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Precise 3D segmentation of infant brain tissues is an essential step towards comprehensive volumetric studies and quantitative analysis of early brain developement. However, computing such segmentations is very challenging, especially for…

The morphological structure of left ventricle segmented from cardiac magnetic resonance images can be used to calculate key clinical parameters, and it is of great significance to the accurate and efficient diagnosis of cardiovascular…

Automatic segmentation of medical images is an important task for many clinical applications. In practice, a wide range of anatomical structures are visualised using different imaging modalities. In this paper, we investigate whether a…

This thesis studies how the segmentation results, produced by convolutional neural networks (CNN), is different from each other when applied to small biomedical datasets. We use different architectures, parameters and hyper-parameters,…

The Pancreatic beta cell is an important target in diabetes research. For scalable modeling of beta cell ultrastructure, we investigate automatic segmentation of whole cell imaging data acquired through soft X-ray tomography. During the…

Deep convolutional neural networks (CNNs) are the backbone of state-of-art semantic image segmentation systems. Recent work has shown that complementing CNNs with fully-connected conditional random fields (CRFs) can significantly enhance…

We present a novel deep convolutional neural network (DCNN) system for fine-grained image classification, called a mixture of DCNNs (MixDCNN). The fine-grained image classification problem is characterised by large intra-class variations…

Sub-cortical brain structure segmentation in Magnetic Resonance Images (MRI) has attracted the interest of the research community for a long time because morphological changes in these structures are related to different neurodegenerative…

Deep convolutional networks have achieved the state-of-the-art for semantic image segmentation tasks. However, training these networks requires access to densely labeled images, which are known to be very expensive to obtain. On the other…

Brain segmentation is a fundamental first step in neuroimage analysis. In the case of fetal MRI, it is particularly challenging and important due to the arbitrary orientation of the fetus, organs that surround the fetal head, and…

We present a method to address the challenging problem of segmentation of lumbar vertebrae from CT images acquired with varying fields of view. Our method is based on cascaded 3D Fully Convolutional Networks (FCNs) consisting of a…

This study explores the potential of graph neural networks (GNNs) to enhance semantic segmentation across diverse image modalities. We evaluate the effectiveness of a novel GNN-based U-Net architecture on three distinct datasets: PascalVOC,…

Accurate segmentation of fetal brain magnetic resonance images is crucial for analyzing fetal brain development and detecting potential neurodevelopmental abnormalities. Traditional deep learning-based automatic segmentation, although…

The quantitative analysis of cellular membranes helps understanding developmental processes at the cellular level. Particularly 3D microscopic image data offers valuable insights into cell dynamics, but error-free automatic segmentation…

In this paper, we propose a novel learning based method for automated segmenta-tion of brain tumor in multimodal MRI images. The machine learned features from fully convolutional neural network (FCN) and hand-designed texton fea-tures are…

Deep Neural Networks (DNN) are widely used to carry out segmentation tasks in biomedical images. Most DNNs developed for this purpose are based on some variation of the encoder-decoder U-Net architecture. Here we show that Res-CR-Net, a new…

Automatic cell detection in histology images is a challenging task due to varying size, shape and features of cells and stain variations across a large cohort. Conventional deep learning methods regress the probability of each pixel…

In this article, we look into some essential aspects of convolutional neural networks (CNNs) with the focus on medical image segmentation. First, we discuss the CNN architecture, thereby highlighting the spatial origin of the data,…

We introduce DeepNAT, a 3D Deep convolutional neural network for the automatic segmentation of NeuroAnaTomy in T1-weighted magnetic resonance images. DeepNAT is an end-to-end learning-based approach to brain segmentation that jointly learns…

While significant attention has been recently focused on designing supervised deep semantic segmentation algorithms for vision tasks, there are many domains in which sufficient supervised pixel-level labels are difficult to obtain. In this…