Automated segmentation of the ex vivo mouse brain

Alize E. H. Scheenstra; Jouke Dijkstra; Rob C. G. van de Ven; Louise van der Weerd; Johan H. C. Reiber

doi:10.1117/12.708867

29 March 2007 Automated segmentation of the ex vivo mouse brain

Alize E. H. Scheenstra, Jouke Dijkstra, Rob C. G. van de Ven, Louise van der Weerd, Johan H. C. Reiber

Author Affiliations +

Proceedings Volume 6511, Medical Imaging 2007: Physiology, Function, and Structure from Medical Images; 651106 (2007) https://doi.org/10.1117/12.708867
Event: Medical Imaging, 2007, San Diego, CA, United States

Abstract

In biological image processing the segmentation of a volume is, although tedious, required for many applications, like the comparison of structures and annotation purposes. To automate this process, we present a segmentation method for various structures of the mouse brain. The segmentation consists of two parts; first a rough affine atlas-based registration was performed and second, the edges between structures were refined by an adapted Markov random field clustering approach. The segmentations results were compared to manual segmentations from two experts. The presented automatic segmentation method is quick, intuitive and suitable for registration purposes, but also for biological objectives, like comparison and annotation.

Citation Download Citation

Alize E. H. Scheenstra, Jouke Dijkstra, Rob C. G. van de Ven, Louise van der Weerd, and Johan H. C. Reiber "Automated segmentation of the ex vivo mouse brain", Proc. SPIE 6511, Medical Imaging 2007: Physiology, Function, and Structure from Medical Images, 651106 (29 March 2007); https://doi.org/10.1117/12.708867

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