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Deep Learning Applications to Cytopathology: A Study on the Detection of Malaria and on the Classification of Leukaemia Cell-Lines

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Handbook of Deep Learning Applications

Part of the book series: Smart Innovation, Systems and Technologies ((SIST,volume 136))

Abstract

This chapter discusses a few applications of deep learning networks in cytopathology. Specifically, the detection of malaria from slide images of blood smear and classification of leukaemia cell-lines are addressed. The chapter starts with relevant theory for traditional (deep) multi-layer neural networks with back-propagation, followed by motivation, theory and training in Convolutional Neural Networks (CNN), the trending deep-learning based classifier. The detection of malaria from blood smear slide images using CNN is addressed followed by a discussion on the transfer learning capability of CNN by taking the classification of leukaemia cell-lines: K562, MOLT & HL60 as an example. The transfer learning capability of CNN is of particular interest especially when there are only very limited number of training samples to come up with a stand alone deep CNN classifier.

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References

  1. R. Nayar, Cytopathology in Oncology (Springer, 2014), http://www.springer.com/medicine/oncology/book/978-3-642-38849-1

  2. PathScope, PathscopeTM slide scanner; digipath inc. Pathology delivered digitally. http://www.digipath.biz/pr/PathScope.pdf. Accessed 7 Dec 2016

  3. M. Rieseberg, C. Kasper, K.F. Reardon, T. Scheper, Flow cytometry in biotechnology. Appl. Microbiol. Biotechnol. 56(3–4), 350–360 (2001)

    Article  Google Scholar 

  4. D.A. Basiji, W.E. Ortyn, L. Liang, V. Venkatachalam, P. Morrissey, Cellular image analysis and imaging by flow cytometry. Clin. Lab. Med. 27(3), 653–670 (2007), https://doi.org/10.1016/j.cll.2007.05.008

    Article  Google Scholar 

  5. E. Schonbrun, S.S. Gorthi, D. Schaak, Microfabricated multiple field of view imaging flow cytometry. Lab Chip 12, 268–273 (2012). https://doi.org/10.1039/C1LC20843H

    Article  Google Scholar 

  6. Amnis Corporation\(^{\textregistered }\) ISX - MKII Brochure (2016), https://www.amnis.com/documents/brochures/ISX-MKII20Brochure_Final_Web.pdf. Accessed 28 July 2016

  7. L. Pantanowitz, P. Valenstein, A. Evans, K. Kaplan, J. Pfeifer, D. Wilbur, L. Collins, T. Colgan, Review of the current state of whole slide imaging in pathology. J. Pathol. Inform. 2(1), 36–45 (2011). https://doi.org/10.4103/2153-3539.83746

    Article  Google Scholar 

  8. M. Rojo, G. Garcia, C. Mateos, J. Garcia, M. Vicente, Critical comparison of 31 commercially available digital slide systems in pathology. Int. J. Surg. Pathol. 14(4), 285–305 (2006). https://doi.org/10.1177/1066896906292274

    Article  Google Scholar 

  9. H. Irshad, A. Veillard, L. Roux, D. Racoceanu, Methods for nuclei detection, segmentation, and classification in digital histopathology: a review - 2014; current status and future potential. IEEE Rev. Biomed. Eng. 7, 97–114 (2014). https://doi.org/10.1109/RBME.2013.2295804

    Article  Google Scholar 

  10. G. Deco, V.K. Jirsa, P.A. Robinson, M. Breakspear, K.J. Friston, The dynamic brain: from spiking neurons to neural masses and cortical fields. PLoS Comput. Biol. 4(8) (2008)

    Article  Google Scholar 

  11. A. Pouliakis, E. Karakitsou, N. Margari, P. Bountris, M. Haritou, J. Panayiotides, D. Koutsouris, P. Karakitsos, Artificial neural networks as decision support tools in cytopathology: past, present, and future. Biomed. Eng. Comput. Biol. 7, 1–18 (2016). https://doi.org/10.4137/BECB.S31601

    Article  Google Scholar 

  12. Z. Shi, L. He, Current status and future potential of neural networks used for medical image processing. J. Multimed. 6(3) (2011)

    Google Scholar 

  13. K. Rohan, Vanishing of gradients (2016), https://ayearofai.com/rohan-4-the-vanishing-gradient-problem-ec68f76ffb9b. accessed: 2017-04-10

  14. H. Greenspan, B. van Ginneken, R.M. Summers, Guest editorial deep learning in medical imaging: overview and future promise of an exciting new technique. IEEE Tran. Med. Imaging 35(5), 1153–1159 (2016). https://doi.org/10.1109/TMI.2016.2553401

    Article  Google Scholar 

  15. WHO, Basic malaria microscopy—Part I: Learner’s guide. World Health Organization (2010)

    Google Scholar 

  16. G. Gopakumar, M. Swetha, G.S. Siva, G.R.K.S. Subrahmanyam, Convolutional neural network-based malaria diagnosis from focus-stack of blood smear images acquired using custom-built slide scanner. J. Biophoton. (2017). https://doi.org/10.1002/jbio.201700003

    Article  Google Scholar 

  17. V.K. Jagannadh, G. Gopakumar, G.R.K.S. Subrahmanyam, S.S. Gorthi, Microfluidic microscopy-assisted label-free approach for cancer screening: automated microfluidic cytology for cancer screening. Med. Biol. Eng. Comput. 1–8 (2016). https://doi.org/10.1007/s11517-016-1549-y

    Article  Google Scholar 

  18. D.E. Rumelhart, G.E. Hinton, R.J. Williams, Learning representations by back-propagating errors, Neurocomputing: Foundations of Research. MIT Press, Cambridge, MA, USA, pp. 696–699, http://dl.acm.org/citation.cfm?id=65669.104451

  19. G. Cybenko, Approximation by superpositions of a sigmoidal function. Math. Control Signals Syst. 2(4), 303–314 (1989). https://doi.org/10.1007/BF02551274

    Article  MathSciNet  Google Scholar 

  20. K. Hornik, Approximation capabilities of multilayer feedforward networks. Neural Netw. 4(2), 251–257 (1991). https://doi.org/10.1016/0893-6080(91)90009-T

    Article  MathSciNet  Google Scholar 

  21. E.A. Buffalo, P. Fries, R. Landman, H. Liang, R. Desimone, A backward progression of attentional effects in the ventral stream. Proc. Natl. Acad. Sci. 107(1), 361–365 (2010). https://doi.org/10.1073/pnas.0907658106

    Article  Google Scholar 

  22. W. Zhang, K. Itoh, J. Tanida, Y. Ichioka, Parallel distributed processing model with local space-invariant interconnections and its optical architecture. Appl. Opt. 29(32), 4790–4797 (1990). https://doi.org/10.1364/AO.29.004790

    Article  Google Scholar 

  23. Y. LeCun, L. Bottou, Y. Bengio, P. Haffner, Gradient-based learning applied to document recognition. Proc. IEEE 86, 2278–2324 (1998)

    Article  Google Scholar 

  24. L. Lu, Y. Zheng, G. Carneiro, L. Yang (eds.), Deep Learning and Convolutional Neural Networks for Medical Image Computing (Springer International Publishing, 2017)

    Google Scholar 

  25. P. Nguyen, T. Tran, N. Wickramasinghe, S. Venkatesh, \(mathtt {Deepr}\): a convolutional net for medical records. IEEE J. Biomed. Health Inform. 21(1), 22–30 (2017). https://doi.org/10.1109/JBHI.2016.2633963

    Article  Google Scholar 

  26. H.C. Shin, H.R. Roth, M. Gao, L. Lu, Z. Xu, I. Nogues, J. Yao, D. Mollura, R.M. Summers, Deep convolutional neural networks for computer-aided detection: CNN architectures, dataset characteristics and transfer learning. IEEE Trans. Med. Imaging 35(5), 1285–1298 (2016). https://doi.org/10.1109/TMI.2016.2528162

    Article  Google Scholar 

  27. N. Tajbakhsh, J.Y. Shin, S.R. Gurudu, R.T. Hurst, C.B. Kendall, M.B. Gotway, J. Liang, Convolutional neural networks for medical image analysis: full training or fine tuning? IEEE Trans. Med. Imaging 35(5), 1299–1312 (2016). https://doi.org/10.1109/TMI.2016.2535302

    Article  Google Scholar 

  28. Q. Dou, H. Chen, L. Yu, J. Qin, P.A. Heng, Multilevel contextual 3-D CNNs for false positive reduction in pulmonary nodule detection. IEEE Trans. Biomed. Eng. 64(7), 1558–1567 (2017). https://doi.org/10.1109/TBME.2016.2613502

    Article  Google Scholar 

  29. L. Yu, H. Chen, Q. Dou, J. Qin, P.A. Heng, Integrating online and offline three-dimensional deep learning for automated polyp detection in colonoscopy videos. IEEE J. Biomed. Health Inform. 21(1), 65–75 (2017). https://doi.org/10.1109/JBHI.2016.2637004

    Article  Google Scholar 

  30. H. Chen, L. Wu, Q. Dou, J. Qin, S. Li, J.Z. Cheng, D. Ni, P.A. Heng, Ultrasound standard plane detection using a composite neural network framework. IEEE Trans. Cybern. 47(6), 1576–1586 (2017). https://doi.org/10.1109/TCYB.2017.2685080

    Article  Google Scholar 

  31. L. Zhang, L. Lu, I. Nogues, R.M. Summers, S. Liu, J. Yao, Deeppap: deep convolutional networks for cervical cell classification. IEEE J. Biomed. Health Inform. 21(6), 1633–1643 (2017a). https://doi.org/10.1109/JBHI.2017.2705583

    Article  Google Scholar 

  32. J.T. Kwak, S.M. Hewitt, Nuclear architecture analysis of prostate cancer via convolutional neural networks. IEEE Access 5, 18,526–18,533 (2017). https://doi.org/10.1109/ACCESS.2017.2747838

    Article  Google Scholar 

  33. R. Zhang, Y. Zheng, T.W.C. Mak, R. Yu, S.H. Wong, J.Y.W. Lau, C.C.Y. Poon, Automatic detection and classification of colorectal polyps by transferring low-level CNN features from nonmedical domain. IEEE J. Biomed. Health Inform. 21(1), 41–47 (2017b). https://doi.org/10.1109/JBHI.2016.2635662

    Article  Google Scholar 

  34. S. Christodoulidis, M. Anthimopoulos, L. Ebner, A. Christe, S. Mougiakakou, Multisource transfer learning with convolutional neural networks for lung pattern analysis. IEEE J. Biomed. Health Inform. 21(1), 76–84 (2017)

    Article  Google Scholar 

  35. H. Chen, D. Ni, J. Qin, S. Li, X. Yang, T. Wang, P.A. Heng, Standard plane localization in fetal ultrasound via domain transferred deep neural networks. IEEE J. Biomed. Health Inform. 19(5), 1627–1636 (2015). https://doi.org/10.1109/JBHI.2015.2425041

    Article  Google Scholar 

  36. S. Albarqouni, C. Baur, F. Achilles, V. Belagiannis, S. Demirci, N. Navab, Aggnet: deep learning from crowds for mitosis detection in breast cancer histology images. IEEE Trans. Med. Imaging 35(5), 1313–1321 (2016). https://doi.org/10.1109/TMI.2016.2528120

    Article  Google Scholar 

  37. S. Sathpathi, A.K. Mohanty, P. Satpathi, S.K. Mishra, P.K. Behera, G. Patel, A.M. Dondorp, Comparing Leishman and Giemsa staining for the assessment of peripheral blood smear preparations in a malaria-endemic region in india. Malar. J. 13(1), 1–5 (2014). https://doi.org/10.1186/1475-2875-13-512

    Article  Google Scholar 

  38. M. Elter, E. HaBlmeyer, T. ZerfaB, Detection of malaria parasites in thick blood films, in 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 5140–5144 (2011). https://doi.org/10.1109/IEMBS.2011.6091273

  39. A. Pinkaew, T. Limpiti, A. Trirat, Automated classification of malaria parasite species on thick blood film using support vector machine, in 2015 8th Biomedical Engineering International Conference (BMEiCON), pp. 1–5 (2015). https://doi.org/10.1109/BMEiCON.2015.7399524

  40. I.K.E. Purnama, F.Z. Rahmanti, M.H. Purnomo, Malaria parasite identification on thick blood film using genetic programming, in 2013 3rd International Conference on Instrumentation, Communications, Information Technology, and Biomedical Engineering (ICICI-BME), pp. 194–198 (2013). https://doi.org/10.1109/ICICI-BME.2013.6698491

  41. V.V. Makkapati, R.M. Rao, Segmentation of malaria parasites in peripheral blood smear images, in 2009 IEEE International Conference on Acoustics, Speech and Signal Processing, pp. 1361–1364 (2009). https://doi.org/10.1109/ICASSP.2009.4959845

  42. A. Mehrjou, T. Abbasian, M. Izadi, Automatic malaria diagnosis system, in 2013 First RSI/ISM International Conference on Robotics and Mechatronics (ICRoM), pp. 205–211 (2013). https://doi.org/10.1109/ICRoM.2013.6510106

  43. Y. Purwar, S.L. Shah, G. Clarke, A. Almugairi, A. Muehlenbachs, Automated and unsupervised detection of malarial parasites in microscopic images. Malar. J. 10(1), 364 (2011). https://doi.org/10.1186/1475-2875-10-364

    Article  Google Scholar 

  44. A. Ravendran, K.W.T.R.T. de Silva, R. Senanayake, Moment invariant features for automatic identification of critical malaria parasites, in 2015 IEEE 10th International Conference on Industrial and Information Systems (ICIIS), pp. 474–479 (2015). https://doi.org/10.1109/ICIINFS.2015.7399058

  45. F.B. Tek, A.G. Dempster, I. Kale, Computer vision for microscopy diagnosis of malaria. Malar. J. 8(1), 153 (2009). https://doi.org/10.1186/1475-2875-8-153

    Article  Google Scholar 

  46. W. Preedanan, M. Phothisonothai, W. Senavongse, S. Tantisatirapong, Automated detection of plasmodium falciparum from Giemsa-stained thin blood films, in 2016 8th International Conference on Knowledge and Smart Technology (KST), pp. 215–218 (2016). https://doi.org/10.1109/KST.2016.7440501

  47. S.S. Savkare, S.P. Narote, Automated system for malaria parasite identification, in 2015 International Conference on Communication, Information Computing Technology (ICCICT), pp. 1–4 (2015). https://doi.org/10.1109/ICCICT.2015.7045660

  48. B.E. Boser, I.M. Guyon , V.N. Vapnik, A training algorithm for optimal margin classifiers, in Proceedings of the Fifth Annual Workshop on Computational Learning Theory, ACM, New York, NY, USA, COLT ’92, pp. 144–152 (1992), https://doi.org/10.1145/130385.130401

  49. Z. Liang, A. Powell, I. Ersoy, M. Poostchi, K. Silamut, K. Palaniappan, P. Guo, M.A. Hossain, A. Sameer, R.J. Maude, J.X. Huang, S. Jaeger, G. Thoma, CNN-based image analysis for malaria diagnosis, in 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 493–496. https://doi.org/10.1109/BIBM.2016.7822567

  50. N. Otsu, A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. 9(1), 62–66 (1979)

    Article  Google Scholar 

  51. G. Gopakumar, V.K. Jagannadh, S.S. Gorthi, G.R.K.S. Subrahmanyam, Framework for morphometric classification of cells in imaging flow cytometry. J. Microsc. 261(3), 307–319 (2016). https://doi.org/10.1111/jmi.12335

    Article  Google Scholar 

  52. A. Vedaldi, K. Lenc, Matconvnet—convolutional neural networks for MATLAB. CoRR abs/1412.4564. http://arxiv.org/abs/1412.4564

  53. N. Linder, R. Turkki, M. Walliander, A. Mårtensson, V. Diwan, E. Rahtu, M. Pietikäinen, M. Lundin, A malaria diagnostic tool based on computer vision screening and visualization of plasmodium falciparum candidate areas in digitized blood smears. PLoS ONE 9(8), e104,855 (2014)

    Article  Google Scholar 

  54. LBP/VAR implementation; centre for machine vision and signal analysis. University of Oulu (2016), http://www.cse.oulu.fi/CMV/Downloads/LBPMatlab. Accessed 15 Oct 2016

  55. T. Ojala, M. Pietikainen, T. Maenpaa, Multiresolution gray-scale and rotation invariant texture classification with local binary patterns. IEEE Trans. Pattern Anal. Mach. Intell. 24(7), 971–987 (2002). https://doi.org/10.1109/TPAMI.2002.1017623

    Article  MATH  Google Scholar 

  56. D.G. Lowe, Distinctive image features from scale-invariant keypoints. Int. J. Comput. Vis. 60(2), 91–110 (2004). https://doi.org/10.1023/B:VISI.0000029664.99615.94

    Article  MathSciNet  Google Scholar 

  57. B.W. Stewart, C. Wild, World Cancer Report 2014 (World Health Organization, 2014)

    Google Scholar 

  58. W. Zhang, R. Li, T. Zeng, Q. Sun, S. Kumar, J. Ye, S. Ji, Deep model based transfer and multi-task learning for biological image analysis, in Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, ACM, New York, NY, USA, KDD ’15, pp. 1475–1484 (2015). https://doi.org/10.1145/2783258.2783304

  59. T. Zeng, R. Li, R. Mukkamala, J. Ye, S. Ji, Deep convolutional neural networks for annotating gene expression patterns in the mouse brain. BMC Bioinform. 16(1), 1–10 (2015). https://doi.org/10.1186/s12859-015-0553-9

    Article  Google Scholar 

  60. K. He, X. Zhang, S. Ren, J. Sun, Delving deep into rectifiers: surpassing human-level performance on imagenet classification. ArXiv e-prints 1502, 01852 (2015)

    Google Scholar 

  61. K. Chatfield, K. Simonyan, A. Vedaldi, A. Zisserman, Return of the devil in the details: delving deep into convolutional nets, in British Machine Vision Conference (2014)

    Google Scholar 

  62. J. Deng, W. Dong, R. Socher, L.J. Li, K. Li, L. Fei-Fei, ImageNet: a large-scale hierarchical image database. In: CVPR09 (2009)

    Google Scholar 

  63. I. Jolliffe, Principal Component Analysis. Springer Series in Statistics (Springer, 2002)

    Google Scholar 

  64. Y. Bar , I. Diamant , L. Wolf , S. Lieberman, E. Konen, H. Greenspan, Chest pathology detection using deep learning with non-medical training, in 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI), pp. 294–297, https://doi.org/10.1109/ISBI.2015.7163871

  65. E.J. Breen, R. Jones, Attribute openings, thinnings, and granulometries. Comput. Vis. Image Underst. 64(3), 377–389 (1996). https://doi.org/10.1006/cviu.1996.0066

    Article  Google Scholar 

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Gopakumar, G., Sai Subrahmanyam, G.R.K. (2019). Deep Learning Applications to Cytopathology: A Study on the Detection of Malaria and on the Classification of Leukaemia Cell-Lines. In: Balas, V., Roy, S., Sharma, D., Samui, P. (eds) Handbook of Deep Learning Applications. Smart Innovation, Systems and Technologies, vol 136. Springer, Cham. https://doi.org/10.1007/978-3-030-11479-4_11

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