Solving the where problem in neuroanatomy: a generative framework with learned mappings to register multimodal, incomplete data into a reference brain

We developed a generative algorithm for registration of micron resolution serial section microscopy images to the Allen reference atlas.

D. J. Tward, X. Li, B. Huo, B. C. Lee, M. Miller, and P. P. Mitra, in bioRxiv.
An optimized protocol for iDISCO+ rat brain clearing, imaging, and analysis
A. Branch, D. Tward, J. T. Vogelstein, Z. Wu, and M. Gallagher, in bioRxiv.
Diffeomorphic Upsampling of Serially Acquired Sparse 2D Cross-Sections in Cardiac MRI

We design diffeomorphic techniques to estimate unobserved data between sparsely sampled slices in cardiac MRI.

B. C. Lee, D. J. Tward, J. Wei, D. Tipre, R. G. Weiss, M. I. Miller, and S. Ardekani, in 2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).
3D Mapping of Serial Histology Sections with Anomalies Using a Novel Robust Deformable Registration Algorithm
D. Tward, X. Li, B. Huo, B. Lee, P. Mitra, and M. Miller, in Multimodal Brain Image Analysis and Mathematical Foundations of Computational Anatomy.
Estimating diffeomorphic mappings between templates and noisy data: Variance bounds on the estimated canonical volume form

We derived the Cramer Rau bound for estimating volume changes from deformable image registration, which is a lower bound on the variance of an estimator. We demonstrated its implications for image registration performance in asymmetric methods versus symmetric methods, the former generally performing better.

D. J. Tward, P. P. Mitra, and M. I. Miller, in Quarterly of applied mathematics.
Expanding the Computational Anatomy Gateway from clinical imaging to basic neuroscience research
D. Tward, A. Kolasny, F. Khan, J. Troncoso, and M. Miller, in Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning).
EM-LDDMM for 3D to 2D registration
D. Tward, and M. Miller, in BioRxiv.
Cortical thickness atrophy in the transentorhinal cortex in mild cognitive impairment
S. Kulason, D. J. Tward, T. Brown, C. S. Sicat, C. Liu, J. T. Ratnanather, L. Younes, A. Bakker, M. Gallagher, M. Albert, and others, in NeuroImage: Clinical.
A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data
R. Burns, E. Perlman, A. Baden, W. G. Roncal, B. Falk, V. Chandrashekhar, F. Collman, S. Seshamani, J. Patsolic, K. Lillaney, and others, in arXiv preprint arXiv:1804.02835.
NeuroStorm: Accelerating Brain Science Discovery in the Cloud
G. Kiar, R. J. Anderson, A. Baden, A. Badea, E. W. Bridgeford, A. Champion, V. Chandrashekhar, F. Collman, B. Duderstadt, A. C. Evans, and others, in arXiv preprint arXiv:1803.03367.

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