Publications

(not updated since 2019, see top page for updates)

• PAT - Probabilistic Axon Tracking for Densely Labeled Neurons in Large 3D Micrographs
  • H. Skibbe, M. Reisert, K. Nakae, A. Watakabe, J. Hata, H. Mizukami, H. Okano, T. Yamamori, S. Ishii
  • In IEEE Trans. Med. Imaging, volume 38, 2019.

• DeTerm: Software for automatic detection of neuronal dendritic branch terminals via an artificial neural network
  • Y. Kanaoka, H. Skibbe, Y. Hayashi, T. Uemura, Y. Hattori
  • Accepted for publication in Genes to Cells, 2019.

• Modelfree global tractography
  • L. Konopleva, K.A. Il'yasov, H. Skibbe, V.G. Kiselev, E. Kellner, B. Dhital, M. Reisert
  • In NeuroImage, Elsevier, 2018.

• Spherical Tensor Algebra: A Toolkit for 3D Image Processing
  • H. Skibbe, M. Reisert
  • In Journal of Mathematical Imaging and Vision, 2017
  • Please find the corresponding source code here : STA-ImageToolbox

• An occlusion-aware particle filter tracker to handle complex and persistent occlusions
  • K. Meshgi, S. Maeda, S. Oba, H. Skibbe, Y. Li, S. Ishii
  • In Computer Vision and Image Understanding, Academic Press, volume 150, 2016.

• Efficient Monte Carlo Image Analysis for the Location of Vascular Entity
  • H. Skibbe, M. Reisert, S. Maeda, M. Koyama, S. Oba, K. Ito, S. Ishii
  • In IEEE Trans. Med. Imaging, volume 34, 2015

• Rotation Covariant Image Processing for Biomedical Applications
  • H. Skibbe, M. Reisert
  • In Computational and Mathematical Methods in Medicine, Special Issue on Mathematical Methods in Biomedical Imaging, Hindawi Publishing Corporation, volume 2013

• Rotation-Invariant HOG Descriptors using Fourier Analysis in Polar and Spherical Coordinates
  • K. Liu, H. Skibbe, T. Schmidt, T. Blein, K. Palme, T. Brox, O. Ronneberger
  • In International Journal of Computer Vision, volume Online First, 2013.

• Fast Rotation Invariant 3D Feature Computation utilizing Efficient Local Neighborhood Operators
  • H. Skibbe, M. Reisert, T. Schmidt, T. Brox, O. Ronneberger, H. Burkhardt
  • In IEEE Trans. Pattern Anal. Mach. Intell., 2012

• ViBE-Z: A Framework for 3D Virtual Colocalization Analysis in Zebrafish Larval Brains
  • 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
  • In Nature Methods, volume 9, 2012.

• Semi-supervised Image-to-Image translation for robust image registration
  • Skibbe, H., Watakabe, A., Rachmadi, F., Gutierrez, C.E, Nakae,K. and Yamamori, T.
  • In Proc. of the Medical Imaging with Deep Learning 2021 2021

• Symmetric Wiener Processes for Probabilistic Tractography and Connectivity Estimation
  • Reisert, M, Dihtal, B, Kellner, E, Skibbe, H and Kaller, C
  • In Medical Image Computing and Computer-Assisted Intervention–MICCAI 2015 Springer International Publishing, 2015

• Efficient Monte Carlo Image Analysis for the Location Of Vascular Entity
  • Skibbe, Henrik, Reisert, Marco and Ishii, Shin
  • In Proc. of the GCPR LNCS, Springer, 2014

• Fiber Continuity based Spherical Deconvolution in Spherical Harmonic Domain
  • Reisert, M. and Skibbe, H.
  • In Medical Image Computing and Computer-Assisted Intervention–MICCAI 2013 2013

• Fiber density estimation by tensor divergence
  • Reisert, M., Skibbe, H. and Kiselev, V. G.
  • In Medical Image Computing and Computer-Assisted Intervention–MICCAI 2012 Springer Berlin Heidelberg, 2012

• Circular Fourier-HOG features for rotation invariant object detection in biomedical images
  • Skibbe, H. and Reisert, M.
  • In Proc. of the ISBI 2012

• Steerable deconvolution feature detection as an inverse problem
  • Reisert, Marco and Skibbe, Henrik
  • In Proc. of the DAGM LNCS, Springer, 2011

• Gaussian Neighborhood Descriptors for Brain Segmentation
  • Skibbe, H., Reisert, M. and Burkhardt, H.
  • In Proc. of the MVA 2011

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

• Spherical Bessel Filter for 3D Object Detection
  • Skibbe, H., Reisert, M., Ronneberger, O. and Burkhardt, H.
  • In Proc. of the ISBI 2011

• 3D Rotation-Invariant Description from Tensor Operation on Spherical HOG Field
  • K. Liu, H. Skibbe, T. Schmidt, T. Blein, K. Palme and O. Ronneberger
  • In Proc. of the BMVC (Jesse Hoey, Stephen McKenna, Manuel Trucco, Jianguo Zhang, eds.) 2011

• 3D Object Detection using a Fast Voxel-Wise Local Spherical Fourier Tensor Transformation
  • Skibbe, H. and Reisert, M. and Schmidt, T. and Palme, K. and Ronneberger, O. and Burkhardt, H.
  • In Proc. of the DAGM LNCS, Springer, 2010

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

• Increasing the Dimension of Creativity in Rotation Invariant Feature Design Using 3D Tensorial Harmonics
  • Skibbe, H., Reisert, M., Ronneberger, O. and Burkhardt, H.
  • In Proc. of the DAGM LNCS, Springer, 2009

• Unsupervised Learning of Characteristic Object Parts from Videos
  • Skibbe, H., Teynor, A. and Burkhardt, H.
  • In Proc. of the MVA 2009

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

• Probabilistic Deep Learning with Adversarial Training and Volume Interval Estimation-Better Ways to Perform and Evaluate Predictive Models for White Matter Hyperintensities Evolution
  • Rachmadi, Muhammad Febrian, Valdés-Hernández, Maria del C, Maulana, Rizal, Wardlaw, Joanna, Makin, Stephen and Skibbe, Henrik
  • In International Workshop on PRedictive Intelligence In MEdicine 2021

• The Diffusion Dictionary in the Human Brain is Short: Rotation Invariant Learning of Basis Functions
  • Reisert, M., Skibbe, H. and Kiselev, V. G.
  • In Proc. of the Workshop on Computational Diffusion MRI (CDMRI'13), part of the MICCAI 2013 2013

• Detection of Unique Point Landmarks in HARDI Images of the Human Brain
  • Skibbe, H. and Reisert, M.
  • In Proc. of the Workshop on Computational Diffusion MRI (CDMRI'12), part of the MICCAI 2012 2012

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

• MarmoNet: a pipeline for automated projection mapping of the common marmoset brain from whole-brain serial two-photon tomography
  • Skibbe, Henrik, Watakabe, Akiya, Nakae, Ken, Gutierrez, Carlos Enrique, Tsukada, Hiromichi, Hata, Junichiand Kawase, Takashi, Gong, Rui, Woodward, Alexander, Doya, Kenji, Okano, Hideyuki, Yamamori, Tetsuo and Ishii, Shin
  • Technical report, 1, 2019

• HAMLET: Hierarchical Harmonic Filters for Learning Tracts from Diffusion MRI
  • Reisert, Marco, Coenen, Volker A, Kaller, Christoph, Egger, Karl and Skibbe, Henrik
  • Technical report, 1, 2018

• Spherical Tensor Algebra for Biomedical Image Analysis
  • Skibbe, H.
  • PhD thesis, Albert-Ludwigs-Universität Freiburg, 2013

• Left-Invariant Diffusion on the Motion Group in terms of the Irreducible Representations of SO(3)
  • Reisert, M. and Skibbe, H
  • Technical report, 1, 2012

• Multi-objective Parameter Optimization of DWI-based Global Fiber Tracking with Neuronal Tracer Signal as a Reference
  • C. Enrique Gutierrez, H. Skibbe, K. Nakae, J. Liénard, A. Woodward, A. Watakabe, H. Tsukada, J. Hata, H. Okano, T. Yamamori, Y. Yamaguchi, S. Ishii and K. Doya
  • International Symposium of Brain/MINDS ISBM, 2019

• Macro-scale connectome by diffusion MRI of exvivo marmoset brain with a pipeline of global fiber reconstruction
  • K. Nakae, J. Hata, H. Skibbe, A. Woodward, C. E. Gutierrez, H. Tsukada, G. Rui, H. Okano and S. Ishii
  • International Symposium of Brain/MINDS ISBM, 2019

• A fully automated, AI-driven pipeline for the determination of the marmoset brain connectivity based on tracer data obtained with the TissueCyte microscope
  • H Skibbe, A. Watakabe, K. Nakae, C. E. Gutierrez, A. Woodward, H. Tsukada, R. Gong, J. Hata, H. Okano, T. Yamamori and S. Ishii
  • International Symposium of Brain/MINDS ISBM, 2019

• Fully automated data processing for mapping connectivity of the marmoset prefrontal cortex
  • H. Skibbe, A. Watakabe, K. Nakae, C. E. Gutierrez, A. Woodward, H. Tsukada, R. Gong, J. Hata, K. Doya, H. Okano, T. Yamamori and S. Ishii
  • Neuroscience, 2019

• Mapping connectivity of the marmoset prefrontal cortex
  • A. Watakabe, H. Skibbe, K. Nakae, J. Wang, M. Takaji, H. Mizukami, A. Woodward, R. Gong, Y. Yamaguchi, J. Hata, H. Okano, S. Ishii and T. Yamamori
  • Neuroscience, 2019

• Prefrontal projection mapping of the common marmoset
• A. Watakabe, J. Wang, M. Takaji, H. Mizukami, A. Woodward, T. Kawase, H. Skibbe, K. Naka, Y. Yamaguchi, S. Ishii and T. Yamamori
• SfN, 2018

• 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
  • H. Skibbe, K. Nakae, A. Watakabe, A. Woodward, C. E. Gutierrez, H. Tsukada, R. Gong, J. Hata, H. Okano, T. Yamamori and S. Ishii
  • Neuroscience, 2018

• Visualizing an individual diversity of marmoset connectome with a pipeline of tractography by MR
  • K. Nakae, H. Junichi, H. Skibbe, A. Woodward, C. E. Gutierrez, T. Hiromachi, R. Gong, H. Okano and S. Ishii
  • Neuroscience, 2018

• Prefrontal projection mapping of the marmoset
  • A. Watakabe, J. Wang, M. Takaji, H. Mizukami, A. Woodward, H. Skibbe, K. Nakae, Y. Yamaguchi, S. Ishii and T. Yamamori
  • Neuroscience, 2018

• GA-based Parameter Optimization of DWI-based Global Fiber Tracking with Neuronal Tracer Signal as a Reference
  • C. E. Gutierrez, H. Skibbe, K. Nakae, A. Woodward, A. Watakabe, J. Hata, H. Okano, T. Yamamori, Y. Yamaguchi, S. Ishii and K. Doya
  • Cosyne, 2018

• A pipeline for macro-scale connectomics of the common marmoset with global fiber reconstruction from diffusion MRI
• K. Nakae, H. Junichi, H. Skibbe, A. Woodward, C. E. Gutierrez, T. Hiromachi, R. Gong, Ryo Ito, H. Okano and S. Ishii
• CNS, 2018

• Individuality of macro-scale connectome of common marmoset with global fiber reconstruction by diffusion MRI
  • K. Nakae, J. Hata, H. Skibbe, A. Woodward, C. E. Gutierrez, R. Gong, H. Tsukada, H. Okano and S. Ishii
  • INCF, 2018

• Brain Model based on the Common Marmoset MRI Data
  • H. Tsukada, H. Hamada, C. E. Gutierrez, K. Nakae, H. Skibbe, S. Ishii, A. Woodward, J. Hata, H. Okano and K. Doya
  • INCF, 2018

* MarmU-Net: Axon tracer signal detection using an artificial neural network

• H. Skibbe, N. Ken, W. Akiya, C. E. Gutierrez, A. Woodward, H. Tsukada, R. Gong, J. Hata, T. Yamamori and S. Ishii
• INCF, 2018

• Columnar and diffuse connectivity of the marmoset PFC neurons
  • A. Watakabe, J. Wang, M. Takaji, H. Mizukami, A. Woodward, T. Kawase, H. Skibbe, K. Nakae, Y. Yamaguchi, S. Ishii and T. Yamamori
• SFN, 2017

• A model-free supervised learning approach for the estimation of fiber orientation distributions from diffusion-weighted MRI images of the brain white matter
  • K. Matsui, H. Skibbe, M. Reisert and S. Ishii
  • Keystone Symposium on “Connectomics”, 2017

• Mapping connectivity of marmoset prefrontal cortex by serial two-photon tomography
  • A. Watakabe, J. Wang, M. Takaji, H. Mizukami, A. Woodward, T. Kawase, H. Skibbe, Y. Yamaguchi, S. Ishii and T. Yamamori
  • SFN, 2016

• Lending Global Fiber-Tracking to the Tracing Of Dense Neurites in Fluorescence Micrographs
  • H. Skibbe and S. Ishii
  • INCF, 2016

• Model-free Global Tractography
  • H. Skibbe, E. Kellner, V.G. Kiselev and M. Reisert i
  • ISMRM, 2016

• Large-Scale Tracking and Modeling of Neural Networks in 3D Micrographs
  • H. Skibbe, K. Ito and S. Ishii
  • INCF, 2014

松山 (Henrik)

六本木 (Henrik)

井の頭公園 (Henrik)