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Convolutional Neural Networks in Advanced Biomedical Imaging Applications

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Deep Learning for Biomedical Data Analysis

Abstract

Deep learning (DL), in particular Convolutional Neural Networks (CNNs), can be used to build powerful quantitative image analysis tools. To take advantage of these capabilities and establish tractable goals and problem solving approaches, it is crucial to understand how both imaging and computational tools have been developed and used together. Different advanced optical imaging methods, whether invasive or non-invasive, are applicable to a wide variety of biomedical research, and CNN algorithms can be tailored to assist with extracting meaningful results from imaging data.

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References

  1. IBM Watson’s Initiative. https://www.ibm.com/academic/home. Accessed: 2020-07-07.

  2. Paperspace. GPU cloud tools built for developers. Powering next-generation workflows and the future of intelligent applications. https://www.paperspace.com/. Accessed: 2020-07-07.

  3. C. A, W. Z, W. J, and et al. Deep learning for the segmentation of preserved photoreceptors on en face optical coherence tomography in two inherited retinal diseases. Biomed Opt Express, 9(7):3092–3105, 2018.

    Google Scholar 

  4. M. Abadi, A. Agarwal, P. Barham, E. Brevdo, Z. Chen, C. Citro, G. S. Corrado, A. Davis, J. Dean, M. Devin, S. Ghemawat, I. Goodfellow, A. Harp, G. Irving, M. Isard, Y. Jia, R. Jozefowicz, L. Kaiser, M. Kudlur, J. Levenberg, D. Mané, R. Monga, S. Moore, D. Murray, C. Olah, M. Schuster, J. Shlens, B. Steiner, I. Sutskever, K. Talwar, P. Tucker, V. Vanhoucke, V. Vasudevan, F. Viégas, O. Vinyals, P. Warden, M. Wattenberg, M. Wicke, Y. Yu, and X. Zheng. TensorFlow: Large-scale machine learning on heterogeneous systems, 2015. Software available from tensorflow.org.

    Google Scholar 

  5. M. Adhi and J. S. Duker. Optical coherence tomography–current and future applications. Current opinion in ophthalmology, 24(3):213, 2013.

    Google Scholar 

  6. S. U. Akram, J. Kannala, L. Eklund, and J. Heikkilä. Cell segmentation proposal network for microscopy image analysis. In Deep Learning and Data Labeling for Medical Applications, pages 21–29. Springer, 2016.

    Google Scholar 

  7. K. Aljakouch, Z. Hilal, I. Daho, M. Schuler, S. D. Krauß, H. K. Yosef, J. Dierks, A. Mosig, K. Gerwert, and S. F. El-Mashtoly. Fast and noninvasive diagnosis of cervical cancer by coherent anti-stokes raman scattering. Analytical Chemistry, 2019.

    Google Scholar 

  8. L. A. Austin, S. Osseiran, and C. L. Evans. Raman technologies in cancer diagnostics. Analyst, 141(2):476–503, 2016.

    Article  CAS  PubMed  Google Scholar 

  9. H. G. Bezerra, M. A. Costa, G. Guagliumi, A. M. Rollins, and D. I. Simon. Intracoronary optical coherence tomography: a comprehensive review: clinical and research applications. JACC: Cardiovascular Interventions, 2(11):1035–1046, 2009.

    PubMed  Google Scholar 

  10. K. Bhatia, M. Graham, L. Terry, A. Wood, P. Tranos, S. Trikha, and N. Jaccard. Disease Classification of Macular Optical Coherence Tomography Scans Using Deep Learning Software: Validation on Independent, Multicenter Data. Retina, page 1, 2019.

    Google Scholar 

  11. K. K. Bhatia, M. S. Graham, L. Terry, A. Wood, P. Tranos, S. Trikha, and N. Jaccard. Disease classification of macular optical coherence tomography scans using deep learning software: validation on independent, multi-centre data. arXiv preprint arXiv:1907.05164, 2019.

    Google Scholar 

  12. C. Bonnans, J. Chou, and Z. Werb. Remodelling the extracellular matrix in development and disease. Nature reviews Molecular cell biology, 15(12):786, 2014.

    Google Scholar 

  13. B. Bouma, G. Tearney, H. Yabushita, M. Shishkov, C. Kauffman, D. D. Gauthier, B. MacNeill, S. Houser, H. Aretz, E. F. Halpern, et al. Evaluation of intracoronary stenting by intravascular optical coherence tomography. Heart, 89(3):317–320, 2003.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. G. Bradski. The OpenCV Library. Dr. Dobb’s Journal of Software Tools, 2000.

    Google Scholar 

  15. L. Breiman. Random forests. Machine Learning, 45(1):5–32, Oct 2001.

    Article  Google Scholar 

  16. H. G. Breunig, M. Weinigel, R. Bückle, M. Kellner-Höfer, J. Lademann, M. E. Darvin, W. Sterry, and K. König. Clinical coherent anti-stokes raman scattering and multiphoton tomography of human skin with a femtosecond laser and photonic crystal fiber. Laser Physics Letters, 10(2):025604, 2013.

    Google Scholar 

  17. M. Brinkmann, A. Fast, T. Hellwig, I. Pence, C. L. Evans, and C. Fallnich. Portable all-fiber dual-output widely tunable light source for coherent raman imaging. Biomedical optics express, 10(9):4437–4449, 2019.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. P. T. Cagle, R. Barrios, and T. C. Allen. Color atlas and text of pulmonary pathology. Lippincott Williams & Wilkins, 2008.

    Google Scholar 

  19. R. Cairns, R. Khokha, and R. Hill. Molecular mechanisms of tumor invasion and metastasis: an integrated view. Current molecular medicine, 3(7):659–671, 2003.

    Article  CAS  PubMed  Google Scholar 

  20. P. Campagnola. Second harmonic generation imaging microscopy: applications to diseases diagnostics, 2011.

    Google Scholar 

  21. R. Carriles, D. N. Schafer, K. E. Sheetz, J. J. Field, R. Cisek, V. Barzda, A. W. Sylvester, and J. A. Squier. Invited review article: Imaging techniques for harmonic and multiphoton absorption fluorescence microscopy. Review of scientific instruments, 80(8):081101, 2009.

    Google Scholar 

  22. D. Castelvecchi. Can we open the black box of ai? Nature News, 538(7623):20, 2016.

    Google Scholar 

  23. J. Chen, S. Zhuo, X. Jiang, X. Zhu, L. Zheng, S. Xie, B. Lin, and H. Zeng. Multiphoton microscopy study of the morphological and quantity changes of collagen and elastic fiber components in keloid disease. Journal of biomedical optics, 16(5):051305, 2011.

    Google Scholar 

  24. F. Chollet. keras. https://github.com/fchollet/keras, 2015.

  25. T. R. Cox and J. T. Erler. Remodeling and homeostasis of the extracellular matrix: implications for fibrotic diseases and cancer. Disease models & mechanisms, 4(2):165–178, 2011.

    Article  CAS  Google Scholar 

  26. J. Cuadros and G. Bresnick. Eyepacs: an adaptable telemedicine system for diabetic retinopathy screening. Journal of diabetes science and technology, 3(3):509–516, 2009.

    Article  PubMed  PubMed Central  Google Scholar 

  27. M. W. Davidson and M. Abramowitz. Optical microscopy. Encyclopedia of imaging science and technology, 2002.

    Google Scholar 

  28. E. Decencière, G. Cazuguel, X. Zhang, G. Thibault, J.-C. Klein, F. Meyer, B. Marcotegui, G. Quellec, M. Lamard, R. Danno, et al. Teleophta: Machine learning and image processing methods for teleophthalmology. Irbm, 34(2):196–203, 2013.

    Article  Google Scholar 

  29. E. Decencière, X. Zhang, G. Cazuguel, B. Lay, B. Cochener, C. Trone, P. Gain, R. Ordonez, P. Massin, A. Erginay, et al. Feedback on a publicly distributed image database: the messidor database. Image Analysis & Stereology, 33(3):231–234, 2014.

    Article  Google Scholar 

  30. W. Denk, J. H. Strickler, and W. W. Webb. Two-photon laser scanning fluorescence microscopy. Science, 248(4951):73–76, 1990.

    Article  CAS  PubMed  Google Scholar 

  31. S. K. Devalla, P. K. Renukanand, B. K. Sreedhar, G. Subramanian, L. Zhang, S. Perera, J.-M. Mari, K. S. Chin, T. A. Tun, N. G. Strouthidis, T. Aung, A. H. Thiéry, and M. J. A. Girard. Drunet: a dilated-residual u-net deep learning network to segment optic nerve head tissues in optical coherence tomography images. Biomed. Opt. Express, 9(7):3244–3265, Jul 2018.

    Article  PubMed  PubMed Central  Google Scholar 

  32. J. Donahue, Y. Jia, O. Vinyals, J. Hoffman, N. Zhang, E. Tzeng, and T. Darrell. Decaf: A deep convolutional activation feature for generic visual recognition. In International conference on machine learning, pages 647–655, 2014.

    Google Scholar 

  33. W. Drexler and J. G. Fujimoto. Optical coherence tomography: technology and applications. Springer Science & Business Media, 2008.

    Google Scholar 

  34. T. Eto, H. Suzuki, A. Honda, and Y. Nagashima. The changes of the stromal elastotic framework in the growth of peripheral lung adenocarcinomas. Cancer: Interdisciplinary International Journal of the American Cancer Society, 77(4):646–656, 1996.

    Article  CAS  Google Scholar 

  35. C. L. Evans, E. O. Potma, M. Puoris’ haag, D. Côté, C. P. Lin, and X. S. Xie. Chemical imaging of tissue in vivo with video-rate coherent anti-stokes raman scattering microscopy. Proceedings of the national academy of sciences, 102(46):16807–16812, 2005.

    Google Scholar 

  36. C. L. Evans and X. S. Xie. Coherent anti-stokes raman scattering microscopy: chemical imaging for biology and medicine. Annu. Rev. Anal. Chem., 1:883–909, 2008.

    Article  CAS  Google Scholar 

  37. C. L. Evans, X. Xu, S. Kesari, X. S. Xie, S. T. Wong, and G. S. Young. Chemically-selective imaging of brain structures with cars microscopy. Optics express, 15(19):12076–12087, 2007.

    Article  CAS  PubMed  Google Scholar 

  38. J. A. Evans, B. E. Bouma, J. Bressner, M. Shishkov, G. Y. Lauwers, M. Mino-Kenudson, N. S. Nishioka, and G. J. Tearney. Identifying intestinal metaplasia at the squamocolumnar junction by using optical coherence tomography. Gastrointestinal endoscopy, 65(1):50–56, 2007.

    Article  PubMed  Google Scholar 

  39. J. A. Evans, J. M. Poneros, B. E. Bouma, J. Bressner, E. F. Halpern, M. Shishkov, G. Y. Lauwers, M. Mino-Kenudson, N. S. Nishioka, and G. J. Tearney. Optical coherence tomography to identify intramucosal carcinoma and high-grade dysplasia in barrett’s esophagus. Clinical Gastroenterology and Hepatology, 4(1):38–43, 2006.

    Article  PubMed  PubMed Central  Google Scholar 

  40. S. Farsiu, S. J. Chiu, R. V. O’Connell, F. A. Folgar, E. Yuan, J. A. Izatt, C. A. Toth, A.-R. E. D. S. . A. S. D. O. C. T. S. Group, et al. Quantitative classification of eyes with and without intermediate age-related macular degeneration using optical coherence tomography. Ophthalmology, 121(1):162–172, 2014.

    Google Scholar 

  41. A. F. Fercher, W. Drexler, C. K. Hitzenberger, and T. Lasser. Optical coherence tomography-principles and applications. Reports on progress in physics, 66(2):239, 2003.

    Google Scholar 

  42. D. C. Fernández, H. M. Salinas, and C. A. Puliafito. Automated detection of retinal layer structures on optical coherence tomography images. Opt. Express, 13(25):10200–10216, Dec 2005.

    Article  Google Scholar 

  43. e. P. Franken, A. E. Hill, C. e. Peters, and G. Weinreich. Generation of optical harmonics. Physical Review Letters, 7(4):118, 1961.

    Google Scholar 

  44. C. W. Freudiger, W. Min, B. G. Saar, S. Lu, G. R. Holtom, C. He, J. C. Tsai, J. X. Kang, and X. S. Xie. Label-free biomedical imaging with high sensitivity by stimulated raman scattering microscopy. Science, 322(5909):1857–1861, 2008.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. C. W. Freudiger, R. Pfannl, D. A. Orringer, B. G. Saar, M. Ji, Q. Zeng, L. Ottoboni, W. Ying, C. Waeber, J. R. Sims, et al. Multicolored stain-free histopathology with coherent raman imaging. Laboratory investigation, 92(10):1492, 2012.

    Google Scholar 

  46. Y. Fu, T. B. Huff, H.-W. Wang, H. Wang, and J.-X. Cheng. Ex vivo and in vivo imaging of myelin fibers in mouse brain by coherent anti-stokes raman scattering microscopy. Optics express, 16(24):19396–19409, 2008.

    Article  CAS  PubMed  Google Scholar 

  47. J. G. Fujimoto, C. Pitris, S. A. Boppart, and M. E. Brezinski. Optical coherence tomography: an emerging technology for biomedical imaging and optical biopsy. Neoplasia (New York, NY), 2(1–2):9, 2000.

    Google Scholar 

  48. G. González and C. L. Evans. Biomedical image processing with containers and deep learning: An automated analysis pipeline: Data architecture, artificial intelligence, automated processing, containerization, and clusters orchestration ease the transition from data acquisition to insights in medium-to-large datasets. BioEssays, page 1900004, 2019.

    Google Scholar 

  49. I. Goodfellow, Y. Bengio, and A. Courville. Deep Learning. The MIT Press, 2016.

    Google Scholar 

  50. A. Gulli and S. Pal. Deep learning with Keras. Packt Publishing Ltd, 2017.

    Google Scholar 

  51. V. Gulshan, L. Peng, M. Coram, M. C. Stumpe, D. Wu, A. Narayanaswamy, S. Venugopalan, K. Widner, T. Madams, J. Cuadros, R. Kim, R. Raman, P. C. Nelson, J. L. Mega, and D. R. Webster. Development and validation of a deep learning algorithm for detection of diabetic retinopathy in retinal fundus photographs. JAMA - Journal of the American Medical Association, 316(22):2402–2410, 2016.

    Article  PubMed  Google Scholar 

  52. V. Gulshan, R. P. Rajan, K. Widner, D. Wu, P. Wubbels, T. Rhodes, K. Whitehouse, M. Coram, G. Corrado, K. Ramasamy, R. Raman, L. Peng, and D. R. Webster. Performance of a Deep-Learning Algorithm vs Manual Grading for Detecting Diabetic Retinopathy in India. JAMA Ophthalmology, 137(9):987–993, 2019.

    Article  PubMed  PubMed Central  Google Scholar 

  53. L. Hamers et al. Similarity measures in scientometric research: The jaccard index versus salton’s cosine formula. Information Processing and Management, 25(3):315–18, 1989.

    Article  Google Scholar 

  54. F. Hausdorff. Dimension und äußeres maß. Mathematische Annalen, 79(1–2):157–179, 1918.

    Article  Google Scholar 

  55. K. He, X. Zhang, S. Ren, and J. Sun. Deep residual learning for image recognition. CoRR, abs/1512.03385, 2015.

    Google Scholar 

  56. J. I. Hoffman. Biostatistics for medical and biomedical practitioners. Academic press, 2015.

    Google Scholar 

  57. K. Hornik. Approximation capabilities of multilayer feedforward networks. Neural networks, 4(2):251–257, 1991.

    Article  Google Scholar 

  58. K. Hornik, M. Stinchcombe, and H. White. Multilayer feedforward networks are universal approximators. Neural Networks, 2(5):359–366, 1989.

    Article  Google Scholar 

  59. N. G. Horton, K. Wang, D. Kobat, C. G. Clark, F. W. Wise, C. B. Schaffer, and C. Xu. In vivo three-photon microscopy of subcortical structures within an intact mouse brain. Nature photonics, 7(3):205, 2013.

    Google Scholar 

  60. M. Huttunen, A. Hassan, C. McCloskey, S. Fasih, J. Upham, B. Venderhyden, R. Boyd, and S. Murugkar. Automated classification of multiphoton microscopy images of ovarian tissue using deep learning. Journal of Biomedical Optics, 23(6), 2018.

    Google Scholar 

  61. H. Iqbal. Plot neural net, 2018. Latex code for drawing neural networks for reports and presentation.

    Google Scholar 

  62. A. Işın, C. Direkoğlu, and M. Şah. Review of mri-based brain tumor image segmentation using deep learning methods. Procedia Computer Science, 102:317–324, 2016.

    Article  Google Scholar 

  63. M. Ji, D. A. Orringer, C. W. Freudiger, S. Ramkissoon, X. Liu, D. Lau, A. J. Golby, I. Norton, M. Hayashi, N. Y. Agar, et al. Rapid, label-free detection of brain tumors with stimulated raman scattering microscopy. Science translational medicine, 5(201):201ra119–201ra119, 2013.

    Google Scholar 

  64. Y. Jia, E. Shelhamer, J. Donahue, S. Karayev, J. Long, R. Girshick, S. Guadarrama, and T. Darrell. Caffe: Convolutional architecture for fast feature embedding, 2014.

    Google Scholar 

  65. K. Kawaguchi, L. P. Kaelbling, and Y. Bengio. Generalization in deep learning. arXiv preprint arXiv:1710.05468, 2017.

    Google Scholar 

  66. T. Kepp, C. Droigk, M. Casper, M. Evers, G. Hüttmann, N. Salma, D. Manstein, M. P. Heinrich, and H. Handels. Segmentation of mouse skin layers in optical coherence tomography image data using deep convolutional neural networks. Biomed. Opt. Express, 10(7):3484–3496, Jul 2019.

    Article  PubMed  PubMed Central  Google Scholar 

  67. W. Kirch. Pearson’s correlation coefficient. Encyclopedia of Public Health; Springer: Dordrecht, The Netherlands, pages 1090–2013, 2008.

    Google Scholar 

  68. N. D. Kirkpatrick, M. A. Brewer, and U. Utzinger. Endogenous optical biomarkers of ovarian cancer evaluated with multiphoton microscopy. Cancer Epidemiology and Prevention Biomarkers, 16(10):2048–2057, 2007.

    Article  CAS  Google Scholar 

  69. A. Krizhevsky, I. Sutskever, and G. E. Hinton. Imagenet classification with deep convolutional neural networks. In Proceedings of the 25th International Conference on Neural Information Processing Systems - Volume 1, NIPS’12, pages 1097–1105, USA, 2012. Curran Associates Inc.

    Google Scholar 

  70. N. Kumar, R. Verma, S. Sharma, S. Bhargava, A. Vahadane, and A. Sethi. A dataset and a technique for generalized nuclear segmentation for computational pathology. IEEE transactions on medical imaging, 36(7):1550–1560, 2017.

    Article  PubMed  Google Scholar 

  71. Y. LeCun, P. Haffner, L. Bottou, and Y. Bengio. Object recognition with gradient-based learning. Feature Grouping, 1999.

    Google Scholar 

  72. K. Lee, M. Garvin, S. Russell, M. Sonka, and M. Abràmoff. Automated intraretinal layer segmentation of 3-d macular oct scans using a multiscale graph search. Investigative Ophthalmology & Visual Science, 51(13):1767–1767, 2010.

    Google Scholar 

  73. J. Li, F. Luisier, and T. Blu. Pure-let image deconvolution. IEEE Transactions on Image Processing, 27(1):92–105, 2017.

    Article  Google Scholar 

  74. H. Lin, F. Deng, K. Huang, H. J. Lee, and J. Cheng. High-speed, high-sensitivity spectroscopic stimulated raman scattering microscopy by ultrafast delay-line tuning and deep learning. In 2019 Conference on Lasers and Electro-Optics (CLEO), pages 1–2, May 2019.

    Google Scholar 

  75. S. Lundberg and S. Lee. A unified approach to interpreting model predictions. CoRR, abs/1705.07874, 2017.

    Google Scholar 

  76. F. Mahmood, D. Borders, R. J. Chen, G. N. McKay, K. J. Salimian, A. S. Baras, and N. J. Durr. Deep adversarial training for multi-organ nuclei segmentation in histopathology images. CoRR, abs/1810.00236, 2018.

    Google Scholar 

  77. B. Manifold, E. Thomas, A. T. Francis, A. H. Hill, and D. Fu. Denoising of stimulated raman scattering microscopy images via deep learning. Biomed. Opt. Express, 10(8):3860–3874, Aug 2019.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. S. Mannor, D. Peleg, and R. Rubinstein. The cross entropy method for classification. In Proceedings of the 22nd international conference on Machine learning, pages 561–568, 2005.

    Google Scholar 

  79. B. Masters, P. So, and E. Gratton. Optical biopsy of in vivo human skin: multi-photon excitation microscopy. Lasers in Medical Science, 13(3):196–203, 1998.

    Article  Google Scholar 

  80. M. Mirza and S. Osindero. Conditional generative adversarial nets. CoRR, abs/1411.1784, 2014.

    Google Scholar 

  81. A. Mishra, A. Wong, K. Bizheva, and D. A. Clausi. Intra-retinal layer segmentation in optical coherence tomography images. Opt. Express, 17(26):23719–23728, Dec 2009.

    Article  CAS  PubMed  Google Scholar 

  82. D. Mojahed, P. Chang, Y. Gan, X. Yao, B. Angelini, H. Hibshoosh, R. Ha, and C. P. Hendon. Convolutional neural network (cnn) classification of breast cancer in optical coherence tomography (oct) images. In Optical Coherence Tomography and Coherence Domain Optical Methods in Biomedicine XXIII, volume 10867, page 108671N. International Society for Optics and Photonics, 2019.

    Google Scholar 

  83. W. J. Murdoch, C. Singh, K. Kumbier, R. Abbasi-Asl, and B. Yu. Definitions, methods, and applications in interpretable machine learning. Proceedings of the National Academy of Sciences, 116(44):22071–22080, 2019.

    Article  CAS  Google Scholar 

  84. O. Nadiarnykh, R. B. LaComb, M. A. Brewer, and P. J. Campagnola. Alterations of the extracellular matrix in ovarian cancer studied by second harmonic generation imaging microscopy. BMC cancer, 10(1):94, 2010.

    Google Scholar 

  85. N. Nassif, B. Cense, B. Park, M. Pierce, S. Yun, B. Bouma, G. Tearney, T. Chen, and J. De Boer. In vivo high-resolution video-rate spectral-domain optical coherence tomography of the human retina and optic nerve. Optics express, 12(3):367–376, 2004.

    Article  CAS  PubMed  Google Scholar 

  86. A. Y. Ng. Feature selection, l 1 vs. l 2 regularization, and rotational invariance. In Proceedings of the twenty-first international conference on Machine learning, page 78, 2004.

    Google Scholar 

  87. S. J. Pan and Q. Yang. A survey on transfer learning. IEEE Transactions on knowledge and data engineering, 22(10):1345–1359, 2009.

    Article  Google Scholar 

  88. A. Paszke, S. Gross, S. Chintala, G. Chanan, E. Yang, Z. DeVito, Z. Lin, A. Desmaison, L. Antiga, and A. Lerer. Automatic differentiation in PyTorch. In NIPS Autodiff Workshop, 2017.

    Google Scholar 

  89. S. W. Perry, R. M. Burke, and E. B. Brown. Two-photon and second harmonic microscopy in clinical and translational cancer research. Annals of biomedical engineering, 40(2):277–291, 2012.

    Article  PubMed  PubMed Central  Google Scholar 

  90. P. Porwal, S. Pachade, R. Kamble, M. Kokare, G. Deshmukh, V. Sahasrabuddhe, and F. Meriaudeau. Indian diabetic retinopathy image dataset (idrid): A database for diabetic retinopathy screening research. Data, 3(3):25, 2018.

    Google Scholar 

  91. P. P. Provenzano, D. R. Inman, K. W. Eliceiri, J. G. Knittel, L. Yan, C. T. Rueden, J. G. White, and P. J. Keely. Collagen density promotes mammary tumor initiation and progression. BMC medicine, 6(1):11, 2008.

    Google Scholar 

  92. K. P. Quinn, G. V. Sridharan, R. S. Hayden, D. L. Kaplan, K. Lee, and I. Georgakoudi. Quantitative metabolic imaging using endogenous fluorescence to detect stem cell differentiation. Scientific reports, 3:3432, 2013.

    Article  PubMed  PubMed Central  Google Scholar 

  93. M. T. Ribeiro, S. Singh, and C. Guestrin. “why should I trust you?”: Explaining the predictions of any classifier. CoRR, abs/1602.04938, 2016.

    Google Scholar 

  94. T. W. Rogers, N. Jaccard, F. Carbonaro, H. G. Lemij, K. A. Vermeer, N. J. Reus, and S. Trikha. Evaluation of an ai system for the automated detection of glaucoma from stereoscopic optic disc photographs: the european optic disc assessment study. Eye, 33(11):1791–1797, 2019.

    Article  PubMed  PubMed Central  Google Scholar 

  95. O. Ronneberger, P. Fischer, and T. Brox. U-net: Convolutional networks for biomedical image segmentation. CoRR, abs/1505.04597, 2015.

    Google Scholar 

  96. C. Ross and I. Swetlitz. Ibm’s watson supercomputer recommended ‘unsafe and incorrect’cancer treatments, internal documents show, 2018.

    Google Scholar 

  97. C. Rudin. Stop explaining black box machine learning models for high stakes decisions and use interpretable models instead. Nature Machine Intelligence, 1(5):206–215, 2019.

    Article  PubMed  PubMed Central  Google Scholar 

  98. D. Rumelhart and J. McClelland. Parallel Distributed Processing: Explorations in the Microstructure of Cognition, Vol. 1: Foundations. Cambridge, MA: Bradford Books/MIT Press, 1985.

    Google Scholar 

  99. O. Russakovsky, J. Deng, H. Su, J. Krause, S. Satheesh, S. Ma, Z. Huang, A. Karpathy, A. Khosla, M. Bernstein, et al. Imagenet large scale visual recognition challenge. International Journal of Computer Vision, 115(3):211–252, 2015.

    Article  Google Scholar 

  100. B. G. Saar, C. W. Freudiger, J. Reichman, C. M. Stanley, G. R. Holtom, and X. S. Xie. Video-rate molecular imaging in vivo with stimulated raman scattering. science, 330(6009):1368–1370, 2010.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. J. M. Schmitt. Optical coherence tomography (oct): a review. IEEE Journal of selected topics in quantum electronics, 5(4):1205–1215, 1999.

    Article  CAS  Google Scholar 

  102. A. Shah, L. Zhou, M. D. Abrámoff, and X. Wu. Multiple surface segmentation using convolution neural nets: application to retinal layer segmentation in oct images. Biomed. Opt. Express, 9(9):4509–4526, Sep 2018.

    Article  PubMed  PubMed Central  Google Scholar 

  103. W. Shi and S. Dustdar. The promise of edge computing. Computer, 49(5):78–81, 2016.

    Article  Google Scholar 

  104. K. Sies, J. K. Winkler, C. Fink, F. Bardehle, F. Toberer, T. Buhl, A. Enk, A. Blum, A. Rosenberger, and H. A. Haenssle. Past and present of computer-assisted dermoscopic diagnosis: performance of a conventional image analyser versus a convolutional neural network in a prospective data set of 1,981 skin lesions. European Journal of Cancer, 135:39–46, 2020.

    Article  PubMed  Google Scholar 

  105. K. Simonyan, A. Vedaldi, and A. Zisserman. Deep inside convolutional networks: Visualising image classification models and saliency maps. CoRR, abs/1312.6034, 2013.

    Google Scholar 

  106. K. Simonyan and A. Zisserman. Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556, 2014.

    Google Scholar 

  107. K. Simonyan and A. Zisserman. Very deep convolutional networks for large-scale image recognition. arXiv preprint arXiv:1409.1556, 2014.

    Google Scholar 

  108. S. W. Smith et al. The scientist and engineer’s guide to digital signal processing. California Technical Pub. San Diego, 1997.

    Google Scholar 

  109. C. Szegedy, V. Vanhoucke, S. Ioffe, J. Shlens, and Z. Wojna. Rethinking the inception architecture for computer vision. In Proceedings of IEEE Conference on Computer Vision and Pattern Recognition, 2016.

    Google Scholar 

  110. C. Szegedy, Wei Liu, Yangqing Jia, P. Sermanet, S. Reed, D. Anguelov, D. Erhan, V. Vanhoucke, and A. Rabinovich. Going deeper with convolutions. In 2015 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pages 1–9, June 2015.

    Google Scholar 

  111. L. Torrey and J. Shavlik. Transfer learning. In Handbook of research on machine learning applications and trends: algorithms, methods, and techniques, pages 242–264. IGI Global, 2010.

    Google Scholar 

  112. B. van Ginneken, S. Kerkstra, and J. Meakin. Grand challenges in biomedical image analysis, 2015.

    Google Scholar 

  113. D. A. Van Valen, T. Kudo, K. M. Lane, D. N. Macklin, N. T. Quach, M. M. DeFelice, I. Maayan, Y. Tanouchi, E. A. Ashley, and M. W. Covert. Deep learning automates the quantitative analysis of individual cells in live-cell imaging experiments. PLOS Computational Biology, 12:1–24, 11 2016.

    Google Scholar 

  114. D. Wang, A. Khosla, R. Gargeya, H. Irshad, and A. H. Beck. Deep learning for identifying metastatic breast cancer. arXiv preprint arXiv:1606.05718, 2016.

    Google Scholar 

  115. H. Wang, S. Osseiran, V. Igras, A. J. Nichols, E. M. Roider, J. Pruessner, H. Tsao, D. E. Fisher, and C. L. Evans. In vivo coherent raman imaging of the melanomagenesis-associated pigment pheomelanin. Scientific reports, 6:37986, 2016.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. J. Welzel. Optical coherence tomography in dermatology: a review. Skin Research and Technology: Review article, 7(1):1–9, 2001.

    Article  CAS  Google Scholar 

  117. S. Weng, X. Xu, J. Li, and S. T. C. Wong. Combining deep learning and coherent anti-Stokes Raman scattering imaging for automated differential diagnosis of lung cancer. Journal of Biomedical Optics, 22(10):1–10, 2017.

    Article  PubMed  Google Scholar 

  118. R. M. Williams, A. Flesken-Nikitin, L. H. Ellenson, D. C. Connolly, T. C. Hamilton, A. Y. Nikitin, and W. R. Zipfel. Strategies for high-resolution imaging of epithelial ovarian cancer by laparoscopic nonlinear microscopy. Translational Oncology, 3(3):181, 2010.

    Google Scholar 

  119. J. K. Winkler, C. Fink, F. Toberer, A. Enk, T. Deinlein, R. Hofmann-Wellenhof, L. Thomas, A. Lallas, A. Blum, W. Stolz, and H. A. Haenssle. Association between Surgical Skin Markings in Dermoscopic Images and Diagnostic Performance of a Deep Learning Convolutional Neural Network for Melanoma Recognition. JAMA Dermatology, 155(10):1135–1141, 2019.

    Article  PubMed  PubMed Central  Google Scholar 

  120. R. Yamashita, M. Nishio, R. K. G. Do, and K. Togashi. Convolutional neural networks: an overview and application in radiology. Insights into imaging, 9(4):611–629, 2018.

    Article  PubMed  PubMed Central  Google Scholar 

  121. C. Zhang, D. Zhang, and J.-X. Cheng. Coherent raman scattering microscopy in biology and medicine. Annual review of biomedical engineering, 17:415–445, 2015.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. A. P. Zijdenbos, B. M. Dawant, R. A. Margolin, and A. C. Palmer. Morphometric analysis of white matter lesions in mr images: method and validation. IEEE transactions on medical imaging, 13(4):716–724, 1994.

    Article  CAS  PubMed  Google Scholar 

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Greenfield, D.A., González, G., Evans, C.L. (2021). Convolutional Neural Networks in Advanced Biomedical Imaging Applications. In: Elloumi, M. (eds) Deep Learning for Biomedical Data Analysis. Springer, Cham. https://doi.org/10.1007/978-3-030-71676-9_9

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