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[[members:henrik|{{members:member_henrik.jpg}}]]
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**Henrik SKIBBE**\\
Unit Leader\\
Brain Image Analysis Unit\\
Center for Brain Science\\
email: henrik.skibbe😀riken.jp
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{{ :members:henrik_cat.png?nolink&200|}}
====== Publications ======
(not updated since 2019, see [[:top|top page]] for updates)
===== Refereed Articles =====




==== 2019 ====

  * **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.


==== 2018 ====
  * **Modelfree global tractography**
    * L. Konopleva, K.A. Il'yasov, H. Skibbe, V.G. Kiselev, E. Kellner, B. Dhital, M. Reisert
    * In NeuroImage, Elsevier, 2018. 
==== 2017 ====
  * **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 : [[https://bitbucket.org/skibbe/sta-toolbox/wiki/Home|STA-ImageToolbox]]
==== 2016 ====
  * **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. 
==== 2015 ====
  * **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
==== 2013 ====
  * **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. 

==== 2012 ====

  * **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. 
===== Refereed Conference Papers =====

==== 2021 ====

  * **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

==== 2015 ====


  * **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
==== 2014 ====
  * **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
==== 2013 ====
  * **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
==== 2012 ====

  * **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
==== 2011 ====
  * **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
==== 2010 ====
  * **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
==== 2009 ====
  * **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

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

====  2021 ==== 
  * **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
==== 2013 ====
  * **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
==== 2012 ====
  * **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
==== 2011 ====

  * **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
===== Other Publications =====

==== 2019 ====
  * **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
==== 2018 ====
  * **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
==== 2013 ====
  * **Spherical Tensor Algebra for Biomedical Image Analysis**
      * Skibbe, H.
      * PhD thesis, Albert-Ludwigs-Universität Freiburg, 2013
==== 2012 ====
  * **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
=====Abstracts =====

==== 2019 ====
  * **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

==== 2018 ====
  * **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
==== 2017 ====
  * **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
==== 2016 ====
  * **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
==== 2014 ====
  * **Large-Scale Tracking and Modeling of Neural Networks in 3D Micrographs**
      * H. Skibbe, K. Ito and S. Ishii
      * INCF, 2014


===== Fotos =====


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松山 (Henrik)

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六本木 (Henrik)

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井の頭公園 (Henrik)