Abstract
Inflammatory myopathy (IM) is a kind of heterogeneous disease that relates to disorders of muscle functionalities. The identification of IM subtypes is critical to guide effective patient treatment since each subtype requires distinct therapy. Image analysis of hematoxylin and eosin (H&E)-stained whole-slide specimens of muscle biopsies are considered as a gold standard for effective IM diagnosis. Accurate segmentation of perimysium plays an important role in early diagnosis of many muscle inflammation diseases. However, it remains as a challenging task due to the complex appearance of the perimysium morphology and its ambiguity to the background area. The muscle perimysium also exhibits strong structure spanned in the entire tissue, which makes it difficult for current local patch-based methods to capture this long-range context information. In this book chapter, we propose a novel spatial clockwork recurrent neural network (spatial CW-RNN) to address those issues. Besides perimysium segmentation, we also introduce a fully automatic whole-slide image analysis framework for IM subtype classification using deep convolutional neural networks (DCNNs).
Y. Xie and F. Liu contributed equally to this work.
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References
Dalakas MC, Hohlfeld R (2003) Polymyositis and dermatomyositis 362:971–982
Dalakas MC (2002) Muscle biopsy findings in inflammatory myopathies. Rheum Dis Clin N Am 28(4):779–798
Dalakas MC (2015) Inflammatory muscle diseases. N Engl J Med 372(18):1734–1747
Hinton GE, Salakhutdinov RR (2006) Reducing the dimensionality of data with neural networks. Science 313(5786):504–507
Krizhevsky A, Sutskever I, Hinton GE (2012) Imagenet classification with deep convolutional neural networks. In: Advances in neural information processing systems, pp 1097–1105
Farabet C, Couprie C, Najman L, LeCun Y (2013) Learning hierarchical features for scene labeling. IEEE Trans Pattern Anal Mach Intell 35(8):1915–1929
Simonyan K, Zisserman A (2014) Very deep convolutional networks for large-scale image recognition. arXiv:1409.1556
Szegedy C, Liu W, Jia Y, Sermanet P, Reed S, Anguelov D, Erhan D, Vanhoucke V, Rabinovich A (2015) Going deeper with convolutions. In: Proceedings of the IEEE conference on computer vision and pattern recognition, pp 1–9
He K, Zhang X, Ren S, Sun J (2016) Deep residual learning for image recognition. In: Proceedings of the IEEE conference on computer vision and pattern recognition, pp 770–778
Visin F, Kastner K, Courville AC, Bengio Y, Matteucci M, Cho K (2015) Reseg: a recurrent neural network for object segmentation, vol 1. arXiv:1511.07053
Cho K, van Merrienboer B, Bahdanau D, Bengio Y (2014) On the properties of neural machine translation: encoder-decoder approaches, vol 1. arXiv:1409.1259
Graves A, Fernández S, Schmidhuber J (2007) Multi-dimensional recurrent neural networks. In: 17th International Conference on Artificial Neural Networks, pp 549–558
Byeon W, Breuel TM, Raue F, Liwicki M (2015) Scene labeling with LSTM recurrent neural networks. In: IEEE conference on computer vision and pattern recognition, pp 3547–3555
Koutník J, Greff K, Gomez F, Schmidhuber J (2014) A clockwork RNN. In: Proceedings of the 31st international conference on machine learning, vol 32, pp 1863–1871
Xie Y, Xing F, Kong X, Su H, Yang L (2015) Beyond classification: Structured regression for robust cell detection using convolutional neural network. In: MICCAI, vol 9351, pp 358–365
Werbos PJ (1990) Backpropagation through time: what it does and how to do it. Proc IEEE 78(10):1550–1560
Hochreiter S, Schmidhuber J (1997) Long short-term memory. Neural Comput 9(8):1735–1780
Ciresan D, Giusti A, Gambardella LM, Schmidhuber J (2012) Deep neural networks segment neuronal membranes in electron microscopy images. In: Advances in neural information processing systems, pp 2843–2851
Ronneberger O, Fischer P, Brox T (2015) U-net: Convolutional networks for biomedical image segmentation. In: MICCAI, pp 234–241
Xie W, Noble JA, Zisserman A (2015) Microscopy cell counting with fully convolutional regression networks. In: MICCAI 1st workshop on deep learning in medical image analysis
Zhou B, Khosla A, Lapedriza A, Oliva A, Torralba A (2016) Learning deep features for discriminative localization. In: Proceedings of the IEEE conference on computer vision and pattern recognition, pp 2921–2929
Sivic J, Zisserman A et al (2003) Video google: a text retrieval approach to object matching in videos
Hou L, Samaras D, Kurc TM, Gao Y, Davis JE, Saltz JH (2016) Patch-based convolutional neural network for whole slide tissue image classification. In: Proceedings of the IEEE conference on computer vision and pattern recognition, pp 2424–2433
van der Maaten L, Hinton G (2008) Visualizing data using t-sne. J Mach Learn Res 9(Nov):2579–2605
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Xie, Y., Liu, F., Xing, F., Yang, L. (2019). Deep Learning for Muscle Pathology Image Analysis. In: Lu, L., Wang, X., Carneiro, G., Yang, L. (eds) Deep Learning and Convolutional Neural Networks for Medical Imaging and Clinical Informatics. Advances in Computer Vision and Pattern Recognition. Springer, Cham. https://doi.org/10.1007/978-3-030-13969-8_2
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