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Henrik Skibbe



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Publications @Google Scholar

Refereed Articles

2018
  • L. Konopleva, K.A. Il'yasov, H. Skibbe, V.G. Kiselev, E. Kellner, B. Dhital, M. Reisert
    Modelfree global tractography
    In NeuroImage, Elsevier, 2018.
  • H. Skibbe, M. Reisert, K. Nakae, A. Watakabe, J. Hata, H. Mizukami, H. Okano, T. Yamamori, S. Ishii
    PAT - Probabilistic Axon Tracking for Densely Labeled Neurons in Large 3D Micrographs
    In accepted for publication in IEEE Trans. Med. Imaging, 2018. [doi]


    Axon configuration from full brain images.


    Global energy minimization based on stochastic optimization.

2017
  • H. Skibbe, M. Reisert
    Spherical Tensor Algebra: A Toolkit for 3D Image Processing
    In Journal of Mathematical Imaging and Vision, 2017. [doi]

    Please find the corresponding source code here : STA-ImageToolbox
2016
  • K. Meshgi, S. Maeda, S. Oba, H. Skibbe, Y. Li, S. Ishii
    An occlusion-aware particle filter tracker to handle complex and persistent occlusions
    In Computer Vision and Image Understanding, Academic Press, volume 150, 2016.
2015
  • H. Skibbe, M. Reisert, S. Maeda, M. Koyama, S. Oba, K. Ito, S. Ishii
    Efficient Monte Carlo Image Analysis for the Location of Vascular Entity
    In IEEE Trans. Med. Imaging, volume 34, 2015. [doi]


2013
  • H. Skibbe, M. Reisert
    Rotation Covariant Image Processing for Biomedical Applications
    In Computational and Mathematical Methods in Medicine, Special Issue on Mathematical Methods in Biomedical Imaging, Hindawi Publishing Corporation, volume 2013, 2013. [pdf]
  • K. Liu, H. Skibbe, T. Schmidt, T. Blein, K. Palme, T. Brox, O. Ronneberger
    Rotation-Invariant HOG Descriptors using Fourier Analysis in Polar and Spherical Coordinates
    In International Journal of Computer Vision, volume Online First, 2013.
2012
  • O. Ronneberger, K. Liu, M. Rath, D. Rueß, T. Mueller, H. Skibbe, B. Drayer, T. Schmidt, A. Filippi, R. Nitschke, T. Brox, H. Burkhardt, W. Driever
    ViBE-Z: A Framework for 3D Virtual Colocalization Analysis in Zebrafish Larval Brains
    In Nature Methods, volume 9, 2012.
Refereed Conference Papers

2015
  • M. Reisert, B. Dihtal, E. Kellner, H. Skibbe, C. Kaller
    Symmetric Wiener Processes for Probabilistic Tractography and Connectivity Estimation
    In Medical Image Computing and Computer-Assisted Intervention--MICCAI 2015, Springer International Publishing, 2015.
2014
  • H. Skibbe, M. Reisert, S. Ishii
    Efficient Monte Carlo Image Analysis for the Location Of Vascular Entity
    In Proc. of the GCPR, LNCS, Springer, 2014.
2013
  • M. Reisert, H. Skibbe
    Fiber Continuity based Spherical Deconvolution in Spherical Harmonic Domain
    In Medical Image Computing and Computer-Assisted Intervention–MICCAI 2013, 2013.
2012
  • M. Reisert, H. Skibbe, V.G. Kiselev
    Fiber density estimation by tensor divergence
    In Medical Image Computing and Computer-Assisted Intervention--MICCAI 2012, Springer Berlin Heidelberg, 2012.
2011
  • K. Liu, H. Skibbe, T. Schmidt, T. Blein, K. Palme, O. Ronneberger
    3D Rotation-Invariant Description from Tensor Operation on Spherical HOG Field
    In Proc. of the BMVC (S.M.K.M.T. Jesse Hoey, J. Zhang, eds.), 2011.
  • H. Skibbe, M. Reisert, O. Ronneberger, H. Burkhardt
    Spherical Bessel Filter for 3D Object Detection
    In Proc. of the ISBI, 2011. [pdf]


  • H. Skibbe, M. Reisert, H. Burkhardt
    SHOG - Spherical HOG Descriptors for Rotation Invariant 3D Object Detection
    In Proc. of the DAGM, LNCS, Springer, 2011. [pdf]


    You can find code samples here: https://bitbucket.org/skibbe/sta-toolbox/ (matlab/octave/c++). They include the demo: SHOG-DEMO.
  • H. Skibbe, M. Reisert, H. Burkhardt
    Gaussian Neighborhood Descriptors for Brain Segmentation
    In Proc. of the MVA, 2011. [pdf]


  • M. Reisert, H. Skibbe
    Steerable deconvolution feature detection as an inverse problem
    In Proc. of the DAGM, LNCS, Springer, 2011.
2010
  • H. Skibbe, M. Reisert, T. Schmidt, K. Palme, O. Ronneberger, H. Burkhardt
    3D Object Detection using a Fast Voxel-Wise Local Spherical Fourier Tensor Transformation
    In Proc. of the DAGM, LNCS, Springer, 2010. [pdf]


2009
  • H. Skibbe, A. Teynor, H. Burkhardt
    Unsupervised Learning of Characteristic Object Parts from Videos
    In Proc. of the MVA, 2009. [pdf]
  • H. Skibbe, M. Reisert, O. Ronneberger, H. Burkhardt
    Increasing the Dimension of Creativity in Rotation Invariant Feature Design Using 3D Tensorial Harmonics
    In Proc. of the DAGM, LNCS, Springer, 2009. [pdf]


  • H. Skibbe, M. Reisert, Q. Wang, O. Ronneberger, H. Burkhardt
    Fast Computation of 3D Spherical Fourier Harmonic Descriptors - A Complete Orthonormal Basis for a Rotational Invariant Representation of Three-Dimensional Objects.
    In Proc. of the 3DIM , part of the ICCV, 2009. [pdf]


2005
  • Z. Lu, H. Skibbe, H. Burkhardt
    Image retrieval based on a multipurpose watermarking scheme
    In Knowledge-Based Intelligent Information and Engineering Systems, 2005.
Refereed Workshop Papers

2013
  • M. Reisert, H. Skibbe, V.G. Kiselev
    The Diffusion Dictionary in the Human Brain is Short: Rotation Invariant Learning of Basis Functions
    In Proc. of the Workshop on Computational Diffusion MRI (CDMRI'13), part of the MICCAI 2013, 2013.
2012
  • H. Skibbe, M. Reisert
    Detection of Unique Point Landmarks in HARDI Images of the Human Brain
    In Proc. of the Workshop on Computational Diffusion MRI (CDMRI'12), part of the MICCAI 2012, 2012. [pdf]


2011
  • H. Skibbe, M. Reisert
    Dense Rotation Invariant Brain Pyramids for Automated Human Brain Parcellation
    In Proc. of the Informatik 2011, Workshop on Emerging Technologies for Medical Diagnosis and Therapy, 2011. [pdf]


Other Publications

2018
  • M. Reisert, V.A. Coenen, C. Kaller, K. Egger, H. Skibbe
    HAMLET: Hierarchical Harmonic Filters for Learning Tracts from Diffusion MRI
    Technical report, 1, 2018.
    online: https://arxiv.org/abs/1807.01068

2013
2012
  • M. Reisert, H. Skibbe
    Left-Invariant Diffusion on the Motion Group in terms of the Irreducible Representations of SO(3)
    Technical report, 1, 2012.
    online: https://arxiv.org/abs/1202.5414

Abstracts

2018
  • K. Nakae, H. Junichi, H. Skibbe, A. Woodward, C.E. Gutierrez, T. Hiromachi, R. Gong, R. Ito, H. Okano, S. Ishii
    A pipeline for macro-scale connectomics of the common marmoset with global fiber reconstruction from diffusion MRI
    CNS, 2018. (Seattle, USA)
  • C.E. Gutierrez, H. Skibbe, K. Nakae, A. Woodward, A. Watakabe, J. Hata, H. Okano, T. Yamamori, Y. Yamaguchi, S. Ishii, K. Doya
    GA-based Parameter Optimization of DWI-based Global Fiber Tracking with Neuronal Tracer Signal as a Reference
    Cosyne, 2018. (Denver, Colorado, USA)
  • A. Watakabe, J. Wang, M. Takaji, H. Mizukami, A. Woodward, H. Skibbe, K. Nakae, Y. Yamaguchi, S. Ishii, T. Yamamori
    Prefrontal projection mapping of the marmose
    Neuroscience, 2018. (Kobe, Japan)
  • K. Nakae, H. Junichi, H. Skibbe, A. Woodward, C.E. Gutierrez, T. Hiromachi, R. Gong, H. Okano, S. Ishii
    Visualizing an individual diversity of marmoset connectome with a pipeline of tractography by MR
    Neuroscience, 2018. (Kobe, Japan)
  • H. Skibbe, K. Nakae, A. Watakabe, A. Woodward, C.E. Gutierrez, H. Tsukada, R. Gong, J. Hata, H. Okano, T. Yamamori, S. Ishii
    A pipeline for the automated integration of individual structural information from images of axonal tracer projections in marmoset brains into a structural map of full brain connectivity
    Neuroscience, 2018. (Kobe, Japan)
  • A. Watakabe, J. Wang, M. Takaji, H. Mizukami, A. Woodward, T. Kawase, H. Skibbe, K. Naka, Y. Yamaguchi, S. Ishii, T. Yamamori
    Prefrontal projection mapping of the common marmoset
    SfN, 2018. (San Diego, USA)
2017
  • K. Matsui, H. Skibbe, M. Reisert, S. Ishii
    A model-free supervised learning approach for the estimation of fiber orientation distributions from diffusion-weighted MRI images of the brain white matter
    Keystone Symposium on "Connectomics", 2017. (Santa Fe, New Mexico USA)
  • A. Watakabe, J. Wang, M. Takaji, H. Mizukami, A. Woodward, T. Kawase, H. Skibbe, K. Nakae, Y. Yamaguchi, S. Ishii, T. Yamamori
    Columnar and diffuse connectivity of the marmoset PFC neurons
    SFN, 2017. (Washington DC, USA)
2016
  • H. Skibbe, E. Kellner, V.G. Kiselev, M.R. i
    Model-free Global Tractography
    ISMRM, 2016. (Singapore)
  • H. Skibbe, S. Ishii
    Lending Global Fiber-Tracking to the Tracing Of Dense Neurites in Fluorescence Micrographs
    INCF, 2016. (Wako, Japan)
  • A. Watakabe, J. Wang, M. Takaji, H. Mizukami, A. Woodward, T. Kawase, H. Skibbe, Y. Yamaguchi, S. Ishii, T. Yamamori
    Mapping connectivity of marmoset prefrontal cortex by serial two-photon tomography
    SFN, 2016. (San Diego, USA)
2014
  • H. Skibbe, K. Ito, S. Ishii
    Large-Scale Tracking and Modeling of Neural Networks in 3D Micrographs
    ISMRM, 2014. (INCF)


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