Atlas guided navigation of brain image repositories using NeuroTerrain
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1
Drexel University College of Medicine, United States
Access to a repository of brain imagery can be made efficient if the data is annotated, spatially normalized, or both. If the transformation mapping points between library entries and reference spatial coordinates is known, then one can retrieve relevant views from multiple brain volumes based on coordinate specification. If the volumes are annotated, retrieval can rely on anatomical labels. This presentation will focus on use of NeuroTerrain, an atlas-browsing environment [1], to selectively view desired planes from the Mouse Brain Library (MBL) [2], an image repository containing 2D brain images.
MBL contains images of histological sections from a large number of mice strains. It was specifically design for functional genomics mapping studies. NeuroTerrain utilizes a reference 3D mouse brain atlas and was developed to serve as MBL’s spatial index. Once entries in the library are aligned to the Atlas, bidirectional spatial navigation is possible–one can automatically display arbitrary planes of view in the atlas corresponding to given MBL entry as well as retrieve entries in the library matching a given atlas plane. Registration between atlas and MBL entries also enables automatic annotation of the latter using Atlas anatomical templates and work is ongoing to support label-based navigation.
NeuroTerrain also supports co-navigation of aligned 3D volumes: arbitrary planes of view selected in one invokes selection of the equivalent planes in the others. The collection of open volumes can also share available delineation templates and the desired set of volumes of interest can be visualized overlaying each of them.
NeuroTerrain is composed of a server and light Java client. The server generates arbitrary slices of 3D volumes including those of the atlas and its anatomical templates. The client provides the user interface to control navigation and to visualize the results. The client can be readily instantiated in other Java applications. This greatly simplifies migration of these capibilities into diverse analysis and visualization environments.
References
1. Gustafson, C., W.J. Bug, and J. Nissanov, NeuroTerrain--a client-server system for browsing 3D biomedical image data sets. BMC Bioinformatics, 2007. 8: p. 40
2. Rosen, G., et al., Informatics center for mouse genomics: the dissection of complex traits of the nervous system. Neuroinformatics, 2003. 1(4): p. 327-342
Conference:
Neuroinformatics 2008, Stockholm, Sweden, 7 Sep - 9 Sep, 2008.
Presentation Type:
Oral Presentation
Topic:
Live Demonstrations
Citation:
Nissanov
J,
Gustafson
C,
Burstein
PD and
Bertrand
L
(2008). Atlas guided navigation of brain image repositories using NeuroTerrain.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2008.
doi: 10.3389/conf.neuro.11.2008.01.129
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Received:
28 Jul 2008;
Published Online:
28 Jul 2008.
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Correspondence:
Jonathan Nissanov, Drexel University College of Medicine, Drexel, United States, nemoABS01@frontiersin.org