Deep collaborative network with alpha matte for precise knee tissue segmentation from MRI

Sheheryar Khan, Basim Azam, Yongcheng Yao, Weitian Chen

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)


Background and objective: Precise segmentation of knee tissues from magnetic resonance imaging (MRI) is critical in quantitative imaging and diagnosis. Convolutional neural networks (CNNs), being state of the art, often challenged by the lack of image-specific adaptation, such as low tissue contrasts and structural inhomogeneities, thereby leading to incomplete segmentation results. Methods: This paper presents a deep learning–based automatic segmentation framework for precise knee tissue segmentation. A novel deep collaborative 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 morphological variations in knee tissues. To model the tissue boundary regions and effectively utilize the superimposed regions, trimap generation 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. Results: Experiments on Osteoarthritis Initiative (OAI) datasets with all the 6 musculoskeletal tissues provide an overall segmentation dice score of 0.8925, where Femoral and Tibial part of cartilage achieving an average dice exceeding 0.9. The volumetric metrics also indicate the superior performances in all tissue compartments. Conclusions: Experiments on Osteoarthritis Initiative (OAI) datasets and a self-prepared scan validate the effectiveness of the proposed method. Inclusion of extra prediction scale allowed the model to distinguish and segment the tissue boundary accurately. We specifically demonstrate the application of the proposed method in a cartilage segmentation–based thickness map for diagnosis purposes.

Original languageEnglish
Article number106963
JournalComputer Methods and Programs in Biomedicine
Publication statusPublished - 16 Jun 2022


  • Alpha matting
  • Cartilage and meniscus segmentation
  • Convolutional neural network
  • Knee MRI
  • Low rank decomposition
  • Trimap


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