Volume quantization of the mouse cerebellum by semiautomatic 3D segmentation of magnetic resonance images

Jan Sijbers; Anne-Marie Van der Linden; Paul Scheunders; Johan Van Audekerke; Dirk Van Dyck; Erik R.R. Raman

doi:10.1117/12.237958

16 April 1996 Volume quantization of the mouse cerebellum by semiautomatic 3D segmentation of magnetic resonance images

Jan Sijbers, Anne-Marie Van der Linden, Paul Scheunders, Johan Van Audekerke, Dirk Van Dyck, Erik R.R. Raman

Proceedings Volume 2710, Medical Imaging 1996: Image Processing; (1996) https://doi.org/10.1117/12.237958
Event: Medical Imaging 1996, 1996, Newport Beach, CA, United States

Abstract

The aim of this work is the development of a non-invasive technique for efficient and accurate volume quantization of the cerebellum of mice. This enables an in-vivo study on the development of the cerebellum in order to define possible alterations in cerebellum volume of transgenic mice. We concentrate on a semi-automatic segmentation procedure to extract the cerebellum from 3D magnetic resonance data. The proposed technique uses a 3D variant of Vincent and Soille's immersion based watershed algorithm which is applied to the gradient magnitude of the MR data. The algorithm results in a partitioning of the data in volume primitives. The known drawback of the watershed algorithm, over-segmentation, is strongly reduced by a priori application of an adaptive anisotropic diffusion filter on the gradient magnitude data. In addition, over-segmentation is a posteriori contingently reduced by properly merging volume primitives, based on the minimum description length principle. The outcome of the preceding image processing step is presented to the user for manual segmentation. The first slice which contains the object of interest is quickly segmented by the user through selection of basic image regions. In the sequel, the subsequent slices are automatically segmented. The segmentation results are contingently manually corrected. The technique is tested on phantom objects, where segmentation errors less than 2% were observed. Three-dimensional reconstructions of the segmented data are shown for the mouse cerebellum and the mouse brains in toto.

Citation Download Citation

Jan Sijbers, Anne-Marie Van der Linden, Paul Scheunders, Johan Van Audekerke, Dirk Van Dyck, and Erik R.R. Raman "Volume quantization of the mouse cerebellum by semiautomatic 3D segmentation of magnetic resonance images", Proc. SPIE 2710, Medical Imaging 1996: Image Processing, (16 April 1996); https://doi.org/10.1117/12.237958

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