6. Publications

6.1. Journal Articles

  • Gray B, Smith AW, MacKenzie-Graham A, Shattuck DW, Tward DJ (2025) Validation of structure tensor analysis for orientation estimation in brain tissue microscopy. J Neurosci Methods. 423:110539. Epub 20250728. doi: 10.1016/j.jneumeth.2025.110539. PMCID: PMC12903131.

  • Joshi AA, Salloum R, Bhushan C, Wisnowski JL, Choi S, Shattuck DW, Leahy RM (2025) Robust cortical thickness estimation in the presence of partial volumes using adaptive diffusion equation. J Neurosci Methods. 2025;423:110552. Epub 20250822. doi: 10.1016/j.jneumeth.2025.110552. PMCID: PMC12707779.

  • Tward DJ, Gray BDP, Li X, Huo BX, Banerjee S, Savoia S, Mezias C, Das S, Miller MI, Mitra PP (2025) Solving the where problem and quantifying geometric variation in neuroanatomy using generative diffeomorphic mapping. Nat Commun. 16(1):10398. Epub 20251124. doi: 10.1038/s41467-025-65317-7. PMCID: PMC12645051.

6.2. Preprints

  • Banerjee S, Stam C, Tward DJ, Savoia S, Wang Y, Mitra PP (2025) Skeletonization of neuronal processes using Discrete Morse techniques from computational topology. arXiv (in review at Nature Computational Science). 2025:arXiv:2505.07754. doi: 10.48550/arXiv.2505.07754. PMCID: PMC12133097.

  • Kim Y, Hrncir H, Meyer CE, Tabbaa M, Moats RA, Levitt Pat, Harris NG, MacKenzie-Graham AJ, Shattuck DW (2024) Mouse Brain Extractor: Brain segmentation of mouse MRI using global positional encoding and SwinUNETR. bioRxiv 2024.09.03.611106; doi: 10.1101/2023.03.14.532686 PMCID: PMC11398355.

  • Kim Y, Joshi AA, Choi S, Joshi SH, Bhushan C, Varadarajan D, Haldar JP, Leahy RM, Shattuck DW (2024) BrainSuite BIDS App: Containerized Workflows for MRI Analysis. bioRxiv 2023.03.14.532686; doi: 10.1101/2023.03.14.532686 PMCID: PMC10055125.

6.3. Conference Papers and Abstracts

  • Gray B and Tward DJ (2025) A Reinforcement Learning Based 3D Neuron Tracing Method. International Symposium on Biomedical Imaging; April 14 – 17, 2025; Houston, TX, USA.

  • Fang S and Tward DJ (2025) A deep learning approach for deformable alignment of 2d microscopy images without training data applied to mouse and marmoset. Society for Neuroscience Annual Meeting; October 2025; San Diego, CA 2025.

  • Gray B and Tward DJ (2025) Automated Neuron Tracing with Reinforcement Learning and Branch Point Classification. Organization for Human Brain Mapping; June 24-28, 2025; Brisbane, Australia: Aperture Neuro.

  • Joshi A, Harris N, Leahy R, Shattuck D, (forthcoming) Brainsync Transform Improves Sensitivity and Effect-size in rs-fMRI Analysis of TBI in Rodents. Organization for Human Brain Mapping 2026 Annual Meeting; June 14-18, 2026; Bordeaux, France (forthcoming).

  • Joshi A, MacKenzie-Graham A, Leahy R, Shattuck D. (forthcoming) Functional Brain Alterations in Preclinical Alzheimer’s Disease Model. Organization for Human Brain Mapping 2026 Annual Meeting; June 14-18, 2026; Bordeaux, France.