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Segmentation of brain structures in a large dataset of magnetic resonance images (MRI) necessitates automatic segmentation instead of manual tracing. Automatic segmentation methods provide a much-needed alternative to manual segmentation…

Background: For the clinical adoption of stress-based rupture risk estimation in abdominal aortic aneurysms (AAAs), a fully automated pipeline, from clinical imaging to biomechanical stress computation, is essential. To this end, we…

A major challenge in stroke research and stroke recovery predictions is the determination of a stroke lesion's extent and its impact on relevant brain systems. Manual segmentation of stroke lesions from 3D magnetic resonance (MR) imaging…

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…

Magnetic Resonance Imaging (MRI) is pivotal in radiology, offering non-invasive and high-quality insights into the human body. Precise segmentation of MRIs into different organs and tissues would be highly beneficial since it would allow…

Glioma is the most deadly brain tumor with high mortality. Treatment planning by human experts depends on the proper diagnosis of physical symptoms along with Magnetic Resonance(MR) image analysis. Highly variability of a brain tumor in…

Recent studies have shown that ensemble approaches could not only improve accuracy and but also estimate model uncertainty in deep learning. However, it requires a large number of parameters according to the increase of ensemble models for…

Segmentation is essential for medical image analysis tasks such as intervention planning, therapy guidance, diagnosis, treatment decisions. Deep learning is becoming increasingly prominent for segmentation, where the lack of annotations,…

Segmenting a structural magnetic resonance imaging (MRI) scan is an important pre-processing step for analytic procedures and subsequent inferences about longitudinal tissue changes. Manual segmentation defines the current gold standard in…

Segmentation of anatomical structures and pathologies is inherently ambiguous. For instance, structure borders may not be clearly visible or different experts may have different styles of annotating. The majority of current state-of-the-art…

Brain Tumor Segmentation from magnetic resonance imaging (MRI) is a critical technique for early diagnosis. However, rather than having complete four modalities as in BraTS dataset, it is common to have missing modalities in clinical…

Early diagnosis and accurate segmentation of brain tumors are imperative for successful treatment. Unfortunately, manual segmentation is time consuming, costly and despite extensive human expertise often inaccurate. Here, we present an…

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…

Lung segmentation in computerized tomography (CT) images is an important procedure in various lung disease diagnosis. Most of the current lung segmentation approaches are performed through a series of procedures with manually empirical…

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment…

Neuroimaging data, particularly from techniques like MRI or PET, offer rich but complex information about brain structure and activity. To manage this complexity, latent representation models - such as Autoencoders, Generative Adversarial…

Deep neural networks are powerful tools for biomedical image segmentation. These models are often trained with heavy supervision, relying on pairs of images and corresponding voxel-level labels. However, obtaining segmentations of…

In this paper we propose a novel method for the segmentation of longitudinal brain MRI scans of patients suffering from Multiple Sclerosis. The method builds upon an existing cross-sectional method for simultaneous whole-brain and lesion…

Fluorescence microscopy images contain several channels, each indicating a marker staining the sample. Since many different marker combinations are utilized in practice, it has been challenging to apply deep learning based segmentation…

Automatic segmentation of brain tumors in intra-operative ultrasound (iUS) images could facilitate localization of tumor tissue during resection surgery. The lack of large annotated datasets limits the current models performances. In this…