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Reconstructing Portal Vein and Hepatic Vein trees from contrast enhanced abdominal CT scans is a prerequisite for preoperative liver surgery simulation. Existing deep learning based methods treat vascular tree reconstruction as a semantic…

Biological membranes are one of the most basic structures and regions of interest in cell biology. In the study of membranes, segment extraction is a well-known and difficult problem because of impeding noise, directional and thickness…

We demonstrate the use of deep learning for fast spectral deconstruction of speckle patterns. The artificial neural network can be effectively trained using numerically constructed multispectral datasets taken from a measured spectral…

In this paper, we consider the problem of automatically segmenting neuronal cells in dual-color confocal microscopy images. This problem is a key task in various quantitative analysis applications in neuroscience, such as tracing cell…

We propose a deep learning approach for finding dense correspondences between 3D scans of people. Our method requires only partial geometric information in the form of two depth maps or partial reconstructed surfaces, works for humans in…

In this paper, we propose a deep convolutional neural network for learning the embeddings of images in order to capture the notion of visual similarity. We present a deep siamese architecture that when trained on positive and negative pairs…

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…

Reconstructing neuron morphology from 3D light microscope imaging data is critical to aid neuroscientists in analyzing brain networks and neuroanatomy. With the boost from deep learning techniques, a variety of learning-based segmentation…

Convolutional neural networks (CNNs) allow for parameter sharing and translational equivariance by using convolutional kernels in their linear layers. By restricting these kernels to be SO(3)-steerable, CNNs can further improve parameter…

Deep neural networks have recently achieved state of the art performance thanks to new training algorithms for rapid parameter estimation and new regularization methods to reduce overfitting. However, in practice the network architecture…

Automated detection of curvilinear structures, e.g., blood vessels or nerve fibres, from medical and biomedical images is a crucial early step in automatic image interpretation associated to the management of many diseases. Precise…

This paper presents a new framework for human body part segmentation based on Deep Convolutional Neural Networks trained using only synthetic data. The proposed approach achieves cutting-edge results without the need of training the models…

Semantic segmentation is pixel-wise classification which retains critical spatial information. The "feature map reuse" has been commonly adopted in CNN based approaches to take advantage of feature maps in the early layers for the later…

The study of neurodegenerative diseases relies on the reconstruction and analysis of the brain cortex from magnetic resonance imaging (MRI). Traditional frameworks for this task like FreeSurfer demand lengthy runtimes, while its accelerated…

Accurate retinal vessel segmentation is an important task for many computer-aided diagnosis systems. Yet, it is still a challenging problem due to the complex vessel structures of an eye. Numerous vessel segmentation methods have been…

Multimode fibers (MMFs) have the potential to carry complex images for endoscopy and related applications, but decoding the complex speckle patterns produced by mode-mixing and modal dispersion in MMFs is a serious challenge. Several groups…

In this work, we focus on the task of learning and representing dense correspondences in deformable object categories. While this problem has been considered before, solutions so far have been rather ad-hoc for specific object types (i.e.,…

The majority of descriptor-based methods for geometric processing of non-rigid shape rely on hand-crafted descriptors. Recently, learning-based techniques have been shown effective, achieving state-of-the-art results in a variety of tasks.…

Learning latent representations of registered meshes is useful for many 3D tasks. Techniques have recently shifted to neural mesh autoencoders. Although they demonstrate higher precision than traditional methods, they remain unable to…

Automated construction of surface geometries of cardiac structures from volumetric medical images is important for a number of clinical applications. While deep-learning-based approaches have demonstrated promising reconstruction precision,…