative analysis,(2009), pp. 1107–1110

    Google Scholar 

  25. D. Magee, D. Treanor, D. Crellin, M. Shires, K. Smith, K. Mohee, et al., in Proc Optical Tissue Image analysis in Microscopy, Histopathology and Endoscopy (MICCAI Workshop), Colour Normalisation in Digital Histopathology Images, (2009), pp. 100–111

    Google Scholar 

  26. K. Jun, H. Shimada, K. Boyer, J. Saltz, M. Gurcan, in 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Image analysis for automated assessment of grade of neuroblastic differentiation, (2007), pp. 61–64

    Google Scholar 

  27. Q. Chaudry, S. Raza, A. Young, M. Wang, Automated renal cell carcinoma subtype classification using morphological, textural and wavelets based features. J. Sig Proc. Syst. 55, 15–23 (2009)

    Article  Google Scholar 

  28. C. Meurie, G. Lebrun, O. Lezoray, A. Elmoataz, A comparison of supervised pixels-based color image segmentation methods. application in cancerology. WSEAS Trans. Comput. 2, 44–739 (2003)

    Google Scholar 

  29. K. Mao, P. Zhao, P. Tan, Supervised learning-based cell image segmentation for P53 immunohistochemistry. IEEE Trans. Biomed. Eng. 53, 1153–1163 (2006)

    Article  Google Scholar 

  30. P. Ranefalla, L. Egevadb, B. Nordina, E. Bengtssona, A new method for segmentation of colour images applied to immunohistochemically stained cell nuclei. Anal. Cell. Pathol. 15, 145–156 (1997)

    Article  Google Scholar 

  31. Y. Al-Kofahi, W. Lassoued, W. Lee, B. Roysam, Improved automatic detection and segmentation of cell nuclei in histopathology images. IEEE Trans. Biomed. Eng. 57, 841–852 (2010)

    Article  Google Scholar 

  32. O. Sertel, J. Kong, U. Catalyurek, G. Lozanski, J. Saltz, M. Gurcan, Histopathological image analysis using model-based intermediate representations and color texture: follicular lymphoma grading. J. Sig. Process. Syst. 55, 169–183 (2009)

    Article  Google Scholar 

  33. C. Gunduz-Demir, M. Kandemir, A. Tosun, C. Sokmensuer, Automatic segmentation of colon glands using object-graphs. Med. Image Anal. 14, 1–12 (2010)

    Article  Google Scholar 

  34. J.P. Monaco, J.E. Tomaszewski, M.D. Feldman, I. Hagemann, M. Moradi, P. Mousavi et al., High-throughput detection of prostate cancer in histological sections using probabilistic pairwise Markov models. Med. Image Anal. 14, 617–629 (2010)

    Article  Google Scholar 

  35. P. Thevenaz, M. Unser, Snakuscules. IEEE Trans. Image Process. 17, 585–593 (2008)

    Article  MathSciNet  Google Scholar 

  36. H. Kong, M. Gurcan, K. Belkacem-Boussaid, Partitioning histopathological images: an integrated framework for supervised color-texture segmentation and cell splitting. IEEE Trans. Med. Imaging 30, 1661–1677 (2011)

    Article  Google Scholar 

  37. A. Tabesh, M. Teverovskiy, P. Ho-Yuen, V.P. Kumar, D. Verbel, A. Kotsianti et al., Multifeature prostate cancer diagnosis and gleason grading of histological images. IEEE Trans. Med. Imaging 26, 1366–1378 (2007)

    Article  Google Scholar 

  38. T. Fuchs, P. Wild, H. Moch, J. Buhmann, in Medical Image Computing and Computer-Assisted Intervention, Computational Pathology Analysis of Tissue Microarrays Predicts Survival of Renal Clear Cell Carcinoma Patients, (2008), pp. 1–8

    Google Scholar 

  39. M. Rahman, P. Bhattacharya, B.C. Desai, A framework for medical image retrieval using machine learning and statistical similarity matching techniques with relevance feedback. IEEE Trans. Inf Technol. Biomed. 11, 58–69 (2007)

    Article  Google Scholar 

  40. L. Yang, O. Tuzel, W. Chen, P. Meer, G. Salaru, L.A. Goodell et al., PathMiner: a web-based tool for computer-assisted diagnostics in pathology. IEEE Trans. Inf Technol. Biomed. 13, 291–299 (2009)

    Article  Google Scholar 

  41. V. Kovalev, A. Dmitruk, I. Safonau, M. Frydman, and S. Shelkovich, in Computer Analysis of Images and Patterns, A Method for Identification and Visualization of Histological Image Structures Relevant to the Cancer Patient Conditions, vol. 6854, ed. by P. Real, D. Diaz-Pernil, H. Molina-Abril, A. Berciano, W. Kropatsch (Springer Berlin/Heidelberg, 2011), pp. 460–468

    Google Scholar 

  42. J. Kong, O. Sertel, H. Shimada, K.L. Boyer, J.H. Saltz, M.N. Gurcan, Computer-aided evaluation of neuroblastoma on whole-slide histology images: classifying grade of neuroblastic differentiation. Pattern Recogn. 42, 1080–1092 (2009)

    Article  Google Scholar 

  43. M.E. Celebi, H.A. Kingravi, B. Uddin, H. Iyatomi, Y.A. Aslandogan, W.V. Stoecker et al., A methodological approach to the classification of dermoscopy images. Comput. Med. Imaging Graph. 31, 362–373 (2007)

    Article  Google Scholar 

  44. M. Muthu Rama Krishnan, M. Pal, R. R. Paul, C. Chakraborty, J. Chatterjee, and A. K. Ray, in Journal of Medical Systems, Computer Vision Approach to Morphometric Feature Analysis of Basal Cell Nuclei for Evaluating Malignant Potentiality of Oral Submucous Fibrosis, vol. 36 (2012), pp. 1746–1756

    Google Scholar 

  45. L.A.D. Cooper, K. Jun, D.A. Gutman, W. Fusheng, S.R. Cholleti, T.C. Pan et al., An integrative approach for in silico glioma research. IEEE Trans. Biomed. Eng. 57, 2617–2621 (2010)

    Article  Google Scholar 

  46. S. Doyle, M. Feldman, J. Tomaszewski, A. Madabhushi, A boosted bayesian multi-resolution classifier for prostate cancer detection from digitized needle biopsies. IEEE Trans. Biomed. Eng. 59, 1205–1218 (2010)

    Article  Google Scholar 

  47. P.W. Huang, C.H. Lee, Automatic classification for pathological prostate images based on fractal analysis. IEEE Trans. Med. Imaging 28, 1037–1050 (2009)

    Article  Google Scholar 

  48. K. Jafari-Khouzani, H. Soltanian-Zadeh, Multiwavelet grading of pathological images of prostate. IEEE Trans. Biomed. Eng. 50, 697–704 (2003)

    Article  Google Scholar 

  49. D. Zhang, G. Lu, Review of shape representation and description techniques. Pattern Recogn. 37, 1 (2004)

    Article  Google Scholar 

  50. L. Boucheron, Object-and spatial-level quantitative analysis of multispectral histopathology images for detection and characterization of cancer, Ph.D thesis, University of California, Santa Barbara, 2008

    Google Scholar 

  51. C. Gunduz, B. Yener, H.S. Gultekin, The cell graphs of cancer. Bioinformatics 20, i145–i151 (2004)

    Article  Google Scholar 

  52. C.C. Bilgin, P. Bullough, G.E. Plopper, B. Yener, ECM-aware cell-graph mining for bone tissue modeling and classification. Data Min. Knowl. Disc. 20, 416–438 (2009)

    Article  MathSciNet  Google Scholar 

  53. A.N. Basavanhally, S. Ganesan, S. Agner, J.P. Monaco, M.D. Feldman, J.E. Tomaszewski et al., Computerized image-based detection and grading of lymphocytic infiltration in HER2 + breast cancer histopathology. IEEE Trans. Biomed. Eng. 57, 642–653 (2010)

    Article  Google Scholar 

  54. J. Sudbø, R. Marcelpoil, A. Reith, New algorithms based on the Voronoi Diagram applied in a pilot study on normal mucosa and carcinomas. Anal. Cell. Pathol. 21, 71–86 (2000)

    Article  Google Scholar 

  55. J. Sudbo, A. Bankfalvi, M. Bryne, R. Marcelpoil, M. Boysen, J. Piffko et al., Prognostic value of graph theory-based tissue architecture analysis in carcinomas of the tongue. Lab. Invest. 80, 1881–1889 (2000)

    Article  Google Scholar 

  56. I. Guyon, A. Elisseeff, An introduction to variable and feature selection. J. Mach. Learn. Res. 3, 1157–1182 (2003)

    MATH  Google Scholar 

  57. M. A. Hall, “Correlation-based feature selection for machine learning,” Department of Computer Science, Waikato University, New Zealand, 1999

    Google Scholar 

  58. C. Ding, H. Peng, Minimum redundancy feature selection from microarray gene expression data. J. Bioinf. Comput. Biol. 3, 185–205 (2005)

    Article  Google Scholar 

  59. I. Kononenko, in Machine Learning: ECML-94, ed. by F. Bergadano, L. De Raedt. Estimating attributes: Analysis and extensions of RELIEF, vol. 784 (Springer Berlin/Heidelberg, 1994), pp. 171–182

    Google Scholar 

  60. D. B. Skalak, in Conference Processing on Machine Learning, Prototype and Feature Selection by Sampling and Random Mutation Hill Climbing Algorithms, (1994), pp. 293–301

    Google Scholar 

  61. J.H. Holland, Adaptation in natural and artificial systems: an introductory analysis with applications to biology, control, and artificial intelligence (Michigan University, Ann Arbor, 1975)

    MATH  Google Scholar 

  62. S. Kirkpatrick, C.D. Gelatt, M.P. Vecchi, Optimization by simulated annealing. Science 220, 671 (1983)

    Article  MathSciNet  MATH  Google Scholar 

  63. I. Guyon, J. Weston, S. Barnhill, V. Vapnik, Gene selection for cancer classification using support vector machines. Mach. Learn. 46, 389–422 (2002)

    Article  MATH  Google Scholar 

  64. S. B. Kotsiantis, in Informatica (03505596), Supervised machine learning: a review of classification techniques, vol. 31 (2007)

    Google Scholar 

  65. R. Bellazzi, B. Zupan, Predictive data mining in clinical medicine: current issues and guidelines. Int. J. Med. Inform. 77, 81–97 (2008)

    Article  Google Scholar 

  66. R. Hoffman, S. Kothari, J. Phan, M. D. Wang, in The International Conference on Health Informatics, ed. by Y.T. Zhang. A High-Resolution Tile-Based Approach for Classifying Biological Regions in Whole-Slide Histopathological Images, (Springer International Publishing, 2014), pp. 280–283

    Google Scholar 

  67. C.-C. Chang, C.-J. Lin, in ACM Transactions on Intelligent Systems and Technology (TIST), LIBSVM: a library for support vector machines, vol. 2 (2011), p. 27

    Google Scholar 

  68. S. Kothari, J. H. Phan, A. O. Osunkoya, M. D. Wang, in Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, Biological interpretation of morphological patterns in histopathological whole-slide images, (2012), pp. 218–225

    Google Scholar 

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Phan, S.K., Hoffman, R., Wang, M.D. (2017). Biomedical Imaging Informatics for Diagnostic Imaging Marker Selection. In: Xu, D., Wang, M., Zhou, F., Cai, Y. (eds) Health Informatics Data Analysis. Health Information Science. Springer, Cham. https://doi.org/10.1007/978-3-319-44981-4_8

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