| 1. |
Marcus N. Leiwe, Satoshi Fujimoto, Toshikazu Baba, Daichi Moriyasu, Biswanath Saha, Richi Sakaguchi, Shigenori Inagaki, Takeshi Imai, Automated neuronal reconstruction with super-multicolour fluorescence imaging, 10.1101/2022.10.20.512984, 2022.10, ABSTRACT
Fluorescence imaging is widely used for the mesoscopic mapping of neuronal connectivity. However, neurite reconstruction is challenging, especially when neurons are densely labelled. Here we report a strategy for the fully automated reconstruction of densely labelled neuronal circuits. Firstly, we established stochastic “super-multicolour” labelling with up to seven different fluorescent proteins using the Tetbow method. With this method, each neuron was labelled with a unique combination of fluorescent proteins, which were then imaged and separated by linear unmixing. We also established an automated neurite reconstruction pipeline based on the quantitative analysis of multiple dyes (QDyeFinder). To classify colour combinations, we used a newly developed unsupervised clustering algorithm, dCrawler, in which data points in multi-dimensional space were clustered based on a given threshold distance. Our new strategy allows for the reconstruction of neurites for up to hundreds of neurons at a millimetre scale without manual tracing.. |
| 2. |
Shigenori Inagaki, Ryo Iwata, Takeshi Imai, In vivo Optical Access to Olfactory Sensory Neurons in the Mouse Olfactory Epithelium, bio-protocol, 10.21769/bioprotoc.4055, 11, 12, 2021.06. |
| 3. |
Shigenori Inagaki, Ryo Iwata, Masakazu Iwamoto, Takeshi Imai, Widespread Inhibition, Antagonism, and Synergy in Mouse Olfactory Sensory Neurons In Vivo, Cell Reports, 10.1016/j.celrep.2020.107814, 31, 13, 107814-107814, 2020.06. |
| 4. |
Shigenori Inagaki, Masakazu Agetsuma, Shinya Ohara, Toshio Iijima, Hideo Yokota, Tetsuichi Wazawa, Yoshiyuki Arai, Takeharu Nagai, Imaging local brain activity of multiple freely moving mice sharing the same environment., Scientific reports, 10.1038/s41598-019-43897-x, 9, 1, 7460-7460, 2019.05. |
| 5. |
Jun Matsushita, Shigenori Inagaki, Tomomi Nishie, Tomoki Sakasai, Junko Tanaka, Chisato Watanabe, Ken-Ichi Mizutani, Yoshihiro Miwa, Ken Matsumoto, Kazuhiro Takara, Hisamichi Naito, Hiroyasu Kidoya, Nobuyuki Takakura, Takeharu Nagai, Satoru Takahashi, Masatsugu Ema, Fluorescence and Bioluminescence Imaging of Angiogenesis in Flk1-Nano-lantern Transgenic Mice., Scientific reports, 10.1038/srep46597, 7, 46597, 46597-46597, 2017.04. |
| 6. |
Shigenori Inagaki, Hidekazu Tsutsui, Kazushi Suzuki, Masakazu Agetsuma, Yoshiyuki Arai, Yuka Jinno, Guirong Bai, Matthew J. Daniels, Yasushi Okamura, Tomoki Matsuda, Takeharu Nagai, Genetically encoded bioluminescent voltage indicator for multi-purpose use in wide range of bioimaging, Scientific Reports, 10.1038/srep42398, 7, 42398, 2017.02. |
