Faculty Information - Henrik SKIBBE

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（Last updated : 2026-03-31 20:00:52）

Henrik SKIBBE
Department Matsuyama University Department of Informatics, Faculty of Informatics

Position Professor

Publications

1.	2026/03	Article	Memory efficient training for 3D brain image registration networks using PatchMorph (Collaboration)
2.	2025/10	Article	The astrocytic ensemble acts as a multiday trace to stabilize memory Nature (Collaboration)
3.	2017/07	Article	Spherical tensor algebra: a toolkit for 3D image processing Journal of Mathematical Imaging and Vision 58(3),pp.349-381 (Collaboration)
4.	2023/10	Article	Exploring the performance of implicit neural representations for brain image registration Scientific Reports 13(1) (Collaboration)
5.	2023/06	Article	The Brain/MINDS Marmoset Connectivity Resource: An open-access platform for cellular-level tracing and tractography in the primate brain PLoS biology 21(6) (Collaboration)
6.	2024/12	Article	Multi-scale Stochastic Generation of Labelled Microscopy Images for Neuron Segmentation Medical Imaging with Deep Learning pp.352-366 (Collaboration)
7.	2023/10	Article	Implicit neural representations for joint decomposition and registration of gene expression images in the marmoset brain International Conference on Medical Image Computing and Computer-Assisted Intervention 645 (Collaboration)
8.	2024/01	Article	Improving segmentation of objects with varying sizes in biomedical images using instance-wise and center-of-instance segmentation loss function Medical Imaging with Deep Learnin pp.286-300 (Collaboration)
9.	2023/04	Article	An automated pipeline to create an atlas of in situ hybridization gene expression data in the adult marmoset brain 2023 IEEE 20th International Symposium on Biomedical Imaging (ISBI) pp.1-5 (Collaboration)
10.	2018/07	Article	PAT—Probabilistic axon tracking for densely labeled neurons in large 3-D micrographs IEEE transactions on medical imaging 38(1),pp.69-78 (Collaboration)
11.	2011/12	Article	Fast rotation invariant 3D feature computation utilizing efficient local neighborhood operators IEEE Transactions on Pattern Analysis and Machine Intelligence 34(8),pp.1563-1575 (Collaboration)
12.	2014/10	Article	Efficient Monte Carlo image analysis for the location of vascular entity IEEE Transactions on medical imaging 34(2),pp.628-643 (Collaboration)
13.	2025/01	Article	Prediction of white matter hyperintensities evolution one-year post-stroke from a single-point brain MRI and stroke lesions information Scientific Reports 15(1) (Collaboration)
14.	2023/07	Article	Local and long-distance organization of prefrontal cortex circuits in the marmoset brain Neuron 111(14),pp.2258-2273 (Collaboration)
15.	2025/10	Article	Benchmarking Evaluation Metrics for Tubular Structure Segmentation in Biomedical Images Lecture Notes in Computer Science 16171,pp.87-102 (Collaboration)
16.	2025/09	Article	Implicit Neural Representations for Brain Image Registration Between Human and Marmoset Lecture Notes in Computer Science 16310,pp.585-599 (Collaboration)
17.	2025/01	Article	Serial Two-Photon Tomography of the Whole Marmoset Brain for Neuroanatomical Analyses Journal of Visualized Experiments (JoVE) (Collaboration)
18.	2024/10	Article	Machine learning-guided reconstruction of cytoskeleton network from Machine learning-guided reconstruction of cytoskeleton network from live-cell AFM images 27(10) (Collaboration)
19.	2024/05	Article	A new family of instance-level loss functions for improving instance-level segmentation and detection of white matter hyperintensities in routine clinical brain MRI Computers in Biology and Medicine 174 (Collaboration)
20.	2023/12	Article	Use of DeTerm for Automated Drosophila Dendrite Arbor Terminal Counts Cold Spring Harbor Protocols (Collaboration)
21.	2023/10	Article	Distinctiveness and continuity in transcriptome and connectivity in the anterior-posterior axis of the paraventricular nucleus of the thalamus Cell Reports 42(10) (Collaboration)
22.	2023/03	Article	A dataset of rodent cerebrovasculature from in vivo multiphoton fluorescence microscopy imaging Scientific Data 10 (Collaboration)
23.	2023/03	Article	Tomographic tract tracing and data driven approaches to unravel complex 3D fiber anatomy of DBS relevant prefrontal projections to the diencephalic-mesencephalic junction in the marmoset Brain Stimulation 16(2),pp.670-681 (Collaboration)
24.	2022/07	Article	A spiking neural network builder for systematic data-to-model workflow Frontiers in Neuroinformatics 16 (Collaboration)
25.	2021/09	Article	Probabilistic Deep Learning with Adversarial Training and Volume Interval Estimation - Better Ways to Perform and Evaluate Predictive Models for White Matter Hyperintensities Evolution Predictive Intelligence in Medicine: 4th International Workshop, PRIME 2021, Held in Conjunction wit pp.168-180 (Collaboration)
26.	2020/12	Article	Optimization and validation of diffusion MRI-based fiber tracking with neural tracer data as a reference Scientific reports 10 (Collaboration)
27.	2020/09	Article	Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species-and region-specific differences Proceedings of the National Academy of Sciences 118(18) (Collaboration)
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