A context based deep learning approach for unbalanced medical image segmentation

Automated medical image segmentation is an important step in many medical procedures. Recently, deep learning networks have been widely used for various medical image segmentation tasks, with U-Net and generative adversarial nets (GANs) being some of the commonly used ones. Foreground-background class imbalance is a common occurrence in medical images, and U-Net has difficulty in handling class imbalance because of its cross entropy (CE) objective function. Similarly, GAN also suffers from class imbalance because the discriminator looks at the entire image to classify it as real or fake. Since the discriminator is essentially a deep learning classifier, it is incapable of correctly identifying minor changes in small structures. To address these issues, we propose a novel context based CE loss function for U-Net, and a novel architecture Seg-GLGAN. The context based CE is a linear combination of CE obtained over the entire image and its region of interest (ROI). In Seg-GLGAN, we introduce a novel context discriminator to which the entire image and its ROI are fed as input, thus enforcing local context. We conduct extensive experiments using two challenging unbalanced datasets: PROMISE12 and ACDC. We observe that segmentation results obtained from our methods give better segmentation metrics as compared to various baseline methods.

Recon-GLGAN: A Global-Local context based Generative Adversarial Network for MRI Reconstruction

Magnetic resonance imaging (MRI) is one of the best medical imaging modalities as it offers excellent spatial resolution and soft-tissue contrast. But, the usage of MRI is limited by its slow acquisition time, which makes it expensive and causes patient discomfort. In order to accelerate the acquisition, multiple deep learning networks have been proposed. Recently, Generative Adversarial Networks (GANs) have shown promising results in MRI reconstruction. The drawback with the proposed GAN based methods is it does not incorporate the prior information about the end goal which could help in better reconstruction. For instance, in the case of cardiac MRI, the physician would be interested in the heart region which is of diagnostic relevance while excluding the peripheral regions. In this work, we show that incorporating prior information about a region of interest in the model would offer better performance. Thereby, we propose a novel GAN based architecture, Reconstruction Global-Local GAN (Recon-GLGAN) for MRI reconstruction. The proposed model contains a generator and a context discriminator which incorporates global and local contextual information from images. Our model offers significant performance improvement over the baseline models. Our experiments show that the concept of a context discriminator can be extended to existing GAN based reconstruction models to offer better performance. We also demonstrate that the reconstructions from the proposed method give segmentation results similar to fully sampled images.