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
ORCID: 0000-0001-6114-7100

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  1. Published

    Jet-based local image descriptors. / Boesen Lindbo Larsen, Anders; Darkner, Sune; Dahl, Anders Lindbjerg; Pedersen, Kim Steenstrup.

    Computer Vision – ECCV 2012: 12th European Conference on Computer Vision, Florence, Italy, October 7-13, 2012, Proceedings, Part III. ed. / Andrew Fitzgibbon; Svetlana Lazebnik; Pietro Perona; Yoichi Sato; Cardelia Schmid. Springer, 2012. p. 638-650 (Lecture notes in computer science, Vol. 7574).

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

  2. Published

    Generalized Partial Volume : an inferior density estimator to Parzen Windows for normalized mutual information. / Darkner, Sune; Sporring, Jon.

    Information Processing in Medical Imaging: 22nd International Conference, IPMI 2011, Kloster Irsee, Germany, July 3-8, 2011. Proceedings. ed. / Gáboe Székely; Horst K. Hahn. Springer, 2011. p. 436-447 (Lecture notes in computer science, Vol. 6801).

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

  3. 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 journal › Journal article › Research › peer-review

  4. 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 proceeding › Article in proceedings › Research › peer-review

  5. Published

    Locally orderless registration. / Darkner, Sune; Sporring, Jon.

    In: I E E E Transactions on Pattern Analysis and Machine Intelligence, Vol. 35, No. 6, 2013, p. 1437-1450.

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

  6. 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 journal › Journal article › Research › peer-review

  7. 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 proceeding › Article in proceedings › Research › peer-review

  8. Published
    Locally orderless registration code : fast normalized mutual information and P-Norm for MATLAB. Darkner, Sune (Producer); Sporring, Jon (Producer). 2012.

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

  9. Published
    FDG-PET template MNI152 1mm. Darkner, Sune (Producer). 2013.

    Research output: Non-textual form › Dataset › Research

  10. Published

    First-in-man mesenchymal stem cells for radiation-induced xerostomia (MESRIX) : study protocol for a randomized controlled trial. / Grønhøj, Christian; Jensen, David Hebbelstrup; Glovinski, Peter Viktor; mpw981, mpw981; Jensen, Allan Bardow; Oliveri, Roberto Stefan; Specht, Lena; Thomsen, Carsten; Darkner, Sune; Kiss, Katalin; Fischer-Nielsen, Anne; von Buchwald, Christian.

    In: Trials, Vol. 18, No. 1, 108, 2017.

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

  11. Published

    Safety and Efficacy of Mesenchymal Stem Cells for Radiation-Induced Xerostomia : A Randomized, Placebo-Controlled Phase 1/2 Trial (MESRIX). / Grønhøj, Christian; Jensen, David H; Vester-Glowinski, Peter; Jensen, Siri Beier; Bardow, Allan; Oliveri, Roberto S; Fog, Lea Munthe; Specht, Lena; Thomsen, Carsten; Darkner, Sune; Jensen, Michael; Müller, Vera; Kiss, Katalin; Agander, Tina; Andersen, Elo; Fischer-Nielsen, Anne; von Buchwald, Christian.

    In: International Journal of Radiation Oncology, Biology, Physics, Vol. 101, No. 3, 01.07.2018, p. 581-592.

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

  12. 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 proceeding › Article in proceedings › Research › peer-review

  13. 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 proceeding › Article in proceedings › Research › peer-review

  14. 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 conference › Conference abstract for conference › Research › peer-review

  15. Published

    Multimodal brain extraction from structural MRI using co-registered FDG-PET. / Jensen, Henrik Grønholt; Federspiel, Frederik Vilhelm Koch; Ptito, Maurice; Nielsen, Mads; Gjedde, Albert; Keller, Sune Høgild; Law, Ian; Kupers, Ron; Darkner, Sune.

    2015. Paper presented at Computational Methods for Molecular Imaging (CMMI) 2015, .

    Research output: Contribution to conference › Paper › Research

  16. Published

    Locally orderless registration for diffusion weighted images. / Jensen, Henrik Grønholt; Lauze, Francois Bernard; Nielsen, Mads; Darkner, Sune.

    Medical Image Computing and Computer-Assisted Intervention -- MICCAI 2015: 18th international conference, Munich, Germany, October 5-9, 2015, Proceedings, Part II. ed. / Nassir Navab; Joachim Hornegger; William M. Wells; Alejandro F. Frangi. Springer, 2015. p. 305-312 (Lecture notes in computer science, Vol. 9350).

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

  17. Published

    Finding significantly connected voxels based on histograms of connection strengths. / Kasenburg, Niklas; Pedersen, Morten Vester; Darkner, Sune.

    Medical Imaging 2016: Image Processing. ed. / Martin A. Styner; Elsa D. Angelini. SPIE - International Society for Optical Engineering, 2016. 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

  18. Published

    Structural parcellation of the thalamus using shortest-path tractography. / Kasenburg, Niklas; Darkner, Sune; Hahn, Ute; Liptrot, Matthew George; Feragen, Aasa.

    2016 IEEE 13th International Symposium on Biomedical Imaging (ISBI). IEEE, 2016. p. 559-563 7493330.

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

  19. 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 journal › Journal article › Research › peer-review

  20. 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 conference › Conference abstract for conference › Research › peer-review

  21. 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 journal › Journal article › Research › peer-review

  22. 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 conference › Conference abstract for conference › Research › peer-review

  23. Published

    Streamlet Tractography. / Liptrot, Matthew George; Darkner, Sune; Feragen, Aasa; Lauze, Francois Bernard.

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

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

  24. 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 proceeding › Article in proceedings › Research › peer-review

  25. 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 proceeding › Article in proceedings › Research › peer-review

  26. Published

    The cartilage bone junction and its implications for deep canal hearing instrument fittings. / Nielsen, Claus; Darkner, Sune.

    In: Hearing Journal, Vol. 64, No. 3, 2011, p. 35-42.

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

  27. Published

    Localized cerebral atrophy acceleration during Alzheimer’s disease. / Pai, Akshay Sadananda Uppinakudru; Sørensen, Lauge; Darkner, Sune; Lillholm, Martin; Dam, Erik B.; Sporring, Jon; Nielsen, Mads.

    In: Alzheimer's & Dementia, Vol. 9, No. 4, Supplement, IC-P-059, 2013, p. P36–P37.

    Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

  28. Published

    White matter hypointensity growth rate correlates with rate of brain atrophy. / Pai, Akshay Sadananda Uppinakudru; Sørensen, Lauge; Darkner, Sune; Sporring, Jon; Rostrup, Egill; Nielsen, Mads.

    In: Alzheimer's & Dementia, Vol. 10, No. 4, Supplement, P1-285, 2014, p. P414.

    Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

  29. 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 proceeding › Book chapter › Research › peer-review

  30. 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 conference › Conference abstract for conference › Research › peer-review

  31. Published

    Evaluation of bias in brain atrophy estimation. / Pai, Akshay Sadananda Uppinakudru; Darkner, Sune; Sørensen, Lauge; Erleben, Lene Lillemark; Mysling, Peter; Sporring, Jon; Dam, Erik; Nielsen, Mads.

    NIBAD '12: MICCAI 2012 Workshop on Novel Imaging Biomarkers for Alzheimer’s Disease and Related Disorders. ed. / L. Wang; P. Yushkevich; S. Ourselin. MICCAI , 2012. p. 198-206.

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

  32. Published

    Localized cerebral atrophy acceleration during Alzheimer’s disease. / Pai, Akshay Sadananda Uppinakudru; Sørensen, Lauge; Darkner, Sune; Lillholm, Martin; Dam, Erik B.; Sporring, Jon; Nielsen, Mads.

    In: Alzheimer's & Dementia, Vol. 9, No. 4, Supplement, O1-10-06, 2013, p. P151.

    Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

  33. Published

    Kernel bundle diffeomorphic image registration using stationary velocity fields and Wendland basis functions. / Pai, Akshay Sadananda Uppinakudru; Sommer, Stefan Horst; Sørensen, Lauge; Darkner, Sune; Sporring, Jon; Nielsen, Mads.

    In: IEEE transactions on medical imaging, Vol. 35, No. 6, 2016, p. 1369-1380.

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

  34. Published

    White matter hypointensity growth rate correlates with rate of brain atrophy. / Pai, Akshay Sadananda Uppinakudru; Sørensen, Lauge; Darkner, Sune; Sporring, Jon; Rostrup, Egill; Nielsen, Mads.

    In: Alzheimer's & Dementia, Vol. 10, No. 4, Supplement, IC-P-131, 2014, p. P75-P76.

    Research output: Contribution to journal › Conference abstract in journal › Research › peer-review

  35. Published

    Hippocampal texture predicts rate of cognitive decline in mild cognitive impairment. / Pai, Akshay Sadananda Uppinakudru; Pillai, Jagan A.; Sørensen, Lauge; Darkner, Sune; Sommer, Stefan Horst; Nielsen, Mads.

    In: Alzheimer's & Dementia, Vol. 13, No. 7, supplement, P4-225, 07.2017, p. P1356.

    Research output: Contribution to journal › Conference abstract in journal › Research

  36. Published

    Stepwise inverse consistent Euler’s scheme for diffeomorphic image registration. / Pai, Akshay Sadananda Uppinakudru; Sommer, Stefan Horst; Darkner, Sune; Sørensen, Lauge; Sporring, Jon; Nielsen, Mads.

    Biomedical Image Registration: 6th International Workshop, WBIR 2014, London, UK, July 7-8, 2014. Proceedings. ed. / Sébastien Ourselin; Marc Modat. Springer, 2014. p. 223-230 (Lecture notes in computer science, Vol. 8545).

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

  37. 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 proceeding › Article in proceedings › Research › peer-review

  38. 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 proceeding › Article in proceedings › Research › peer-review

  39. 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 journal › Journal article › Research › peer-review

  40. 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 proceeding › Article in proceedings › Research › peer-review

  41. Published

    Image registration using stationary velocity fields parameterized by norm-minimizing Wendland kernel. / Pai, Akshay Sadananda Uppinakudru; Sommer, Stefan Horst; Sørensen, Lauge; Darkner, Sune; Sporring, Jon; Nielsen, Mads.

    2015. Poster session presented at SPIE Medical Imaging 2015, Denmark.

    Research output: Contribution to conference › Poster › Research › peer-review

  42. 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 proceeding › Article in proceedings › Research › peer-review

  43. 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 proceeding › Article in proceedings › Research › peer-review

  44. 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 conference › Conference abstract for conference › Research › peer-review

  45. Published

    Higher-order momentum distributions and locally affine LDDMM registration. / Sommer, Stefan Horst; Nielsen, Mads; Darkner, Sune; Pennec, Xavier.

    In: S I A M Journal on Imaging Sciences, Vol. 6, No. 1, 2013, p. 341-367.

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

  46. 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 proceeding › Article in proceedings › Research › peer-review

  47. Published

    Jacobians for Lebesgue registration for a range of similarity measures. / Sporring, Jon; Darkner, Sune.

    Department of Computer Science, University of Copenhagen, 2011. 8 p. (Koebenhavns Universitet. Datalogisk Institut. Rapport; No. 04/2011).

    Research output: Book/Report › Report

  48. Published

    The minimal energetic requirement of sustained awareness after brain injury. / Stender, Johan; Mortensen, Kristian Nygaard; Thibaut, Aurore; Darkner, Sune; Laureys, Steven; Gjedde, Albert; Kupers, Ron.

    In: Current Biology, Vol. 26, No. 11, 06.06.2016, p. 1494-1499.

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

  49. 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 journal › Journal article › Research

  50. Published

    Hippocampal texture provides volume-independent information for Alzheimer's disease diagnosis. / Sørensen, Lauge; Pai, Akshay Sadananda Uppinakudru; Darkner, Sune; Suhy, Joyce; Oh, Joonmi; Chen, Gennan; Igel, Christian; Nielsen, Mads.

    In: Alzheimer's & Dementia, Vol. 8, No. 4, Supplement, 2012, p. P162–P163.

    Research output: Contribution to journal › Conference abstract in journal › Research

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