Abstract
Automatic segmentation of challenging biomedical volumes with multiple objects is still an open research field. Automatic approaches usually require a large amount of training data to be able to model the complex and often noisy appearance and structure of biological organelles and their boundaries. However, due to the variety of different biological specimens and the large volume sizes of the datasets, training data is costly to produce, error prone and sparsely available. Here, we propose a novel Selective Labeling algorithm to overcome these challenges; an unsupervised sub-volume proposal method that identifies the most representative regions of a volume. This massively-reduced subset of regions are then manually labeled and combined with an active learning procedure to fully segment the volume. Results on a publicly available EM dataset demonstrate the quality of our approach by achieving equivalent segmentation accuracy with only 5 % of the training data.
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Notes
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The terms sub-volume and window will be used interchangeably along the document.
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References
Karasev, P., Kolesov, I., Fritscher, K., Vela, P., Mitchell, P., Tannenbaum, A.: Interactive medical image segmentation using PDE control of active contours. IEEE Trans. Med. Imaging 32, 2127–2139 (2013)
Beichel, R., et al.: Liver segmentation in CT data: a segmentation refinement approach. In: Proceedings of 3D Segmentation in the Clinic: A Grand Challenge, pp. 235–245 (2007)
Uijlings, J.R.R., van de Sande, K.E.A., Gevers, T., Smeulders, A.W.M.: Selective search for object recognition. IJCV 104, 154–171 (2013)
Top, A., Hamarneh, G., Abugharbieh, R.: Active learning for interactive 3D image segmentation. In: Fichtinger, G., Martel, A., Peters, T. (eds.) MICCAI 2011. LNCS, vol. 6893, pp. 603–610. Springer, Heidelberg (2011). doi:10.1007/978-3-642-23626-6_74
Top, A., Hamarneh, G., Abugharbieh, R.: Spotlight: automated confidence-based user guidance for increasing efficiency in interactive 3D image segmentation. In: Menze, B., Langs, G., Tu, Z., Criminisi, A. (eds.) MICCAI 2010. LNCS, vol. 6533, pp. 204–213. Springer, Heidelberg (2011)
Lucchi, A., et al.: Supervoxel-based segmentation of mitochondria in EM image stacks with learned shape features. IEEE Trans. Med. Imaging 31(2), 474–486 (2012)
Hong, X., Chang, H., Shan, S., Chen, X., Gao, W.: Sigma set: a small second order statistical region descriptor. In: CVPR 2009 (2009)
Luengo, I., Basham, M., French, A.P.: Fast global interactive volume segmentation with regional supervoxel descriptors. In: SPIE Medical Imaging, pp. 97842D–97842D. International Society for Optics and Photonics (2016)
Geurts, P., Ernst, D., Wehenkel, L.: Extremely randomized trees. Mach. Learn. 63(1), 3–42 (2006)
Frey, B.J., Dueck, D.: Clustering by passing messages between data points. Science 315(5814), 972–976 (2007)
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Luengo, I., Basham, M., French, A.P. (2016). Selective Labeling: Identifying Representative Sub-volumes for Interactive Segmentation. In: Wu, G., Coupé, P., Zhan, Y., Munsell, B., Rueckert, D. (eds) Patch-Based Techniques in Medical Imaging. Patch-MI 2016. Lecture Notes in Computer Science(), vol 9993. Springer, Cham. https://doi.org/10.1007/978-3-319-47118-1_3
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DOI: https://doi.org/10.1007/978-3-319-47118-1_3
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