Multipath CNN with alpha matte inference for knee tissue segmentation from MRI

Precise segmentation of knee tissues from magnetic resonance imaging (MRI) is critical in quantitative imaging and diagnosis. Convolutional neural networks (CNNs), which are state of the art, have limitations owing to the lack of image-specific adaptation, such as low tissue contrasts and structural inhomogeneities, thereby leading to incomplete segmentation results. This paper presents a deep learning based automatic segmentation framework for knee tissue segmentation. A novel multipath CNN-based method is proposed, which consists of an encoder decoder-based segmentation network in combination with a low rank tensor-reconstructed segmentation network. Low rank reconstruction in MRI tensor sub-blocks is introduced to exploit the structural and morphological variations in knee tissues. To further improve the segmentation from CNNs, trimap generation, which effectively utilizes superimposed regions, is proposed for defining high, medium and low confidence regions from the multipath CNNs. The secondary path with low rank reconstructed input mitigates the conditions in which the primary segmentation network can potentially fail and overlook the boundary regions. The outcome of the segmentation is solved as an alpha matting problem by blending the trimap with the source input. Experiments on Osteoarthritis Initiative (OAI) datasets and a self prepared scan validate the effectiveness of the proposed method. We specifically demonstrate the application of the proposed method in a cartilage segmentation based thickness map for diagnosis purposes.