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Brain MR image segmentation is a key task in neuroimaging studies. It is commonly conducted using standard computational tools, such as FSL, SPM, multi-atlas segmentation etc, which are often registration-based and suffer from expensive…

A major challenge in brain tumor treatment planning and quantitative evaluation is determination of the tumor extent. The noninvasive magnetic resonance imaging (MRI) technique has emerged as a front-line diagnostic tool for brain tumors…

Brain extraction or whole brain segmentation is an important first step in many of the neuroimage analysis pipelines. The accuracy and robustness of brain extraction, therefore, is crucial for the accuracy of the entire brain analysis…

High-level shape understanding and technique evaluation on large repositories of 3D shapes often benefit from additional information known about the shapes. One example of such information is the semantic segmentation of a shape into…

The throughput of electron microscopes has increased significantly in recent years, enabling detailed analysis of cell morphology and ultrastructure. Analysis of neural circuits at single-synapse resolution remains the flagship target of…

Convolutional neural networks (CNNs) are increasingly being used to automate segmentation of organs-at-risk in radiotherapy. Since large sets of highly curated data are scarce, we investigated how much data is required to train accurate and…

Medical image segmentation is vital to the area of medical imaging because it enables professionals to more accurately examine and understand the information offered by different imaging modalities. The technique of splitting a medical…

Magnetic resonance imaging (MRI) is critically important for brain mapping in both scientific research and clinical studies. Precise segmentation of brain tumors facilitates clinical diagnosis, evaluations, and surgical planning. Deep…

The automatic detection and localization of anatomical features in retinal imaging data are relevant for many aspects. In this work, we follow a data-centric approach to optimize classifier training for optic nerve head detection and…

Deep convolutional neural networks (CNNs) have shown excellent performance in object recognition tasks and dense classification problems such as semantic segmentation. However, training deep neural networks on large and sparse datasets is…

Brain extraction in magnetic resonance imaging (MRI) data is an important segmentation step in many neuroimaging preprocessing pipelines. Image segmentation is one of the research fields in which deep learning had the biggest impact in…

We propose a segmentation framework that uses deep neural networks and introduce two innovations. First, we describe a biophysics-based domain adaptation method. Second, we propose an automatic method to segment white and gray matter, and…

Neuroanatomical segmentation in magnetic resonance imaging (MRI) of the brain is a prerequisite for volume, thickness and shape measurements. This work introduces a new highly accurate and versatile method based on 3D convolutional neural…

Magnetic Resonance Images (MRIs) are extremely used in the medical field to detect and better understand diseases. In order to fasten automatic processing of scans and enhance medical research, this project focuses on automatically…

Deploying neural networks to different devices or platforms is in general challenging, especially when the model size is large or model complexity is high. Although there exist ways for model pruning or distillation, it is typically…

Deep learning methods are actively used for brain lesion segmentation. One of the most popular models is DeepMedic, which was developed for segmentation of relatively large lesions like glioma and ischemic stroke. In our work, we consider…

For complex segmentation tasks, fully automatic systems are inherently limited in their achievable accuracy for extracting relevant objects. Especially in cases where only few data sets need to be processed for a highly accurate result,…

We show dense voxel embeddings learned via deep metric learning can be employed to produce a highly accurate segmentation of neurons from 3D electron microscopy images. A "metric graph" on a set of edges between voxels is constructed from…

Tumor segmentation from multi-modal brain MRI images is a challenging task due to the limited samples, high variance in shapes and uneven distribution of tumor morphology. The performance of automated medical image segmentation has been…

Detection and segmentation of the hippocampal structures in volumetric brain images is a challenging problem in the area of medical imaging. In this paper, we propose a two-stage 3D fully convolutional neural network that efficiently…