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. 2012 Nov 15;28(22):3009-11.
doi: 10.1093/bioinformatics/bts543. Epub 2012 Sep 8.

ImgLib2--generic image processing in Java

Tobias Pietzsch  1 , Stephan Preibisch, Pavel Tomancák, Stephan Saalfeld
Affiliations

ImgLib2--generic image processing in Java

Tobias Pietzsch et al. Bioinformatics. .

Erratum in

  • Bioinformatics. 2013 Jan 15;29(2):298

Abstract

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 pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins.

Availability: ImgLib2 is licensed under BSD. Documentation and source code are available at http://imglib2.net and in a public repository at https://github.com/imagej/imglib.

Supplementary information: Supplementary data are available at Bioinformatics Online.

Contact: saalfeld@mpi-cbg.de

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Figures

Fig. 1.
Fig. 1.
Visualizes exemplarily the capabilities of ImgLib2. (a) shows an image, virtually extended by a mirroring strategy, arrows mark the original image boundaries. Four algorithms were applied to sub-image views: (from left to right) anisotropic diffusion, maximally stable extremal regions, Sobel filtering, Gaussian convolution. (b) shows an extrapolation of sparse data where 2,000 points were randomly sampled from the larger area indicated in (a). (c) shows an interpolated and affine transformed view of the smaller tilted area indicated in (a)
See this image and copyright information in PMC

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Publication types