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The wiring and connectivity of neurons form a structural basis for the function of the nervous system. Advances in volume electron microscopy (EM) and image segmentation have enabled mapping of circuit diagrams (connectomics) within local…
The response of adult human bone marrow stromal stem cells to surface topographies generated through femtosecond laser machining can be predicted by a deep neural network. The network is capable of predicting cell response to a…
We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy (EM) in accuracy and scalability. Our method consists of a…
The article explores an encoding and structural information processing approach using sparse bit vectors and fixed-length linear vectors. The following are presented: a discrete method of speculative stochastic dimensionality reduction of…
Neuroscientists have devoted significant effort into the creation of standard brain reference atlases for high-throughput registration of anatomical regions of interest. However, variability in brain size and form across individuals poses a…
Deep cerebellar nuclei are a key structure of the cerebellum that are involved in processing motor and sensory information. It is thus a crucial step to accurately segment deep cerebellar nuclei for the understanding of the cerebellum…
Deep learning has been shown to produce state of the art results in many tasks in biomedical imaging, especially in segmentation. Moreover, segmentation of the cerebrovascular structure from magnetic resonance angiography is a challenging…
In this paper, we present an automated approach for segmenting multiple sclerosis (MS) lesions from multi-modal brain magnetic resonance images. Our method is based on a deep end-to-end 2D convolutional neural network (CNN) for slice-based…
We propose a new algorithm for curve skeleton computation which differs from previous algorithms by being based on the notion of local separators. The main benefits of this approach are that it is able to capture relatively fine details and…
Recent advances in deep learning algorithms have led to significant benefits for solving many medical image analysis problems. Training deep learning models commonly requires large datasets with expert-labeled annotations. However,…
Accurate segmentation of MR brain tissue is a crucial step for diagnosis,surgical planning, and treatment of brain abnormalities. However,it is a time-consuming task to be performed by medical experts. So, automatic and reliable…
Segmenting deep brain structures from magnetic resonance images is important for patient diagnosis, surgical planning, and research. Most current state-of-the-art solutions follow a segmentation-by-registration approach, where subject MRIs…
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…
This paper introduces Smart-Tree, a supervised method for approximating the medial axes of branch skeletons from a tree point cloud. Smart-Tree uses a sparse voxel convolutional neural network to extract the radius and direction towards the…
Deep learning segmentation relies heavily on labeled data, but manual labeling is laborious and time-consuming, especially for volumetric images such as brain magnetic resonance imaging (MRI). While recent domain-randomization techniques…
We present an interactive approach to train a deep neural network pixel classifier for the segmentation of neuronal structures. An interactive training scheme reduces the extremely tedious manual annotation task that is typically required…
In this paper we give a new, efficient algorithm for computing curve skeletons, based on local separators. Our efficiency stems from a multilevel approach, where we solve small problems across levels of detail and combine these in order to…
Purpose: Conventional automated segmentation of the head anatomy in MRI distinguishes different brain and non-brain tissues based on image intensities and prior tissue probability maps (TPM). This works well for normal head anatomies, but…
Manual annotation of vertebrae on spinal X-ray imaging is costly and time-consuming due to bone shape complexity and image quality variations. In this study, we address this challenge by proposing an ensemble method called VertXNet, to…
Currently, most bone implants used in orthopedics and traumatology are non-degradable and may need to be surgically removed later on e.g. in the case of children. This removal is associated with health risks which could be minimized by…