@article{beyondlumir,
  title={Beyond the LUMIR challenge: The pathway to foundational registration models},
  author={Chen, Junyu and Wei, Shuwen and Honkamaa, Joel and Marttinen, Pekka and Zhang, Hang and Liu, Min and Zhou, Yichao and Tan, Zuopeng and Wang, Zhuoyuan and Wang, Yi and others},
  journal={arXiv preprint arXiv:2505.24160},
  year={2025}
}

@article{ants,
  title={Advanced normalization tools (ANTS)},
  author={Avants, Brian B and Tustison, Nick and Song, Gang and others},
  journal={Insight j},
  volume={2},
  number={365},
  pages={1--35},
  year={2009}
}

@online{antsgithub,
  title = {ANTsX: Advanced Normalization Tools (ANTs)},
  author = {{ANTsX}},
  url = {https://github.com/ANTsX/ANTs},
  note = {GitHub repository},
}

@article{ashburner2007fast,
  title={A fast diffeomorphic image registration algorithm},
  author={Ashburner, John},
  journal={Neuroimage},
  volume={38},
  number={1},
  pages={95--113},
  year={2007},
  publisher={Elsevier}
}


@article{avants2004geodesic,
  title={Geodesic estimation for large deformation anatomical shape averaging and interpolation},
  author={Avants, Brian and Gee, James C},
  journal={Neuroimage},
  volume={23},
  pages={S139--S150},
  year={2004},
  publisher={Elsevier}
}

@article{avants2008symmetric,
  title={Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain},
  author={Avants, Brian B and Epstein, Charles L and Grossman, Murray and Gee, James C},
  journal={Medical image analysis},
  volume={12},
  number={1},
  pages={26--41},
  year={2008},
  publisher={Elsevier}
}

@article{bai2020population,
  title={A population-based phenome-wide association study of cardiac and aortic structure and function},
  author={Bai, Wenjia and Suzuki, Hideaki and Huang, Jian and Francis, Catherine and Wang, Shuo and Tarroni, Giacomo and Guitton, Florian and Aung, Nay and Fung, Kenneth and Petersen, Steffen E and others},
  journal={Nature medicine},
  volume={26},
  number={10},
  pages={1654--1662},
  year={2020},
  publisher={Nature Publishing Group US New York}
}

@inproceedings{bai2022deep,
  title={Deep equilibrium optical flow estimation},
  author={Bai, Shaojie and Geng, Zhengyang and Savani, Yash and Kolter, J Zico},
  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
  pages={620--630},
  year={2022}
}

@article{bajcsy1983computerized,
  title={A computerized system for the elastic matching of deformed radiographic images to idealized atlas images.},
  author={Bajcsy, Ruzena and Lieberson, Robert and Reivich, Martin},
  journal={Journal of computer assisted tomography},
  volume={7},
  number={4},
  pages={618--625},
  year={1983}
}

@article{balakrishnan2019voxelmorph,
  title={VoxelMorph: a learning framework for deformable medical image registration},
  author={Balakrishnan, Guha and Zhao, Amy and Sabuncu, Mert R and Guttag, John and Dalca, Adrian V},
  journal={IEEE transactions on medical imaging},
  volume={38},
  number={8},
  pages={1788--1800},
  year={2019},
  publisher={IEEE}
}

@article{balta20203d,
  title={3D registration and integrated segmentation framework for heterogeneous unmanned robotic systems},
  author={Balta, Haris and Velagic, Jasmin and Beglerovic, Halil and De Cubber, Geert and Siciliano, Bruno},
  journal={Remote Sensing},
  volume={12},
  number={10},
  pages={1608},
  year={2020},
  publisher={MDPI}
}

@book{banyaga2013structure,
  title={The structure of classical diffeomorphism groups},
  author={Banyaga, Augustin},
  volume={400},
  year={2013},
  publisher={Springer Science \& Business Media}
}

@article{becigneul2018riemannian,
  title={Riemannian adaptive optimization methods},
  author={B{\'e}cigneul, Gary and Ganea, Octavian-Eugen},
  journal={arXiv preprint arXiv:1810.00760},
  year={2018}
}

@article{beg2005computing,
  title={Computing large deformation metric mappings via geodesic flows of diffeomorphisms},
  author={Beg, M Faisal and Miller, Michael I and Trouv{\'e}, Alain and Younes, Laurent},
  journal={International journal of computer vision},
  volume={61},
  pages={139--157},
  year={2005},
  publisher={Springer}
}

@article{bentoutou2005automatic,
  title={An automatic image registration for applications in remote sensing},
  author={Bentoutou, Youcef and Taleb, Nasreddine and Kpalma, Kidiyo and Ronsin, Joseph},
  journal={IEEE transactions on geoscience and remote sensing},
  volume={43},
  number={9},
  pages={2127--2137},
  year={2005},
  publisher={IEEE}
}

@article{beroiz2020astroalign,
  title={Astroalign: A Python module for astronomical image registration},
  author={Beroiz, Martin and Cabral, Juan B and Sanchez, Bruno},
  journal={Astronomy and Computing},
  volume={32},
  pages={100384},
  year={2020},
  publisher={Elsevier}
}

@misc{bigstream,
  author = {Fleishman, Greg M.},
  title = {Bigstream},
  year = {2023},
  note = {GitHub repository},
  howpublished = {\url{https://github.com/GFleishman/bigstream}}
}

@misc{bloch2023stochastic,
    author = {Andrea Bloch},
    title = {Stochastic Gradient Descent on Riemannian Manifolds},
    url = {https://andbloch.github.io/Stochastic-Gradient-Descent-on-Riemannian-Manifolds/},
}

@article{bonnabel2013stochastic,
  title={Stochastic gradient descent on Riemannian manifolds},
  author={Bonnabel, Silvere},
  journal={IEEE Transactions on Automatic Control},
  volume={58},
  number={9},
  pages={2217--2229},
  year={2013},
  publisher={IEEE}
}

@article{borovec2020anhir,
  title={ANHIR: automatic non-rigid histological image registration challenge},
  author={Borovec, Ji{\v{r}}{\'\i} and Kybic, Jan and Arganda-Carreras, Ignacio and Sorokin, Dmitry V and Bueno, Gloria and Khvostikov, Alexander V and Bakas, Spyridon and Eric, I and Chang, Chao and Heldmann, Stefan and others},
  journal={IEEE transactions on medical imaging},
  volume={39},
  number={10},
  pages={3042--3052},
  year={2020},
  publisher={IEEE}
}

@book{brunelli2009template,
  title={Template matching techniques in computer vision: theory and practice},
  author={Brunelli, Roberto},
  year={2009},
  publisher={John Wiley \& Sons}
}

@book{carrivick2016structure,
  title={Structure from Motion in the Geosciences},
  author={Carrivick, Jonathan L and Smith, Mark W and Quincey, Duncan J},
  year={2016},
  publisher={John Wiley \& Sons}
}

@article{chen2015expansion,
  title={Expansion microscopy},
  author={Chen, Fei and Tillberg, Paul W and Boyden, Edward S},
  journal={Science},
  volume={347},
  number={6221},
  pages={543--548},
  year={2015},
  publisher={American Association for the Advancement of Science}
}

@article{chen2015sirf,
  title={SIRF: Simultaneous satellite image registration and fusion in a unified framework},
  author={Chen, Chen and Li, Yeqing and Liu, Wei and Huang, Junzhou},
  journal={IEEE Transactions on Image Processing},
  volume={24},
  number={11},
  pages={4213--4224},
  year={2015},
  publisher={IEEE}
}

@inproceedings{chen2016full,
  title={Full flow: Optical flow estimation by global optimization over regular grids},
  author={Chen, Qifeng and Koltun, Vladlen},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition},
  pages={4706--4714},
  year={2016}
}

@article{chen2016nanoscale,
  title={Nanoscale imaging of RNA with expansion microscopy},
  author={Chen, Fei and Wassie, Asmamaw T and Cote, Allison J and Sinha, Anubhav and Alon, Shahar and Asano, Shoh and Daugharthy, Evan R and Chang, Jae-Byum and Marblestone, Adam and Church, George M and others},
  journal={Nature methods},
  volume={13},
  number={8},
  pages={679--684},
  year={2016},
  publisher={Nature Publishing Group US New York}
}

@article{chen2020functional,
  title={Functional near-infrared spectroscopy and its clinical application in the field of neuroscience: advances and future directions},
  author={Chen, Wei-Liang and Wagner, Julie and Heugel, Nicholas and Sugar, Jeffrey and Lee, Yu-Wen and Conant, Lisa and Malloy, Marsha and Heffernan, Joseph and Quirk, Brendan and Zinos, Anthony and others},
  journal={Frontiers in neuroscience},
  volume={14},
  pages={724},
  year={2020},
  publisher={Frontiers Media SA}
}

@article{chen2022transmorph,
  title={Transmorph: Transformer for unsupervised medical image registration},
  author={Chen, Junyu and Frey, Eric C and He, Yufan and Segars, William P and Li, Ye and Du, Yong},
  journal={Medical image analysis},
  volume={82},
  pages={102615},
  year={2022},
  publisher={Elsevier}
}

@article{chevalley1951theorie,
  title={Th{\'e}orie des groupes de Lie},
  author={Chevalley, Claude},
  journal={(No Title)},
  year={1951}
}

@article{miller2006geodesic,
  title={Geodesic shooting for computational anatomy},
  author={Miller, Michael I and Trouv{\'e}, Alain and Younes, Laurent},
  journal={Journal of mathematical imaging and vision},
  volume={24},
  number={2},
  pages={209--228},
  year={2006},
  publisher={Springer}
}

@article{christensen1996deformable,
  title={Deformable templates using large deformation kinematics},
  author={Christensen, Gary E and Rabbitt, Richard D and Miller, Michael I},
  journal={IEEE transactions on image processing},
  volume={5},
  number={10},
  pages={1435--1447},
  year={1996},
  publisher={IEEE}
}

@article{christensen1997volumetric,
  title={Volumetric transformation of brain anatomy},
  author={Christensen, Gary E and Joshi, Sarang C and Miller, Michael I},
  journal={IEEE transactions on medical imaging},
  volume={16},
  number={6},
  pages={864--877},
  year={1997},
  publisher={IEEE}
}

@article{christensen2001consistent,
  title={Consistent image registration},
  author={Christensen, Gary E and Johnson, Hans J},
  journal={IEEE transactions on medical imaging},
  volume={20},
  number={7},
  pages={568--582},
  year={2001},
  publisher={IEEE}
}

@incollection{clarenz2006computational,
  title={Computational methods for nonlinear image registration},
  author={Clarenz, Ulrich and Droske, Marc and Henn, Stefan and Rumpf, Martin and Witsch, Kristian},
  booktitle={Mathematical Models for Registration and Applications to Medical Imaging},
  pages={81--101},
  year={2006},
  publisher={Springer}
}

@inproceedings{collet2009object,
  title={Object recognition and full pose registration from a single image for robotic manipulation},
  author={Collet, Alvaro and Berenson, Dmitry and Srinivasa, Siddhartha S and Ferguson, Dave},
  booktitle={2009 IEEE International Conference on Robotics and Automation},
  pages={48--55},
  year={2009},
  organization={IEEE}
}

@article{convexadam,
  title={ConvexAdam: Self-Configuring Dual-Optimisation-Based 3D Multitask Medical Image Registration},
  author={Siebert, Hanna and Gro{\ss}br{\"o}hmer, Christoph and Hansen, Lasse and Heinrich, Mattias P},
  journal={IEEE Transactions on Medical Imaging},
  year={2024},
  publisher={IEEE}
}

@article{d2003viscous,
  title={A viscous fluid model for multimodal non-rigid image registration using mutual information},
  author={D'agostino, Emiliano and Maes, Frederik and Vandermeulen, Dirk and Suetens, Paul},
  journal={Medical image analysis},
  volume={7},
  number={4},
  pages={565--575},
  year={2003},
  publisher={Elsevier}
}

@article{dice,
 ISSN = {00129658, 19399170},
 URL = {http://www.jstor.org/stable/1932409},
 author = {Lee R. Dice},
 journal = {Ecology},
 number = {3},
 pages = {297--302},
 publisher = {Ecological Society of America},
 title = {Measures of the Amount of Ecologic Association Between Species},
 urldate = {2023-09-04},
 volume = {26},
 year = {1945}
}

@article{duchi2011adaptive,
  title={Adaptive subgradient methods for online learning and stochastic optimization.},
  author={Duchi, John and Hazan, Elad and Singer, Yoram},
  journal={Journal of machine learning research},
  volume={12},
  number={7},
  year={2011}
}

@inproceedings{evans19933d,
  title={3D statistical neuroanatomical models from 305 MRI volumes},
  author={Evans, Alan C and Collins, D Louis and Mills, SR and Brown, Edward D and Kelly, Ryan L and Peters, Terry M},
  booktitle={1993 IEEE conference record nuclear science symposium and medical imaging conference},
  pages={1813--1817},
  year={1993},
  organization={IEEE}
}

@misc{fireantsissue1,
  author={GitHub},
  title={FireANTS Github issues},
  year={2024},
  note = {GitHub repository issues},
  howpublished = {\url{https://github.com/rohitrango/FireANTs/issues/15}},
}

@article{fireants,
  title={Fireants: Adaptive riemannian optimization for multi-scale diffeomorphic matching},
  author={Jena, Rohit and Chaudhari, Pratik and Gee, James C},
  journal={arXiv preprint arXiv:2404.01249},
  year={2024}
}


@misc{fireantsissue2,
  author={GitHub},
  title={FireANTS Github issues},
  year={2024},
  note = {GitHub repository issues},
  howpublished = {\url{https://github.com/rohitrango/FireANTs/pull/10}},
}

@article{fmost1,
  title={High-throughput dual-colour precision imaging for brain-wide connectome with cytoarchitectonic landmarks at the cellular level},
  author={Gong, Hui and Xu, Dongli and Yuan, Jing and Li, Xiangning and Guo, Congdi and Peng, Jie and Li, Yuxin and Schwarz, Lindsay A and Li, Anan and Hu, Bihe and others},
  journal={Nature communications},
  volume={7},
  number={1},
  pages={12142},
  year={2016},
  publisher={Nature Publishing Group UK London}
}

@article{fortun2015optical,
  title={Optical flow modeling and computation: A survey},
  author={Fortun, Denis and Bouthemy, Patrick and Kervrann, Charles},
  journal={Computer Vision and Image Understanding},
  volume={134},
  pages={1--21},
  year={2015},
  publisher={Elsevier}
}

@article{fu2020lungregnet,
  title={LungRegNet: an unsupervised deformable image registration method for 4D-CT lung},
  author={Fu, Yabo and Lei, Yang and Wang, Tonghe and Higgins, Kristin and Bradley, Jeffrey D and Curran, Walter J and Liu, Tian and Yang, Xiaofeng},
  journal={Medical physics},
  volume={47},
  number={4},
  pages={1763--1774},
  year={2020},
  publisher={Wiley Online Library}
}

@incollection{whitney1992analytic,
  title={Analytic extensions of differentiable functions defined in closed sets},
  author={Whitney, Hassler},
  booktitle={Hassler Whitney Collected Papers},
  pages={228--254},
  year={1992},
  publisher={Springer}
}

@incollection{lorenz2017deterministic,
  title={Deterministic nonperiodic flow 1},
  author={Lorenz, Edward N},
  booktitle={Universality in Chaos, 2nd edition},
  pages={367--378},
  year={2017},
  publisher={Routledge}
}

@article{zhu2008sensitivity,
  title={The sensitivity of the exponential of an essentially nonnegative matrix},
  author={Zhu, Weifang and Xue, Jungong and Gao, Weiguo},
  journal={Journal of Computational Mathematics},
  pages={250--258},
  year={2008},
  publisher={JSTOR}
}

@article{leonov2015differences,
  title={On differences and similarities in the analysis of Lorenz, Chen, and Lu systems},
  author={Leonov, Gennady A and Kuznetsov, Nikolay V},
  journal={Applied Mathematics and Computation},
  volume={256},
  pages={334--343},
  year={2015},
  publisher={Elsevier}
}

@article{rossler1976equation,
  title={An equation for continuous chaos},
  author={R{\"o}ssler, Otto E},
  journal={Physics Letters A},
  volume={57},
  number={5},
  pages={397--398},
  year={1976},
  publisher={Elsevier}
}

@article{ebin2006singularities,
  title={Singularities of the exponential map on the volume-preserving diffeomorphism group},
  author={Ebin, DAVID G and Misio? ek, G and Preston, STEPHEN C},
  journal={Geometric and Functional Analysis},
  volume={16},
  number={4},
  pages={850--868},
  year={2006},
  publisher={Basel; Boston: Birkhauser, c1991-}
}

@article{van1977sensitivity,
  title={The sensitivity of the matrix exponential},
  author={Van Loan, Charles},
  journal={SIAM Journal on Numerical Analysis},
  volume={14},
  number={6},
  pages={971--981},
  year={1977},
  publisher={SIAM}
}

@book{milnor1984,
title={Remarks on infinite-dimensional Lie groups},
publisher={North-Holland.},
author={Milnor, J.},
year={1984},
pages={p. 1007–1057.}
}

@article{Hadamard1906,
author = {Hadamard},
journal = {Bulletin de la Société Mathématique de France},
language = {fre},
pages = {71-84},
publisher = {Société mathématique de France},
title = {Sur les transformations ponctuelles},
url = {http://eudml.org/doc/86165},
volume = {34},
year = {1906},
}

@article{ultracortex,
  author = {Lucas Mahler and Julius Steiglechner and Benjamin Bender and Tobias Lindig and Dana Ramadan and Jonas Bause and Florian Birk and Rahel Heule and Edyta Charyasz and Michael Erb and Vinod Jangir Kumar and Gisela E Hagberg and Pascal Martin and Gabriele Lohmann and Klaus Scheffler},
  title = {"UltraCortex: Submillimeter Ultra-High Field 9.4T Brain MR Image Collection and Manual Cortical Segmentations"},
  year = {2024},
  doi = {doi:10.18112/openneuro.ds005216.v1.1.0},
  publisher = {OpenNeuro}
}

@article{wu2024neural,
  title={Neural ordinary differential equation based sequential image registration for dynamic characterization},
  author={Wu, Yifan and Dong, Mengjin and Jena, Rohit and Qin, Chen and Gee, James C},
  journal={arXiv preprint arXiv:2404.02106},
  year={2024}
}

@inproceedings{wu2022nodeo,
  title={Nodeo: A neural ordinary differential equation based optimization framework for deformable image registration},
  author={Wu, Yifan and Jiahao, Tom Z and Wang, Jiancong and Yushkevich, Paul A and Hsieh, M Ani and Gee, James C},
  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
  pages={20804--20813},
  year={2022}
}

@inproceedings{alegro2016multimodal,
  title={Multimodal whole brain registration: MRI and high resolution histology},
  author={Alegro, Maryana and Amaro-Jr, Edson and Loring, Burlen and Heinsen, Helmut and Alho, Eduardo and Zollei, Lilla and Ushizima, Daniela and Grinberg, Lea T},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition workshops},
  pages={194--202},
  year={2016}
}

@article{gambarotto2019imaging,
  title={Imaging cellular ultrastructures using expansion microscopy (U-ExM)},
  author={Gambarotto, Davide and Zwettler, Fabian U and Le Guennec, Maeva and Schmidt-Cernohorska, Marketa and Fortun, Denis and Borgers, Susanne and Heine, J{\"o}rn and Schloetel, Jan-Gero and Reuss, Matthias and Unser, Michael and others},
  journal={Nature methods},
  volume={16},
  number={1},
  pages={71--74},
  year={2019},
  publisher={Nature Publishing Group US New York}
}

@article{fletcher2004principal,
  title={Principal geodesic analysis for the study of nonlinear statistics of shape},
  author={Fletcher, P Thomas and Lu, Conglin and Pizer, Stephen M and Joshi, Sarang},
  journal={IEEE transactions on medical imaging},
  volume={23},
  number={8},
  pages={995--1005},
  year={2004},
  publisher={IEEE}
}

@inproceedings{gee1993elastically,
  title={Elastically deforming a three-dimensional atlas to match anatomical brain images},
  author={Gee, James C and Reivich, Martin and Bajcsy, Ruzena},
  year={1993}
}

@article{gee1998elastic,
  title={Elastic matching: Continuum mechanical and probabilistic analysis},
  author={Gee, James C and Bajcsy, Ruzena K},
  journal={Brain warping},
  volume={2},
  pages={183--197},
  year={1998},
  publisher={Citeseer}
}

@misc{geoopt2020kochurov,
    title={Geoopt: Riemannian Optimization in PyTorch},
    author={Max Kochurov and Rasul Karimov and Serge Kozlukov},
    year={2020},
    eprint={2005.02819},
    archivePrefix={arXiv},
    primaryClass={cs.CG}
}

@article{gholipour2007brain,
  title={Brain functional localization: a survey of image registration techniques},
  author={Gholipour, Ali and Kehtarnavaz, Nasser and Briggs, Richard and Devous, Michael and Gopinath, Kaundinya},
  journal={IEEE transactions on medical imaging},
  volume={26},
  number={4},
  pages={427--451},
  year={2007},
  publisher={IEEE}
}

@article{nbest,
  title={nBEST: Deep-learning-based non-human primates Brain Extraction and Segmentation Toolbox across ages, sites and species},
  author={Zhong, Tao and Wu, Xueyang and Liang, Shujun and Ning, Zhenyuan and Wang, Li and Niu, Yuyu and Yang, Shihua and Kang, Zhuang and Feng, Qianjin and Li, Gang and others},
  journal={NeuroImage},
  volume={295},
  pages={120652},
  year={2024},
  publisher={Elsevier}
}

@inproceedings{glocker2008optical,
  title={Optical flow estimation with uncertainties through dynamic MRFs},
  author={Glocker, Ben and Paragios, Nikos and Komodakis, Nikos and Tziritas, Georgios and Navab, Nassir},
  booktitle={2008 IEEE Conference on Computer Vision and Pattern Recognition},
  pages={1--8},
  year={2008},
  organization={IEEE}
}

@article{goubran2019multimodal,
  title={Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI},
  author={Goubran, Maged and Leuze, Christoph and Hsueh, Brian and Aswendt, Markus and Ye, Li and Tian, Qiyuan and Cheng, Michelle Y and Crow, Ailey and Steinberg, Gary K and McNab, Jennifer A and others},
  journal={Nature communications},
  volume={10},
  number={1},
  pages={5504},
  year={2019},
  publisher={Nature Publishing Group UK London}
}

@article{grenander1998computational,
  title={Computational anatomy: An emerging discipline},
  author={Grenander, Ulf and Miller, Michael I},
  journal={Quarterly of applied mathematics},
  volume={56},
  number={4},
  pages={617--694},
  year={1998}
}

@book{grinfeld2013introduction,
  title={Introduction to tensor analysis and the calculus of moving surfaces},
  author={Grinfeld, Pavel},
  year={2013},
  publisher={Springer}
}

@article{haber2004numerical,
  title={Numerical methods for volume preserving image registration},
  author={Haber, Eldad and Modersitzki, Jan},
  journal={Inverse problems},
  volume={20},
  number={5},
  pages={1621},
  year={2004},
  publisher={IOP Publishing}
}

@article{hall2000elementary,
  title={An elementary introduction to groups and representations},
  author={Hall, Brian C},
  journal={arXiv preprint math-ph/0005032},
  year={2000}
}

@book{hall2013lie,
  title={Lie groups, Lie algebras, and representations},
  author={Hall, Brian C and Hall, Brian C},
  year={2013},
  publisher={Springer}
}

@article{hamid2022stereo,
  title={Stereo matching algorithm based on deep learning: A survey},
  author={Hamid, Mohd Saad and Abd Manap, NurulFajar and Hamzah, Rostam Affendi and Kadmin, Ahmad Fauzan},
  journal={Journal of King Saud University-Computer and Information Sciences},
  volume={34},
  number={5},
  pages={1663--1673},
  year={2022},
  publisher={Elsevier}
}

@article{hand2009automated,
  title={Automated tracking of migrating cells in phase-contrast video microscopy sequences using image registration},
  author={Hand, AJ and Sun, Tao and Barber, DC and Hose, DR and MacNeil, Sheila},
  journal={Journal of microscopy},
  volume={234},
  number={1},
  pages={62--79},
  year={2009},
  publisher={Wiley Online Library}
}

@article{synthseg,
  title={SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining},
  author={Billot, Benjamin and Greve, Douglas N and Puonti, Oula and Thielscher, Axel and Van Leemput, Koen and Fischl, Bruce and Dalca, Adrian V and Iglesias, Juan Eugenio and others},
  journal={Medical image analysis},
  volume={86},
  pages={102789},
  year={2023},
  publisher={Elsevier}
}

@inproceedings{zhang2015finite,
  title={Finite-dimensional lie algebras for fast diffeomorphic image registration},
  author={Zhang, Miaomiao and Fletcher, P Thomas},
  booktitle={International conference on information processing in medical imaging},
  pages={249--260},
  year={2015},
  organization={Springer}
}

@article{anatomix,
  title={Learning general-purpose biomedical volume representations using randomized synthesis},
  author={Dey, Neel and Billot, Benjamin and Wong, Hallee E and Wang, Clinton J and Ren, Mengwei and Grant, P Ellen and Dalca, Adrian V and Golland, Polina},
  journal={arXiv preprint arXiv:2411.02372},
  year={2024}
}

@misc{ultrascaleplaybook,
  title={The Ultra-Scale Playbook: Training LLMs on GPU Clusters},
  author={Nouamane, Tazi and Ferdinand, Mom and Haojun, Zhao and Phuc, Nguyen and Mohamed, Mekkouri and Leandro, Werra and Thomas, Wolf},
  year={2025},
}

@article{polypose,
  title={PolyPose: Localizing Deformable Anatomy in 3D from Sparse 2D X-ray Images using Polyrigid Transforms},
  author={Gopalakrishnan, Vivek and Dey, Neel and Golland, Polina},
  journal={ArXiv},
  pages={arXiv--2505},
  year={2025}
}

@article{bailiang,
  title={Disentangling Progress in Medical Image Registration: Beyond Trend-Driven Architectures towards Domain-Specific Strategies},
  author={Jian, Bailiang and Pan, Jiazhen and Jena, Rohit and Ghahremani, Morteza and Li, Hongwei Bran and Rueckert, Daniel and Wachinger, Christian and Wiestler, Benedikt},
  journal={arXiv preprint arXiv:2512.01913},
  year={2025}
}

@article{dio,
  title={Deep implicit optimization enables robust learnable features for deformable image registration},
  author={Jena, Rohit and Chaudhari, Pratik and Gee, James C},
  journal={Medical Image Analysis},
  pages={103577},
  year={2025},
  publisher={Elsevier}
}

@article{reducingactivation,
  title={Reducing activation recomputation in large transformer models},
  author={Korthikanti, Vijay Anand and Casper, Jared and Lym, Sangkug and McAfee, Lawrence and Andersch, Michael and Shoeybi, Mohammad and Catanzaro, Bryan},
  journal={Proceedings of Machine Learning and Systems},
  volume={5},
  pages={341--353},
  year={2023}
}

@article{hering2022learn2reg,
  title={Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning},
  author={Hering, Alessa and Hansen, Lasse and Mok, Tony CW and Chung, Albert CS and Siebert, Hanna and H{\"a}ger, Stephanie and Lange, Annkristin and Kuckertz, Sven and Heldmann, Stefan and Shao, Wei and others},
  journal={IEEE Transactions on Medical Imaging},
  volume={42},
  number={3},
  pages={697--712},
  year={2022},
  publisher={IEEE}
}

@article{hillman2019light,
  title={Light-sheet microscopy in neuroscience},
  author={Hillman, Elizabeth MC and Voleti, Venkatakaushik and Li, Wenze and Yu, Hang},
  journal={Annual review of neuroscience},
  volume={42},
  pages={295--313},
  year={2019},
  publisher={Annual Reviews}
}

@article{hoffmann2021synthmorph,
  title={SynthMorph: learning contrast-invariant registration without acquired images},
  author={Hoffmann, Malte and Billot, Benjamin and Greve, Douglas N and Iglesias, Juan Eugenio and Fischl, Bruce and Dalca, Adrian V},
  journal={IEEE transactions on medical imaging},
  volume={41},
  number={3},
  pages={543--558},
  year={2021},
  publisher={IEEE}
}

@inproceedings{hypermorph,
  title={Hypermorph: Amortized hyperparameter learning for image registration},
  author={Hoopes, Andrew and Hoffmann, Malte and Fischl, Bruce and Guttag, John and Dalca, Adrian V},
  booktitle={International conference on information processing in medical imaging},
  pages={3--17},
  year={2021},
  organization={Springer}
}

@inproceedings{im2grid,
  title={Coordinate translator for learning deformable medical image registration},
  author={Liu, Yihao and Zuo, Lianrui and Han, Shuo and Xue, Yuan and Prince, Jerry L and Carass, Aaron},
  booktitle={International workshop on multiscale multimodal medical imaging},
  pages={98--109},
  year={2022},
  organization={Springer}
}

@misc{itkguide,
  title={The ITK software guide},
  author={Ibanez, Luis and Schroeder, Will and Ng, Lydia and Cates, Josh and others},
  year={2003},
  publisher={Kitware, Incorporated Clifton Park, New York}
}

@article{joshi2000landmark,
  title={Landmark matching via large deformation diffeomorphisms},
  author={Joshi, Sarang C and Miller, Michael I},
  journal={IEEE transactions on image processing},
  volume={9},
  number={8},
  pages={1357--1370},
  year={2000},
  publisher={IEEE}
}

@article{kingma2014adam,
  title={Adam: A method for stochastic optimization},
  author={Kingma, Diederik P and Ba, Jimmy},
  journal={arXiv preprint arXiv:1412.6980},
  year={2014}
}

@article{klein2009evaluation,
  title={Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration},
  author={Klein, Arno and Andersson, Jesper and Ardekani, Babak A and Ashburner, John and Avants, Brian and Chiang, Ming-Chang and Christensen, Gary E and Collins, D Louis and Gee, James and Hellier, Pierre and others},
  journal={Neuroimage},
  volume={46},
  number={3},
  pages={786--802},
  year={2009},
  publisher={Elsevier}
}

@article{azba,
  title={A 3D adult zebrafish brain atlas (AZBA) for the digital age},
  author={Kenney, Justin W and Steadman, Patrick E and Young, Olivia and Shi, Meng Ting and Polanco, Maris and Dubaishi, Saba and Covert, Kristopher and Mueller, Thomas and Frankland, Paul W},
  journal={Elife},
  volume={10},
  pages={e69988},
  year={2021},
  publisher={eLife Sciences Publications, Ltd}
}

@article{kleven2023waxholm,
  title={Waxholm Space atlas of the rat brain: a 3D atlas supporting data analysis and integration},
  author={Kleven, Heidi and Bjerke, Ingvild E and Clasc{\'a}, Francisco and Groenewegen, Henk J and Bjaalie, Jan G and Leergaard, Trygve B},
  journal={Nature methods},
  volume={20},
  number={11},
  pages={1822--1829},
  year={2023},
  publisher={Nature Publishing Group US New York}
}

@article{krebs2019learning,
  title={Learning a probabilistic model for diffeomorphic registration},
  author={Krebs, Julian and Delingette, Herv{\'e} and Mailh{\'e}, Boris and Ayache, Nicholas and Mansi, Tommaso},
  journal={IEEE transactions on medical imaging},
  volume={38},
  number={9},
  pages={2165--2176},
  year={2019},
  publisher={IEEE}
}

@misc{hastie2009elements,
  title={The elements of statistical learning: data mining, inference, and prediction},
  author={Hastie, Trevor},
  year={2009},
  publisher={Springer}
}

@article{vapnik1998statistical,
  title={Statistical learning theory},
  author={Vapnik, Vladimir Naumovich},
  journal={(No Title)},
  year={1998}
}

@article{beery2020iwildcam,
    title={The iWildCam 2020 Competition Dataset},
    author={Beery, Sara and Cole, Elijah and Gjoka, Arvi},
    journal={arXiv preprint arXiv:2004.10340},
    year={2020}
}

@article{zech2018variable,
  title={Variable generalization performance of a deep learning model to detect pneumonia in chest radiographs: a cross-sectional study},
  author={Zech, John R and Badgeley, Marcus A and Liu, Manway and Costa, Anthony B and Titano, Joseph J and Oermann, Eric Karl},
  journal={PLoS medicine},
  volume={15},
  number={11},
  pages={e1002683},
  year={2018},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{albadawy2018deep,
  title={Deep learning for segmentation of brain tumors: Impact of cross-institutional training and testing},
  author={AlBadawy, Ehab A and Saha, Ashirbani and Mazurowski, Maciej A},
  journal={Medical physics},
  volume={45},
  number={3},
  pages={1150--1158},
  year={2018},
  publisher={Wiley Online Library}
}

@article{malinin2018predictive,
  title={Predictive uncertainty estimation via prior networks},
  author={Malinin, Andrey and Gales, Mark},
  journal={Advances in neural information processing systems},
  volume={31},
  year={2018}
}

@article{maddox2019simple,
  title={A simple baseline for bayesian uncertainty in deep learning},
  author={Maddox, Wesley J and Izmailov, Pavel and Garipov, Timur and Vetrov, Dmitry P and Wilson, Andrew Gordon},
  journal={Advances in neural information processing systems},
  volume={32},
  year={2019}
}

@article{lakshminarayanan2017simple,
  title={Simple and scalable predictive uncertainty estimation using deep ensembles},
  author={Lakshminarayanan, Balaji and Pritzel, Alexander and Blundell, Charles},
  journal={Advances in neural information processing systems},
  volume={30},
  year={2017}
}

@article{jadon2025realdrivesim,
  title={RealDriveSim: A Realistic Multi-Modal Multi-Task Synthetic Dataset for Autonomous Driving},
  author={Jadon, Arpit and Wang, Haoran and Thomas, Phillip and Stanley, Michael and Cibik, S Nathaniel and Laurat, Rachel and Maher, Omar and Hoyer, Lukas and Unal, Ozan and Dai, Dengxin},
  journal={arXiv preprint arXiv:2506.16319},
  year={2025}
}

@article{kronman2023developmental,
  title={Developmental Mouse Brain Common Coordinate Framework},
  author={Kronman, Fae A and Liwang, Josephine K and Betty, Rebecca and Vanselow, Daniel J and Wu, Yuan-Ting and Tustison, Nicholas J and Bhandiwad, Ashwin and Manjila, Steffy B and Minteer, Jennifer A and Shin, Donghui and others},
  journal={bioRxiv},
  year={2023},
  publisher={Cold Spring Harbor Laboratory Preprints}
}

@inproceedings{kwitt2017fast,
  title={Fast predictive simple geodesic regression},
  author={Kwitt, Roland and Niethammer, Marc},
  booktitle={third International Workshop DLMIA},
  pages={267},
  year={2017}
}

@inproceedings{lee2019sfnet,
  title={Sfnet: Learning object-aware semantic correspondence},
  author={Lee, Junghyup and Kim, Dohyung and Ponce, Jean and Ham, Bumsub},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages={2278--2287},
  year={2019}
}

@article{lefebure2001image,
  title={Image registration, optical flow and local rigidity},
  author={Lef{\'e}bure, Martin and Cohen, Laurent D},
  journal={Journal of mathematical imaging and vision},
  volume={14},
  pages={131--147},
  year={2001},
  publisher={Springer}
}

@article{leon2021review,
  title={A review of tracking and trajectory prediction methods for autonomous driving},
  author={Leon, Florin and Gavrilescu, Marius},
  journal={Mathematics},
  volume={9},
  number={6},
  pages={660},
  year={2021},
  publisher={MDPI}
}

@article{leslie1967differential,
  title={On a differential structure for the group of diffeomorphisms},
  author={Leslie, JA},
  journal={Topology},
  volume={6},
  number={2},
  pages={263--271},
  year={1967},
  publisher={Pergamon}
}

@article{li2018super,
  title={Super resolution for astronomical observations},
  author={Li, Zhan and Peng, Qingyu and Bhanu, Bir and Zhang, Qingfeng and He, Haifeng},
  journal={Astrophysics and Space Science},
  volume={363},
  pages={1--15},
  year={2018},
  publisher={Springer}
}

@article{linger2014aerial,
  title={Aerial image registration for tracking},
  author={Linger, Michael E and Goshtasby, A Ardeshir},
  journal={IEEE Transactions on Geoscience and Remote Sensing},
  volume={53},
  number={4},
  pages={2137--2145},
  year={2014},
  publisher={IEEE}
}

@article{lku,
  title={U-Net vs Transformer: Is U-Net Outdated in Medical Image Registration?},
  author={Jia, Xi and Bartlett, Joseph and Zhang, Tianyang and Lu, Wenqi and Qiu, Zhaowen and Duan, Jinming},
  journal={arXiv preprint arXiv:2208.04939},
  volume={1},
  year={2022}
}

@inproceedings{makovoz2006mopex,
  title={MOPEX: a software package for astronomical image processing and visualization},
  author={Makovoz, David and Roby, Trey and Khan, Iffat and Booth, Hartley},
  booktitle={Advanced Software and Control for Astronomy},
  volume={6274},
  pages={93--102},
  year={2006},
  organization={SPIE}
}

@incollection{mang2024claire,
  title={CLAIRE: Scalable GPU-Accelerated Algorithms for Diffeomorphic Image Registration in 3D},
  author={Mang, Andreas},
  booktitle={Explorations in the Mathematics of Data Science: The Inaugural Volume of the Center for Approximation and Mathematical Data Analytics},
  pages={167--215},
  year={2024},
  publisher={Springer}
}

@article{sitreg,
  title={SITReg: Multi-resolution architecture for symmetric, inverse consistent, and topology preserving image registration},
  author={Honkamaa, Joel and Marttinen, Pekka},
  journal={arXiv preprint arXiv:2303.10211},
  year={2023}
}

@article{mang2017lagrangian,
  title={A Lagrangian Gauss--Newton--Krylov solver for mass-and intensity-preserving diffeomorphic image registration},
  author={Mang, Andreas and Ruthotto, Lars},
  journal={SIAM Journal on Scientific Computing},
  volume={39},
  number={5},
  pages={B860--B885},
  year={2017},
  publisher={SIAM}
}

@article{mang2017semi,
  title={A semi-Lagrangian two-level preconditioned Newton--Krylov solver for constrained diffeomorphic image registration},
  author={Mang, Andreas and Biros, George},
  journal={SIAM Journal on Scientific Computing},
  volume={39},
  number={6},
  pages={B1064--B1101},
  year={2017},
  publisher={SIAM}
}

@Article{manopt,
    author = {Boumal, N. and Mishra, B. and Absil, P.-A. and Sepulchre, R.},
    journal = {Journal of Machine Learning Research},
    title = {{M}anopt, a {M}atlab Toolbox for Optimization on Manifolds},
    year = {2014},
    number = {42},
    pages = {1455--1459},
    volume = {15},
    url = {https://www.manopt.org}
}

@article{mezias2024establishing,
  title={Establishing neuroanatomical correspondences across mouse and marmoset brain structures},
  author={Mezias, Christopher and Huo, Bingxing and Bota, Mihail and Jayakumar, Jaikishan and Mitra, Partha P},
  journal={Research Square},
  pages={rs--3},
  year={2024}
}

@article{beauchamp2022whole,
  title={Whole-brain comparison of rodent and human brains using spatial transcriptomics},
  author={Beauchamp, Antoine and Yee, Yohan and Darwin, Ben C and Raznahan, Armin and Mars, Rogier B and Lerch, Jason P},
  journal={elife},
  volume={11},
  pages={e79418},
  year={2022},
  publisher={eLife Sciences Publications Limited}
}

@article{mertzios1986generalized,
  title={On the generalized Cayley-Hamilton theorem},
  author={Mertzios, B and Christodoulou, M},
  journal={IEEE transactions on automatic control},
  volume={31},
  number={2},
  pages={156--157},
  year={1986},
  publisher={IEEE}
}

@inproceedings{mok2020large,
  title={Large deformation diffeomorphic image registration with laplacian pyramid networks},
  author={Mok, Tony CW and Chung, Albert CS},
  booktitle={Medical Image Computing and Computer Assisted Intervention--MICCAI 2020: 23rd International Conference, Lima, Peru, October 4--8, 2020, Proceedings, Part III 23},
  pages={211--221},
  year={2020},
  organization={Springer}
}

@inproceedings{jia2023fourier,
  title={Fourier-net: Fast image registration with band-limited deformation},
  author={Jia, Xi and Bartlett, Joseph and Chen, Wei and Song, Siyang and Zhang, Tianyang and Cheng, Xinxing and Lu, Wenqi and Qiu, Zhaowen and Duan, Jinming},
  booktitle={Proceedings of the AAAI Conference on Artificial Intelligence},
  volume={37},
  number={1},
  pages={1015--1023},
  year={2023}
}

@inproceedings{wang2020deepflash,
  title={Deepflash: An efficient network for learning-based medical image registration},
  author={Wang, Jian and Zhang, Miaomiao},
  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
  pages={4444--4452},
  year={2020}
}

@inproceedings{mok2021conditional,
  title={Conditional deformable image registration with convolutional neural network},
  author={Mok, Tony CW and Chung, Albert CS},
  booktitle={Medical Image Computing and Computer Assisted Intervention--MICCAI 2021: 24th International Conference, Strasbourg, France, September 27--October 1, 2021, Proceedings, Part IV 24},
  pages={35--45},
  year={2021},
  organization={Springer}
}

@article{moler2003nineteen,
  title={Nineteen dubious ways to compute the exponential of a matrix, twenty-five years later},
  author={Moler, Cleve and Van Loan, Charles},
  journal={SIAM review},
  volume={45},
  number={1},
  pages={3--49},
  year={2003},
  publisher={SIAM}
}

@article{moter2000fluorescence,
  title={Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms},
  author={Moter, Annette and G{\"o}bel, Ulf B},
  journal={Journal of microbiological methods},
  volume={41},
  number={2},
  pages={85--112},
  year={2000},
  publisher={Elsevier}
}

@article{murphy2011evaluation,
  title={Evaluation of registration methods on thoracic CT: the EMPIRE10 challenge},
  author={Murphy, Keelin and Van Ginneken, Bram and Reinhardt, Joseph M and Kabus, Sven and Ding, Kai and Deng, Xiang and Cao, Kunlin and Du, Kaifang and Christensen, Gary E and Garcia, Vincent and others},
  journal={IEEE transactions on medical imaging},
  volume={30},
  number={11},
  pages={1901--1920},
  year={2011},
  publisher={IEEE}
}

@article{magicormirage,
  title={Deep learning in medical image registration: Magic or mirage?},
  author={Jena, Rohit and Sethi, Deeksha and Chaudhari, Pratik and Gee, James},
  journal={Advances in Neural Information Processing Systems},
  volume={37},
  pages={108331--108353},
  year={2024}
}

@article{nenoff2020deformable,
  title={Deformable image registration uncertainty for inter-fractional dose accumulation of lung cancer proton therapy},
  author={Nenoff, Lena and Ribeiro, C{\'a}ssia O and Matter, Michael and Hafner, Luana and Josipovic, Mirjana and Langendijk, Johannes A and Persson, Gitte F and Walser, Marc and Weber, Damien Charles and Lomax, Antony John and others},
  journal={Radiotherapy and Oncology},
  volume={147},
  pages={178--185},
  year={2020},
  publisher={Elsevier}
}

@inproceedings{nextbrain,
  title={An open-source tool for fast segmentation of any brain MR scan with the NextBrain histological atlas},
  author={Puonti, Oula and Nolan, Jackson and Dicamillo, Robert and Balbastre, Yael and Casamitjana, Adria and MatteoMancini and Robinson, Eleanor and Peter, Loic and Annunziata, Roberto and Althonayan, Juri and ShaunaCrampsie and Blackburn, Emily and Billot, Benjamin and Atzeni, Alessia and Schmidt, Peter and Hughes, James and Augustinack, Jean and Edlow, Brian and Zöllei, Lilla and Thomas, David and Kliemann, Dorit and MartinaBocchetta and Strand, Catherine and Holton, Janice and Jaunmuktane, Zane and Iglesias, Juan Eugenio},
  booktitle={31th Annual Meeting of the Organization for Human Brain Mapping (OHBM 2025)},
  year={2025}
}

@inproceedings{niethammer2011geodesic,
  title={Geodesic regression for image time-series},
  author={Niethammer, Marc and Huang, Yang and Vialard, Fran{\c{c}}ois-Xavier},
  booktitle={Medical Image Computing and Computer-Assisted Intervention--MICCAI 2011: 14th International Conference, Toronto, Canada, September 18-22, 2011, Proceedings, Part II 14},
  pages={655--662},
  year={2011},
  organization={Springer}
}

@inproceedings{Niethammer_2019_CVPR,
  title={Metric learning for image registration},
  author={Niethammer, Marc and Kwitt, Roland and Vialard, Francois-Xavier},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages={8463--8472},
  year={2019}
}

 @misc{nlst, title={Data from the National Lung Screening Trial (NLST)}, url={https://www.cancerimagingarchive.net/collection/nlst/}, DOI={10.7937/TCIA.HMQ8-J677}, publisher={The Cancer Imaging Archive}, author={National Lung Screening Trial Research Team}, year={2013} }


@article{oasisdataset,
  title={Open Access Series of Imaging Studies (OASIS): cross-sectional MRI data in young, middle aged, nondemented, and demented older adults},
  author={Marcus, Daniel S and Wang, Tracy H and Parker, Jamie and Csernansky, John G and Morris, John C and Buckner, Randy L},
  journal={Journal of cognitive neuroscience},
  volume={19},
  number={9},
  pages={1498--1507},
  year={2007},
  publisher={MIT Press One Rogers Street, Cambridge, MA 02142-1209, USA journals-info~…}
}

@article{oh2014mesoscale,
  title={A mesoscale connectome of the mouse brain},
  author={Oh, Seung Wook and Harris, Julie A and Ng, Lydia and Winslow, Brent and Cain, Nicholas and Mihalas, Stefan and Wang, Quanxin and Lau, Chris and Kuan, Leonard and Henry, Alex M and others},
  journal={Nature},
  volume={508},
  number={7495},
  pages={207--214},
  year={2014},
  publisher={Nature Publishing Group UK London}
}

@inproceedings{braincolor,
  title={Open labels: online feedback for a public resource of manually labeled brain images},
  author={Klein, Arno and Dal Canton, Tito and Ghosh, Satrajit S and Landman, Bennett and Lee, Joel and Worth, Andrew},
  booktitle={16th annual meeting for the organization of human brain mapping},
  volume={84358},
  pages={6},
  year={2010}
}

@article{olarte2018light,
  title={Light-sheet microscopy: a tutorial},
  author={Olarte, Omar E and Andilla, Jordi and Gualda, Emilio J and Loza-Alvarez, Pablo},
  journal={Advances in Optics and Photonics},
  volume={10},
  number={1},
  pages={111--179},
  year={2018},
  publisher={Optica Publishing Group}
}

@article{slant,
  title={3D whole brain segmentation using spatially localized atlas network tiles},
  author={Huo, Yuankai and Xu, Zhoubing and Xiong, Yunxi and Aboud, Katherine and Parvathaneni, Prasanna and Bao, Shunxing and Bermudez, Camilo and Resnick, Susan M and Cutting, Laurie E and Landman, Bennett A},
  journal={NeuroImage},
  volume={194},
  pages={105--119},
  year={2019},
  publisher={Elsevier}
}

@InProceedings{pmlr-v97-lezcano-casado19a,
  title = 	 {Cheap Orthogonal Constraints in Neural Networks: A Simple Parametrization of the Orthogonal and Unitary Group},
  author =       {Lezcano-Casado, Mario and Mart\'{\i}nez-Rubio, David},
  booktitle = 	 {Proceedings of the 36th International Conference on Machine Learning},
  pages = 	 {3794--3803},
  year = 	 {2019},
  editor = 	 {Chaudhuri, Kamalika and Salakhutdinov, Ruslan},
  volume = 	 {97},
  series = 	 {Proceedings of Machine Learning Research},
  month = 	 {09--15 Jun},
  publisher =    {PMLR},
  pdf = 	 {http://proceedings.mlr.press/v97/lezcano-casado19a/lezcano-casado19a.pdf},
  url = 	 {https://proceedings.mlr.press/v97/lezcano-casado19a.html},
  abstract = 	 {We introduce a novel approach to perform first-order optimization with orthogonal and unitary constraints. This approach is based on a parametrization stemming from Lie group theory through the exponential map. The parametrization transforms the constrained optimization problem into an unconstrained one over a Euclidean space, for which common first-order optimization methods can be used. The theoretical results presented are general enough to cover the special orthogonal group, the unitary group and, in general, any connected compact Lie group. We discuss how this and other parametrizations can be computed efficiently through an implementation trick, making numerically complex parametrizations usable at a negligible runtime cost in neural networks. In particular, we apply our results to RNNs with orthogonal recurrent weights, yielding a new architecture called expRNN. We demonstrate how our method constitutes a more robust approach to optimization with orthogonal constraints, showing faster, accurate, and more stable convergence in several tasks designed to test RNNs.}
}

@article{pomerleau2015review,
  title={A review of point cloud registration algorithms for mobile robotics},
  author={Pomerleau, Francois and Colas, Francis and Siegwart, Roland and others},
  journal={Foundations and Trends in Robotics},
  volume={4},
  number={1},
  pages={1--104},
  year={2015},
  publisher={Now Publishers, Inc.}
}

@article{primate,
  title={An open resource for non-human primate imaging},
  author={Milham, Michael P and Ai, Lei and Koo, Bonhwang and Xu, Ting and Amiez, C{\'e}line and Balezeau, Fabien and Baxter, Mark G and Blezer, Erwin LA and Brochier, Thomas and Chen, Aihua and others},
  journal={Neuron},
  volume={100},
  number={1},
  pages={61--74},
  year={2018},
  publisher={Elsevier}
}

@article{pytorch,
  title={Pytorch: An imperative style, high-performance deep learning library},
  author={Paszke, Adam and Gross, Sam and Massa, Francisco and Lerer, Adam and Bradbury, James and Chanan, Gregory and Killeen, Trevor and Lin, Zeming and Gimelshein, Natalia and Antiga, Luca and others},
  journal={Advances in neural information processing systems},
  volume={32},
  year={2019}
}

@article{qiao2019efficient,
  title={An efficient preconditioner for stochastic gradient descent optimization of image registration},
  author={Qiao, Yuchuan and Lelieveldt, Boudewijn PF and Staring, Marius},
  journal={IEEE transactions on medical imaging},
  volume={38},
  number={10},
  pages={2314--2325},
  year={2019},
  publisher={IEEE}
}

@inproceedings{qiu2021learning,
  title={Learning diffeomorphic and modality-invariant registration using b-splines},
  author={Qiu, Huaqi and Qin, Chen and Schuh, Andreas and Hammernik, Kerstin and Rueckert, Daniel},
  booktitle={Medical Imaging with Deep Learning},
  year={2021}
}

@article{ragan2012serial,
  title={Serial two-photon tomography for automated ex vivo mouse brain imaging},
  author={Ragan, Timothy and Kadiri, Lolahon R and Venkataraju, Kannan Umadevi and Bahlmann, Karsten and Sutin, Jason and Taranda, Julian and Arganda-Carreras, Ignacio and Kim, Yongsoo and Seung, H Sebastian and Osten, Pavel},
  journal={Nature methods},
  volume={9},
  number={3},
  pages={255--258},
  year={2012},
  publisher={Nature Publishing Group US New York}
}

@inproceedings{rivenson2020emerging,
  title={Emerging advances to transform histopathology using virtual staining},
  author={Rivenson, Yair and de Haan, Kevin and Wallace, W Dean and Ozcan, Aydogan},
  journal={BME frontiers},
  year={2020},
  publisher={AAAS}
}

@article{rmsprop,
  title={Lecture 6.5-rmsprop: Divide the gradient by a running average of its recent magnitude},
  author={Tieleman, Tijmen and Hinton, Geoffrey and others},
  journal={COURSERA: Neural networks for machine learning},
  volume={4},
  number={2},
  pages={26--31},
  year={2012}
}

@online{rnrexm,
    title = {RNR-EXM Grand Challenge},
    url = {https://rnr-exm.grand-challenge.org/},
}

@article{routier2021clinica,
  title={Clinica: An open-source software platform for reproducible clinical neuroscience studies},
  author={Routier, Alexandre and Burgos, Ninon and D{\'\i}az, Mauricio and Bacci, Michael and Bottani, Simona and El-Rifai, Omar and Fontanella, Sabrina and Gori, Pietro and Guillon, J{\'e}r{\'e}my and Guyot, Alexis and others},
  journal={Frontiers in Neuroinformatics},
  volume={15},
  pages={689675},
  year={2021},
  publisher={Frontiers Media SA}
}

@article{rwcnet,
  title={Recurrence With Correlation Network for Medical Image Registration},
  author={Sivan, Vignesh and Vujovic, Teodora and Ranabhat, Raj and Wong, Alexander and Mclachlin, Stewart and Hardisty, Michael},
  journal={arXiv preprint arXiv:2302.02283},
  year={2023}
}

@article{schmid1987infinite,
  title={Infinite dimensional Hamiltonian systems},
  author={Schmid, Rudolf and others},
  journal={(No Title)},
  volume={-},
  year={1987}
}

@inproceedings{sentker2018gdl,
  title={GDL-FIRE: Deep Learning-Based Fast 4D CT Image Registration},
  author={Sentker, Thilo and Madesta, Frederic and Werner, Ren{\'e}},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={765--773},
  year={2018},
  organization={Springer}
}

@article{smith2016structure,
  title={Structure from motion photogrammetry in physical geography},
  author={Smith, Mark William and Carrivick, Jonathan L and Quincey, Duncan J},
  journal={Progress in physical geography},
  volume={40},
  number={2},
  pages={247--275},
  year={2016},
  publisher={SAGE Publications Sage UK: London, England}
}

@article{sorensen1948method,
  title={A method of establishing groups of equal amplitude in plant sociology based on similarity of species content and its application to analyses of the vegetation on Danish commons},
  author={Sorensen, Thorvald},
  journal={Biologiske skrifter},
  volume={5},
  pages={1--34},
  year={1948}
}

@article{sotiras2013deformable,
  title={Deformable medical image registration: A survey},
  author={Sotiras, Aristeidis and Davatzikos, Christos and Paragios, Nikos},
  journal={IEEE transactions on medical imaging},
  volume={32},
  number={7},
  pages={1153--1190},
  year={2013},
  publisher={IEEE}
}

@article{thirion1998image,
  title={Image matching as a diffusion process: an analogy with Maxwell's demons},
  author={Thirion, J-P},
  journal={Medical image analysis},
  volume={2},
  number={3},
  pages={243--260},
  year={1998},
  publisher={Elsevier}
}

@inproceedings{tian2024unigradicon,
  title={unigradicon: A foundation model for medical image registration},
  author={Tian, Lin and Greer, Hastings and Kwitt, Roland and Vialard, Fran{\c{c}}ois-Xavier and San Jos{\'e} Est{\'e}par, Ra{\'u}l and Bouix, Sylvain and Rushmore, Richard and Niethammer, Marc},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={749--760},
  year={2024},
  organization={Springer}
}

@article{toga2001role,
  title={The role of image registration in brain mapping},
  author={Toga, Arthur W and Thompson, Paul M},
  journal={Image and vision computing},
  volume={19},
  number={1-2},
  pages={3--24},
  year={2001},
  publisher={Elsevier}
}

@article{troglio2011automatic,
  title={Automatic extraction of ellipsoidal features for planetary image registration},
  author={Troglio, Giulia and Le Moigne, Jacqueline and Benediktsson, J{\'o}n Atli and Moser, Gabriele and Serpico, Sebastiano B},
  journal={IEEE Geoscience and remote sensing letters},
  volume={9},
  number={1},
  pages={95--99},
  year={2011},
  publisher={IEEE}
}

@article{deepatropos,
  title={The ANTsX ecosystem for quantitative biological and medical imaging},
  author={Tustison, Nicholas J and Cook, Philip A and Holbrook, Andrew J and Johnson, Hans J and Muschelli, John and Devenyi, Gabriel A and Duda, Jeffrey T and Das, Sandhitsu R and Cullen, Nicholas C and Gillen, Daniel L and others},
  journal={Scientific reports},
  volume={11},
  number={1},
  pages={9068},
  year={2021},
  publisher={Nature Publishing Group UK London}
}

@article{trouve1998diffeomorphisms,
  title={Diffeomorphisms groups and pattern matching in image analysis},
  author={Trouv{\'e}, Alain},
  journal={International journal of computer vision},
  volume={28},
  pages={213--221},
  year={1998},
  publisher={Springer}
}

@article{tustison2024antsx,
  title={The ANTsX Ecosystem for Mapping the Mouse Brain},
  author={Tustison, Nicholas J and Chen, Min and Kronman, Fae N and Duda, Jeffrey T and Gamlin, Clare and Tustison, Mia G and Kunst, Michael and Dalley, Rachel and Sorenson, Staci and Wang, Quanxin and others},
  journal={bioRxiv},
  pages={2024--05},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}

@article{ueda2020tissue,
  title={Tissue clearing and its applications in neuroscience},
  author={Ueda, Hiroki R and Ert{\"u}rk, Ali and Chung, Kwanghun and Gradinaru, Viviana and Ch{\'e}dotal, Alain and Tomancak, Pavel and Keller, Philipp J},
  journal={Nature Reviews Neuroscience},
  volume={21},
  number={2},
  pages={61--79},
  year={2020},
  publisher={Nature Publishing Group UK London}
}

@inproceedings{van2011survey,
  title={A survey on shape correspondence},
  author={Van Kaick, Oliver and Zhang, Hao and Hamarneh, Ghassan and Cohen-Or, Daniel},
  booktitle={Computer graphics forum},
  volume={30},
  number={6},
  pages={1681--1707},
  year={2011},
  organization={Wiley Online Library}
}

@article{vercauteren2007diffeomorphic,
  title={Diffeomorphic demons using ITK’s finite difference solver hierarchy},
  author={Vercauteren, Tom and Pennec, Xavier and Perchant, Aymeric and Ayache, Nicholas and others},
  journal={The Insight Journal},
  volume={1},
  year={2007}
}

@inproceedings{menke2004using,
  title={Using permutations instead of student's t distribution for p-values in paired-difference algorithm comparisons},
  author={Menke, Joshua and Martinez, Tony R},
  booktitle={2004 IEEE international joint conference on neural networks (IEEE Cat. No. 04CH37541)},
  volume={2},
  pages={1331--1335},
  year={2004},
  organization={IEEE}
}

@article{vfa,
  title={Vector field attention for deformable image registration},
  author={Liu, Yihao and Chen, Junyu and Zuo, Lianrui and Carass, Aaron and Prince, Jerry L},
  journal={Journal of Medical Imaging},
  volume={11},
  number={6},
  pages={064001--064001},
  year={2024},
  publisher={Society of Photo-Optical Instrumentation Engineers}
}

@phdthesis{Wang-thesis,
author = {Xiaolong Wang},
title = {Learning and Reasoning with Visual Correspondence in Time},
year = {2019},
month = {September},
school = {Carnegie Mellon University},
address = {Pittsburgh, PA},
number = {CMU-RI-TR-19-75},
keywords = {Video; Correspondence; Self-Supervised Learning; Interaction Reasoning},
}

@article{wang2020allen,
  title={The Allen mouse brain common coordinate framework: a 3D reference atlas},
  author={Wang, Quanxin and Ding, Song-Lin and Li, Yang and Royall, Josh and Feng, David and Lesnar, Phil and Graddis, Nile and Naeemi, Maitham and Facer, Benjamin and Ho, Anh and others},
  journal={Cell},
  volume={181},
  number={4},
  pages={936--953},
  year={2020},
  publisher={Elsevier}
}

@article{wassie2019expansion,
  title={Expansion microscopy: principles and uses in biological research},
  author={Wassie, Asmamaw T and Zhao, Yongxin and Boyden, Edward S},
  journal={Nature methods},
  volume={16},
  number={1},
  pages={33--41},
  year={2019},
  publisher={Nature Publishing Group US New York}
}

@inproceedings{liu2025unsupervised,
title={Unsupervised Deformable Image Registration Revisited: Enhancing Performance with Registration-Specific Designs},
author={Liu, Hengjie and Ruan, Dan and Sheng, Ke},
booktitle={Medical Imaging with Deep Learning - Short Papers},
year={2025}
}

@inproceedings{jian2024mamba,
  title={Mamba? catch the hype or rethink what really helps for image registration},
  author={Jian, Bailiang and Pan, Jiazhen and Ghahremani, Morteza and Rueckert, Daniel and Wachinger, Christian and Wiestler, Benedikt},
  booktitle={International Workshop on Biomedical Image Registration},
  pages={86--97},
  year={2024},
  organization={Springer}
}

@article{xia2019spatial,
  title={Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression},
  author={Xia, Chenglong and Fan, Jean and Emanuel, George and Hao, Junjie and Zhuang, Xiaowei},
  journal={Proceedings of the National Academy of Sciences},
  volume={116},
  number={39},
  pages={19490--19499},
  year={2019},
  publisher={National Acad Sciences}
}

@article{yang2008fast,
  title={A fast inverse consistent deformable image registration method based on symmetric optical flow computation},
  author={Yang, Deshan and Li, Hua and Low, Daniel A and Deasy, Joseph O and El Naqa, Issam},
  journal={Physics in Medicine \& Biology},
  volume={53},
  number={21},
  pages={6143},
  year={2008},
  publisher={IOP Publishing}
}

@inproceedings{yoo2017ssemnet,
  title={ssEMnet: Serial-section electron microscopy image registration using a spatial transformer network with learned features},
  author={Yoo, Inwan and Hildebrand, David GC and Tobin, Willie F and Lee, Wei-Chung Allen and Jeong, Won-Ki},
  booktitle={Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support: Third International Workshop, DLMIA 2017, and 7th International Workshop, ML-CDS 2017, Held in Conjunction with MICCAI 2017, Qu{\'e}bec City, QC, Canada, September 14, Proceedings 3},
  pages={249--257},
  year={2017},
  organization={Springer}
}

@book{younes2010shapes,
  title={Shapes and diffeomorphisms},
  author={Younes, Laurent},
  volume={171},
  year={2010},
  publisher={Springer}
}

@article{zbrain,
  title={Whole-brain activity mapping onto a zebrafish brain atlas},
  author={Randlett, Owen and Wee, Caroline L and Naumann, Eva A and Nnaemeka, Onyeka and Schoppik, David and Fitzgerald, James E and Portugues, Ruben and Lacoste, Alix MB and Riegler, Clemens and Engert, Florian and others},
  journal={Nature methods},
  volume={12},
  number={11},
  pages={1039--1046},
  year={2015},
  publisher={Nature Publishing Group US New York}
}

@article{zhang2016riemannian,
  title={Riemannian SVRG: Fast stochastic optimization on Riemannian manifolds},
  author={Zhang, Hongyi and J Reddi, Sashank and Sra, Suvrit},
  journal={Advances in Neural Information Processing Systems},
  volume={29},
  year={2016}
}

@inproceedings{zhao2019recursive,
  title={Recursive cascaded networks for unsupervised medical image registration},
  author={Zhao, Shengyu and Dong, Yue and Chang, Eric I and Xu, Yan and others},
  booktitle={Proceedings of the IEEE/CVF international conference on computer vision},
  pages={10600--10610},
  year={2019}
}

@article{zheng2013visualization,
  title={Visualization of brain circuits using two-photon fluorescence micro-optical sectioning tomography},
  author={Zheng, Ting and Yang, Zhongqing and Li, Anan and Lv, Xiaohua and Zhou, Zhenqiao and Wang, Xiaojun and Qi, Xiaoli and Li, Shiwei and Luo, Qingming and Gong, Hui and others},
  journal={Optics express},
  volume={21},
  number={8},
  pages={9839--9850},
  year={2013},
  publisher={Optica Publishing Group}
}

@article{zhou2008human,
  title={Human motion tracking for rehabilitation—A survey},
  author={Zhou, Huiyu and Hu, Huosheng},
  journal={Biomedical signal processing and control},
  volume={3},
  number={1},
  pages={1--18},
  year={2008},
  publisher={Elsevier}
}

@article{zhu2019applications,
  title={Applications of deep learning to neuro-imaging techniques},
  author={Zhu, Guangming and Jiang, Bin and Tong, Liz and Xie, Yuan and Zaharchuk, Greg and Wintermark, Max},
  journal={Frontiers in neurology},
  volume={10},
  pages={869},
  year={2019},
  publisher={Frontiers Media SA}
}
