Sune Darkner

Sune Darkner

Associate Professor

ORCID: 0000-0001-6114-7100

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  1. Published

    3D analysis of synaptic vesicle density and distribution after acute foot-shock stress by using serial section transmission electron microscopy

    Khanmohammadi, M., Darkner, Sune, Nava, N., Nyengaard, J. R., Wegener, G., Popoli, M. & Sporring, Jon, 2017, In: Journal of Microscopy. 265, 1, p. 101–110 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  2. Published

    3D estimation of synaptic vesicle distributions in serial section transmission electron microscopy

    Khanmohammadi, M., Darkner, Sune, Nava, N., Nyengaard, J. R., Wegener, G., Popoli, M. & Sporring, Jon, 2017, In: Journal of Microscopy. 265, 1, p. 101–110 1 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    A Direct Geometry Processing Cartilage Generation Method Using Segmented Bone Models from Datasets with Poor Cartilage Visibility

    nsv780, nsv780, Nielsen, M. K., Tascon Vidarte, J. D., Darkner, Sune & Erleben, Kenny, 2022, Computational Biomechanics for Medicine: Towards Translation and Better Patient Outcomes. Springer, p. 155.169

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  4. Published

    A Highly Accurate Model Based Registration Method for FIB-SEM Images of Neurons

    Stephensen, Hans Jacob Teglbjærg, Darkner, Sune & Sporring, Jon, 2020, 8 p. (arXiv.org).

    Research output: Book/Report › Report › Research

  5. Published

    A framework for voxel-based assessment of biological effect after proton radiotherapy in pediatric brain cancer patients using multi-modal imaging

    Skaarup, M., Lundemann, M. J., Darkner, Sune, Jorgensen, M., Marner, Lisbeth, Mirkovic, D., Grosshans, D., Peeler, C., Mohan, R., Vogelius, Ivan R. & Appelt, A., 10 Jun 2021, In: Medical Physics. 48, 7, 12 p., 4110-4121.

    Research output: Contribution to journal › Journal article › Research › peer-review

  6. Published

    A hybrid approach to full-scale reconstruction of renal arterial network

    Xu, Peidi, von Holstein-Rathlou, Niels-Henrik, Søgaard, S. B., Gundlach, C., Sorensen, Charlotte Mehlin, Erleben, Kenny, Sosnovtseva, Olga & Darkner, Sune, 9 May 2023, In: Scientific Reports. 13, 1, 15 p., 7569.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    A hyper elasticity method for interactive virtual design of hearing aids: a parallel method for general non-linear hyper elasticity modeling

    Darkner, Sune & Erleben, Kenny, 2011, In: Visual Computer. 27, 6, p. 645-653 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    A multi-patient analysis of the center of rotation trajectories using finite element models of the human mandible

    Gholamalizadeh, T., Darkner, Sune, Søndergaard, P. L. & Erleben, Kenny, 2021, In: PLoS ONE. 16, 11 November, 16 p., e0259794.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    A statistical model for simultaneous template estimation, bias correction, and registration of 3D brain images

    Pai, A. S. U., Sommer, Stefan Horst, Raket, L. L., Kühnel, L., Darkner, Sune, Sørensen, L. & Nielsen, Mads, 2017, Medical Computer Vision and Bayesian and Graphical Models for Biomedical Imaging: MICCAI 2016 International Workshops, MCV and BAMBI, Athens, Greece, October 21, 2016, Revised Selected Papers. Müller, H., Kelm, B. M., Arbel, T., Cai, W., Cardoso, M. J., Langs, G., Menze, B., Metaxas, D., Montillo, A., Wells, W. M., Zhang, S., Chung, A. C. S., Jenkinson, M. & Ribbens, A. (eds.). Springer, p. 151-159 9 p. (Lecture notes in computer science, Vol. 10081).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  10. Published

    Accuracy and consistency of intensity-based deformable image registration in 4DCT for tumor motion estimation in liver radiotherapy planning

    Tascon-Vidarte, J. D., Stick, L. B., Josipovic, Mirjana, Risum, S., Jomier, J., Erleben, Kenny, Vogelius, Ivan R. & Darkner, Sune, Jul 2022, In: PLoS ONE. 17, 7 July, p. 1-15 e0271064.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Published

    Adaptive time-stepping in dieomorphic image registration with bounded inverse consistency error

    Pai, A. S. U., Klein, S., Sommer, Stefan Horst, Sørensen, L., Darkner, Sune, Sporring, Jon & Nielsen, Mads, 2015, Proceedings of the fifth international workshop on Mathematical Foundations of Computational Anatomy (MFCA 2015) . INRIA, p. 35-47

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  12. Published

    Adaptive time-stepping in diffeomorphic image registration with bounded inverse consistency error

    Pai, A. S. U., Klein, S., Sommer, Stefan Horst, Sørensen, L. E. B. L., Darkner, Sune, Sporring, Jon & Nielsen, Mads, 2015, The 18th International Conference on Medical Image Computing and Computer Assisted Intervention: proceedings. Technische Universität München , p. 35-47 13 p.

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  13. Published

    An Automatic DWI/FLAIR Mismatch Assessment of Stroke Patients

    Johansen, Jacob, Offersen, C. M., Carlsen, Jonathan Frederik, Ingala, S., Hansen, Adam Espe, Nielsen, Michael Bachmann, Darkner, Sune & Pai, A., 2024, In: Diagnostics. 14, 1, 12 p., 69.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    An algebra for local histograms

    Sporring, Jon & Darkner, Sune, 2022, In: Frontiers in Computer Science. 4, p. 1-9 939563.

    Research output: Contribution to journal › Journal article › Research › peer-review

  15. Published

    Auto-segmentation of Hip Joints Using MultiPlanar UNet with Transfer Learning

    Xu, Peidi, nsv780, nsv780, Gholamalizadeh, T., Nielsen, Michael Bachmann, Erleben, Kenny & Darkner, Sune, 2022, Medical Image Learning with Limited and Noisy Data: First International Workshop, MILLanD 2022 Held in Conjunction with MICCAI 2022 Singapore, September 22, 2022 Proceedings. Zamzmi, G., Antani, S., Rajaraman, S., Xue, Z., Bagci, U. & Linguraru, M. G. (eds.). Springer Science and Business Media Deutschland GmbH, p. 153-162 10 p. (Medical Image Learning with Limited and Noisy Data, Vol. 13559).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  16. Published

    Automatic FDG-PET-based tumor and metastatic lymph node segmentation in cervical cancer

    Rodríguez Arbonès, D., Jensen, H. G., Loft, A., af Rosenschöld, P. M., Hansen, A. E., Igel, Christian & Darkner, Sune, 2014, Medical Imaging 2014: Image Processing. Ourselin, S. & Styner, M. A. (eds.). SPIE - International Society for Optical Engineering, 8 p. 903441. (Progress in Biomedical Optics and Imaging; No. 35, Vol. 15).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  17. Published

    Automatic correction of dental artifacts in PET/MRI

    Ladefoged, C. N., Andersen, F. L., Keller, S., Beyer, T., Law, I., Højgaard, Liselotte, Darkner, Sune & Lauze, Francois Bernard, 2015, In: SPIE Journal of Medical Imaging. 2, 2, 13 p., 024009.

    Research output: Contribution to journal › Journal article › Research › peer-review

  18. Published

    Automatic measurement of wrist synovitis from contrast-enhanced MRI: a registration-centered approach

    Mysling, P., Darkner, Sune, Sporring, Jon, Dam, E. & Lillholm, Martin, 2013, Medical Imaging 2013: Image Processing. Ourselin, S. & Haynor, D. R. (eds.). SPIE - International Society for Optical Engineering, 6 p. 86692U. (Progress in Biomedical Optics and Imaging; No. 36, Vol. 14).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  19. Published

    Brain Segmentation in Rodent MR-Images Using Convolutional Neural Networks

    Sigurdsson, B., Darkner, Sune, Sommer, Stefan Horst, Mortensen, K. N., Sanggaard, S., Kostrikov, S. & Nedergaard, Maiken, 2018.

    Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

  20. Published

    Bundle Geodesic Convolutional Neural Network for DWI Segmentation from Single Scan Learning

    Liu, Renfei, Lauze, Francois Bernard, Erleben, Kenny & Darkner, Sune, 2021, Computational Diffusion MRI - 12th International Workshop, CDMRI 2021, Held in Conjunction with MICCAI 2021, Proceedings. Cetin-Karayumak, S., Christiaens, D., Figini, M., Guevara, P., Gyori, N., Nath, V. & Pieciak, T. (eds.). Springer, p. 121-132 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 13006 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  21. Published

    Bundle geodesic convolutional neural network for diffusion-weighted imaging segmentation

    Liu, Renfei, Lauze, Francois Bernard, Erleben, Kenny, Berg, Rune W. & Darkner, Sune, 2022, In: Journal of Medical Imaging. 9, 6, 14 p., 064002.

    Research output: Contribution to journal › Journal article › Research › peer-review

  22. Published

    Cine-MRI Simulation to Evaluate Tumor Tracking

    Tascón-Vidarte, J. D., Wahlstedt, I., Jomier, J., Erleben, Kenny, Vogelius, Ivan R. & Darkner, Sune, 2021, Simulation and Synthesis in Medical Imaging - 6th International Workshop, SASHIMI 2021, Held in Conjunction with MICCAI 2021, Proceedings. Svoboda, D., Burgos, N., Wolterink, J. M. & Zhao, C. (eds.). Springer, p. 131-141 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 12965 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  23. Published

    Collision-constrained deformable image registration framework for discontinuity management

    Alscher, Thomas Michael, Erleben, Kenny & Darkner, Sune, 2023, In: PLoS ONE. 18, 8, 15 p., e0290243.

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Published

    Collocation for diffeomorphic deformations in medical image registration

    Darkner, Sune, Pai, A. S. U., Liptrot, M. G. & Sporring, Jon, 2018, In: I E E E Transactions on Pattern Analysis and Machine Intelligence. 40, 7, p. 1570-1583

    Research output: Contribution to journal › Journal article › Research › peer-review

  25. Published

    Combining the boundary shift integral and tensor-based morphometry for brain atrophy estimation

    Michalkiewicz, M. D., Pai, A. S. U., Leung, K. K., Sommer, Stefan Horst, Darkner, Sune, Sørensen, L., Sporring, Jon & Nielsen, Mads, 2016, Medical imaging 2016: Image processing. Styner, M. A. & Angelini, E. D. (eds.). SPIE - International Society for Optical Engineering, 6 p. 978406. (Progress in Biomedical Optics and Imaging).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  26. Published

    Comparison of several computational pipelines for atrophy computation in longitudinal Alzheimers studies

    Pai, A. S. U., Sommer, Stefan Horst, Darkner, Sune, Sørensen, L. E. B. L., Sporring, Jon & Nielsen, Mads, 2015. 1 p.

    Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

  27. Published

    Conforming contact manifolds for multibody simulations

    Visseq, V., Bonde, U., Erleben, Kenny & Darkner, Sune, 2014. 2 p.

    Research output: Contribution to conference › Conference abstract for conference › Research

  28. Published

    Contact modeling from images using cut finite element solvers

    Claus, S., Kerfriden, P., nsv780, nsv780, Darkner, Sune, Erleben, Kenny & Wong, Christian, 2021, In: Advanced Modeling and Simulation in Engineering Sciences. 8, 1, p. 1-23 13.

    Research output: Contribution to journal › Journal article › Research › peer-review

  29. Published

    Cube propagation for focal brain atrophy estimation

    Pai, A. S. U., Sørensen, L., Darkner, Sune, Mysling, P., Jørgensen, D. R., Dam, E. B., Lillholm, Martin, Oh, J., Chen, G., Suhy, J., Sporring, Jon & Nielsen, Mads, 2013, 2013 IEEE 10th International Symposium on Biomedical Imaging. IEEE, p. 402-405 4 p.

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  30. Published

    Data Driven Inverse Kinematics of Soft Robots using Local Models

    Holsten, F., Engell-norregard, M. P., Darkner, Sune & Erleben, Kenny, 2019, 2019 International Conference on Robotics and Automation (ICRA). IEEE, p. 6251-6257

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  31. Published

    Data driven constraints for the SVM

    Darkner, Sune & Clemmensen, L. H., 2012, Machine Learning in Medical Imaging: Third International Workshop, MLMI 2012, Held in Conjunction with MICCAI 2012, Nice, France, October 1, 2012, Revised Selected Papers. Wang, F., Shen, D., Yan, P. & Suzuki, K. (eds.). Springer, p. 70-77 8 p. (Lecture notes in computer science, Vol. 7588).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  32. Published

    Deep Learning-Assisted Localisation of Nanoparticles in synthetically generated two-photon microscopy images

    Netterstrøm, R., Kutuzov, Nikolay, Darkner, Sune, Pallesen, M. J., Lauritzen, Martin, Erleben, Kenny & Lauze, Francois Bernard, 2023, arXiv.org, 1 p.

    Research output: Working paper › Preprint › Research

  33. Published

    Deep-learning-based segmentation of individual tooth and bone with periodontal ligament interface details for simulation purposes

    Xu, Peidi, Gholamalizadeh, T., nsv780, nsv780, Darkner, Sune & Erleben, Kenny, 2023, In: IEEE Access. 11, p. 102460-102470

    Research output: Contribution to journal › Journal article › Research › peer-review

  34. Published

    Deformation-based atrophy computation by surface propagation and its application to Alzheimer’s disease

    Pai, A. S. U., Sporring, Jon, Darkner, Sune, Dam, Erik Bjørnager, Lillholm, Martin, Jørgensen, D., Oh, J., Chen, G., Suhy, J., Sørensen, L. & Nielsen, Mads, 2016, In: SPIE Journal of Medical Imaging. 3, 1, 11 p., 014005.

    Research output: Contribution to journal › Journal article › Research › peer-review

  35. Published

    Density-based non-rigid registration of diffusion-weighted images

    Jensen, H. G., Lauze, Francois Bernard, Nielsen, Mads & Darkner, Sune, Apr 2017.

    Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

  36. Published

    Deterministic Group Tractography with Local Uncertainty Quantification

    Holm, Andreas Nugaard, Feragen, A., Dela Haije, T. & Darkner, Sune, 2019, Computational Diffusion: International MICCAI Workshop, Granada,. Bonet-Carne, E., Grussu, F., Ning, L., Sepehrband, F. & Tax, C. M. W. (eds.). 226249 ed. Springer, p. 377-386 (Mathematics and Visualization).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  37. Published

    Diffeomorphic image registration with automatic time-step adjustment

    Pai, A. S. U., Klein, S., Sommer, Stefan Horst, Darkner, Sune, Sporring, Jon & Nielsen, Mads, 2015, 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI). IEEE, p. 1085-1088 4 p.

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  38. Published

    Drift Corrector Software

    Stephensen, Hans Jacob Teglbjærg, Darkner, Sune & Sporring, Jon, 20 Aug 2019

    Research output: Non-textual form › Computer programme › Research

  39. Published

    Efficient hyperelastic regularization for registration

    Darkner, Sune, Hansen, M. S., Larsen, R. & Hansen, M. F., 2011, Image Analysis: 17th Scandinavian Conference, SCIA 2011, Ystad, Sweden, May 2011. Proceedings. Heyden, A. & Kahl, F. (eds.). Springer, p. 295-305 11 p. (Lecture notes in computer science, Vol. 6688).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  40. Published

    Estimating the thickness of ultra thin sections for electron microscopy by image statistics

    Sporring, Jon, Khanmohammadi, M., Darkner, Sune, Nava, N., Nyengaard, J. R. & Jensen, E. B. V., 2014, 2014 IEEE International Symposium on Biomedical Imaging. IEEE, p. 157-160 4 p.

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  41. Published

    Evaluation of WBAA with registration-based cube propagation for brain atrophy quantification

    Lillholm, Martin, Pai, A. S. U., Sørensen, L., Nielsen, Mads, Sporring, Jon, Darkner, Sune & Dam, E., 2013. 1 p.

    Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

  42. Published

    Evaluation of bias in brain atrophy estimation

    Pai, A. S. U., Darkner, Sune, Sørensen, L., Erleben, L. L., Mysling, P., Sporring, Jon, Dam, E. & Nielsen, Mads, 2012, NIBAD '12: MICCAI 2012 Workshop on Novel Imaging Biomarkers for Alzheimer’s Disease and Related Disorders. Wang, L., Yushkevich, P. & Ourselin, S. (eds.). MICCAI , p. 198-206 9 p.

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  43. Published

    Extremely Weakly-Supervised Blood Vessel Segmentation with Physiologically Based Synthesis and Domain Adaptation

    Xu, Peidi, Lee, B., Sosnovtseva, Olga, Sorensen, Charlotte Mehlin, Erleben, Kenny & Darkner, Sune, 2023, Medical Image Learning with Limited and Noisy Data - 2nd International Workshop, MILLanD 2023, Held in Conjunction with MICCAI 2023, Proceedings. Xue, Z., Antani, S., Zamzmi, G., Yang, F., Rajaraman, S., Liang, Z., Huang, S. X. & Linguraru, M. G. (eds.). Springer, p. 191-201 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 14307 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  44. Published

    FDG-PET template MNI152 1mm

    Darkner, Sune, 2013

    Research output: Non-textual form › Dataset › Research

  45. Published

    Fast Vortex Particle Method for Fluid-Character Interaction

    Meldgaard, A., Darkner, Sune & Erleben, Kenny, 2022, In: OpenReview.net. 2022, 7 p.

    Research output: Contribution to journal › Conference article › Research

  46. Published

    Fast Vortex Particle Method for Fluid-Character Interaction

    Meldgaard, A., Erleben, Kenny & Darkner, Sune, 2022, In: Proceedings - Graphics Interface. 2022-May, 10.

    Research output: Contribution to journal › Conference article › Research › peer-review

  47. Published

    Finding significantly connected voxels based on histograms of connection strengths

    Kasenburg, N., Pedersen, M. V. & Darkner, Sune, 2016, Medical Imaging 2016: Image Processing. Styner, M. A. & Angelini, E. D. (eds.). SPIE - International Society for Optical Engineering, 7 p. 978431. (Progress in Biomedical Optics and Imaging; No. 39, Vol. 17).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  48. Published

    First Order Locally Orderless Registration

    Darkner, Sune, Vidarte, J. D. T. & Lauze, Francois Bernard, 2021, Scale Space and Variational Methods in Computer Vision - 8th International Conference, SSVM 2021, Proceedings. Elmoataz, A., Fadili, J., Quéau, Y., Rabin, J. & Simon, L. (eds.). Springer, p. 177-188 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 12679 LNCS).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

  49. Published

    First-in-man mesenchymal stem cells for radiation-induced xerostomia (MESRIX): study protocol for a randomized controlled trial.

    Grønhøj, C., Jensen, D. H., Glovinski, P. V., mpw981, M., Jensen, A. B., Oliveri, R. S., Specht, Lena, Thomsen, C., Darkner, Sune, Kiss, K., Fischer-Nielsen, A. & von Buchwald, Christian, 2017, In: Trials. 18, 1, 10 p., 108.

    Research output: Contribution to journal › Journal article › Research › peer-review

  50. Published

    Generalized Partial Volume: an inferior density estimator to Parzen Windows for normalized mutual information

    Darkner, Sune & Sporring, Jon, 2011, Information Processing in Medical Imaging: 22nd International Conference, IPMI 2011, Kloster Irsee, Germany, July 3-8, 2011. Proceedings. Székely, G. & Hahn, H. K. (eds.). Springer, p. 436-447 12 p. (Lecture notes in computer science, Vol. 6801).

    Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

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