3D Convolutional Neural Networks for Tumor Segmentation using Long-range 2D Context

We present an efficient deep learning approach for the challenging task of tumor segmentation in multisequence MR images. In recent years, Convolutional Neural Networks (CNN) have achieved state-of-the-art performances in a large variety of recognition tasks in medical imaging. Because of the considerable computational cost of CNNs, large volumes such as MRI are typically processed by subvolumes, for instance slices (axial, coronal, sagittal) or small 3D patches. In this paper we introduce a CNN-based model which efficiently combines the advantages of the short-range 3D context and the long-range 2D context. To overcome the limitations of specific choices of neural network architectures, we also propose to merge outputs of several cascaded 2D-3D models by a voxelwise voting strategy. Furthermore, we propose a network architecture in which the different MR sequences are processed by separate subnetworks in order to be more robust to the problem of missing MR sequences. Finally, a simple and efficient algorithm for training large CNN models is introduced. We evaluate our method on the public benchmark of the BRATS 2017 challenge on the task of multiclass segmentation of malignant brain tumors. Our method achieves good performances and produces accurate segmentations with median Dice scores of 0.918 (whole tumor), 0.883 (tumor core) and 0.854 (enhancing core). Our approach can be naturally applied to various tasks involving segmentation of lesions or organs.Comment: Submitted to the journal Computerized Medical Imaging and Graphic

3D Anisotropic Hybrid Network: Transferring Convolutional Features from 2D Images to 3D Anisotropic Volumes

While deep convolutional neural networks (CNN) have been successfully applied for 2D image analysis, it is still challenging to apply them to 3D anisotropic volumes, especially when the within-slice resolution is much higher than the between-slice resolution and when the amount of 3D volumes is relatively small. On one hand, direct learning of CNN with 3D convolution kernels suffers from the lack of data and likely ends up with poor generalization; insufficient GPU memory limits the model size or representational power. On the other hand, applying 2D CNN with generalizable features to 2D slices ignores between-slice information. Coupling 2D network with LSTM to further handle the between-slice information is not optimal due to the difficulty in LSTM learning. To overcome the above challenges, we propose a 3D Anisotropic Hybrid Network (AH-Net) that transfers convolutional features learned from 2D images to 3D anisotropic volumes. Such a transfer inherits the desired strong generalization capability for within-slice information while naturally exploiting between-slice information for more effective modelling. The focal loss is further utilized for more effective end-to-end learning. We experiment with the proposed 3D AH-Net on two different medical image analysis tasks, namely lesion detection from a Digital Breast Tomosynthesis volume, and liver and liver tumor segmentation from a Computed Tomography volume and obtain the state-of-the-art results

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

Interactive Medical Image Segmentation using Deep Learning with Image-specific Fine-tuning

Convolutional neural networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they have not demonstrated sufficiently accurate and robust results for clinical use. In addition, they are limited by the lack of image-specific adaptation and the lack of generalizability to previously unseen object classes. To address these problems, we propose a novel deep learning-based framework for interactive segmentation by incorporating CNNs into a bounding box and scribble-based segmentation pipeline. We propose image-specific fine-tuning to make a CNN model adaptive to a specific test image, which can be either unsupervised (without additional user interactions) or supervised (with additional scribbles). We also propose a weighted loss function considering network and interaction-based uncertainty for the fine-tuning. We applied this framework to two applications: 2D segmentation of multiple organs from fetal MR slices, where only two types of these organs were annotated for training; and 3D segmentation of brain tumor core (excluding edema) and whole brain tumor (including edema) from different MR sequences, where only tumor cores in one MR sequence were annotated for training. Experimental results show that 1) our model is more robust to segment previously unseen objects than state-of-the-art CNNs; 2) image-specific fine-tuning with the proposed weighted loss function significantly improves segmentation accuracy; and 3) our method leads to accurate results with fewer user interactions and less user time than traditional interactive segmentation methods.Comment: 11 pages, 11 figure