Region Competition: Unifying Snakes, Region Growing, and Bayes/MDL for Multiband Image Segmentation
IEEE Transactions on Pattern Analysis and Machine Intelligence
MICCAI '01 Proceedings of the 4th International Conference on Medical Image Computing and Computer-Assisted Intervention
Smooth 3-D Reconstruction for 2-D Histological Images
IPMI '09 Proceedings of the 21st International Conference on Information Processing in Medical Imaging
Automatic hippocampus localization in histological images using PSO-based deformable models
Proceedings of the 13th annual conference companion on Genetic and evolutionary computation
Reconstruction of 3-D histology images by simultaneous deformable registration
MICCAI'11 Proceedings of the 14th international conference on Medical image computing and computer-assisted intervention - Volume Part II
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The Allen Brain Atlas project aims to bridge the divide between genomics and neuroanatomy by mapping the expression of the entire C57BL/6J mouse genome onto a high-resolution 3D anatomical reference atlas of the mouse brain. We present the image registration approach used to generate this anatomical reference from histological sections. Due to the large number of sections (525) and the presence of debris and distortions, a straightforward alignment of each slice to its neighbors fails to accurately recover the 3D shape of the brain. On the other hand, multimodality registration of histology slices to an MRI reference compromises correspondences between neighboring slices. Our approach combines the high-frequency component of slice-to-slice histology registration with the low-frequency component of the histology-to-MRI registration to produce a coarse-to-fine reconstruction that is accurate both in its global shape and in the alignment of local features.