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Register a new userBinary segmentation of medical images using implicit spline representations and deep learning
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We propose a novel approach to image segmentation based on combining implicit spline representations with deep convolutional neural networks. This is done by predicting the control points of a bivariate spline function whose zero-set represents the segmentation boundary. We adapt several existing neural network architectures and design novel loss functions that are tailored towards providing implicit spline curve approximations. The method is evaluated on a congenital heart disease computed tomography medical imaging dataset. Experiments are carried out by measuring performance in various standard metrics for different networks and loss functions. We determine that splines of bidegree $(1,1)$ with $128times128$ coefficient resolution performed optimally for $512times 512$ resolution CT images. For our best network, we achieve an average volumetric test Dice score of almost 92%, which reaches the state of the art for this congenital heart disease dataset.
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Deep learning has been widely used for medical image segmentation and a large number of papers has been presented recording the success of deep learning in the field. In this paper, we present a comprehensive thematic survey on medical image segmentation using deep learning techniques. This paper makes two original contributions. Firstly, compared to traditional surveys that directly divide literatures of deep learning on medical image segmentation into many groups and introduce literatures in detail for each group, we classify currently popular literatures according to a multi-level structure from coarse to fine. Secondly, this paper focuses on supervised and weakly supervised learning approaches, without including unsupervised approaches since they have been introduced in many old surveys and they are not popular currently. For supervised learning approaches, we analyze literatures in three aspects: the selection of backbone networks, the design of network blocks, and the improvement of loss functions. For weakly supervised learning approaches, we investigate literature according to data augmentation, transfer learning, and interactive segmentation, separately. Compared to existing surveys, this survey classifies the literatures very differently from before and is more convenient for readers to understand the relevant rationale and will guide them to think of appropriate improvements in medical image segmentation based on deep learning approaches.
Accurate image segmentation is crucial for medical imaging applications. The prevailing deep learning approaches typically rely on very large training datasets with high-quality manual annotations, which are often not available in medical imaging. We introduce Annotation-effIcient Deep lEarning (AIDE) to handle imperfect datasets with an elaborately designed cross-model self-correcting mechanism. AIDE improves the segmentation Dice scores of conventional deep learning models on open datasets possessing scarce or noisy annotations by up to 30%. For three clinical datasets containing 11,852 breast images of 872 patients from three medical centers, AIDE consistently produces segmentation maps comparable to those generated by the fully supervised counterparts as well as the manual annotations of independent radiologists by utilizing only 10% training annotations. Such a 10-fold improvement of efficiency in utilizing experts labels has the potential to promote a wide range of biomedical applications.
As AI-based medical devices are becoming more common in imaging fields like radiology and histology, interpretability of the underlying predictive models is crucial to expand their use in clinical practice. Existing heatmap-based interpretability methods such as GradCAM only highlight the location of predictive features but do not explain how they contribute to the prediction. In this paper, we propose a new interpretability method that can be used to understand the predictions of any black-box model on images, by showing how the input image would be modified in order to produce different predictions. A StyleGAN is trained on medical images to provide a mapping between latent vectors and images. Our method identifies the optimal direction in the latent space to create a change in the model prediction. By shifting the latent representation of an input image along this direction, we can produce a series of new synthetic images with changed predictions. We validate our approach on histology and radiology images, and demonstrate its ability to provide meaningful explanations that are more informative than GradCAM heatmaps. Our method reveals the patterns learned by the model, which allows clinicians to build trust in the models predictions, discover new biomarkers and eventually reveal potential biases.
Since the introduction of optical coherence tomography (OCT), it has been possible to study the complex 3D morphological changes of the optic nerve head (ONH) tissues that occur along with the progression of glaucoma. Although several deep learning (DL) techniques have been recently proposed for the automated extraction (segmentation) and quantification of these morphological changes, the device specific nature and the difficulty in preparing manual segmentations (training data) limit their clinical adoption. With several new manufacturers and next-generation OCT devices entering the market, the complexity in deploying DL algorithms clinically is only increasing. To address this, we propose a DL based 3D segmentation framework that is easily translatable across OCT devices in a label-free manner (i.e. without the need to manually re-segment data for each device). Specifically, we developed 2 sets of DL networks. The first (referred to as the enhancer) was able to enhance OCT image quality from 3 OCT devices, and harmonized image-characteristics across these devices. The second performed 3D segmentation of 6 important ONH tissue layers. We found that the use of the enhancer was critical for our segmentation network to achieve device independency. In other words, our 3D segmentation network trained on any of 3 devices successfully segmented ONH tissue layers from the other two devices with high performance (Dice coefficients > 0.92). With such an approach, we could automatically segment images from new OCT devices without ever needing manual segmentation data from such devices.
Automatic tumor segmentation is a crucial step in medical image analysis for computer-aided diagnosis. Although the existing methods based on convolutional neural networks (CNNs) have achieved the state-of-the-art performance, many challenges still remain in medical tumor segmentation. This is because regular CNNs can only exploit translation invariance, ignoring further inherent symmetries existing in medical images such as rotations and reflections. To mitigate this shortcoming, we propose a novel group equivariant segmentation framework by encoding those inherent symmetries for learning more precise representations. First, kernel-based equivariant operations are devised on every orientation, which can effectively address the gaps of learning symmetries in existing approaches. Then, to keep segmentation networks globally equivariant, we design distinctive group layers with layerwise symmetry constraints. By exploiting further symmetries, novel segmentation CNNs can dramatically reduce the sample complexity and the redundancy of filters (by roughly 2/3) over regular CNNs. More importantly, based on our novel framework, we show that a newly built GER-UNet outperforms its regular CNN-based counterpart and the state-of-the-art segmentation methods on real-world clinical data. Specifically, the group layers of our segmentation framework can be seamlessly integrated into any popular CNN-based segmentation architectures.
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