Related papers: Organelle-specific segmentation, spatial analysis,…

Volumetric cell segmentation in fluorescence microscopy images is important to study a wide variety of cellular processes. Applications range from the analysis of cancer cells to behavioral studies of cells in the embryonic stage. Like in…

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…

With the introduction of spectral-domain optical coherence tomography (OCT), much larger image datasets are routinely acquired compared to what was possible using the previous generation of time-domain OCT. Thus, the need for 3-D…

Existing approaches for the problem of ultrasound image segmentation, whether supervised or semi-supervised, are typically specialized for specific anatomical structures or tasks, limiting their practical utility in clinical settings. In…

Due to the intensive cost of labor and expertise in annotating 3D medical images at a voxel level, most benchmark datasets are equipped with the annotations of only one type of organs and/or tumors, resulting in the so-called partially…

Fluorescence microscopy is an essential tool for the analysis of 3D subcellular structures in tissue. An important step in the characterization of tissue involves nuclei segmentation. In this paper, a two-stage method for segmentation of…

We propose a novel hands-free method to interactively segment 3D medical volumes. In our scenario, a human user progressively segments an organ by answering a series of questions of the form "Is this voxel inside the object to segment?". At…

Deep learning has shown great promise in the ability to automatically annotate organs in magnetic resonance imaging (MRI) scans, for example, of the brain. However, despite advancements in the field, the ability to accurately segment…

The objective of this paper is to significantly reduce the manual workload required from medical professionals in complex 3D segmentation tasks that cannot be yet fully automated. For instance, in radiotherapy planning, organs at risk must…

Deep neural networks enable highly accurate image segmentation, but require large amounts of manually annotated data for supervised training. Few-shot learning aims to address this shortcoming by learning a new class from a few annotated…

Despite the considerable progress in automatic abdominal multi-organ segmentation from CT/MRI scans in recent years, a comprehensive evaluation of the models' capabilities is hampered by the lack of a large-scale benchmark from diverse…

Morphology of mitochondria plays critical roles in mediating their physiological functions. Accurate segmentation of mitochondria from 3D electron microscopy (EM) images is essential to quantitative characterization of their morphology at…

Segmentation of multiple organs-at-risk (OARs) is essential for radiation therapy treatment planning and other clinical applications. We developed an Automated deep Learning-based Abdominal Multi-Organ segmentation (ALAMO) framework based…

Recent advances in bioimaging have provided scientists a superior high spatial-temporal resolution to observe dynamics of living cells as 3D volumetric videos. Unfortunately, the 3D biomedical video analysis is lagging, impeded by resource…

Automatic localization and segmentation of organs-at-risk (OAR) in CT are essential pre-processing steps in medical image analysis tasks, such as radiation therapy planning. For instance, the segmentation of OAR surrounding tumors enables…

Reconstructing a synaptic wiring diagram, or connectome, from electron microscopy (EM) images of brain tissue currently requires many hours of manual annotation or proofreading (Kasthuri and Lichtman, 2010; Lichtman and Sanes, 2008; Seung,…

Optimal surface segmentation is a state-of-the-art method used for segmentation of multiple globally optimal surfaces in volumetric datasets. The method is widely used in numerous medical image segmentation applications. However, nodes in…

Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most…

This paper presents a new technique for the virtual reality (VR) visu-alization of complex volume images obtained from computer tomography (CT) and Magnetic Resonance Imaging (MRI) by combining three-dimensional (3D) mesh processing and…

The lack of sufficient annotated image data is a common issue in medical image segmentation. For some organs and densities, the annotation may be scarce, leading to poor model training convergence, while other organs have plenty of…