Automated reconstruction of three-dimensional brain structures based on 2D histological atlases.
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1
Nencki Institute of Experimental Biology, Department of Neurophysiology, Poland
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2
University of Warsaw, Faculty of Mathematics Informatics and Mechanics, Poland
Brain activity data obtained with various neurophysiological methods must be precisely localized in neuroanatomical context in order to make the interpretation of the results correct or even possible. Traditionally, such context was provided by 2D planes of the atlases of brain structures. Recent development of modern recording techniques (MRI, PET, multichannel LFP), leading to spatially distributed data, brought a necessity of three-dimensional brain atlases of various species. Creating three-dimensional atlases is not a new problem in itself (e.g. SMART Atlas, NESYS Atlas3D). However, large part of available software gives only the option of viewing already prepared structures rather than creating new 3D models of these structures. Moreover, common practice in creating such atlases is to do it manually by tracing contours of desired structures on all slices and creating 3D models in commercial software (e.g. Amira). This approach leads to many inconveniences. First of all it is time consuming and tedious task which is hard to record and repeat afterwards by other people or by computer. It is also not customizable as constructing the 3D model again means conducting the whole manual process from scratch. All of those disadvantages result in difficulties in spotting and eliminating reconstruction errors. Obviously, in case of atypical species the tracing stage is necessary, but for many standard laboratory animals existing 2D atlases could be employed. Here we propose software, 3D Brain Atlas Reconstructor (3dBAR) dedicated to automated reconstruction of three-dimensional brain structures based on 2D histological atlases. Our goal is a framework for generation of 3D models of chosen brain structures based on 2D representations (either vector or bitmap formats) of slices. Implemented methods allow to generate 3D models in reproducible and configurable way as well as track and review the whole reconstruction process in order to find and correct errors. Some typical simple errors which may be noticed in 2D digital atlases, such as open boundaries between regions or incorrectly placed labels, can be highlighted or eliminated by the software. Our workflow allows for manual corrections when automatic reconstruction is not good enough. The software takes into consideration many collaborative features: it allows exchanging content (complete models as well as data from intermediate stages of processing) and may easily integrate with other atlasing systems by using open file formats (SVG, XML, VRML). The framework allows for adding new public or proprietary content and supports an open file definition based on SVG for 2D input data. Moreover, on-line service with dedicated API will be created allowing downloading desired structures via http queries. At present, our software package consists of graphical interface for generating and previewing models and it contains wrappers for two atlases: Paxinos and Franklin Mouse atlas and Paxinos and Watson Rat atlas. We are working towards integrating other data in particular in collaboration with Scalable Brain Atlas project. Ultimately, the tools will be published as open source. Supported from grant POIG.02.03.00-00-003/09.
Conference:
Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.
Presentation Type:
Poster Presentation
Topic:
Digital atlasing
Citation:
Majka
P,
Furga
G,
Kublik
E and
Wójcik
D
(2010). Automated reconstruction of three-dimensional brain structures based on 2D histological atlases..
Front. Neurosci.
Conference Abstract:
Neuroinformatics 2010 .
doi: 10.3389/conf.fnins.2010.13.00044
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Received:
10 Jun 2010;
Published Online:
10 Jun 2010.
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Correspondence:
Piotr Majka, Nencki Institute of Experimental Biology, Department of Neurophysiology, Warsaw, Poland, p.majka@nencki.edu.pl