Abstract
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.
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References
Ng, L., Hawrylycz, M., Haynor, D.: Automated high-throughput registration for localizing 3D mouse brain gene expression using ITK. Insight Jounral 1 (2005) (Special Issue on ISC/NA-MIC/MICCAI Workshop on Open-Source Software)
Ourselin, S., Roche, A., Subsol, G., Pennec, X., Ayache, N.: Reconstructing a 3D structure from serial histological sections. Image and Vision Computing 19(1), 25–31 (2001)
MacKenzie-Graham, A., Lee, E.-F., Dinov, I.D., Bota, M., Shattuck, D.W., Ruffins, S., Yuan, H., Konstantinidis, F., Pitiot, A., Ding, Y., Hu, G., Jacobs, R.E., Toga, A.W.: A multimodal, multidimensional atlas of the C57BL/6J mouse brain. J. Anat. 204(2), 93–102 (2004)
Ourselin, S., Bardinet, E., Dormont, D., Malandain, G., Roche, A., Ayache, N., Tande, D., Parain, K., Yelnik, J.: Fusion of histological sections and mr images: Towards the construction of an atlas of the human basal ganglia. In: Niessen, W.J., Viergever, M.A. (eds.) MICCAI 2001. LNCS, vol. 2208, pp. 743–751. Springer, Heidelberg (2001)
Wirtz, S., Papenberg, N., Fischer, B., Schmitt, O.: Robust and staining-invariant elastic registration of a series of images from histologic slices. In: Fitzpatrick, J.M., Reinhardt, J.M. (eds.) Medical Imaging 2005: Image Processing. SPIE, vol. 5747, pp. 1256–1262 (2005)
Sidman, R.L., Kosaras, B., Misra, B., Senft, S.: High resolution mouse brain atlas (2005), http://www.hms.harvard.edu/research/brain
Jacobs, M.A., Windham, J.P., Soltanian-Zadeh, H., Peck, D.J., Knight, R.A.: Registration and warping of magnetic resonance images to histological sections. Med. Phys. 26(8), 1568–1578 (1999)
Zhu, S.C., Yuille, A.: Region competition: Unifying snakes, region growing, and bayes/mdl for multiband image segmentation. IEEE Trans. Pattern Anal. Mach. Intell. 18(9), 884–900 (1996)
Ibanez, L., Schroeder, W., Ng, L., Cates, J.: The ITK Software Guide. Kitware, Inc. (2003)
Mattes, D., Haynor, D.R., Vesselle, H., Lewellyn, T.K., Eubank, W.: Nonrigid multimodality image registration. In: Sonka, M., Hanson, K.M. (eds.) Medical Imaging 2001: Image Processing, vol. 4322, pp. 1609–1620. SPIE (2001)
Avants, B., Schoenemann, P.T., Gee, J.C.: Lagrangian frame diffeomorphic image registration: Morphometric comparison of human and chimpanzee cortex. Medical Image Analysis (in press, 2005)
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Yushkevich, P.A. et al. (2006). 3D Mouse Brain Reconstruction from Histology Using a Coarse-to-Fine Approach. In: Pluim, J.P.W., Likar, B., Gerritsen, F.A. (eds) Biomedical Image Registration. WBIR 2006. Lecture Notes in Computer Science, vol 4057. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11784012_28
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DOI: https://doi.org/10.1007/11784012_28
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-35648-6
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