Sune Darkner

Sune Darkner

Associate Professor

  • Image Analysis, Computational Modelling and Geometry

    Universitetsparken 5, 2100 København Ø

    Phone: +45 35 33 57 02Mobile: +45 21 30 85 84

  1. Published

    3D analysis of synaptic vesicle density and distribution after acute foot-shock stress by using serial section transmission electron microscopy. / Khanmohammadi, Mahdieh; Darkner, Sune; Nava, Nicoletta; Nyengaard, J. R.; Wegener, G.; Popoli, M.; Sporring, Jon.

    In: Journal of Microscopy, Vol. 265, No. 1, 2017, p. 101–110.

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. Published

    3D estimation of synaptic vesicle distributions in serial section transmission electron microscopy. / Khanmohammadi, Mahdieh; Darkner, Sune; Nava, Nicoletta; Nyengaard, Jens Randel; Sporring, Jon.

    2013. Abstract from European Congress of Stereology and Image Analysis, Kaiserslautern, Germany.

    Research output: Contribution to conferenceConference abstract for conferenceResearchpeer-review

  3. Published

    A Highly Accurate Model Based Registration Method for FIB-SEM Images of Neurons. / Stephensen, Hans Jacob Teglbjærg; Darkner, Sune; Sporring, Jon.

    In: arXiv.org, 2019.

    Research output: Contribution to journalJournal articleResearch

  4. 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.

    In: Visual Computer, Vol. 27, No. 6, 2011, p. 645-653.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Published

    A statistical model for simultaneous template estimation, bias correction, and registration of 3D brain images. / Pai, Akshay Sadananda Uppinakudru; Sommer, Stefan Horst; Raket, Lars Lau; Kühnel, Line; Darkner, Sune; Sørensen, Lauge; Nielsen, Mads.

    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. ed. / Henning Müller; B. Michael Kelm; Tal Arbel; Weidong Cai; M. Jorge Cardoso; Georg Langs; Bjoern Menze; Dmitris Metaxas; Albert Montillo; William M. Wells; Shaoting Zhang; Albert C. S. Chung; Mark Jenkinson; Annemie Ribbens. Springer, 2017. p. 151-159 (Lecture notes in computer science, Vol. 10081).

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  6. Published

    Adaptive time-stepping in dieomorphic image registration with bounded inverse consistency error. / Pai, Akshay Sadananda Uppinakudru; Klein, Stefan; Sommer, Stefan Horst; Sørensen, Lauge; Darkner, Sune; Sporring, Jon; Nielsen, Mads.

    Proceedings of the fifth international workshop on Mathematical Foundations of Computational Anatomy (MFCA 2015) . INRIA, 2015. p. 35-47.

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  7. Published

    Adaptive time-stepping in diffeomorphic image registration with bounded inverse consistency error. / Pai, Akshay Sadananda Uppinakudru; Klein, Stefan; Sommer, Stefan Horst; Sørensen, Lauge Emil Borch Laurs; Darkner, Sune; Sporring, Jon; Nielsen, Mads.

    The 18th International Conference on Medical Image Computing and Computer Assisted Intervention: proceedings. Technische Universität München , 2015. p. 35-47.

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  8. Published

    Automatic FDG-PET-based tumor and metastatic lymph node segmentation in cervical cancer. / Rodríguez Arbonès, Dídac; Jensen, Henrik Grønholt; Loft, Annika; af Rosenschöld, Per Munck; Hansen, Anders Elias; Igel, Christian; Darkner, Sune.

    Medical Imaging 2014: Image Processing. ed. / Sebastian Ourselin; Martin A. Styner. SPIE - International Society for Optical Engineering, 2014. 903441 (Progress in Biomedical Optics and Imaging; No. 35, Vol. 15).

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  9. Published

    Automatic correction of dental artifacts in PET/MRI. / Ladefoged, Claes N.; Andersen, Flemming L.; Keller, Sune; Beyer, Thomas; Law, Ian; Højgaard, Liselotte; Darkner, Sune; Lauze, Francois Bernard.

    In: SPIE Journal of Medical Imaging, Vol. 2, No. 2, 024009, 2015.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Published

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

    Medical Imaging 2013: Image Processing. ed. / Sebastien Ourselin; David R. Haynor. SPIE - International Society for Optical Engineering, 2013. 86692U (Progress in Biomedical Optics and Imaging; No. 36, Vol. 14).

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  11. Published

    Brain Segmentation in Rodent MR-Images Using Convolutional Neural Networks. / Sigurdsson, Björn; Darkner, Sune; Sommer, Stefan Horst; Mortensen, Kristian Nygaard; Sanggaard, Simon; Kostrikov, Serhii; Nedergaard, Maiken.

    2018. Abstract from Joint Annual Meeting ISMRM-ESMRMB 2018, Paris, France.

    Research output: Contribution to conferenceConference abstract for conferenceResearchpeer-review

  12. Published

    Collocation for diffeomorphic deformations in medical image registration. / Darkner, Sune; Pai, Akshay Sadananda Uppinakudru; Liptrot, Matthew George; Sporring, Jon.

    In: I E E E Transactions on Pattern Analysis and Machine Intelligence, Vol. 40, No. 7, 2018, p. 1570-1583.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Published

    Combining the boundary shift integral and tensor-based morphometry for brain atrophy estimation. / Michalkiewicz, Mateusz Dawid; Pai, Akshay Sadananda Uppinakudru; Leung, Kelvin K.; Sommer, Stefan Horst; Darkner, Sune; Sørensen, Lauge; Sporring, Jon; Nielsen, Mads.

    Medical imaging 2016: Image processing. ed. / Martin A. Styner; Elsa D. Angelini. SPIE - International Society for Optical Engineering, 2016. 978406 (Progress in Biomedical Optics and Imaging).

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  14. Published

    Comparison of several computational pipelines for atrophy computation in longitudinal Alzheimers studies. / Pai, Akshay Sadananda Uppinakudru; Sommer, Stefan Horst; Darkner, Sune; Sørensen, Lauge Emil Borch Laurs; Sporring, Jon; Nielsen, Mads.

    2015. Abstract from 101st Scientific Assembly and Annual Meeting of the Radiological Society of North America , Chicago, United States.

    Research output: Contribution to conferenceConference abstract for conferenceResearchpeer-review

  15. Published

    Conforming contact manifolds for multibody simulations. / Visseq, Vincent; Bonde, Ulrik; Erleben, Kenny; Darkner, Sune.

    2014. Abstract from World Congress on Computational Mechanics (WCCM XI), Barcelona, Spain.

    Research output: Contribution to conferenceConference abstract for conferenceResearch

  16. Published

    Cube propagation for focal brain atrophy estimation. / Pai, Akshay Sadananda Uppinakudru; Sørensen, Lauge; Darkner, Sune; Mysling, Peter; Jørgensen, Dan Richter; Dam, Erik B.; Lillholm, Martin; Oh, Joonmi; Chen, Gennan; Suhy, Joyce; Sporring, Jon; Nielsen, Mads.

    2013 IEEE 10th International Symposium on Biomedical Imaging. IEEE, 2013. p. 402-405.

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  17. Published

    Data Driven Inverse Kinematics of Soft Robots using Local Models. / Holsten, Fredrik; Engell-norregard, Morten Pol; Darkner, Sune; Erleben, Kenny.

    2019 International Conference on Robotics and Automation (ICRA). IEEE, 2019. p. 6251-6257.

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  18. Published

    Data driven constraints for the SVM. / Darkner, Sune; Clemmensen, Line H.

    Machine Learning in Medical Imaging: Third International Workshop, MLMI 2012, Held in Conjunction with MICCAI 2012, Nice, France, October 1, 2012, Revised Selected Papers. ed. / Fei Wang; Dinggang Shen; Pingkun Yan; Kenji Suzuki. Springer, 2012. p. 70-77 (Lecture notes in computer science, Vol. 7588).

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  19. Published

    Deformation-based atrophy computation by surface propagation and its application to Alzheimer’s disease. / Pai, Akshay Sadananda Uppinakudru; Sporring, Jon; Darkner, Sune; Dam, Erik Bjørnager; Lillholm, Martin; Jørgensen, Dan; Oh, Joonmi; Chen, Gennan; Suhy, Joyce; Sørensen, Lauge; Nielsen, Mads.

    In: SPIE Journal of Medical Imaging, Vol. 3, No. 1, 014005, 2016.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Published

    Density-based non-rigid registration of diffusion-weighted images. / Jensen, Henrik Grønholt; Lauze, Francois Bernard; Nielsen, Mads; Darkner, Sune.

    2017. Abstract from 25th ISMRM Annual Meeting, Honolulu, United States.

    Research output: Contribution to conferenceConference abstract for conferenceResearchpeer-review

  21. Published

    Deterministic Group Tractography with Local Uncertainty Quantification. / Holm, Andreas Nugaard; Feragen, Aasa; Dela Haije, Tom; Darkner, Sune.

    Computational Diffusion: International MICCAI Workshop, Granada,. ed. / Elisenda Bonet-Carne; Francesco Grussu; Lipeng Ning; Farshid Sepehrband; Chantal M. W. Tax. 226249. ed. Springer, 2019. p. 377-386 (Mathematics and Visualization).

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  22. Published

    Diffeomorphic image registration with automatic time-step adjustment. / Pai, Akshay Sadananda Uppinakudru; Klein, S.; Sommer, Stefan Horst; Darkner, Sune; Sporring, Jon; Nielsen, Mads.

    Biomedical Imaging (ISBI), 2015 IEEE 12th International Symposium on. IEEE, 2015. p. 1085-1088.

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  23. Published

    Efficient hyperelastic regularization for registration. / Darkner, Sune; Hansen, Michael Sass; Larsen, Rasmus; Hansen, Mads F.

    Image Analysis: 17th Scandinavian Conference, SCIA 2011, Ystad, Sweden, May 2011. Proceedings. ed. / Anders Heyden; Fredrik Kahl. Springer, 2011. p. 295-305 (Lecture notes in computer science, Vol. 6688).

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  24. Published

    Estimating the thickness of ultra thin sections for electron microscopy by image statistics. / Sporring, Jon; Khanmohammadi, Mahdieh; Darkner, Sune; Nava, Nicoletta; Nyengaard, Jens Randel; Jensen, Eva B. Vedel.

    2014 IEEE International Symposium on Biomedical Imaging. IEEE, 2014. p. 157-160.

    Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

  25. Published

    Evaluation of WBAA with registration-based cube propagation for brain atrophy quantification. / Lillholm, Martin; Pai, Akshay Sadananda Uppinakudru; Sørensen, Lauge; Nielsen, Mads; Sporring, Jon; Darkner, Sune; Dam, Erik.

    2013. Abstract from 99th Scientific Assembly and Annual Meeting of the Radiological Society of North America, Chicago, United States.

    Research output: Contribution to conferenceConference abstract for conferenceResearchpeer-review

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