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363 results on '"Hata, Junichi"'

6. Multi-modal brain magnetic resonance imaging database covering marmosets with a wide age range

Author

Hata, Junichi, Nakae, Ken, Tsukada, Hiromichi, Woodward, Alexander, Haga, Yawara, Iida, Mayu, Uematsu, Akiko, Seki, Fumiko, Ichinohe, Noritaka, Gong, Rui, Kaneko, Takaaki, Yoshimaru, Daisuke, Watakabe, Akiya, Abe, Hiroshi, Tani, Toshiki, Hamda, Hiro Taiyo, Gutierrez, Carlos Enrique, Skibbe, Henrik, Maeda, Masahide, Papazian, Frederic, Hagiya, Kei, Kishi, Noriyuki, Ishii, Shin, Doya, Kenji, Shimogori, Tomomi, Yamamori, Tetsuo, Tanaka, Keiji, Okano, Hirotaka James, and Okano, Hideyuki

Published
2023
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11. Optimization and Validation of Diffusion MRI-based Fiber Tracking with Neural Tracer Data as a Reference

Author

Gutierrez, Carlos Enrique, Skibbe, Henrik, Nakae, Ken, Tsukada, Hiromichi, Lienard, Jean, Watakabe, Akiya, Hata, Junichi, Reisert, Marco, Woodward, Alexander, Okano, Hideyuki, Yamamori, Tetsuo, Yamaguchi, Yoko, Ishii, Shin, and Doya, Kenji

Subjects
Physics - Medical Physics, Electrical Engineering and Systems Science - Image and Video Processing, Quantitative Biology - Quantitative Methods
Abstract

Diffusion-weighted magnetic resonance imaging (dMRI) allows non-invasive investigation of whole-brain connectivity, which can potentially help to reveal the brain's global network architecture and abnormalities involved in neurological and mental disorders. However, the reliability of connection inferences from dMRI-based fiber tracking is still debated, due to low sensitivity, dominance of false positives, and inaccurate and incomplete reconstruction of long-range connections. Furthermore, parameters of tracking algorithms are typically tuned in a heuristic way, which leaves room for manipulation of an intended result. Here we propose a data-driven framework to optimize and validate parameters of dMRI-based fiber-tracking algorithms using neural tracer data as a reference. Japan's Brain/MINDS Project provides invaluable datasets containing both dMRI and neural tracer data from the same primates. We considered four criteria for goodness of fiber tracking: distance-weighted coverage, true/false positive ratio, projection coincidence, and commissural passage, applied using a multi-objective optimization algorithm. We implemented a variant of non-dominated sorting genetic algorithm II (NSGA-II) to optimize five major parameters of a global fiber-tracking algorithm over multiple brain samples in parallel. Using optimized parameters compared to the default parameters, dMRI-based fiber tracking performance was significantly improved, while minimizing false positives and impossible cross-hemisphere connections. Parameters optimized for 10 tracer injection sites showed good generalization capability for other brain samples. These results demonstrate the importance of data-driven adjustment of fiber-tracking algorithms and support the validity of dMRI-based tractography, if appropriate adjustments are employed.

Published
2019

12. MarmoNet: a pipeline for automated projection mapping of the common marmoset brain from whole-brain serial two-photon tomography

Author

Skibbe, Henrik, Watakabe, Akiya, Nakae, Ken, Gutierrez, Carlos Enrique, Tsukada, Hiromichi, Hata, Junichi, Kawase, Takashi, Gong, Rui, Woodward, Alexander, Doya, Kenji, Okano, Hideyuki, Yamamori, Tetsuo, and Ishii, Shin

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Machine Learning, Quantitative Biology - Neurons and Cognition, Statistics - Machine Learning
Abstract

Understanding the connectivity in the brain is an important prerequisite for understanding how the brain processes information. In the Brain/MINDS project, a connectivity study on marmoset brains uses two-photon microscopy fluorescence images of axonal projections to collect the neuron connectivity from defined brain regions at the mesoscopic scale. The processing of the images requires the detection and segmentation of the axonal tracer signal. The objective is to detect as much tracer signal as possible while not misclassifying other background structures as the signal. This can be challenging because of imaging noise, a cluttered image background, distortions or varying image contrast cause problems. We are developing MarmoNet, a pipeline that processes and analyzes tracer image data of the common marmoset brain. The pipeline incorporates state-of-the-art machine learning techniques based on artificial convolutional neural networks (CNN) and image registration techniques to extract and map all relevant information in a robust manner. The pipeline processes new images in a fully automated way. This report introduces the current state of the tracer signal analysis part of the pipeline.

Published
2019

15. Multimodal Cross-registration and Quantification of Metric Distortions in Whole Brain Histology of Marmoset using Diffeomorphic Mappings

Author

Lee, Brian C., Lin, Meng Kuan, Fu, Yan, Hata, Junichi, Miller, Michael I., and Mitra, Partha P.

Subjects
Quantitative Biology - Neurons and Cognition
Abstract

Whole brain neuroanatomy using tera-voxel light-microscopic data sets is of much current interest. A fundamental problem in this field is the mapping of individual brain data sets to a reference space. Previous work has not rigorously quantified the distortions in brain geometry from in-vivo to ex-vivo brains due to the tissue processing, which will be important when computing properties such as local cell and process densities at the voxel level in creating reference brain maps. Further, existing approaches focus on registering uni-modal volumetric data; however, given the increasing interest in the marmoset model for neuroscience research, it is necessary to cross-register multi-modal data sets including MRIs and multiple histological series that can help address individual variations in brain architecture. Here we present a computational approach for same-subject multimodal MRI guided reconstruction of a histological series, jointly with diffeomorphic mapping to a reference atlas. We quantify the scale change during the different stages of histological processing of the brains using the Jacobian determinant of the diffeomorphic transformations involved. There are two major steps in the histology process with associated scale distortions (a) brain perfusion (b) histological sectioning and reassembly. By mapping the final image stacks to the ex-vivo post fixation MRI, we show that tape-transfer histology can be reassembled accurately into 3D volumes with a local scale change of 2.0 $\pm$ 0.4% per axis dimension. In contrast, the perfusion step, as assessed by mapping the in-vivo MRIs to the ex-vivo post fixation MRIs, shows a larger local scale change of 6.9 $\pm$ 2.1% per axis dimension. This is the first systematic quantification of the local metric distortions associated with whole-brain histological processing, and we expect that the results will generalize to other species.

Published
2018

28. A shift of brain network hub after spinal cord injury

Author

Matsubayashi, Kohei, primary, Shinozaki, Munehisa, additional, Hata, Junichi, additional, Komaki, Yuji, additional, Nagoshi, Narihito, additional, Tsuji, Osahiko, additional, Fujiyoshi, Kanehiro, additional, Nakamura, Masaya, additional, and Okano, Hideyuki, additional

Published
2023
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29. Single-cell bioluminescence imaging of deep tissue in freely moving animals

Author

Iwano, Satoshi, Sugiyama, Mayu, Hama, Hiroshi, Watakabe, Akiya, Hasegawa, Naomi, Kuchimaru, Takahiro, Tanaka, Kazumasa Z., Takahashi, Megumu, Ishida, Yoko, Hata, Junichi, Shimozono, Satoshi, Namiki, Kana, Fukano, Takashi, Kiyama, Masahiro, Okano, Hideyuki, Kizaka-Kondoh, Shinae, McHugh, Thomas J., Yamamori, Tetsuo, Hioki, Hiroyuki, Maki, Shojiro, and Miyawaki, Atsushi

Published
2018

34. The Brain/MINDS Marmoset Connectivity Resource: An open-access platform for cellular-level tracing and tractography in the primate brain

Author

Skibbe, Henrik, primary, Rachmadi, Muhammad Febrian, additional, Nakae, Ken, additional, Gutierrez, Carlos Enrique, additional, Hata, Junichi, additional, Tsukada, Hiromichi, additional, Poon, Charissa, additional, Schlachter, Matthias, additional, Doya, Kenji, additional, Majka, Piotr, additional, Rosa, Marcello G. P., additional, Okano, Hideyuki, additional, Yamamori, Tetsuo, additional, Ishii, Shin, additional, Reisert, Marco, additional, and Watakabe, Akiya, additional

Published
2023
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37. The Brain/MINDS Marmoset Connectivity Resource: an open access platform for cellular-level tracing and tractography in the primate brain

Author

0000-0002-2857-6023, Skibbe, Henrik, Rachmadi, Febrian Muhammad, Nakae, Ken, Gutierrez, Enrique Carlos, Hata, Junichi, Tsukada, Hiromichi, Poon, Charissa, Schlachter, Matthias, Doya, Kenji, Majka, Piotr, Rosa, G. P. Marcello, Okano, Hideyuki, Yamamori, Tetsuo, Ishii, Shin, Reisert, Marco, Watakabe, Akiya, 0000-0002-2857-6023, Skibbe, Henrik, Rachmadi, Febrian Muhammad, Nakae, Ken, Gutierrez, Enrique Carlos, Hata, Junichi, Tsukada, Hiromichi, Poon, Charissa, Schlachter, Matthias, Doya, Kenji, Majka, Piotr, Rosa, G. P. Marcello, Okano, Hideyuki, Yamamori, Tetsuo, Ishii, Shin, Reisert, Marco, and Watakabe, Akiya

Abstract

The primate brain has unique anatomical characteristics, which translate into advanced cognitive, sensory and motor abilities. Thus, it is important that we gain insight on its structure, to provide a solid basis for models that will clarify function. Here we report on the implementation and features of the Brain/MINDS Marmoset Connectivity Resource (BMCR), a new open-access platform that provides access to high-resolution anterograde neuronal tracer data in the marmoset brain, integrated to retrograde tracer and tractography data. Unlike other existing image explorers, the BMCR allows visualization of data from different individuals and modalities in a common reference space. This feature, allied to an unprecedented high resolution, enables analyses of features such as reciprocity, directionality and spatial segregation of connections. The present release of the BMCR focuses on the prefrontal cortex, a uniquely developed region of the primate brain which is linked to advanced cognition, including the results of 52 anterograde and 164 retrograde tracer injections in the cortex of the marmoset. Moreover, the inclusion of tractography data from diffusion MRI allows systematic analyses of this non-invasive modality against gold-standard cellular connectivity data, enabling detection of false positives and negatives, which provide a basis for future development of tractography. This paper introduces the BMCR image pre-processing pipeline and resources, which include new tools for exploring and reviewing the data.

Published
2023

40. MRI検査の安全管理に対する全国多施設フォローアップ調査研究

Author

AZUMA, Minako, primary, DOI, Tsukasa, additional, TAKAHASHI, Mitsuyuki, additional, HATA, Hirofumi, additional, UEYAMA, Tsuyoshi, additional, TAKAHASHI, Junji, additional, SAKAI, Kazuyuki, additional, OYAMA-MANABE, Noriko, additional, HATA, Junichi, additional, KATAOKA, Masako, additional, KURODA, Kagayaki, additional, IJICHI, Shinpei, additional, AOKI, Shigeki, additional, and HIRAI, Toshinori, additional

Published
2023
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44. Effect of sedatives or anesthetics on the measurement of resting brain function in common marmosets

Author

Muta, Kanako, primary, Hata, Junichi, additional, Kawaguchi, Naoki, additional, Haga, Yawara, additional, Yoshimaru, Daisuke, additional, Hagiya, Kei, additional, Kaneko, Takaaki, additional, Miyabe-Nishiwaki, Takako, additional, Komaki, Yuji, additional, Seki, Fumiko, additional, Okano, Hirotaka James, additional, and Okano, Hideyuki, additional

Published
2022
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45. Multi-modal brain magnetic resonance imaging database covering marmosets with a wide age range

Author

Hata, Junichi, primary, Nakae, Ken, additional, Tsukada, Hiromichi, additional, Woodward, Alexander, additional, Haga, Yawara, additional, Iida, Mayu, additional, Uematsu, Akiko, additional, Seki, Fumiko, additional, Ichinohe, Noritaka, additional, Gong, Rui, additional, Kaneko, Takaaki, additional, Yoshimaru, Daisuke, additional, Watakabe, Akiya, additional, Abe, Hiroshi, additional, Tani, Toshiki, additional, Skibbe, Henrik, additional, Maeda, Masahide, additional, Papazian, Frederic, additional, Hagiya, Kei, additional, Kishi, Noriyuki, additional, Shimogori, Tomomi, additional, Yamamori, Tetsuo, additional, Okano, Hirotaka James, additional, and Okano, Hideyuki, additional

Published
2022
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47. The Brain/MINDS Marmoset Connectivity Atlas: exploring bidirectional tracing and tractography in the same stereotaxic space

Author

Skibbe, Henrik, primary, Rachmadi, Muhammad Febrian, additional, Nakae, Ken, additional, Gutierrez, Carlos Enrique, additional, Hata, Junichi, additional, Tsukada, Hiromichi, additional, Poon, Charissa, additional, Doya, Kenji, additional, Majka, Piotr, additional, Rosa, Marcello G. P., additional, Okano, Hideyuki, additional, Yamamori, Tetsuo, additional, Ishii, Shin, additional, Reisert, Marco, additional, and Watakabe, Akiya, additional

Published
2022
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