Ishii Laboratory
@Google Maps
Kyoto University
Faculty of Informatics
Building of Engineering No.1(Kogakubu 1 gokan)
Yoshida-honmachi, sakyo-ku, Kyoto, 606-8501 JAPAN
e-mail: skibbe-h (at sign) sys.i.kyoto-u.ac.jp
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
H. Skibbe, M. Reisert, T. Schmidt, T. Brox, O. Ronneberger, H. Burkhardt Fast Rotation Invariant 3D Feature Computation utilizing Efficient Local Neighborhood Operators In IEEE Trans. Pattern Anal. Mach. Intell., 2012. [pdf]
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
H. Skibbe, M. Reisert Circular Fourier-HOG features for rotation invariant object detection in biomedical images In Proc. of the ISBI, 2012. [pdf]
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]
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
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
H. Skibbe, N. Ken, W. Akiya, C.E. Gutierrez, A. Woodward, H. Tsukada, R. Gong, J. Hata, T. Yamamori, S. Ishii MarmU-Net: Axon tracer signal detection using an artificial neural network INCF, 2018. (Wako, Japan)
H. Tsukada, H. Hamada, C.E. Gutierrez, K. Nakae, H. Skibbe, S. Ishii, A. Woodward, J. Hata, H. Okano, K. Doya Brain Model based on the Common Marmoset MRI Data INCF, 2018. (Wako, Japan)
K. Nakae, J. Hata, H. Skibbe, A. Woodward, C.E. Gutierrez, R. Gong, H. Tsukada, H. Okano, S. Ishii Individuality of macro-scale connectome of common marmoset with global fiber reconstruction by diffusion MRI INCF, 2018. (Wako, Japan)
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 INCF, 2014. (Wako, Japan)