Some Issues of Biological Shape Modelling with Applications. - Rasmus Larsen 001; Klaus Baggesen Hilger; Karl Skoglund; Sune Darkner; Rasmus R. Paulsen; Mikkel B. Stegmann; Brian Lading; Hans Henrik Thodberg; Hrafnkell Eiriksson (SCIA, 2003)

Wedgelet Enhanced Appearance Models. - Sune Darkner; Rasmus Larsen 001; Mikkel B. Stegmann; Bjarne K. Ersbøll (CVPR Workshops, 2004)

An Active Illumination and Appearance (AIA) Model for Face Alignment. - Fatih Kahraman; Muhittin Gökmen; Sune Darkner; Rasmus Larsen 001 (CVPR, 2007)

Analysis of Deformation of the Human Ear and Canal Caused by Mandibular Movement. - Sune Darkner; Rasmus Larsen 001; Rasmus R. Paulsen (MICCAI (2), 2007)

Evaluating a method for automated rigid registration. - Sune Darkner; Martin Vester-Christensen; Rasmus Larsen 001; Rasmus R. Paulsen (Image Processing, 2007)

Accelerated 3D image registration. - Martin Vester-Christensen; Søren G. H. Erbou; Sune Darkner; Rasmus Larsen 001 (Image Processing, 2007)

Texture enhanced appearance models. - Rasmus Larsen 001; Mikkel B. Stegmann; Sune Darkner; Søren Forchhammer; Timothy F. Cootes; Bjarne K. Ersbøll (Comput. Vis. Image Underst., 2007)

Estimation of shape model parameters for 3D surfaces. - Søren G. H. Erbou; Sune Darkner; Jurgen Fripp; Sébastien Ourselin; Bjarne K. Ersbøll (ISBI, 2008)

Analysis of Surfaces Using Constrained Regression Models. - Sune Darkner; Mert R. Sabuncu; Polina Golland; Rasmus R. Paulsen; Rasmus Larsen 001 (MICCAI (1), 2008)

Robust registration for change detection. - Sune Darkner; Dan Witzner Hansen; Rasmus R. Paulsen; Rasmus Larsen 001 (Image Processing, 2008)

Non-rigid registration of 2D manifolds in 3D Euclidian space. - Sune Darkner; Martin Vester-Christensen; Rasmus R. Paulsen; Rasmus Larsen 001 (Image Processing, 2008)

Registration-based interpolation applied to cardiac MRI. - Hildur Ólafsdóttir; Henrik Pedersen; Michael Sass Hansen; Mark Lyksborg; Mads Fogtmann Hansen; Sune Darkner; Rasmus Larsen 001 (Image Processing, 2010)

Local Segmentation by Large Scale Hypothesis Testing - Segmentation as Outlier Detection. - Sune Darkner; Anders Bjorholm Dahl; Rasmus Larsen 001; Arnold Skimminge; Ellen Garde; Gunhild Waldemar (VISAPP (2), 2010)

Generalized Partial Volume: An Inferior Density Estimator to Parzen Windows for Normalized Mutual Information. - Sune Darkner; Jon Sporring (IPMI, 2011)

Efficient Hyperelastic Regularization for Registration. - Sune Darkner; Michael Sass Hansen; Rasmus Larsen 001; Mads Fogtmann Hansen (SCIA, 2011)

Higher Order Kernels and Locally Affine LDDMM Registration - Stefan Sommer; Mads Nielsen; Sune Darkner; Xavier Pennec (CoRR, 2011)

A hyper elasticity method for interactive virtual design of hearing aids - A parallel method for general non-linear hyper elasticity modeling. - Sune Darkner; Kenny Erleben (Vis. Comput., 2011)

Jet-Based Local Image Descriptors. - Anders Boesen Lindbo Larsen; Sune Darkner; Anders Lindbjerg Dahl; Kim Steenstrup Pedersen (ECCV (3), 2012)

Data Driven Constraints for the SVM. - Sune Darkner; Line Harder Clemmensen (MLMI, 2012)

Cube propagation for focal brain atrophy estimation. - Akshay Pai; Lauge Sørensen; Sune Darkner; Peter Mysling; Dan R. Jørgensen; Erik B. Dam; Martin Lillholm; Joonmi Oh; Gennan Chen; Joyce Suhy; Jon Sporring; Mads Nielsen (ISBI, 2013)

Automatic measurement of wrist synovitis from contrast-enhanced MRI: a registration-centered approach. - Peter Mysling; Sune Darkner; Jon Sporring; Erik Dam; Martin Lillholm (Image Processing, 2013)

Locally Orderless Registration. - Sune Darkner; Jon Sporring (IEEE Trans. Pattern Anal. Mach. Intell., 2013)

Higher-Order Momentum Distributions and Locally Affine LDDMM Registration. - Stefan Sommer; Mads Nielsen; Sune Darkner; Xavier Pennec (SIAM J. Imaging Sci., 2013)

Estimating the thickness of ultra thin sections for electron microscopy by image statistics. - Jon Sporring; Mahdieh Khanmohammadi; Sune Darkner; Nicoletta Nava; Jens Rondel Nyengaard; Eva Bjorn Wedel Jensen (ISBI, 2014)

Automatic FDG-PET-based tumor and metastatic lymph node segmentation in cervical cancer. - Dídac R. Arbonès; Henrik G. Jensen; Annika Loft; Per Munck af Rosenschöld; Anders E. Hansen; Christian Igel; Sune Darkner (Image Processing, 2014)

Stepwise Inverse Consistent Euler's Scheme for Diffeomorphic Image Registration. - Akshay Pai; Stefan Sommer; Sune Darkner; Lauge Sørensen; Jon Sporring; Mads Nielsen (WBIR, 2014)

Diffeomorphic image registration with automatic time-step adjustment. - Akshay Pai; Stefan Klein 001; Stefan Sommer; Sune Darkner; Jon Sporring; Mads Nielsen (ISBI, 2015)

Locally Orderless Registration for Diffusion Weighted Images. - Henrik G. Jensen; François Lauze; Mads Nielsen; Sune Darkner (MICCAI (2), 2015)

Image registration using stationary velocity fields parameterized by norm-minimizing Wendland kernel. - Akshay Pai; Stefan Sommer; Lauge Sørensen; Sune Darkner; Jon Sporring; Mads Nielsen (Image Processing, 2015)

Structural parcellation of the thalamus using shortest-path tractography. - Niklas Kasenburg; Sune Darkner; Ute Hahn; Matthew G. Liptrot; Aasa Feragen (ISBI, 2016)

A Statistical Model for Simultaneous Template Estimation, Bias Correction, and Registration of 3D Brain Images. - Akshay Pai; Stefan Sommer; Lars Lau Rakêt; Line Kühnel; Sune Darkner; Lauge Sørensen; Mads Nielsen (MCV/BAMBI@MICCAI, 2016)

Finding significantly connected voxels based on histograms of connection strengths. - Niklas Kasenburg; Morten Vester Pedersen; Sune Darkner (Image Processing, 2016)

Combining the boundary shift integral and tensor-based morphometry for brain atrophy estimation. - Mateusz Michalkiewicz; Akshay Pai; Kelvin K. Leung; Stefan Sommer; Sune Darkner; Lauge Sørensen; Jon Sporring; Mads Nielsen (Image Processing, 2016)

Kernel Bundle Diffeomorphic Image Registration Using Stationary Velocity Fields and Wendland Basis Functions. - Akshay Pai; Stefan Sommer; Lauge Sørensen; Sune Darkner; Jon Sporring; Mads Nielsen (IEEE Trans. Medical Imaging, 2016)

Local Models for Data Driven Inverse Kinematics of Soft Robots. - Fredrik Holsten; Sune Darkner; Morten Pol Engell-Nørregård; Kenny Erleben (Symposium on Computer Animation (Posters), 2018)

An Average of the Human Ear Canal: Recovering Acoustical Properties via Shape Analysis. - Sune Darkner; Stefan Sommer; Andreas Schuhmacher; Henrik Ingerslev Anders O. Baandrup; Carsten Thomsen; Søren Jønsson (CoRR, 2018)

Collocation for Diffeomorphic Deformations in Medical Image Registration. - Sune Darkner; Akshay Pai; Matthew G. Liptrot; Jon Sporring (IEEE Trans. Pattern Anal. Mach. Intell., 2018)

Data Driven Inverse Kinematics of Soft Robots using Local Models. - Fredrik Holsten; Morten Pol Engell-Nørregård; Sune Darkner; Kenny Erleben (ICRA, 2019)

TopAwaRe: Topology-Aware Registration. - Rune Kok Nielsen; Sune Darkner; Aasa Feragen (MICCAI (2), 2019)

U-Time: A Fully Convolutional Network for Time Series Segmentation Applied to Sleep Staging. - Mathias Perslev; Michael Hejselbak Jensen; Sune Darkner; Poul Jørgen Jennum; Christian Igel (NeurIPS, 2019)

Mandibular Teeth Movement Variations in Tipping Scenario: A Finite Element Study on Several Patients. - Torkan Gholamalizadeh; Sune Darkner; Paolo Maria Cattaneo; Peter Lempel Søndergaard; Kenny Erleben (CoRR, 2020)

Bundle Geodesic Convolutional Neural Network for DWI Segmentation from Single Scan Learning. - Renfei Liu; François Lauze; Kenny Erleben; Sune Darkner (CDMRI@MICCAI, 2021)

Cine-MRI Simulation to Evaluate Tumor Tracking. - José D. Tascón-Vidarte; Isak Wahlstedt; Julien Jomier; Kenny Erleben; Ivan R. Vogelius; Sune Darkner (SASHIMI@MICCAI, 2021)

First Order Locally Orderless Registration. - Sune Darkner; José D. Tascón-Vidarte; François Lauze (SSVM, 2021)

Contact modeling from images using cut finite element solvers. - Susanne Claus; Pierre Kerfriden; Faezeh Moshfeghifar; Sune Darkner; Kenny Erleben; Christian Wong (Adv. Model. Simul. Eng. Sci., 2021)

RootPainter3D: Interactive-machine-learning enables rapid and accurate contouring for radiotherapy. - Abraham George Smith; Jens Petersen; Cynthia Terrones-Campos; Anne Kiil Berthelsen; Nora Jarrett Forbes; Sune Darkner; Lena Specht; Ivan Richter Vogelius (CoRR, 2021)

First Order Locally Orderless Registration. - Sune Darkner; Jose D. Tascon; François Lauze (CoRR, 2021)

U-Sleep: resilient high-frequency sleep staging. - Mathias Perslev; Sune Darkner; Lykke Kempfner; Miki Nikolic; Poul Jørgen Jennum; Christian Igel (npj Digit. Medicine, 2021)

Global Position Prediction for Interactive Motion Capture. - Paul Schreiner; Maksym Perepichka; Hayden Lewis; Sune Darkner; Paul G. Kry; Kenny Erleben; Victor B. Zordan (Proc. ACM Comput. Graph. Interact. Tech., 2021)

Revisiting Transformer-based Models for Long Document Classification. - Xiang Dai; Ilias Chalkidis; Sune Darkner; Desmond Elliott (EMNLP (Findings), 2022)

Group Convolutional Neural Networks for DWI Segmentation. - Renfei Liu; François Lauze; Erik J. Bekkers; Kenny Erleben; Sune Darkner (GeoMedIA, 2022)

Fast Vortex Particle Method for Fluid-Character Interaction. - Asger Meldgaard; Sune Darkner; Kenny Erleben (Graphics Interface, 2022)

Reducing Annotation Need in Self-explanatory Models for Lung Nodule Diagnosis. - Jiahao Lu; Chong Yin; Oswin Krause; Kenny Erleben; Michael Bachmann Nielsen; Sune Darkner (iMIMIC@MICCAI, 2022)

Auto-segmentation of Hip Joints Using MultiPlanar UNet with Transfer Learning. - Peidi Xu; Faezeh Moshfeghifar; Torkan Gholamalizadeh; Michael Bachmann Nielsen; Kenny Erleben; Sune Darkner (MILLanD@MICCAI, 2022)

Open-Full-Jaw: An open-access dataset and pipeline for finite element models of human jaw. - Torkan Gholamalizadeh; Faezeh Moshfeghifar; Zachary Ferguson; Teseo Schneider; Daniele Panozzo; Sune Darkner; Masrour Makaremi; François Chan; Peter Lempel Søndergaard; Kenny Erleben (Comput. Methods Programs Biomed., 2022)

LibHip: An open-access hip joint model repository suitable for finite element method simulation. - Faezeh Moshfeghifar; Torkan Gholamalizadeh; Zachary Ferguson; Teseo Schneider; Michael Bachmann Nielsen; Daniele Panozzo; Sune Darkner; Kenny Erleben (Comput. Methods Programs Biomed., 2022)

A direct geometry processing cartilage generation method using segmented bone models from datasets with poor cartilage visibility. - Faezeh Moshfeghifar; Max Kragballe Nielsen; José D. Tascón-Vidarte; Sune Darkner; Kenny Erleben (CoRR, 2022)

A multi-patient analysis of the center of rotation trajectories using finite element models of the human mandible. - Torkan Gholamalizadeh; Sune Darkner; Peter Lempel Søndergaard; Kenny Erleben (CoRR, 2022)

Reconstructing Binary Signals from Local Histograms. - Jon Sporring; Sune Darkner (Entropy, 2022)

An algebra for local histograms. - Jon Sporring; Sune Darkner (Frontiers Comput. Sci., 2022)

Information-Theoretic Registration with Explicit Reorientation of Diffusion-Weighted Images. - Henrik G. Jensen; François Lauze; Sune Darkner (J. Math. Imaging Vis., 2022)

cRedAnno+: Annotation Exploitation In Self-Explanatory Lung Nodule Diagnosis. - Jiahao Lu; Chong Yin; Kenny Erleben; Michael Bachmann Nielsen; Sune Darkner (ISBI, 2023)

Extremely Weakly-Supervised Blood Vessel Segmentation with Physiologically Based Synthesis and Domain Adaptation. - Peidi Xu; Blaire Lee; Olga V. Sosnovtseva; Charlotte Mehlin Sørensen; Kenny Erleben; Sune Darkner (MILLanD@MICCAI, 2023)

Deep-Learning-Based Segmentation of Individual Tooth and Bone With Periodontal Ligament Interface Details for Simulation Purposes. - Peidi Xu; Torkan Gholamalizadeh; Faezeh Moshfeghifar; Sune Darkner; Kenny Erleben (IEEE Access, 2023)

A Hybrid Approach to Full-Scale Reconstruction of Renal Arterial Network. - Peidi Xu; Niels-Henrik Holstein-Rathlou; Stinne Byrholdt Søgaard; Carsten Gundlach; Charlotte Mehlin Sørensen; Kenny Erleben; Olga V. Sosnovtseva; Sune Darkner (CoRR, 2023)

Deep Learning-Assisted Localisation of Nanoparticles in synthetically generated two-photon microscopy images. - Rasmus Netterstrøm; Nikolay Kutuzov; Sune Darkner; Maurits Jørring Pallesen; Martin Johannes Lauritzen; Kenny Erleben; François Lauze (CoRR, 2023)

Localise to segment: crop to improve organ at risk segmentation accuracy. - Abraham George Smith; Denis Kutnár; Ivan Richter Vogelius; Sune Darkner; Jens Petersen (CoRR, 2023)

Extremely weakly-supervised blood vessel segmentation with physiologically based synthesis and domain adaptation. - Peidi Xu; Olga V. Sosnovtseva; Charlotte Mehlin Sørensen; Kenny Erleben; Sune Darkner (CoRR, 2023)

Pseudo-Label Guided Image Synthesis for Semi-Supervised COVID-19 Pneumonia Infection Segmentation. - Fei Lyu 004; Mang Ye; Jonathan Frederik Carlsen; Kenny Erleben; Sune Darkner; Pong C. Yuen (IEEE Trans. Medical Imaging, 2023)

XFibrosis: Explicit Vessel-Fiber Modeling for Fibrosis Staging from Liver Pathology Images. - Chong Yin; Siqi Liu 003; Fei Lyu 004; Jiahao Lu; Sune Darkner; Vincent Wai-Sun Wong; Pong C. Yuen (CVPR, 2024)

In Vivo Deep Learning Estimation of Diffusion Coefficients of Nanoparticles. - Julius B. Kirkegaard; Nikolay Kutuzov; Rasmus Netterstrøm; Sune Darkner; Martin Johannes Lauritzen; François Lauze (MICCAI (2), 2024)

ADAPT: AI-Driven Artefact Purging Technique for IMU Based Motion Capture. - Paul Schreiner; Rasmus Netterstrøm; Hang Yin 001; Sune Darkner; Kenny Erleben (Comput. Graph. Forum, 2024)

Locally orderless networks. - Jon Sporring; Peidi Xu; Jiahao Lu; François Bernard Lauze; Sune Darkner (NLDL, 2025)

Collision Constraints and Diffeomorphisms: Dealing With Physics in Deformable Image Registration. - Thomas Alscher; Jens Petersen; François Lauze; Kenny Erleben; Sune Darkner (IEEE Access, 2025)

SE(3) group convolutional neural networks and a study on group convolutions and equivariance for DWI segmentation. - Renfei Liu; François Lauze; Erik J. Bekkers; Sune Darkner; Kenny Erleben (Frontiers Artif. Intell., 2025)

Neural Kinematic Bases for Fluids. - Yibo Liu; Paul Kry; Kenny Erleben; Noam Aigerman; Sune Darkner; Teseo Schneider (CoRR, 2025)

MERA: Multimodal and Multiscale Self-Explanatory Model with Considerably Reduced Annotation for Lung Nodule Diagnosis. - Jiahao Lu; Chong Yin; Silvia Ingala; Kenny Erleben; Michael Bachmann Nielsen; Sune Darkner (CoRR, 2025)

Policy-Space Diffusion for Physics-Based Character Animation. - Michele Rocca; Sune Darkner; Kenny Erleben; Sheldon Andrews (ACM Trans. Graph., 2025)