DeepOrgan: Multi-level Deep Convolutional Networks for Automated Pancreas Segmentation

Automatic organ segmentation is an important yet challenging problem for medical image analysis. The pancreas is an abdominal organ with very high anatomical variability. This inhibits previous segmentation methods from achieving high accuracies, especially compared to other organs such as the liver, heart or kidneys. In this paper, we present a probabilistic bottom-up approach for pancreas segmentation in abdominal computed tomography (CT) scans, using multi-level deep convolutional networks (ConvNets). We propose and evaluate several variations of deep ConvNets in the context of hierarchical, coarse-to-fine classification on image patches and regions, i.e. superpixels. We first present a dense labeling of local image patches via $P{-}\mathrm{ConvNet}$ and nearest neighbor fusion. Then we describe a regional ConvNet ($R_1{-}\mathrm{ConvNet}$) that samples a set of bounding boxes around each image superpixel at different scales of contexts in a "zoom-out" fashion. Our ConvNets learn to assign class probabilities for each superpixel region of being pancreas. Last, we study a stacked $R_2{-}\mathrm{ConvNet}$ leveraging the joint space of CT intensities and the $P{-}\mathrm{ConvNet}$ dense probability maps. Both 3D Gaussian smoothing and 2D conditional random fields are exploited as structured predictions for post-processing. We evaluate on CT images of 82 patients in 4-fold cross-validation. We achieve a Dice Similarity Coefficient of 83.6$\pm$6.3% in training and 71.8$\pm$10.7% in testing.Comment: To be presented at MICCAI 2015 - 18th International Conference on Medical Computing and Computer Assisted Interventions, Munich, German

Morphological and multi-level geometrical descriptor analysis in CT and MRI volumes for automatic pancreas segmentation

Automatic pancreas segmentation in 3D radiological scans is a critical, yet challenging task. As a prerequisite for computer-aided diagnosis (CADx) systems, accurate pancreas segmentation could generate both quantitative and qualitative information towards establishing the severity of a condition, and thus provide additional guidance for therapy planning. Since the pancreas is an organ of high inter-patient anatomical variability, previous segmentation approaches report lower quantitative accuracy scores in comparison to abdominal organs such as the liver or kidneys. This paper presents a novel approach for automatic pancreas segmentation in magnetic resonance imaging (MRI) and computer tomography (CT) scans. This method exploits 3D segmentation that, when coupled with geometrical and morphological characteristics of abdominal tissue, classifies distinct contours in tight pixel-range proximity as “pancreas” or “non-pancreas”. There are three main stages to this approach: (1) identify a major pancreas region and apply contrast enhancement to differentiate between pancreatic and surrounding tissue; (2) perform 3D segmentation via continuous max-flow and min-cuts approach, structured forest edge detection, and a training dataset of annotated pancreata; (3) eliminate non-pancreatic contours from resultant segmentation via morphological operations on area, structure and connectivity between distinct contours. The proposed method is evaluated on a dataset containing 82 CT image volumes, achieving mean Dice Similarity coefficient (DSC) of 79.3 ± 4.4%. Two MRI datasets containing 216 and 132 image volumes are evaluated, achieving mean DSC 79.6 ± 5.7% and 81.6 ± 5.1% respectively. This approach is statistically stable, reflected by lower metrics in standard deviation in comparison to state-of-the-art approaches

A Survey on Deep Learning-based Architectures for Semantic Segmentation on 2D images

Semantic segmentation is the pixel-wise labelling of an image. Since the problem is defined at the pixel level, determining image class labels only is not acceptable, but localising them at the original image pixel resolution is necessary. Boosted by the extraordinary ability of convolutional neural networks (CNN) in creating semantic, high level and hierarchical image features; excessive numbers of deep learning-based 2D semantic segmentation approaches have been proposed within the last decade. In this survey, we mainly focus on the recent scientific developments in semantic segmentation, specifically on deep learning-based methods using 2D images. We started with an analysis of the public image sets and leaderboards for 2D semantic segmantation, with an overview of the techniques employed in performance evaluation. In examining the evolution of the field, we chronologically categorised the approaches into three main periods, namely pre-and early deep learning era, the fully convolutional era, and the post-FCN era. We technically analysed the solutions put forward in terms of solving the fundamental problems of the field, such as fine-grained localisation and scale invariance. Before drawing our conclusions, we present a table of methods from all mentioned eras, with a brief summary of each approach that explains their contribution to the field. We conclude the survey by discussing the current challenges of the field and to what extent they have been solved.Comment: Updated with new studie

Efficient extraction of semantic information from medical images in large datasets using random forests

Large datasets of unlabelled medical images are increasingly becoming available; however only a small subset tend to be manually semantically labelled as it is a tedious and extremely time-consuming task to do for large datasets. This thesis aims to tackle the problem of efficiently extracting semantic information in the form of image segmentations and organ localisations from large datasets of unlabelled medical images. To do so, we investigate the suitability of supervoxels and random classification forests for the task. The first contribution of this thesis is a novel method for efficiently estimating coarse correspondences between pairs of images that can handle difficult cases that exhibit large variations in fields of view. The proposed methods adapts the random forest framework, which is a supervised learning algorithm, to work in an unsupervised manner by automatically generating labels for training via the use of supervoxels. The second contribution of this thesis is a method that extends our first contribution so as to be applicable efficiently on a large dataset of images. The proposed method is efficient and can be used to obtain correspondences between a large number of object-like supervoxels that are representative of organ structures in the images. The method is evaluated for the applications of organ-based image retrieval and weakly-supervised image segmentation using extremely minimal user input. While the method does not achieve image segmentation accuracies for all organs in an abdominal CT dataset compared to current fully-supervised state-of-the-art methods, it does provide a promising way for efficiently extracting and parsing a large dataset of medical images for the purpose of further processing.Open Acces

Deep learning for image-based liver analysis — A comprehensive review focusing on malignant lesions

Deep learning-based methods, in particular, convolutional neural networks and fully convolutional networks are now widely used in the medical image analysis domain. The scope of this review focuses on the analysis using deep learning of focal liver lesions, with a special interest in hepatocellular carcinoma and metastatic cancer; and structures like the parenchyma or the vascular system. Here, we address several neural network architectures used for analyzing the anatomical structures and lesions in the liver from various imaging modalities such as computed tomography, magnetic resonance imaging and ultrasound. Image analysis tasks like segmentation, object detection and classification for the liver, liver vessels and liver lesions are discussed. Based on the qualitative search, 91 papers were filtered out for the survey, including journal publications and conference proceedings. The papers reviewed in this work are grouped into eight categories based on the methodologies used. By comparing the evaluation metrics, hybrid models performed better for both the liver and the lesion segmentation tasks, ensemble classifiers performed better for the vessel segmentation tasks and combined approach performed better for both the lesion classification and detection tasks. The performance was measured based on the Dice score for the segmentation, and accuracy for the classification and detection tasks, which are the most commonly used metrics.publishedVersio