Brain Tumor Synthetic Segmentation in 3D Multimodal MRI Scans

The magnetic resonance (MR) analysis of brain tumors is widely used for diagnosis and examination of tumor subregions. The overlapping area among the intensity distribution of healthy, enhancing, non-enhancing, and edema regions makes the automatic segmentation a challenging task. Here, we show that a convolutional neural network trained on high-contrast images can transform the intensity distribution of brain lesions in its internal subregions. Specifically, a generative adversarial network (GAN) is extended to synthesize high-contrast images. A comparison of these synthetic images and real images of brain tumor tissue in MR scans showed significant segmentation improvement and decreased the number of real channels for segmentation. The synthetic images are used as a substitute for real channels and can bypass real modalities in the multimodal brain tumor segmentation framework. Segmentation results on BraTS 2019 dataset demonstrate that our proposed approach can efficiently segment the tumor areas. In the end, we predict patient survival time based on volumetric features of the tumor subregions as well as the age of each case through several regression models

Massively Parallel Video Networks

We introduce a class of causal video understanding models that aims to improve efficiency of video processing by maximising throughput, minimising latency, and reducing the number of clock cycles. Leveraging operation pipelining and multi-rate clocks, these models perform a minimal amount of computation (e.g. as few as four convolutional layers) for each frame per timestep to produce an output. The models are still very deep, with dozens of such operations being performed but in a pipelined fashion that enables depth-parallel computation. We illustrate the proposed principles by applying them to existing image architectures and analyse their behaviour on two video tasks: action recognition and human keypoint localisation. The results show that a significant degree of parallelism, and implicitly speedup, can be achieved with little loss in performance.Comment: Fixed typos in densenet model definition in appendi

Intelligent Data Networking for the Earth System Science Community

Earth system science (ESS) research is generally very data intense. To enable detailed discovery and transparent access of the data stored in heterogeneous and organisationally separated data centres common data and metadata community interfaces are needed. This paper describes the development of a coherent data discovery and data access infrastructure for the ESS community in Germany. To comprehensively and consistently describe the characteristics of geographic data, required for their discovery (discovery metadata) and for their usage (use metadata) the ISO standard 19115 is adopted. Webservice technology is used to hide the details of heterogeneous data access mechanisms and preprocessing implementations. The commitment to international standards and the modular character of the approach facilitates the expandability of the infrastructure as well as the interoperability with international partners and other communities

Improving Whole Slide Segmentation Through Visual Context - A Systematic Study

While challenging, the dense segmentation of histology images is a necessary first step to assess changes in tissue architecture and cellular morphology. Although specific convolutional neural network architectures have been applied with great success to the problem, few effectively incorporate visual context information from multiple scales. With this paper, we present a systematic comparison of different architectures to assess how including multi-scale information affects segmentation performance. A publicly available breast cancer and a locally collected prostate cancer datasets are being utilised for this study. The results support our hypothesis that visual context and scale play a crucial role in histology image classification problems

End-to-End Boundary Aware Networks for Medical Image Segmentation

Fully convolutional neural networks (CNNs) have proven to be effective at representing and classifying textural information, thus transforming image intensity into output class masks that achieve semantic image segmentation. In medical image analysis, however, expert manual segmentation often relies on the boundaries of anatomical structures of interest. We propose boundary aware CNNs for medical image segmentation. Our networks are designed to account for organ boundary information, both by providing a special network edge branch and edge-aware loss terms, and they are trainable end-to-end. We validate their effectiveness on the task of brain tumor segmentation using the BraTS 2018 dataset. Our experiments reveal that our approach yields more accurate segmentation results, which makes it promising for more extensive application to medical image segmentation.Comment: Accepted to MICCAI Machine Learning in Medical Imaging (MLMI 2019

Synaptic partner prediction from point annotations in insect brains

High-throughput electron microscopy allows recording of lar- ge stacks of neural tissue with sufficient resolution to extract the wiring diagram of the underlying neural network. Current efforts to automate this process focus mainly on the segmentation of neurons. However, in order to recover a wiring diagram, synaptic partners need to be identi- fied as well. This is especially challenging in insect brains like Drosophila melanogaster, where one presynaptic site is associated with multiple post- synaptic elements. Here we propose a 3D U-Net architecture to directly identify pairs of voxels that are pre- and postsynaptic to each other. To that end, we formulate the problem of synaptic partner identification as a classification problem on long-range edges between voxels to encode both the presence of a synaptic pair and its direction. This formulation allows us to directly learn from synaptic point annotations instead of more ex- pensive voxel-based synaptic cleft or vesicle annotations. We evaluate our method on the MICCAI 2016 CREMI challenge and improve over the current state of the art, producing 3% fewer errors than the next best method

TuNet: End-to-end Hierarchical Brain Tumor Segmentation using Cascaded Networks

Glioma is one of the most common types of brain tumors; it arises in the glial cells in the human brain and in the spinal cord. In addition to having a high mortality rate, glioma treatment is also very expensive. Hence, automatic and accurate segmentation and measurement from the early stages are critical in order to prolong the survival rates of the patients and to reduce the costs of the treatment. In the present work, we propose a novel end-to-end cascaded network for semantic segmentation that utilizes the hierarchical structure of the tumor sub-regions with ResNet-like blocks and Squeeze-and-Excitation modules after each convolution and concatenation block. By utilizing cross-validation, an average ensemble technique, and a simple post-processing technique, we obtained dice scores of 88.06, 80.84, and 80.29, and Hausdorff Distances (95th percentile) of 6.10, 5.17, and 2.21 for the whole tumor, tumor core, and enhancing tumor, respectively, on the online test set.Comment: Accepted at MICCAI BrainLes 201

Improving the Segmentation of Anatomical Structures in Chest Radiographs using U-Net with an ImageNet Pre-trained Encoder

Accurate segmentation of anatomical structures in chest radiographs is essential for many computer-aided diagnosis tasks. In this paper we investigate the latest fully-convolutional architectures for the task of multi-class segmentation of the lungs field, heart and clavicles in a chest radiograph. In addition, we explore the influence of using different loss functions in the training process of a neural network for semantic segmentation. We evaluate all models on a common benchmark of 247 X-ray images from the JSRT database and ground-truth segmentation masks from the SCR dataset. Our best performing architecture, is a modified U-Net that benefits from pre-trained encoder weights. This model outperformed the current state-of-the-art methods tested on the same benchmark, with Jaccard overlap scores of 96.1% for lung fields, 90.6% for heart and 85.5% for clavicles.Comment: Presented at the First International Workshop on Thoracic Image Analysis (TIA), MICCAI 201

Unsupervised Holistic Image Generation from Key Local Patches

We introduce a new problem of generating an image based on a small number of key local patches without any geometric prior. In this work, key local patches are defined as informative regions of the target object or scene. This is a challenging problem since it requires generating realistic images and predicting locations of parts at the same time. We construct adversarial networks to tackle this problem. A generator network generates a fake image as well as a mask based on the encoder-decoder framework. On the other hand, a discriminator network aims to detect fake images. The network is trained with three losses to consider spatial, appearance, and adversarial information. The spatial loss determines whether the locations of predicted parts are correct. Input patches are restored in the output image without much modification due to the appearance loss. The adversarial loss ensures output images are realistic. The proposed network is trained without supervisory signals since no labels of key parts are required. Experimental results on six datasets demonstrate that the proposed algorithm performs favorably on challenging objects and scenes.Comment: 16 page