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Cellular-resolution connectomics is an ambitious research direction with the goal of generating comprehensive brain connectivity maps using high-throughput, nano-scale electron microscopy. One of the main challenges in connectomics research is developing scalable image analysis algorithms that require minimal user intervention. Deep learning has provided exceptional performance in image classification tasks in computer vision, leading to a recent explosion in popularity. Similarly, its applicati

In this paper we propose a novel computational technique to solve the Eikonal equation efficiently on parallel architectures. The proposed method manages the list of active nodes and iteratively updates the solutions on those nodes until they converge. Nodes are added to or removed from the list based on a convergence measure, but the management of this list does not entail an extra burden of expensive ordered data structures or special updating sequences. The proposed method has suboptimal wors

Data sets imaged with modern electron microscopes can range from tens of terabytes to about one petabyte. Two new tools, Ssecrett and NeuroTrace, support interactive exploration and analysis of large-scale optical-and electron-microscopy images to help scientists reconstruct complex neural circuits of the mammalian nervous system.

Recent advances in scanning technology provide high resolution EM (Electron Microscopy) datasets that allow neuro-scientists to reconstruct complex neural connections in a nervous system. However, due to the enormous size and complexity of the resulting data, segmentation and visualization of neural processes in EM data is usually a difficult and very time-consuming task. In this paper, we present NeuroTrace, a novel EM volume segmentation and visualization system that consists of two parts: a s

In this paper we present a method to compute and visualize volumetric white matter connectivity in diffusion tensor magnetic resonance imaging (DT-MRI) using a Hamilton-Jacobi (H-J) solver on the GPU (Graphics Processing Unit). Paths through the volume are assigned costs that are lower if they are consistent with the preferred diffusion directions. The proposed method finds a set of voxels in the DTI volume that contain paths between two regions whose costs are within a threshold of the optimal

This paper presents a 3D, volumetric, seismic fault detection system that relies on a novel set of nonlinear filters combined with a GPU (Graphics Processing Unit) implementation, which makes interactive nonlinear, volumetric processing feasible. The method uses a 3D structure tensor to robustly measure seismic orientations. These tensors guide an anisotropic diffusion, which reduces noise in the data while enhancing the fault discontinuity and coherency along seismic strata. A fault-likelihood

Histology is the study of the structure of biological tissue using microscopy techniques. As digital imaging technology advances, high resolution microscopy of large tissue volumes is becoming feasible; however, new interactive tools are needed to explore and analyze the enormous datasets. In this paper we present a visualization framework that specifically targets interactive examination of arbitrarily large image stacks. Our framework is built upon two core techniques: display-aware processing

An automatic procedure is presented to generate a multiresolution head model from sampled surface data. A generic control mesh serves as the starting point for a fitting algorithm that approximates the points in an unstructured set of surface samples, e.g. a point cloud obtained directly from range scans of an individual. A hierarchical representation of the model is generated by repeated refinement using subdivision rules and measuring displacements to the input data. Key features of our method

We present a method for the adaptive reconstruction of a surface directly from an unorganized point cloud. The algorithm is based on an incrementally expanding neural network and the statistical analysis of its learning process. In particular, we make use of the simple observation that during the learning process the normal of a vertex near a sharp edge or a high curvature area of the target space, statistically, will vary more than the normal of a vertex near a flat area. We use the information

With the advent of unsupervised learning, efficient training of a deep network for image denoising without pairs of noisy and clean images has become feasible. Most current unsupervised denoising methods are built on self-supervised loss with the assumption of zero-mean noise under the signal-independent condition, which causes brightness-shifting artifacts on unconventional noise statistics (i.e., different from commonly used noise models). Moreover, most blind denoising methods require a rando

We describe a set of image editing and viewing tools that explicitly take into account the resolution of the display on which the image is viewed. Our approach is twofold. First, we design editing tools that process only the visible data, which is useful for images larger than the display. This encompasses cases such as multi-image panoramas and high-resolution medical data. Second, we propose an adaptive way to set viewing parameters such brightness and contrast. Because we deal with very large

Abstract Collaborative slide image viewing systems are becoming increasingly important in pathology applications such as telepathology and E‐learning. Despite rapid advances in computing and imaging technology, current digital pathology systems have limited performance with respect to remote viewing of whole slide images on desktop or mobile computing devices. In this paper we present a novel digital pathology client–server system that supports collaborative viewing of multi‐plane whole slide im