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 · Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE · 2007
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.