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1
December 2013
IEEE Transactions on Visualization and Computer Graphics: Volume 19 Issue 12, December 2013
Publisher: IEEE Educational Activities Department
This paper presents ConnectomeExplorer, an application for the interactive exploration and query-guided visual analysis of large volumetric electron microscopy (EM) data sets in connectomics research. Our system incorporates a knowledge-based query algebra that supports the interactive specification of dynamically evaluated queries, which enable neuroscientists to pose and answer domain-specific questions ...
Keywords:
Connectomics, neuroscience, query algebra, visual knowledge discovery, petascale volume analysis
2
W. Jeong,
J. Schneider,
A. Hansen,
M. Lee,
S. G. Turney,
B. E. Faulkner-Jones,
J. L. Hecht,
R. Najarian,
E. Yee,
J. W. Lichtman,
H. Pfister
September 2013
Computer Graphics Forum: Volume 32 Issue 6, September 2013
Publisher: The Eurographs Association & John Wiley & Sons, Ltd.
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 ...
Keywords:
biomedical image visualization, digital pathology, Computer Graphics [I.3.8]: Applications, collaborative visualization, Computer Graphics [I.3.2]: Graphics systems, distributed/network graphics, GPU, image compression
3
Randal Burns,
Kunal Lillaney,
Daniel R. Berger,
Logan Grosenick,
Karl Deisseroth,
R. Clay Reid,
William Gray Roncal,
Priya Manavalan,
Davi D. Bock,
Narayanan Kasthuri,
Michael Kazhdan,
Stephen J. Smith,
Dean Kleissas,
Eric Perlman,
Kwanghun Chung,
Nicholas C. Weiler,
Jeff Lichtman,
Alexander S. Szalay,
Joshua T. Vogelstein,
R. Jacob Vogelstein
July 2013
SSDBM: Proceedings of the 25th International Conference on Scientific and Statistical Database Management
Publisher: ACM
Bibliometrics:
Citation Count: 1
Downloads (6 Weeks): 4, Downloads (12 Months): 41, Downloads (Overall): 250
Full text available:
 PDF
We describe a scalable database cluster for the spatial analysis and annotation of high-throughput brain imaging data, initially for 3-d electron microscopy image stacks, but for time-series and multi-channel data as well. The system was designed primarily for workloads that build connectomes ---neural connectivity maps of the brain---using the parallel ...
Keywords:
connectomics, data-intensive computing
4
July 2013
IEEE Computer Graphics and Applications: Volume 33 Issue 4, July 2013
Publisher: IEEE Computer Society Press
Recent advances in high-resolution microscopy let neuroscientists acquire neural-tissue volume data of extremely large sizes. However, the tremendous resolution and the high complexity of neural structures present big challenges to storage, processing, and visualization at interactive rates. A proposed system provides interactive exploration of petascale (petavoxel) volumes resulting from high-throughput ...
Keywords:
Data visualization,Neuroscience,Image resolution,Rendering (computer graphics),Microscopy,Streaming media,Medical image processing,computer graphics,petascale-volume exploration,segmented volume data,high-resolution microscopy,high-throughput imaging,neuroscience
5
November 2012
Journal of Visual Communication and Image Representation: Volume 23 Issue 8, November, 2012
Publisher: Academic Press, Inc.
In this study, we compare two vectorial tracing methods for 3D color images: (i) a conventional piecewise linear generalized cylinder algorithm that uses color and edge information and (ii) a principal curve tracing algorithm that uses the gradient and Hessian of a given density estimate. We tested the algorithms on ...
Keywords:
Brainbow, Volumetric color images, Axon tracing, Piecewise linear cylinder model, Ridge analysis, Topological skeleton, Principal curve, Connectivity analysis
6
November 2011
ICCV '11: Proceedings of the 2011 International Conference on Computer Vision
Publisher: IEEE Computer Society
We address the problem of automatic 3D segmentation of a stack of electron microscopy sections of brain tissue. Unlike previous efforts, where the reconstruction is usually done on a section-to-section basis, or by the agglomerative clustering of 2D segments, we leverage information from the entire volume to obtain a globally ...
7
September 2011
MICCAI'11: Proceedings of the 14th international conference on Medical image computing and computer-assisted intervention - Volume Part I
Publisher: Springer-Verlag
We present a novel semi-automatic method for segmenting neural processes in large, highly anisotropic EM (electron microscopy) image stacks. Our method takes advantage of sparse scribble annotations provided by the user to guide a 3D variational segmentation model, thereby allowing our method to globally optimally enforce 3D geometric constraints on ...
8
September 2011
XRDS: Crossroads, The ACM Magazine for Students - Neuroscience and Computing: Technology on the Brain: Volume 18 Issue 1, Fall 2011
Publisher: ACM
Bibliometrics:
Citation Count: 1
Downloads (6 Weeks): 2, Downloads (12 Months): 23, Downloads (Overall): 743
Using neuroimaging, researchers are succesfully mapping neural connectivity and in the process creating vivid "brainbows."
9
August 2011
SIGGRAPH '11: ACM SIGGRAPH 2011 Talks
Publisher: ACM
Bibliometrics:
Citation Count: 3
Downloads (6 Weeks): 0, Downloads (12 Months): 8, Downloads (Overall): 150
Full text available:
PDF
In neuroscience, a very promising bottom-up approach to understanding how the brain works is built on acquiring and analyzing electron microscopy (EM) scans of brain tissue, an area known as Connectomics . This results in volume data of extremely high resolution of 3--5nm per pixel and 25--50nm slice thickness, overall ...
10
November 2010
IEEE Transactions on Visualization and Computer Graphics: Volume 16 Issue 6, November 2010
Publisher: IEEE Educational Activities Department
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 ...
Keywords:
biomedical image processing, texture compression, GPU, Gigapixel viewer, biomedical image processing, GPU, texture compression, Gigapixel viewer
11
June 2010
Bioinformatics: Volume 26 Issue 12, June 2010
Publisher: Oxford University Press
Motivation: Unraveling the structure and behavior of the brain and central nervous system (CNS) has always been a major goal of neuroscience. Understanding the wiring diagrams of the neuromuscular junction connectomes (full connectivity of nervous system neuronal components) is a starting point for this, as it helps in the study ...
12
May 2010
IEEE Computer Graphics and Applications: Volume 30 Issue 3, May 2010
Publisher: IEEE Computer Society Press
Recent advances in optical and electron microscopy let scientists acquire extremely high-resolution images for neuroscience research. Data sets imaged with modern electron microscopes can range between tens of terabytes to about one petabyte. These large data sizes and the high complexity of the underlying neural structures make it very challenging ...
Keywords:
connectome, neuroscience, volume rendering, segmentation, computer graphics, graphics and multimedia, graphics hardware, implicit surface rendering, neuroscience, connectome, segmentation, volume rendering, implicit surface rendering, graphics hardware, computer graphics, graphics and multimedia
13
August 2008
Neural Computation: Volume 20 Issue 8, August 2008
Publisher: MIT Press
The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is ...
14
December 1998
CNS '97: Proceedings of the sixth annual conference on Computational neuroscience : trends in research, 1998: trends in research, 1998
Publisher: Plenum Press
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