A novel segmentation framework for uveal melanoma in magnetic resonance imaging based on class activation maps

Huu-Giao Nguyen, Alessia Pica, Jan Hrbacek, Damien C. Weber, Francesco La Rosa, Ann Schalenbourg, Raphael Sznitman, Meritxell Bach Cuadra
Proceedings of The 2nd International Conference on Medical Imaging with Deep Learning, PMLR 102:370-379, 2019.

Abstract

An automatic and accurate eye tumor segmentation from Magnetic Resonance images (MRI) could have a great clinical contribution for the purpose of diagnosis and treatment planning of intra-ocular cancer. For instance, the characterization of uveal melanoma (UM) tumors would allow the integration of 3D information for the radiotherapy and would also support further radiomics studies. In this work, we tackle two major challenges of UM segmentation: 1) the high heterogeneity of tumor characterization in respect to location, size and appearance and, 2) the difficulty in obtaining ground-truth delineations of medical experts for training. We propose a thorough segmentation pipeline consisting of a combination of two Convolutional Neural Networks (CNN). First, we consider the class activation maps (CAM) output from a Resnet classification model and the combination of Dense Conditional Random Field (CRF) with a prior information of sclera and lens from an Active Shape Model (ASM) to automatically extract the tumor location for all MRIs. Then, these immediate results will be inputted into a 2D-Unet CNN whereby using four encoder and decoder layers to produce the tumor segmentation. A clinical data set of 1.5T T1-w and T2-w images of 28 healthy eyes and 24 UM patients is used for validation. We show experimentally in two different MRI sequences that our weakly 2D-Unet approach outperforms previous state-of-the-art methods for tumor segmentation and that it achieves equivalent accuracy as when manual labels are used for training. These results are promising for further large-scale analysis and for introducing 3D ocular tumor information in the therapy planning.

Cite this Paper


BibTeX
@InProceedings{pmlr-v102-nguyen19a, title = {A novel segmentation framework for uveal melanoma in magnetic resonance imaging based on class activation maps}, author = {Nguyen, {Huu-Giao} and Pica, Alessia and Hrbacek, Jan and Weber, {Damien C.} and Rosa, Francesco La and Schalenbourg, Ann and Sznitman, Raphael and {Bach Cuadra}, Meritxell}, booktitle = {Proceedings of The 2nd International Conference on Medical Imaging with Deep Learning}, pages = {370--379}, year = {2019}, editor = {Cardoso, M. Jorge and Feragen, Aasa and Glocker, Ben and Konukoglu, Ender and Oguz, Ipek and Unal, Gozde and Vercauteren, Tom}, volume = {102}, series = {Proceedings of Machine Learning Research}, month = {08--10 Jul}, publisher = {PMLR}, pdf = {http://proceedings.mlr.press/v102/nguyen19a/nguyen19a.pdf}, url = { http://proceedings.mlr.press/v102/nguyen19a.html }, abstract = {An automatic and accurate eye tumor segmentation from Magnetic Resonance images (MRI) could have a great clinical contribution for the purpose of diagnosis and treatment planning of intra-ocular cancer. For instance, the characterization of uveal melanoma (UM) tumors would allow the integration of 3D information for the radiotherapy and would also support further radiomics studies. In this work, we tackle two major challenges of UM segmentation: 1) the high heterogeneity of tumor characterization in respect to location, size and appearance and, 2) the difficulty in obtaining ground-truth delineations of medical experts for training. We propose a thorough segmentation pipeline consisting of a combination of two Convolutional Neural Networks (CNN). First, we consider the class activation maps (CAM) output from a Resnet classification model and the combination of Dense Conditional Random Field (CRF) with a prior information of sclera and lens from an Active Shape Model (ASM) to automatically extract the tumor location for all MRIs. Then, these immediate results will be inputted into a 2D-Unet CNN whereby using four encoder and decoder layers to produce the tumor segmentation. A clinical data set of 1.5T T1-w and T2-w images of 28 healthy eyes and 24 UM patients is used for validation. We show experimentally in two different MRI sequences that our weakly 2D-Unet approach outperforms previous state-of-the-art methods for tumor segmentation and that it achieves equivalent accuracy as when manual labels are used for training. These results are promising for further large-scale analysis and for introducing 3D ocular tumor information in the therapy planning.} }
Endnote
%0 Conference Paper %T A novel segmentation framework for uveal melanoma in magnetic resonance imaging based on class activation maps %A Huu-Giao Nguyen %A Alessia Pica %A Jan Hrbacek %A Damien C. Weber %A Francesco La Rosa %A Ann Schalenbourg %A Raphael Sznitman %A Meritxell Bach Cuadra %B Proceedings of The 2nd International Conference on Medical Imaging with Deep Learning %C Proceedings of Machine Learning Research %D 2019 %E M. Jorge Cardoso %E Aasa Feragen %E Ben Glocker %E Ender Konukoglu %E Ipek Oguz %E Gozde Unal %E Tom Vercauteren %F pmlr-v102-nguyen19a %I PMLR %P 370--379 %U http://proceedings.mlr.press/v102/nguyen19a.html %V 102 %X An automatic and accurate eye tumor segmentation from Magnetic Resonance images (MRI) could have a great clinical contribution for the purpose of diagnosis and treatment planning of intra-ocular cancer. For instance, the characterization of uveal melanoma (UM) tumors would allow the integration of 3D information for the radiotherapy and would also support further radiomics studies. In this work, we tackle two major challenges of UM segmentation: 1) the high heterogeneity of tumor characterization in respect to location, size and appearance and, 2) the difficulty in obtaining ground-truth delineations of medical experts for training. We propose a thorough segmentation pipeline consisting of a combination of two Convolutional Neural Networks (CNN). First, we consider the class activation maps (CAM) output from a Resnet classification model and the combination of Dense Conditional Random Field (CRF) with a prior information of sclera and lens from an Active Shape Model (ASM) to automatically extract the tumor location for all MRIs. Then, these immediate results will be inputted into a 2D-Unet CNN whereby using four encoder and decoder layers to produce the tumor segmentation. A clinical data set of 1.5T T1-w and T2-w images of 28 healthy eyes and 24 UM patients is used for validation. We show experimentally in two different MRI sequences that our weakly 2D-Unet approach outperforms previous state-of-the-art methods for tumor segmentation and that it achieves equivalent accuracy as when manual labels are used for training. These results are promising for further large-scale analysis and for introducing 3D ocular tumor information in the therapy planning.
APA
Nguyen, H., Pica, A., Hrbacek, J., Weber, D.C., Rosa, F.L., Schalenbourg, A., Sznitman, R. & Bach Cuadra, M.. (2019). A novel segmentation framework for uveal melanoma in magnetic resonance imaging based on class activation maps. Proceedings of The 2nd International Conference on Medical Imaging with Deep Learning, in Proceedings of Machine Learning Research 102:370-379 Available from http://proceedings.mlr.press/v102/nguyen19a.html .

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