Multi-planar whole heart segmentation of 3D CT images using 2D spatial propagation CNN

Whole heart segmentation from cardiac CT scans is a prerequisite for many clinical applications, but manual
delineation is a tedious task and subject to both intra- and inter-observer variation. Automating the segmentation process has thus become an increasingly popular task in the field of image analysis, and is generally solved by either using 3D methods, considering the image volume as a whole, or 2D methods, segmenting each slice independently. In the field of deep learning, there are significant limitations regarding 3D networks, including the need for more training examples and GPU memory. The need for GPU memory is usually solved by down sampling the input images, thus losing important information, which is not a necessary sacrifice when employing 2D networks. It would therefore be relevant to exploit the benefits of 2D networks in a configuration, where spatial information across slices is kept, as when employing 3D networks. The proposed method performs multiclass segmentation of cardiac CT scans utilizing 2D convolutional neural networks with a multi-planar approach. Furthermore, spatial propagation is included in the network structure, to ensure spatial consistency through each image volume. The approach keeps the computational assets of 2D methods while addressing 3D issues regarding spatial context. The pipeline is structured in a two-step approach, in which the first step detects the location of the heart and crops a region of interest, and the second step performs multi-class segmentation of the heart structures. The pipeline demonstrated promising results on the MICCAI 2017 Multi-Modality Whole Heart Segmentation challenge data.