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The development of high quality medical image segmentation algorithms depends on the availability of large datasets with pixel-level labels. The challenges of collecting such datasets, especially in case of 3D volumes, motivate to develop…

Pulmonary Embolism (PE) is a life-threatening condition for which accurate and timely detection is critical to patient care. However, our systematic study of PE segmentation algorithms reveals concerning limitations in the current state of…

Volumetric medical image segmentation is a fundamental problem in medical image analysis where the objective is to accurately classify a given 3D volumetric medical image with voxel-level precision. In this work, we propose a novel…

Deep learning techniques have shown their success in medical image segmentation since they are easy to manipulate and robust to various types of datasets. The commonly used loss functions in the deep segmentation task are pixel-wise loss…

With the introduction of fully convolutional neural networks, deep learning has raised the benchmark for medical image segmentation on both speed and accuracy, and different networks have been proposed for 2D and 3D segmentation with…

Tissue stiffness is related to soft tissue pathologies and can be assessed through palpation or via clinical imaging systems, e.g., ultrasound or magnetic resonance imaging. Typically, the image based approaches are not suitable during…

There has been a debate in 3D medical image segmentation on whether to use 2D or 3D networks, where both pipelines have advantages and disadvantages. 2D methods enjoy a low inference time and greater transfer-ability while 3D methods are…

Image segmentation is a fundamental topic in image processing and has been studied for many decades. Deep learning-based supervised segmentation models have achieved state-of-the-art performance but most of them are limited by using…

Deep neural networks have evolved as the leading approach in 3D medical image segmentation due to their outstanding performance. However, the ever-increasing model size and computation cost of deep neural networks have become the primary…

Purpose: Conventional automated segmentation of the head anatomy in MRI distinguishes different brain and non-brain tissues based on image intensities and prior tissue probability maps (TPM). This works well for normal head anatomies, but…

Recently, deep convolutional neural networks have achieved great success for medical image segmentation. However, unlike segmentation of natural images, most medical images such as MRI and CT are volumetric data. In order to make full use…

3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own…

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…

Quantitative assessment of the abdominal region from clinically acquired CT scans requires the simultaneous segmentation of abdominal organs. Thanks to the availability of high-performance computational resources, deep learning-based…

3D medical image processing with deep learning greatly suffers from a lack of data. Thus, studies carried out in this field are limited compared to works related to 2D natural image analysis, where very large datasets exist. As a result,…

In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks…

For 3D medical image (e.g. CT and MRI) segmentation, the difficulty of segmenting each slice in a clinical case varies greatly. Previous research on volumetric medical image segmentation in a slice-by-slice manner conventionally use the…

Many recent medical segmentation systems rely on powerful deep learning models to solve highly specific tasks. To maximize performance, it is standard practice to evaluate numerous pipelines with varying model topologies, optimization…

Although deep neural networks have been a dominant method for many 2D vision tasks, it is still challenging to apply them to 3D tasks, such as medical image segmentation, due to the limited amount of annotated 3D data and limited…

Image segmentation is widely used in a variety of computer vision tasks, such as object localization and recognition, boundary detection, and medical imaging. This thesis proposes deep learning architectures to improve automatic object…