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5. 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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9. 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

10. 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

13. 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

19. 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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21. 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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23. 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

25. 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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33. Abstract P784: A Novel Rat Model of Embolic Cerebral Ischemia Using a Cell-Implantable Radiopaque Hydrogel Micro Fiber

Author

Komatsu, Teppei, primary, Ohta, Hiroki, additional, Takakura, Naoki, additional, Kitagawa, Tomomichi, additional, Hata, Junichi, additional, Terawaki, Koshiro, additional, Koizumi, Makoto, additional, Muta, Kanako, additional, Kurashina, Yuta, additional, Onoe, Hiroaki, additional, Okano, Hirotaka J, additional, and Iguchi, Yasuyuki, additional

Published
2021
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34. The Japan Monkey Centre Primates Brain Imaging Repository for comparative neuroscience: an archive of digital records including records for endangered species

Author

Sakai, Tomoko, Hata, Junichi, Ohta, Hiroki, Shintaku, Yuta, Kimura, Naoto, Ogawa, Yuki, Sogabe, Kazumi, Mori, Susumu, Okano, James, Hirotaka, Hamada, Yuzuru, Shibata, Shinsuke, Okano, Hideyuki, and Oishi, Kenichi

Subjects
Database, Diffusion tensor imaging, Magnetic resonance imaging, Evolution, Primate, Brain samples, Comparative neuroscience, Endangered species
Abstract

Advances in magnetic resonance imaging (MRI) and computational analysis technology have enabled comparisons among various primate brains in a three-dimensional electronic format. Results from comparative studies provide information about common features across primates and species-specific features of neuroanatomy. Investigation of various species of non-human primates is important for understanding such features, but the majority of comparative MRI studies have been based on experimental primates, such as common marmoset, macaques, and chimpanzee. A major obstacle has been the lack of a database that includes non-experimental primates’ brain MRIs. To facilitate scientific discoveries in the field of comparative neuroanatomy and brain evolution, we launched a collaborative project to develop an open-resource repository of non-human primate brain images obtained using ex vivo MRI. As an initial open resource, here we release a collection of structural MRI and diffusion tensor images obtained from 12 species: pygmy marmoset, owl monkey, white-fronted capuchin, crab-eating macaque, Japanese macaque, bonnet macaque, toque macaque, Sykes’ monkey, red-tailed monkey, Schmidt’s guenon, de Brazza’s guenon, and lar gibbon. Sixteen postmortem brain samples from the 12 species, stored in the Japan Monkey Centre (JMC), were scanned using a 9.4-T MRI scanner and made available through the JMC collaborative research program (http://www.j-monkey.jp/BIR/index_e.html). The expected significant contributions of the JMC Primates Brain Imaging Repository include (1) resources for comparative neuroscience research, (2) preservation of various primate brains, including those of endangered species, in a permanent digital form, (3) resources with higher resolution for identifying neuroanatomical features, compared to previous MRI atlases, (4) resources for optimizing methods of scanning large fixed brains, and (5) references for veterinary neuroradiology. User-initiated research projects beyond these contributions are also anticipated.

Published
2018

35. Semiquantitative Evaluation of Muscle Repair by Diffusion Tensor Imaging in Mice

Author

Hata, Junichi, Mizuno, Sakiko, Haga, Yawara, Shimoda, Masayuki, Kanai, Yae, Chiba, Kazuhiro, Okano, Hideyuki, Nakamura, Masaya, and Horiuchi, Keisuke

Subjects
MUSCLE INJURY, MAGNETIC RESONANCE IMAGING, ADAM10, Original Article, MUSCLE REPAIR, Original Articles, DIFFUSION TENSOR IMAGING
Abstract

Muscle injury is one of the most common traumas in orthopedic and sports medicine. However, there are only a few treatment options with marginal clinical benefits for this condition. Muscle repair after injury involves multiple and complex processes, such as the inflammation phase, regeneration phase, and remodeling phase. To develop a treatment modality and to examine the efficacy of novel interventions and agents for patients with muscle injuries, it is essential to establish a reliable and sensitive method to monitor the changes in muscle structure and status during muscle repair. Diffusion‐weighted magnetic resonance imaging has been widely used to assess the diffusivity of water molecules in tissue. When it is used in combination with diffusion tensor imaging (DTI), the microstructure of muscle tissue can be indirectly depicted. In the present study, we evaluated the time‐course changes in the diffusivity and anisotropy in muscles by DTI and histology after injury in mice. We found that the diffusivity and anisotropy exhibit distinct kinetics during muscle repair and that these kinetics were significantly altered in mutant mice with a defect in muscle regeneration. Our data show that muscle repair processes can be readily evaluated and monitored by DTI technique and suggest that DTI can be clinically applied for assessing muscle injury and repair in humans. © 2018 The Authors. JBMR Plus is published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.

Published
2018

45. A high-throughput neurohistological pipeline for brain-wide mesoscale connectivity mapping of the common marmoset

Author

Lin, Meng Kuan, primary, Takahashi, Yeonsook Shin, additional, Huo, Bing-Xing, additional, Hanada, Mitsutoshi, additional, Nagashima, Jaimi, additional, Hata, Junichi, additional, Tolpygo, Alexander S, additional, Ram, Keerthi, additional, Lee, Brian C, additional, Miller, Michael I, additional, Rosa, Marcello GP, additional, Sasaki, Erika, additional, Iriki, Atsushi, additional, Okano, Hideyuki, additional, and Mitra, Partha, additional

Published
2019
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48. Elavl3 is essential for the maintenance of Purkinje neuron axons

Author

Ogawa, Yuki, primary, Kakumoto, Kyoko, additional, Yoshida, Tetsu, additional, Kuwako, Ken-ichiro, additional, Miyazaki, Taisuke, additional, Yamaguchi, Junji, additional, Konno, Ayumu, additional, Hata, Junichi, additional, Uchiyama, Yasuo, additional, Hirai, Hirokazu, additional, Watanabe, Masahiko, additional, Darnell, Robert B., additional, Okano, Hideyuki, additional, and Okano, Hirotaka James, additional

Published
2018
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