ImgLib2 for large scale image analysis and visualization
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1
Max Planck Institute of Molecular Cell Biology and Genetics, Germany
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2
Albert Einstein College of Medicine, United States
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3
Max Planck Institute of Molecular Cell Biology and Genetics, Germany
Today, both connectivity and detailed neuroanatomy of biological nervous tissue are reconstructed from light- and electron-microscopy images. Structures in neuronal tissue span a wide range of scales, they have both fine details and large extent. Accordingly, large volumes need to be imaged at very high resolution resulting in image data of overwhelming and ever increasing size. New approaches to both algorithm development for image analysis and data storage and access management are desperately required.
We propose our Java library ImgLib2 for n-dimensional data representation and manipulation [1] as a valuable tool in this context. ImgLib2 separates pixel-algebra, data access and data representation in memory by virtualization. It makes algorithm development independent of infrastructure design and vice versa, simplifying both lines of development. In consequence, it is easier to express new or existing approaches for image analysis in software. New data sources are immedately available to existing algorithm implementations. ImgLib2 collaborates seamlessly with existing infrastructure. It is typically sufficient to implement one basic accessor to connect an existing data source to the library.
We demonstrate ImgLib2's flexibility in two distinct and relevant contexts: (1) a rich-client visualization and annotation tool for remotely stored image volumes of many terabytes size [2], and (2) as a server-side image processing backend for the browser-based collaborative annotation tool CATMAID [3].
References
[1] Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak, and Stephan Saalfeld, ImgLib2---Generic Image Processing in Java, Bioinformatics, 28(22), 3009–3011 (2012), doi:10.1093/bioinformatics/bts543.
[2] Open Connectome Project (http://openconnecto.me)
[3] Stephan Saalfeld, Albert Cardona, Volker Hartenstein, Pavel Tomancak, CATMAID: Collaborative Annotation Toolkit for Massive Amounts of Image Data, Bioinformatics, 25(19), 1984--1986 (2009).
Keywords:
ImgLib2,
image processing and analysis,
large remote data,
Java,
software engineering,
visualization,
Open Source Software
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Poster
Topic:
Large scale modeling
Citation:
Saalfeld
S,
Pietzsch
T,
Preibisch
S and
Tomancak
P
(2013). ImgLib2 for large scale image analysis and visualization.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00107
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Received:
29 Apr 2013;
Published Online:
11 Jul 2013.
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Correspondence:
Dr. Stephan Saalfeld, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany, saalfeld@mpi-cbg.de