Localization Network and End-to-End Cascaded U-Nets for Kidney Tumor Segmentation

Kidney tumor segmentation emerges as a new frontier of computer vision in medical imaging. This is partly due to its challenging manual annotation and great medical impact. Within the scope of the Kidney Tumor Segmentation Challenge 2019, that is aiming at combined kidney and tumor segmentation, this work proposes a novel combination of 3D U-Nets—collectively denoted TuNet—utilizing the resulting kidney masks for the consecutive tumor segmentation. The proposed method achieves a Sørensen-Dice coefficient score of 0.902 for the kidney, and 0.408 for the tumor segmentation, computed from a five-fold cross-validation on the 210 patients available in the data

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

Medical Image Segmentation Review: The success of U-Net

Automatic medical image segmentation is a crucial topic in the medical domain and successively a critical counterpart in the computer-aided diagnosis paradigm. U-Net is the most widespread image segmentation architecture due to its flexibility, optimized modular design, and success in all medical image modalities. Over the years, the U-Net model achieved tremendous attention from academic and industrial researchers. Several extensions of this network have been proposed to address the scale and complexity created by medical tasks. Addressing the deficiency of the naive U-Net model is the foremost step for vendors to utilize the proper U-Net variant model for their business. Having a compendium of different variants in one place makes it easier for builders to identify the relevant research. Also, for ML researchers it will help them understand the challenges of the biological tasks that challenge the model. To address this, we discuss the practical aspects of the U-Net model and suggest a taxonomy to categorize each network variant. Moreover, to measure the performance of these strategies in a clinical application, we propose fair evaluations of some unique and famous designs on well-known datasets. We provide a comprehensive implementation library with trained models for future research. In addition, for ease of future studies, we created an online list of U-Net papers with their possible official implementation. All information is gathered in https://github.com/NITR098/Awesome-U-Net repository.Comment: Submitted to the IEEE Transactions on Pattern Analysis and Machine Intelligence Journa

A double cascaded framework based on 3D SEAU-Net for kidney and kidney tumor Segmentation

Accurate segmentation of kidney and kidney tumor from CT-volumes is vital to many clinical endpoints, such as differential diagnosis, prognosis and radiation therapy planning. While manual segmentation is subjective and time-consuming, fully automated extraction is quite imperative and challenging due to intrinsic heterogeneity of tumor structures. To address this problem, we propose a double cascaded framework based on 3D SEAU-Net to hierarchically and successively segment the subregions of the target. This double cascaded framework is used to decompose the complex task of multi-class segmentation into two simpler binary segmentation tasks. That is to say, the region of interest (ROI) including kidney and kidney tumor is trained and extracted in the first step, and the pre-trained weights are used as the initial weights of the network that is to segment the kidney tumor in second step. Our proposed network, 3D SEAU-Net, integrates residual network, dilated convolution, squeeze-and-excitation network and attention mechanism to improve segmentation performance. To speed training and improve network generalization, we take advantage of transfer learning (i.e., weight transfer) in the whole training phase. Meanwhile, we use 3D fully connected conditional random field to refine the result in post-processing phase. Eventually, our proposed segmentation method is evaluated on KiTS 2019 dataset and experimental results achieves mean dice scores 93.51% for the whole kidney and tumor, 92.42% for kidney and 74.34% for tumor on the training data

Deep Learning of Unified Region, Edge, and Contour Models for Automated Image Segmentation

Image segmentation is a fundamental and challenging problem in computer vision with applications spanning multiple areas, such as medical imaging, remote sensing, and autonomous vehicles. Recently, convolutional neural networks (CNNs) have gained traction in the design of automated segmentation pipelines. Although CNN-based models are adept at learning abstract features from raw image data, their performance is dependent on the availability and size of suitable training datasets. Additionally, these models are often unable to capture the details of object boundaries and generalize poorly to unseen classes. In this thesis, we devise novel methodologies that address these issues and establish robust representation learning frameworks for fully-automatic semantic segmentation in medical imaging and mainstream computer vision. In particular, our contributions include (1) state-of-the-art 2D and 3D image segmentation networks for computer vision and medical image analysis, (2) an end-to-end trainable image segmentation framework that unifies CNNs and active contour models with learnable parameters for fast and robust object delineation, (3) a novel approach for disentangling edge and texture processing in segmentation networks, and (4) a novel few-shot learning model in both supervised settings and semi-supervised settings where synergies between latent and image spaces are leveraged to learn to segment images given limited training data.Comment: PhD dissertation, UCLA, 202

Identification of space-occupying lesions in medical imaging of the kidney: A review.

Usually, the kidneys can be affected by renal masses or space-occupying lesions (LOE). When reference is made to the term renal mass, all benign and malignant processes that occupy, distort and affect the renal parenchyma and its environment are included, regardless of etiology, shape and volume. Therefore, renal masses include all cystic formations (abscesses), calculi, pseudotumors, neoplasms, inflammatory diseases and traumatic lesions. Thus, for the evaluation of cystic renal masses in medical imaging, according to their characteristics such as their wall (thin, irregular, thickened), septa (thin, irregular, thickened), borders (defined or not) and size, classifications such as Bosniak's classification shown in Table 1 are used, which classifies renal cysts into five categories based on the appearance of the image, to help predict whether it is a benign or malignant tumor

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