• Corpus ID: 1720842

BigDataViewer: Interactive Visualization and Image Processing for Terabyte Data Sets

  title={BigDataViewer: Interactive Visualization and Image Processing for Terabyte Data Sets},
  author={Tobias Pietzsch and Stephan Saalfeld and Stephan Preibisch and Pavel Tomançak},
The increasingly popular light sheet microscopy techniques generate very large 3D time-lapse recordings of living biological specimen. The necessity to make large volumetric datasets available for interactive visualization and analysis has been widely recognized. However, existing solutions build on dedicated servers to generate virtual slices that are transferred to the client applications, practically leading to insufficient frame rates (less than 10 frames per second) for truly interactive… 
Automatische Zusammenfassung von Bild-Datensätzen
The results indicate that the implementation generates diverse and appealing image collages for the tested image datasets, but that there are also some extreme cases for example with misleading symmetry caused by the pre-attentive processing of the human visual system.
Master thesis : Cytomine-Multidim
This work aims at extending the Cytomine software to handle efficiently large hyperspectral datasets and allow their fast storage and visualization, and proposes the development of a new file format called HSDS that stores hyperspectrals data and allows efficient remote access to spectral data.


CATMAID: collaborative annotation toolkit for massive amounts of image data
The CATMAID interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by bookmarking and enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy.
ImgLib2—generic image processing in Java
Summary: ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating
Pyramidal parametrics
This paper advances a “pyramidal parametric” prefiltering and sampling geometry which minimizes aliasing effects and assures continuity within and between target images.
The open connectome project data cluster: scalable analysis and vision for high-throughput neuroscience
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
Efficient Bayesian-based multiview deconvolution
A Bayesian-based derivation of multiview deconvolution is presented that drastically improves the convergence time, and a fast implementation using graphics hardware is provided.
Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy
Large, living biological specimens present challenges to existing optical imaging techniques because of their absorptive and scattering properties. We developed selective plane illumination
ImgLib2 - generic image processing in Java
Extensible markup language (XML) 1.0 (fifth edition)
  • tech. rep., W3C, 2008.
  • 2008
  • HDFView
Chunking in HDF5
  • Chunking in HDF5