Conditional Generative Refinement Adversarial Networks for Unbalanced Medical Image Semantic Segmentation

We propose a new generative adversarial architecture to mitigate imbalance data problem in medical image semantic segmentation where the majority of pixels belongs to a healthy region and few belong to lesion or non-health region. A model trained with imbalanced data tends to bias toward healthy data which is not desired in clinical applications and predicted outputs by these networks have high precision and low sensitivity. We propose a new conditional generative refinement network with three components: a generative, a discriminative, and a refinement network to mitigate unbalanced data problem through ensemble learning. The generative network learns to a segment at the pixel level by getting feedback from the discriminative network according to the true positive and true negative maps. On the other hand, the refinement network learns to predict the false positive and the false negative masks produced by the generative network that has significant value, especially in medical application. The final semantic segmentation masks are then composed by the output of the three networks. The proposed architecture shows state-of-the-art results on LiTS-2017 for liver lesion segmentation, and two microscopic cell segmentation datasets MDA231, PhC-HeLa. We have achieved competitive results on BraTS-2017 for brain tumour segmentation

Which Contrast Does Matter? Towards a Deep Understanding of MR Contrast using Collaborative GAN

Thanks to the recent success of generative adversarial network (GAN) for image synthesis, there are many exciting GAN approaches that successfully synthesize MR image contrast from other images with different contrasts. These approaches are potentially important for image imputation problems, where complete set of data is often difficult to obtain and image synthesis is one of the key solutions for handling the missing data problem. Unfortunately, the lack of the scalability of the existing GAN-based image translation approaches poses a fundamental challenge to understand the nature of the MR contrast imputation problem: which contrast does matter? Here, we present a systematic approach using Collaborative Generative Adversarial Networks (CollaGAN), which enable the learning of the joint image manifold of multiple MR contrasts to investigate which contrasts are essential. Our experimental results showed that the exogenous contrast from contrast agents is not replaceable, but other endogenous contrast such as T1, T2, etc can be synthesized from other contrast. These findings may give important guidance to the acquisition protocol design for MR in real clinical environment.Comment: 32 pages, 6 figure

Missing MRI Pulse Sequence Synthesis using Multi-Modal Generative Adversarial Network

Magnetic resonance imaging (MRI) is being increasingly utilized to assess, diagnose, and plan treatment for a variety of diseases. The ability to visualize tissue in varied contrasts in the form of MR pulse sequences in a single scan provides valuable insights to physicians, as well as enabling automated systems performing downstream analysis. However many issues like prohibitive scan time, image corruption, different acquisition protocols, or allergies to certain contrast materials may hinder the process of acquiring multiple sequences for a patient. This poses challenges to both physicians and automated systems since complementary information provided by the missing sequences is lost. In this paper, we propose a variant of generative adversarial network (GAN) capable of leveraging redundant information contained within multiple available sequences in order to generate one or more missing sequences for a patient scan. The proposed network is designed as a multi-input, multi-output network which combines information from all the available pulse sequences, implicitly infers which sequences are missing, and synthesizes the missing ones in a single forward pass. We demonstrate and validate our method on two brain MRI datasets each with four sequences, and show the applicability of the proposed method in simultaneously synthesizing all missing sequences in any possible scenario where either one, two, or three of the four sequences may be missing. We compare our approach with competing unimodal and multi-modal methods, and show that we outperform both quantitatively and qualitatively.Comment: Accepted for publication in IEEE Transactions on Medical Imagin

Red-GAN: Attacking class imbalance via conditioned generation. Yet another perspective on medical image synthesis for skin lesion dermoscopy and brain tumor MRI

Exploiting learning algorithms under scarce data regimes is a limitation and a reality of the medical imaging field. In an attempt to mitigate the problem, we propose a data augmentation protocol based on generative adversarial networks. We condition the networks at a pixel-level (segmentation mask) and at a global-level information (acquisition environment or lesion type). Such conditioning provides immediate access to the image-label pairs while controlling global class specific appearance of the synthesized images. To stimulate synthesis of the features relevant for the segmentation task, an additional passive player in a form of segmentor is introduced into the adversarial game. We validate the approach on two medical datasets: BraTS, ISIC. By controlling the class distribution through injection of synthetic images into the training set we achieve control over the accuracy levels of the datasets' classes

SegAN: Adversarial Network with Multi-scale L1L_1 Loss for Medical Image Segmentation

Inspired by classic generative adversarial networks (GAN), we propose a novel end-to-end adversarial neural network, called SegAN, for the task of medical image segmentation. Since image segmentation requires dense, pixel-level labeling, the single scalar real/fake output of a classic GAN's discriminator may be ineffective in producing stable and sufficient gradient feedback to the networks. Instead, we use a fully convolutional neural network as the segmentor to generate segmentation label maps, and propose a novel adversarial critic network with a multi-scale $L_1$ loss function to force the critic and segmentor to learn both global and local features that capture long- and short-range spatial relationships between pixels. In our SegAN framework, the segmentor and critic networks are trained in an alternating fashion in a min-max game: The critic takes as input a pair of images, (original_image $*$ predicted_label_map, original_image $*$ ground_truth_label_map), and then is trained by maximizing a multi-scale loss function; The segmentor is trained with only gradients passed along by the critic, with the aim to minimize the multi-scale loss function. We show that such a SegAN framework is more effective and stable for the segmentation task, and it leads to better performance than the state-of-the-art U-net segmentation method. We tested our SegAN method using datasets from the MICCAI BRATS brain tumor segmentation challenge. Extensive experimental results demonstrate the effectiveness of the proposed SegAN with multi-scale loss: on BRATS 2013 SegAN gives performance comparable to the state-of-the-art for whole tumor and tumor core segmentation while achieves better precision and sensitivity for Gd-enhance tumor core segmentation; on BRATS 2015 SegAN achieves better performance than the state-of-the-art in both dice score and precision

An Adversarial Learning Approach to Medical Image Synthesis for Lesion Detection

The identification of lesion within medical image data is necessary for diagnosis, treatment and prognosis. Segmentation and classification approaches are mainly based on supervised learning with well-paired image-level or voxel-level labels. However, labeling the lesion in medical images is laborious requiring highly specialized knowledge. We propose a medical image synthesis model named abnormal-to-normal translation generative adversarial network (ANT-GAN) to generate a normal-looking medical image based on its abnormal-looking counterpart without the need for paired training data. Unlike typical GANs, whose aim is to generate realistic samples with variations, our more restrictive model aims at producing a normal-looking image corresponding to one containing lesions, and thus requires a special design. Being able to provide a "normal" counterpart to a medical image can provide useful side information for medical imaging tasks like lesion segmentation or classification validated by our experiments. In the other aspect, the ANT-GAN model is also capable of producing highly realistic lesion-containing image corresponding to the healthy one, which shows the potential in data augmentation verified in our experiments.Comment: 10 pages, 13 figure

MRI Cross-Modality NeuroImage-to-NeuroImage Translation

We present a cross-modality generation framework that learns to generate translated modalities from given modalities in MR images without real acquisition. Our proposed method performs NeuroImage-to-NeuroImage translation (abbreviated as N2N) by means of a deep learning model that leverages conditional generative adversarial networks (cGANs). Our framework jointly exploits the low-level features (pixel-wise information) and high-level representations (e.g. brain tumors, brain structure like gray matter, etc.) between cross modalities which are important for resolving the challenging complexity in brain structures. Our framework can serve as an auxiliary method in clinical diagnosis and has great application potential. Based on our proposed framework, we first propose a method for cross-modality registration by fusing the deformation fields to adopt the cross-modality information from translated modalities. Second, we propose an approach for MRI segmentation, translated multichannel segmentation (TMS), where given modalities, along with translated modalities, are segmented by fully convolutional networks (FCN) in a multichannel manner. Both of these two methods successfully adopt the cross-modality information to improve the performance without adding any extra data. Experiments demonstrate that our proposed framework advances the state-of-the-art on five brain MRI datasets. We also observe encouraging results in cross-modality registration and segmentation on some widely adopted brain datasets. Overall, our work can serve as an auxiliary method in clinical diagnosis and be applied to various tasks in medical fields. Keywords: image-to-image, cross-modality, registration, segmentation, brain MRIComment: 46 pages, 16 figure

Conditional Adversarial Network for Semantic Segmentation of Brain Tumor

Automated medical image analysis has a significant value in diagnosis and treatment of lesions. Brain tumors segmentation has a special importance and difficulty due to the difference in appearances and shapes of the different tumor regions in magnetic resonance images. Additionally, the data sets are heterogeneous and usually limited in size in comparison with the computer vision problems. The recently proposed adversarial training has shown promising results in generative image modeling. In this paper, we propose a novel end-to-end trainable architecture for brain tumor semantic segmentation through conditional adversarial training. We exploit conditional Generative Adversarial Network (cGAN) and train a semantic segmentation Convolution Neural Network (CNN) along with an adversarial network that discriminates segmentation maps coming from the ground truth or from the segmentation network for BraTS 2017 segmentation task[15, 4, 2, 3]. We also propose an end-to-end trainable CNN for survival day prediction based on deep learning techniques for BraTS 2017 prediction task [15, 4, 2, 3]. The experimental results demonstrate the superior ability of the proposed approach for both tasks. The proposed model achieves on validation data a DICE score, Sensitivity and Specificity respectively 0.68, 0.99 and 0.98 for the whole tumor, regarding online judgment system.Comment: Submitted to BraTS challenges which is part of MICCAI-201

Generative Adversarial Network in Medical Imaging: A Review

Generative adversarial networks have gained a lot of attention in the computer vision community due to their capability of data generation without explicitly modelling the probability density function. The adversarial loss brought by the discriminator provides a clever way of incorporating unlabeled samples into training and imposing higher order consistency. This has proven to be useful in many cases, such as domain adaptation, data augmentation, and image-to-image translation. These properties have attracted researchers in the medical imaging community, and we have seen rapid adoption in many traditional and novel applications, such as image reconstruction, segmentation, detection, classification, and cross-modality synthesis. Based on our observations, this trend will continue and we therefore conducted a review of recent advances in medical imaging using the adversarial training scheme with the hope of benefiting researchers interested in this technique.Comment: 24 pages; v4; added missing references from before Jan 1st 2019; accepted to MedI

Medical Image Generation using Generative Adversarial Networks

Generative adversarial networks (GANs) are unsupervised Deep Learning approach in the computer vision community which has gained significant attention from the last few years in identifying the internal structure of multimodal medical imaging data. The adversarial network simultaneously generates realistic medical images and corresponding annotations, which proven to be useful in many cases such as image augmentation, image registration, medical image generation, image reconstruction, and image-to-image translation. These properties bring the attention of the researcher in the field of medical image analysis and we are witness of rapid adaption in many novel and traditional applications. This chapter provides state-of-the-art progress in GANs-based clinical application in medical image generation, and cross-modality synthesis. The various framework of GANs which gained popularity in the interpretation of medical images, such as Deep Convolutional GAN (DCGAN), Laplacian GAN (LAPGAN), pix2pix, CycleGAN, and unsupervised image-to-image translation model (UNIT), continue to improve their performance by incorporating additional hybrid architecture, has been discussed. Further, some of the recent applications of these frameworks for image reconstruction, and synthesis, and future research directions in the area have been covered.Comment: 19 pages, 3 figures, 5 table