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Seeking effective neural networks is a critical and practical field in deep learning. Besides designing the depth, type of convolution, normalization, and nonlinearities, the topological connectivity of neural networks is also important.…

Deep learning-based approaches to delineating 3D structure depend on accurate annotations to train the networks. Yet, in practice, people, no matter how conscientious, have trouble precisely delineating in 3D and on a large scale, in part…

Accurately segmenting thin tubular structures, such as vessels, nerves, roads or concrete cracks, is a crucial task in computer vision. Standard deep learning-based segmentation loss functions, such as Dice or Cross-Entropy, focus on…

Convolutional neural networks are state-of-the-art for various segmentation tasks. While for 2D images these networks are also computationally efficient, 3D convolutions have huge storage requirements and require long training time. To…

Reconstructing the intricate local morphology of neurons and their long-range projecting axons can address many connectivity related questions in neuroscience. The main bottleneck in connectomics pipelines is correcting topological errors,…

Accurate segmentation of thin, tubular structures (e.g., blood vessels) is challenging for deep neural networks. These networks classify individual pixels, and even minor misclassifications can break the thin connections within these…

Promoting the connectivity of curvilinear structures, such as neuronal processes in biomedical scans and blood vessels in CT images, remains a key challenge in semantic segmentation. Traditional pixel-wise loss functions, including…

Reconstructing 3D objects from 2D images is both challenging for our brains and machine learning algorithms. To support this spatial reasoning task, contextual information about the overall shape of an object is critical. However, such…

Many state-of-the-art delineation methods rely on supervised machine learning algorithms. As a result, they require manually annotated training data, which is tedious to obtain. Furthermore, even minor classification errors may…

Embedding 3D morphable basis functions into deep neural networks opens great potential for models with better representation power. However, to faithfully learn those models from an image collection, it requires strong regularization to…

In many biomedical segmentation tasks, the preservation of elongated structure continuity and length is more important than voxel-wise accuracy. We propose two novel loss functions, Negative Centerline Loss and Simplified Topology Loss,…

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…

Convolutional neural networks are state-of-the-art for various segmentation tasks. While for 2D images these networks are also computationally efficient, 3D convolutions have huge storage requirements and therefore, end-to-end training is…

Due to imaging artifacts and low signal-to-noise ratio in ultrasound images, automatic bone surface segmentation networks often produce fragmented predictions that can hinder the success of ultrasound-guided computer-assisted surgical…

We propose a novel, connectivity-oriented loss function for training deep convolutional networks to reconstruct network-like structures, like roads and irrigation canals, from aerial images. The main idea behind our loss is to express the…

Delineating 3D blood vessels is essential for clinical diagnosis and treatment, however, is challenging due to complex structure variations and varied imaging conditions. Supervised deep learning has demonstrated its superior capacity in…

The difficulty of obtaining annotations to build training databases still slows down the adoption of recent deep learning approaches for biomedical image analysis. In this paper, we show that we can train a Deep Net to perform 3D volumetric…

In image segmentation, preserving the topology of segmented structures like vessels, membranes, or roads is crucial. For instance, topological errors on road networks can significantly impact navigation. Recently proposed solutions are loss…

We propose a neural network-based approach to topology optimization that aims to reduce the use of support structures in additive manufacturing. Our approach uses a network architecture that allows the simultaneous determination of an…

Curvilinear structure segmentation is important in medical imaging, quantifying structures such as vessels, airways, neurons, or organ boundaries in 2D slices. Segmentation via pixel-wise classification often fails to capture the small and…