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

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

OctNetFusion: Learning Depth Fusion from Data

In this paper, we present a learning based approach to depth fusion, i.e., dense 3D reconstruction from multiple depth images. The most common approach to depth fusion is based on averaging truncated signed distance functions, which was originally proposed by Curless and Levoy in 1996. While this method is simple and provides great results, it is not able to reconstruct (partially) occluded surfaces and requires a large number frames to filter out sensor noise and outliers. Motivated by the availability of large 3D model repositories and recent advances in deep learning, we present a novel 3D CNN architecture that learns to predict an implicit surface representation from the input depth maps. Our learning based method significantly outperforms the traditional volumetric fusion approach in terms of noise reduction and outlier suppression. By learning the structure of real world 3D objects and scenes, our approach is further able to reconstruct occluded regions and to fill in gaps in the reconstruction. We demonstrate that our learning based approach outperforms both vanilla TSDF fusion as well as TV-L1 fusion on the task of volumetric fusion. Further, we demonstrate state-of-the-art 3D shape completion results.Comment: 3DV 2017, https://github.com/griegler/octnetfusio