Molecular Computational Anatomy: Unifying the Particle to Tissue Continuum via Measure Representations of the Brain

We formalized the mathematical representation of imaging data features from the molecular to anatomical scales, and showed analysis for several examples including deposition of pathology in Alzheimer's disease.

M. Miller, D. J. Tward, and A. Trouv{\'e}, in BME Frontiers.
3D printing hippocampi to depict atrophy-related Alzheimer's biomarkers

This work discusses the challenges of 3D printing hippocampi from annotated post mortem MRI. This work will help visualize subtle changes to complex anatomy during the disease.

F. Xu, E. Xu, J. Troncoso, M. Albert, D. J. Tward, and M. Miller, in Proceedings of the 2020 Summer Biomechanics, Bioengineering, and Biotransport Conference.
Diffeomorphic registration with intensity transformation and missing data: Application to 3D digital pathology of Alzheimer's disease

We develop methods for accurate image registration between images of different modalities, possibly in the presence of damaged or missing tissue. We use this approach to build the first 3D reconstruction of tau tangle pathology in the medial temporal lobe for an individual who died of Alzheimer's disease.

D. Tward, T. Brown, Y. Kageyama, J. Patel, Z. Hou, S. Mori, M. Albert, J. Troncoso, and M. Miller, in Frontiers in neuroscience.
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.
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.
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.
P3-386: CORTICAL THICKNESS ATROPHY IN THE TRANSENTORHINAL CORTEX IN MILD COGNITIVE IMPAIRMENT
S. Kulason, D. J. Tward, C. S. Sicat, A. Bakker, M. Gallagher, M. S. Albert, and M. Miller, in Alzheimer's \& Dementia.
Quantification OF 3D tangle distribution in medial temporal lobe using multimodal image registration and convolutional neural networks
D. J. Tward, T. Brown, J. Patel, Y. Kageyama, S. Mori, J. C. Troncoso, and M. Miller, in Alzheimer's \& Dementia: The Journal of the Alzheimer's Association.
A community-developed open-source computational ecosystem for big neuro data

A series of open source and web accessible resources for studying neuroscience related data.

J. Vogelstein, E. Perlman, B. Falk, A. Baden, W. G. Roncal, V. Chandreshekhar, F. Collman, S. Seshamani, J. Patsolic, K. Lillaney, M. Kazhdan, R. J. Hider, D. Pryor, J. Matelsky, A. Crow, M. Write, S. Smith, T. Gion, P. Manavalan, B. Wester, M. Chevillet, E. Trautman, K. Khairy, E. Bridgeford, D. Kleissas, D. J. Tward, M. Miller, R. Vogelstein, K. Deisseroth, and R. Burns, in Nature methods.

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