Sequential neural networks for biologically informed glioma segmentation

Andrew Beers; Ken Chang; James Brown; Elizabeth Gerstner; Bruce Rosen; Jayashree Kalpathy-Cramer

doi:10.1117/12.2293941

2 March 2018 Sequential neural networks for biologically informed glioma segmentation

Andrew Beers, Ken Chang, James Brown, Elizabeth Gerstner, Bruce Rosen, Jayashree Kalpathy-Cramer

Proceedings Volume 10574, Medical Imaging 2018: Image Processing; 1057433 (2018) https://doi.org/10.1117/12.2293941
Event: SPIE Medical Imaging, 2018, Houston, Texas, United States

Abstract

In the last five years, advances in processing power and computational efficiency in graphical processing units have catalyzed dozens of deep neural network segmentation algorithms for a variety of target tissues and malignancies. However, few of these algorithms preconfigure any biological context of their chosen segmentation tissues, instead relying on the neural network’s optimizer to develop such associations de novo. We present a novel method for applying deep neural networks to the problem of glioma tissue segmentation that takes into account the structured nature of gliomas – edematous tissue surrounding mutually-exclusive regions of enhancing and non-enhancing tumor. We trained separate deep neural networks with a 3D U-Net architecture in a tree structure to create segmentations for edema, non-enhancing tumor, and enhancing tumor regions. Specifically, training was configured such that the whole tumor region including edema was predicted first, and its output segmentation was fed as input into separate models to predict enhancing and non-enhancing tumor. We trained our model on publicly available pre- and post-contrast T1 images, T2 images, and FLAIR images, and validated our trained model on patient data from an ongoing clinical trial.

Citation Download Citation

Andrew Beers, Ken Chang, James Brown, Elizabeth Gerstner, Bruce Rosen, and Jayashree Kalpathy-Cramer "Sequential neural networks for biologically informed glioma segmentation", Proc. SPIE 10574, Medical Imaging 2018: Image Processing, 1057433 (2 March 2018); https://doi.org/10.1117/12.2293941

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