Ischemic Stroke Lesion Segmentation in CT Perfusion Scans using Pyramid Pooling and Focal Loss

We present a fully convolutional neural network for segmenting ischemic stroke lesions in CT perfusion images for the ISLES 2018 challenge. Treatment of stroke is time sensitive and current standards for lesion identification require manual segmentation, a time consuming and challenging process. Automatic segmentation methods present the possibility of accurately identifying lesions and improving treatment planning. Our model is based on the PSPNet, a network architecture that makes use of pyramid pooling to provide global and local contextual information. To learn the varying shapes of the lesions, we train our network using focal loss, a loss function designed for the network to focus on learning the more difficult samples. We compare our model to networks trained using the U-Net and V-Net architectures. Our approach demonstrates effective performance in lesion segmentation and ranked among the top performers at the challenge conclusion.Comment: BrainLes 2018 MICCAI worksho

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

MDS-Net: A Model-Driven Stack-Based Fully Convolutional Network for Pancreas Segmentation

The irregular geometry and high inter-slice variability in computerized tomography (CT) scans of the human pancreas make an accurate segmentation of this crucial organ a challenging task for existing data-driven deep learning methods. To address this problem, we present a novel model-driven stack-based fully convolutional network with a bi-directional convolutional long short-term memory network for pancreas segmentation, termed MDS-Net. The MDS-Net's cost function includes data approximation term and prior knowledge regularization term combined with a stack scheme for capturing and fusing the two-dimensional (2D) and local three-dimensional (3D) context information. Specifically, 3D CT scans are divided into multiple stacks, and each multi-slice stack is used as a basic unit for network training and modeling of the local spatial context. To highlight the importance of single slices in segmentation, the inter-slice relationships in the stack data are also incorporated in the MDS-Net framework. For implementing this proposed model-driven method, we create a stack-based U-Net architecture and successfully derive its back-propagation procedure for end-to-end training. Furthermore, a bi-directional convolutional long short-term memory (BiCLSTM) network is utilized to integrate upper and lower slice information, thereby ensuring the consistency of adjacent CT slices and intra-stack. Finally, extensive quantitative assessments on the NIH Pancreas-CT dataset demonstrated higher pancreatic segmentation accuracy and reliability of MDS-Net compared to other state-of-the-art methods

Towards Automatic 3D Shape Instantiation for Deployed Stent Grafts: 2D Multiple-class and Class-imbalance Marker Segmentation with Equally-weighted Focal U-Net

Robot-assisted Fenestrated Endovascular Aortic Repair (FEVAR) is currently navigated by 2D fluoroscopy which is insufficiently informative. Previously, a semi-automatic 3D shape instantiation method was developed to instantiate the 3D shape of a main, deployed, and fenestrated stent graft from a single fluoroscopy projection in real-time, which could help 3D FEVAR navigation and robotic path planning. This proposed semi-automatic method was based on the Robust Perspective-5-Point (RP5P) method, graft gap interpolation and semi-automatic multiple-class marker center determination. In this paper, an automatic 3D shape instantiation could be achieved by automatic multiple-class marker segmentation and hence automatic multiple-class marker center determination. Firstly, the markers were designed into five different shapes. Then, Equally-weighted Focal U-Net was proposed to segment the fluoroscopy projections of customized markers into five classes and hence to determine the marker centers. The proposed Equally-weighted Focal U-Net utilized U-Net as the network architecture, equally-weighted loss function for initial marker segmentation, and then equally-weighted focal loss function for improving the initial marker segmentation. This proposed network outperformed traditional Weighted U-Net on the class-imbalance segmentation in this paper with reducing one hyper-parameter - the weight. An overall mean Intersection over Union (mIoU) of 0.6943 was achieved on 78 testing images, where 81.01% markers were segmented with a center position error <1.6mm. Comparable accuracy of 3D shape instantiation was also achieved and stated. The data, trained models and TensorFlow codes are available on-line.Comment: 7 pages, 8 figures, 2 table

Transformation Consistent Self-ensembling Model for Semi-supervised Medical Image Segmentation

Deep convolutional neural networks have achieved remarkable progress on a variety of medical image computing tasks. A common problem when applying supervised deep learning methods to medical images is the lack of labeled data, which is very expensive and time-consuming to be collected. In this paper, we present a novel semi-supervised method for medical image segmentation, where the network is optimized by the weighted combination of a common supervised loss for labeled inputs only and a regularization loss for both labeled and unlabeled data. To utilize the unlabeled data, our method encourages the consistent predictions of the network-in-training for the same input under different regularizations. Aiming for the semi-supervised segmentation problem, we enhance the effect of regularization for pixel-level predictions by introducing a transformation, including rotation and flipping, consistent scheme in our self-ensembling model. With the aim of semi-supervised segmentation tasks, we introduce a transformation consistent strategy in our self-ensembling model to enhance the regularization effect for pixel-level predictions. We have extensively validated the proposed semi-supervised method on three typical yet challenging medical image segmentation tasks: (i) skin lesion segmentation from dermoscopy images on International Skin Imaging Collaboration (ISIC) 2017 dataset, (ii) optic disc segmentation from fundus images on Retinal Fundus Glaucoma Challenge (REFUGE) dataset, and (iii) liver segmentation from volumetric CT scans on Liver Tumor Segmentation Challenge (LiTS) dataset. Compared to the state-of-the-arts, our proposed method shows superior segmentation performance on challenging 2D/3D medical images, demonstrating the effectiveness of our semi-supervised method for medical image segmentation.Comment: Accept at IEEE Transactions on Neural Networks and Learning System

Semantic Segmentation of Pathological Lung Tissue with Dilated Fully Convolutional Networks

Early and accurate diagnosis of interstitial lung diseases (ILDs) is crucial for making treatment decisions, but can be challenging even for experienced radiologists. The diagnostic procedure is based on the detection and recognition of the different ILD pathologies in thoracic CT scans, yet their manifestation often appears similar. In this study, we propose the use of a deep purely convolutional neural network for the semantic segmentation of ILD patterns, as the basic component of a computer aided diagnosis (CAD) system for ILDs. The proposed CNN, which consists of convolutional layers with dilated filters, takes as input a lung CT image of arbitrary size and outputs the corresponding label map. We trained and tested the network on a dataset of 172 sparsely annotated CT scans, within a cross-validation scheme. The training was performed in an end-to-end and semi-supervised fashion, utilizing both labeled and non-labeled image regions. The experimental results show significant performance improvement with respect to the state of the art

Data augmentation using learned transformations for one-shot medical image segmentation

Image segmentation is an important task in many medical applications. Methods based on convolutional neural networks attain state-of-the-art accuracy; however, they typically rely on supervised training with large labeled datasets. Labeling medical images requires significant expertise and time, and typical hand-tuned approaches for data augmentation fail to capture the complex variations in such images. We present an automated data augmentation method for synthesizing labeled medical images. We demonstrate our method on the task of segmenting magnetic resonance imaging (MRI) brain scans. Our method requires only a single segmented scan, and leverages other unlabeled scans in a semi-supervised approach. We learn a model of transformations from the images, and use the model along with the labeled example to synthesize additional labeled examples. Each transformation is comprised of a spatial deformation field and an intensity change, enabling the synthesis of complex effects such as variations in anatomy and image acquisition procedures. We show that training a supervised segmenter with these new examples provides significant improvements over state-of-the-art methods for one-shot biomedical image segmentation. Our code is available at https://github.com/xamyzhao/brainstorm.Comment: 9 pages, CVPR 201

Task Decomposition and Synchronization for Semantic Biomedical Image Segmentation

Semantic segmentation is essentially important to biomedical image analysis. Many recent works mainly focus on integrating the Fully Convolutional Network (FCN) architecture with sophisticated convolution implementation and deep supervision. In this paper, we propose to decompose the single segmentation task into three subsequent sub-tasks, including (1) pixel-wise image segmentation, (2) prediction of the class labels of the objects within the image, and (3) classification of the scene the image belonging to. While these three sub-tasks are trained to optimize their individual loss functions of different perceptual levels, we propose to let them interact by the task-task context ensemble. Moreover, we propose a novel sync-regularization to penalize the deviation between the outputs of the pixel-wise segmentation and the class prediction tasks. These effective regularizations help FCN utilize context information comprehensively and attain accurate semantic segmentation, even though the number of the images for training may be limited in many biomedical applications. We have successfully applied our framework to three diverse 2D/3D medical image datasets, including Robotic Scene Segmentation Challenge 18 (ROBOT18), Brain Tumor Segmentation Challenge 18 (BRATS18), and Retinal Fundus Glaucoma Challenge (REFUGE18). We have achieved top-tier performance in all three challenges.Comment: IEEE Transactions on Medical Imagin

Detecting Scatteredly-Distributed, Small, andCritically Important Objects in 3D OncologyImaging via Decision Stratification

Finding and identifying scatteredly-distributed, small, and critically important objects in 3D oncology images is very challenging. We focus on the detection and segmentation of oncology-significant (or suspicious cancer metastasized) lymph nodes (OSLNs), which has not been studied before as a computational task. Determining and delineating the spread of OSLNs is essential in defining the corresponding resection/irradiating regions for the downstream workflows of surgical resection and radiotherapy of various cancers. For patients who are treated with radiotherapy, this task is performed by experienced radiation oncologists that involves high-level reasoning on whether LNs are metastasized, which is subject to high inter-observer variations. In this work, we propose a divide-and-conquer decision stratification approach that divides OSLNs into tumor-proximal and tumor-distal categories. This is motivated by the observation that each category has its own different underlying distributions in appearance, size and other characteristics. Two separate detection-by-segmentation networks are trained per category and fused. To further reduce false positives (FP), we present a novel global-local network (GLNet) that combines high-level lesion characteristics with features learned from localized 3D image patches. Our method is evaluated on a dataset of 141 esophageal cancer patients with PET and CT modalities (the largest to-date). Our results significantly improve the recall from $45\%$ to $67\%$ at $3$ FPs per patient as compared to previous state-of-the-art methods. The highest achieved OSLN recall of $0.828$ is clinically relevant and valuable.Comment: 14 pages, 4 Figure

Coarse-to-fine volumetric segmentation of teeth in Cone-Beam CT

We consider the problem of localizing and segmenting individual teeth inside 3D Cone-Beam Computed Tomography (CBCT) images. To handle large image sizes we approach this task with a coarse-to-fine framework, where the whole volume is first analyzed as a 33-class semantic segmentation (adults have up to 32 teeth) in coarse resolution, followed by binary semantic segmentation of the cropped region of interest in original resolution. To improve the performance of the challenging 33-class segmentation, we first train the Coarse step model on a large weakly labeled dataset, then fine-tune it on a smaller precisely labeled dataset. The Fine step model is trained with precise labels only. Experiments using our in-house dataset show significant improvement for both weakly-supervised pretraining and for the addition of the Fine step. Empirically, this framework yields precise teeth masks with low localization errors sufficient for many real-world applications