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This study investigates a 3D and fully convolutional neural network (CNN) for subcortical brain structure segmentation in MRI. 3D CNN architectures have been generally avoided due to their computational and memory requirements during…

Automatic medical image segmentation based on Computed Tomography (CT) has been widely applied for computer-aided surgery as a prerequisite. With the development of deep learning technologies, deep convolutional neural networks (DCNNs) have…

Image registration is a key component of various image processing operations which involve the analysis of different image data sets. Automatic image registration domains have witnessed the application of many intelligent methodologies over…

Finding a code to unravel the population of neural responses that leads to a distinct animal behavior has been a long-standing question in the field of neuroscience. With the recent advances in machine learning, it is shown that the…

Caenorhabditis elegans (C. elegans) illustrated remarkable behavioral plasticities including complex non-associative and associative learning representations. Understanding the principles of such mechanisms presumably leads to constructive…

Researchers in the field of connectomics are working to reconstruct a map of neural connections in the brain in order to understand at a fundamental level how the brain processes information. Constructing this wiring diagram is done by…

From human crowds to cells in tissue, the detection and efficient tracking of multiple objects in dense configurations is an important and unsolved problem. In the past, limitations of image analysis have restricted studies of dense groups…

MR images of fetuses allow clinicians to detect brain abnormalities in an early stage of development. The cornerstone of volumetric and morphologic analysis in fetal MRI is segmentation of the fetal brain into different tissue classes.…

In this paper, we propose CLIP-Dissect, a new technique to automatically describe the function of individual hidden neurons inside vision networks. CLIP-Dissect leverages recent advances in multimodal vision/language models to label…

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…

The identification of vascular networks is an important topic in the medical image analysis community. While most methods focus on single vessel tracking, the few solutions that exist for tracking complete vascular networks are usually…

Deformable image registration is a crucial step in medical image analysis for finding a non-linear spatial transformation between a pair of fixed and moving images. Deep registration methods based on Convolutional Neural Networks (CNNs)…

Convolutional neural networks (CNNs) have shown promising results on several segmentation tasks in magnetic resonance (MR) images. However, the accuracy of CNNs may degrade severely when segmenting images acquired with different scanners…

Automated sample preparation and electron microscopy enables acquisition of very large image data sets. These technical advances are of special importance to the field of neuroanatomy, as 3D reconstructions of neuronal processes at the nm…

Accurate analysis and modeling of renal functions require a precise segmentation of the renal blood vessels. Micro-CT scans provide image data at higher resolutions, making more small vessels near the renal cortex visible. Although…

The current neuron reconstruction pipeline for electron microscopy (EM) data usually includes automatic image segmentation followed by extensive human expert proofreading. In this work, we aim to reduce human workload by predicting…

Contemporary approaches to instance segmentation in cell science use 2D or 3D convolutional networks depending on the experiment and data structures. However, limitations in microscopy systems or efforts to prevent phototoxicity commonly…

Convolutional neural network (CNN) driven by image recognition has been shown to be able to explain cortical responses to static pictures at ventral-stream areas. Here, we further showed that such CNN could reliably predict and decode…

Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) automatic 3-D registration is implemented and validated for small animal image volumes so that the high-resolution anatomical MRI information can be fused with the low…

The anatomical location of imaging features is of crucial importance for accurate diagnosis in many medical tasks. Convolutional neural networks (CNN) have had huge successes in computer vision, but they lack the natural ability to…