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1. SYNAPSE: An international roadmap to large brain imaging

Author

Stampfl, Anton P.J., Liu, Zhongdong, Hu, Jun, Sawada, Kei, Takano, H., Kohmura, Yoshiki, Ishikawa, Tetsuya, Lim, Jae-Hong, Je, Jung-Ho, Low, Chian-Ming, Teo, Alvin, Tok, Eng Soon, Tan, Tin Wee, Ban, Kenneth, Libedinsky, Camilo, Tan, Francis Chee Kuan, Chen, Kuan-Peng, Yang, An-Cheng, Chuang, Chao-Chun, Chen, Nan-Yow, Shih, Chi-Tin, Lee, Ting-Kuo, Yang, De-Nian, Lai, Hsu-Chao, Shuai, Hong-Han, Cheng, Chang-Chieh, Ching, Yu-Tai, Li, Chia-Wei, Charng, Ching-Che, Lo, Chung-Chuan, Chiang, Ann-Shyn, Recur, Benoit, Petibois, Cyril, Cheng, Chia-Liang, Chen, Hsiang-Hsin, Yang, Shun-Min, Hwu, Yeukuang, Rojviriya, Catleya, Rugmai, Supagorn, Rujirawat, Saroj, and Margaritondo, Giorgio

Published
2023
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2. A synchrotron X-ray imaging strategy to map large animal brains

Author

Chin, An-Lun, Yang, Shun-Min, Chen, Hsiang-Hsin, Li, Min-Tsang, Lee, Tsung-Tse, Chen, Ying-Jie, Lee, Ting-Kuo, Petibois, Cyril, Cai, Xiaoqing, Low, Chian-Ming, Tan, Francis Chee Kuan, Teo, Alvin, Tok, Eng Soon, Ong, Edwin B.L., Lin, Yen-Yin, Lin, I-Jin, Tseng, Yi-Chi, Chen, Nan-Yow, Shih, Chi-Tin, Lim, Jae-Hong, Lim, Jun, Je, Jung-Ho, Kohmura, Yoshiki, Ishikawa, Tetsuya, Margaritondo, Giorgio, Chiang, Ann-Shyn, and Hwu, Yeukuang

Published
2020
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4. The interplay of mutations and electronic properties in disease-related genes

Author

Shih, Chi-Tin, Wells, Stephen A., Hsu, Ching-Ling, Cheng, Yun-Yin, and Römer, Rudolf A.

Subjects
Quantitative Biology - Other Quantitative Biology, Physics - Biological Physics
Abstract

Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as p53 by detection of oxidative damage. However, the reproducible measurement and modelling of charge migration through DNA molecules at the nanometer scale remains a challenging and controversial subject even after more than a decade of intense efforts. Here we show, by analysing 162 disease-related genes from a variety of medical databases with a total of almost 20,000 observed pathogenic mutations, a significant difference in the electronic properties of the population of observed mutations compared to the set of all possible mutations. Our results have implications for the role of the electronic properties of DNA in cellular processes, and hint at the possibility of prediction, early diagnosis and detection of mutation hotspots.

Published
2011
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5. Electric Transport Properties of the p53 Gene and the Effects of Point Mutations

Author

Shih, Chi-Tin, Römer, Rudolf A., and Roche, Stephan

Subjects
Quantitative Biology - Genomics
Abstract

In this work, charge transport (CT) properties of the p53 gene are numerically studied by the transfer matrix method, and using either single or double strand effective tight-binding models. A statistical analysis of the consequences of known p53 point mutations on CT features is performed. It is found that in contrast to other kind of mutation defects, cancerous mutations result in much weaker changes of CT efficiency. Given the envisioned role played by CT in the DNA-repairing mechanism, our theoretical results suggest an underlying physical explanation at the origin of carcinogenesis., Comment: 5 pages, 4 figures, presented in the conference "Trends in NanoTechnology 2007", submitted to physica status solidi (a)

Published
2007

6. Point Mutations Effects on Charge Transport Properties of the Tumor-Suppressor Gene p53

Author

Shih, Chi-Tin, Roche, Stephan, and Römer, Rudolf A.

Subjects
Quantitative Biology - Genomics, Condensed Matter - Soft Condensed Matter, Quantitative Biology - Quantitative Methods
Abstract

We report on a theoretical study of point mutations effects on charge transfer properties in the DNA sequence of the tumor-suppressor p53 gene. On the basis of effective single-strand or double-strand tight-binding models which simulate hole propagation along the DNA, a statistical analysis of charge transmission modulations associated with all possible point mutations is performed. We find that in contrast to non-cancerous mutations, mutation hotspots tend to result in significantly weaker {\em changes of transmission properties}. This suggests that charge transport could play a significant role for DNA-repairing deficiency yielding carcinogenesis., Comment: 4.1 PR style pages with 5 figures included

Published
2007
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8. SYNAPSE: An international roadmap to large brain imaging

Author

Stampfl, Anton P. J., Liu, Zhongdong, Hu, Jun, Sawada, Kei, Takano, H., Kohmura, Yoshiki, Ishikawa, Tetsuya, Lim, Jae-Hong, Je, Jung-Ho, Low, Chian-Ming, Teo, Alvin, Tok, Eng Soon, Tan, Tin Wee, Ban, Kenneth, Libedinsky, Camilo, Tan, Francis Chee Kuan, Chen, Kuan-Peng, Yang, An-Cheng, Chuang, Chao-Chun, Chen, Nan-Yow, Shih, Chi-Tin, Lee, Ting-Kuo, Yang, De-Nian, Lai, Hsu-Chao, Shuai, Hong-Han, Cheng, Chang-Chieh, Ching, Yu-Tai, Li, Chia-Wei, Charng, Ching-Che, Lo, Chung-Chuan, Chiang, Ann-Shyn, Recur, Benoit, Petibois, Cyril, Cheng, Chia-Liang, Chen, Hsiang-Hsin, Yang, Shun-Min, Hwu, Yeukuang, Rojviriya, Catleya, Rugmai, Supagorn, Rujirawat, Saroj, Margaritondo, Giorgio, Stampfl, Anton P. J., Liu, Zhongdong, Hu, Jun, Sawada, Kei, Takano, H., Kohmura, Yoshiki, Ishikawa, Tetsuya, Lim, Jae-Hong, Je, Jung-Ho, Low, Chian-Ming, Teo, Alvin, Tok, Eng Soon, Tan, Tin Wee, Ban, Kenneth, Libedinsky, Camilo, Tan, Francis Chee Kuan, Chen, Kuan-Peng, Yang, An-Cheng, Chuang, Chao-Chun, Chen, Nan-Yow, Shih, Chi-Tin, Lee, Ting-Kuo, Yang, De-Nian, Lai, Hsu-Chao, Shuai, Hong-Han, Cheng, Chang-Chieh, Ching, Yu-Tai, Li, Chia-Wei, Charng, Ching-Che, Lo, Chung-Chuan, Chiang, Ann-Shyn, Recur, Benoit, Petibois, Cyril, Cheng, Chia-Liang, Chen, Hsiang-Hsin, Yang, Shun-Min, Hwu, Yeukuang, Rojviriya, Catleya, Rugmai, Supagorn, Rujirawat, Saroj, and Margaritondo, Giorgio

Abstract

Since 2020, synchrotron radiation facilities in several Asia-Pacific countries have been collaborating in a major project called "SYNAPSE"(Synchrotrons for Neuroscience: an Asia-Pacific Scientific Enterprise). They use x-ray imaging to attack in a coordinated fashion one of the major issues in modern science: the structure of animal and human brains, including neurons and connections. The objective is to develop Google-like maps also including detailed structural and functional information for selected regions of interest. The sheer mass of data needed for the objective poses huge problems for the acquisition, processing, storage and use of images. In order to complete the task within a reasonable time, the key element of the SYNAPSE strategy is the parallel and coordinated work of several facilities on the same specimens. This article reviews different aspects of the enterprise, including the foundations of synchrotron radiation, coherence and of its role in advanced imaging, electron accelerators, x-ray optics and detectors. This will provide the foundation for an extensive presentation of the different components of SYNAPSE, with an overview of results already obtained within the consortium.

Published
2023
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11. Diverse Community Structures in the Neuronal-Level Connectome of the Drosophila Brain.

Author

Shih, Chi-Tin, Lin, Yen-Jen, Wang, Cheng-Te, Wang, Ting-Yuan, Chen, Chih-Chen, Su, Ta-Shun, Lo, Chung-Chuang, and Chiang, Ann-Shyn

Abstract

Drosophila melanogaster is one of the most important model animals in neurobiology owing to its manageable brain size, complex behaviour, and extensive genetic tools. However, without a comprehensive map of the brain-wide neural network, our ability to investigate brain functions at the systems level is seriously limited. In this study, we constructed a neuron-to-neuron network of the Drosophila brain based on the 28,573 fluorescence images of single neurons in the newly released FlyCircuit v1.2 (http://www.flycircuit.tw) database. By performing modularity and centrality analyses, we identified eight communities (right olfaction, left olfaction, olfactory core, auditory, motor, pre-motor, left vision, and right vision) in the brain-wide network. Further investigation on information exchange and structural stability revealed that the communities of different functions dominated different types of centralities, suggesting a correlation between functions and network structures. Except for the two olfaction and the motor communities, the network is characterized by overall small-worldness. A rich club (RC) structure was also found in this network, and most of the innermost RC members innervated the central complex, indicating its role in information integration. We further identified numerous loops with length smaller than seven neurons. The observation suggested unique characteristics in the information processing inside the fruit fly brain. [ABSTRACT FROM AUTHOR]

Published
2020
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13. 26th Annual Computational Neuroscience Meeting (CNS*2017): Part 2

Author

Rubchinsky, Leonid L., primary, Ahn, Sungwoo, additional, Klijn, Wouter, additional, Cumming, Ben, additional, Yates, Stuart, additional, Karakasis, Vasileios, additional, Peyser, Alexander, additional, Woodman, Marmaduke, additional, Diaz-Pier, Sandra, additional, Deraeve, James, additional, Vassena, Eliana, additional, Alexander, William, additional, Beeman, David, additional, Kudela, Pawel, additional, Boatman-Reich, Dana, additional, Anderson, William S., additional, Luque, Niceto R., additional, Naveros, Francisco, additional, Carrillo, Richard R., additional, Ros, Eduardo, additional, Arleo, Angelo, additional, Huth, Jacob, additional, Ichinose, Koki, additional, Park, Jihoon, additional, Kawai, Yuji, additional, Suzuki, Junichi, additional, Mori, Hiroki, additional, Asada, Minoru, additional, Oprisan, Sorinel A., additional, Dave, Austin I., additional, Babaie, Tahereh, additional, Robinson, Peter, additional, Tabas, Alejandro, additional, Andermann, Martin, additional, Rupp, André, additional, Balaguer-Ballester, Emili, additional, Lindén, Henrik, additional, Christensen, Rasmus K., additional, Nakamura, Mari, additional, Barkat, Tania R., additional, Tosi, Zach, additional, Beggs, John, additional, Lonardoni, Davide, additional, Boi, Fabio, additional, Di Marco, Stefano, additional, Maccione, Alessandro, additional, Berdondini, Luca, additional, Jędrzejewska-Szmek, Joanna, additional, Dorman, Daniel B., additional, Blackwell, Kim T., additional, Bauermeister, Christoph, additional, Keren, Hanna, additional, Braun, Jochen, additional, Dornas, João V., additional, Mavritsaki, Eirini, additional, Aldrovandi, Silvio, additional, Bridger, Emma, additional, Lim, Sukbin, additional, Brunel, Nicolas, additional, Buchin, Anatoly, additional, Kerr, Clifford Charles, additional, Chizhov, Anton, additional, Huberfeld, Gilles, additional, Miles, Richard, additional, Gutkin, Boris, additional, Spencer, Martin J., additional, Meffin, Hamish, additional, Grayden, David B., additional, Burkitt, Anthony N., additional, Davey, Catherine E., additional, Tao, Liangyu, additional, Tiruvadi, Vineet, additional, Ali, Rehman, additional, Mayberg, Helen, additional, Butera, Robert, additional, Gunay, Cengiz, additional, Lamb, Damon, additional, Calabrese, Ronald L., additional, Doloc-Mihu, Anca, additional, López-Madrona, Víctor J., additional, Matias, Fernanda S., additional, Pereda, Ernesto, additional, Mirasso, Claudio R., additional, Canals, Santiago, additional, Geminiani, Alice, additional, Pedrocchi, Alessandra, additional, D’Angelo, Egidio, additional, Casellato, Claudia, additional, Chauhan, Ankur, additional, Soman, Karthik, additional, Srinivasa Chakravarthy, V., additional, Muddapu, Vignayanandam R., additional, Chuang, Chao-Chun, additional, Chen, Nan-yow, additional, Bayati, Mehdi, additional, Melchior, Jan, additional, Wiskott, Laurenz, additional, Azizi, Amir Hossein, additional, Diba, Kamran, additional, Cheng, Sen, additional, Smirnova, Elena Y., additional, Yakimova, Elena G., additional, Chizhov, Anton V., additional, Chen, Nan-Yow, additional, Shih, Chi-Tin, additional, Florescu, Dorian, additional, Coca, Daniel, additional, Courtiol, Julie, additional, Jirsa, Viktor K., additional, Covolan, Roberto J. M., additional, Teleńczuk, Bartosz, additional, Kempter, Richard, additional, Curio, Gabriel, additional, Destexhe, Alain, additional, Parker, Jessica, additional, Klishko, Alexander N., additional, Prilutsky, Boris I., additional, Cymbalyuk, Gennady, additional, Franke, Felix, additional, Hierlemann, Andreas, additional, da Silveira, Rava Azeredo, additional, Casali, Stefano, additional, Masoli, Stefano, additional, Rizza, Martina, additional, Rizza, Martina Francesca, additional, Sun, Yinming, additional, Wong, Willy, additional, Farzan, Faranak, additional, Blumberger, Daniel M., additional, Daskalakis, Zafiris J., additional, Popovych, Svitlana, additional, Viswanathan, Shivakumar, additional, Rosjat, Nils, additional, Grefkes, Christian, additional, Daun, Silvia, additional, Gentiletti, Damiano, additional, Suffczynski, Piotr, additional, Gnatkovski, Vadym, additional, De Curtis, Marco, additional, Lee, Hyeonsu, additional, Paik, Se-Bum, additional, Choi, Woochul, additional, Jang, Jaeson, additional, Park, Youngjin, additional, Song, Jun Ho, additional, Song, Min, additional, Pallarés, Vicente, additional, Gilson, Matthieu, additional, Kühn, Simone, additional, Insabato, Andrea, additional, Deco, Gustavo, additional, Glomb, Katharina, additional, Ponce-Alvarez, Adrián, additional, Ritter, Petra, additional, Campo, Adria Tauste, additional, Thiele, Alexander, additional, Deeba, Farah, additional, Robinson, P. A., additional, van Albada, Sacha J., additional, Rowley, Andrew, additional, Hopkins, Michael, additional, Schmidt, Maximilian, additional, Stokes, Alan B., additional, Lester, David R., additional, Furber, Steve, additional, Diesmann, Markus, additional, Barri, Alessandro, additional, Wiechert, Martin T., additional, DiGregorio, David A., additional, Dimitrov, Alexander G., additional, Vich, Catalina, additional, Berg, Rune W., additional, Guillamon, Antoni, additional, Ditlevsen, Susanne, additional, Cazé, Romain D., additional, Girard, Benoît, additional, Doncieux, Stéphane, additional, Doyon, Nicolas, additional, Boahen, Frank, additional, Desrosiers, Patrick, additional, Laurence, Edward, additional, Dubé, Louis J., additional, Eleonora, Russo, additional, Durstewitz, Daniel, additional, Schmidt, Dominik, additional, Mäki-Marttunen, Tuomo, additional, Krull, Florian, additional, Bettella, Francesco, additional, Metzner, Christoph, additional, Devor, Anna, additional, Djurovic, Srdjan, additional, Dale, Anders M., additional, Andreassen, Ole A., additional, Einevoll, Gaute T., additional, Næss, Solveig, additional, Ness, Torbjørn V., additional, Halnes, Geir, additional, Halgren, Eric, additional, Pettersen, Klas H., additional, Sætra, Marte J., additional, Hagen, Espen, additional, Schiffer, Alina, additional, Grzymisch, Axel, additional, Persike, Malte, additional, Ernst, Udo, additional, Harnack, Daniel, additional, Ernst, Udo A., additional, Tomen, Nergis, additional, Zucca, Stefano, additional, Pasquale, Valentina, additional, Pica, Giuseppe, additional, Molano-Mazón, Manuel, additional, Chiappalone, Michela, additional, Panzeri, Stefano, additional, Fellin, Tommaso, additional, Oie, Kelvin S., additional, Boothe, David L., additional, Crone, Joshua C., additional, Yu, Alfred B., additional, Felton, Melvin A., additional, Zulfiqar, Isma, additional, Moerel, Michelle, additional, De Weerd, Peter, additional, Formisano, Elia, additional, Oie, Kelvin, additional, Franaszczuk, Piotr, additional, Diggelmann, Roland, additional, Fiscella, Michele, additional, Guarino, Domenico, additional, Antolík, Jan, additional, Davison, Andrew P., additional, Frègnac, Yves, additional, Etienne, Benjamin Xavier, additional, Frohlich, Flavio, additional, Lefebvre, Jérémie, additional, Marcos, Encarni, additional, Mattia, Maurizio, additional, Genovesio, Aldo, additional, Fedorov, Leonid A., additional, Dijkstra, Tjeerd M.H., additional, Sting, Louisa, additional, Hock, Howard, additional, Giese, Martin A., additional, Buhry, Laure, additional, Langlet, Clément, additional, Giovannini, Francesco, additional, Verbist, Christophe, additional, Salvadé, Stefano, additional, Giugliano, Michele, additional, Henderson, James A., additional, Wernecke, Hendrik, additional, Sándor, Bulcsú, additional, Gros, Claudius, additional, Voges, Nicole, additional, Dabrovska, Paulina, additional, Riehle, Alexa, additional, Brochier, Thomas, additional, Grün, Sonja, additional, Gu, Yifan, additional, Gong, Pulin, additional, Dumont, Grégory, additional, Novikov, Nikita A., additional, Gutkin, Boris S., additional, Tewatia, Parul, additional, Eriksson, Olivia, additional, Kramer, Andrei, additional, Santos, Joao, additional, Jauhiainen, Alexandra, additional, Kotaleski, Jeanette H., additional, Belić, Jovana J., additional, Kumar, Arvind, additional, Kotaleski, Jeanette Hellgren, additional, Shimono, Masanori, additional, Hatano, Naomichi, additional, Ahmad, Subutai, additional, Cui, Yuwei, additional, Hawkins, Jeff, additional, Senk, Johanna, additional, Korvasová, Karolína, additional, Tetzlaff, Tom, additional, Helias, Moritz, additional, Kühn, Tobias, additional, Denker, Michael, additional, Mana, PierGianLuca, additional, Dahmen, David, additional, Schuecker, Jannis, additional, Goedeke, Sven, additional, Keup, Christian, additional, Heuer, Katja, additional, Bakker, Rembrandt, additional, Tiesinga, Paul, additional, Toro, Roberto, additional, Qin, Wei, additional, Hadjinicolaou, Alex, additional, Ibbotson, Michael R., additional, Kameneva, Tatiana, additional, Lytton, William W., additional, Mulugeta, Lealem, additional, Drach, Andrew, additional, Myers, Jerry G., additional, Horner, Marc, additional, Vadigepalli, Rajanikanth, additional, Morrison, Tina, additional, Walton, Marlei, additional, Steele, Martin, additional, Anthony Hunt, C., additional, Tam, Nicoladie, additional, Amaducci, Rodrigo, additional, Muñiz, Carlos, additional, Reyes-Sánchez, Manuel, additional, Rodríguez, Francisco B., additional, Varona, Pablo, additional, Cronin, Joseph T., additional, Hennig, Matthias H., additional, Iavarone, Elisabetta, additional, Yi, Jane, additional, Shi, Ying, additional, Zandt, Bas-Jan, additional, Van Geit, Werner, additional, Rössert, Christian, additional, Markram, Henry, additional, Hill, Sean, additional, O’Reilly, Christian, additional, Perin, Rodrigo, additional, Lu, Huanxiang, additional, Bryson, Alexander, additional, Hadrava, Michal, additional, Hlinka, Jaroslav, additional, Hosaka, Ryosuke, additional, Olenik, Mark, additional, Houghton, Conor, additional, Iannella, Nicolangelo, additional, Launey, Thomas, additional, Kotsakidis, Rebecca, additional, Soriano, Jaymar, additional, Kubo, Takatomi, additional, Inoue, Takao, additional, Kida, Hiroyuki, additional, Yamakawa, Toshitaka, additional, Suzuki, Michiyasu, additional, Ikeda, Kazushi, additional, Abbasi, Samira, additional, Hudson, Amber E., additional, Heck, Detlef H., additional, Jaeger, Dieter, additional, Lee, Joel, additional, Janušonis, Skirmantas, additional, Saggio, Maria Luisa, additional, Spiegler, Andreas, additional, Stacey, William C., additional, Bernard, Christophe, additional, Lillo, Davide, additional, Petkoski, Spase, additional, Drakesmith, Mark, additional, Jones, Derek K., additional, Zadeh, Ali Sadegh, additional, Kambhampati, Chandra, additional, Karbowski, Jan, additional, Kaya, Zeynep Gokcen, additional, Lakretz, Yair, additional, Treves, Alessandro, additional, Li, Lily W., additional, Lizier, Joseph, additional, Kerr, Cliff C., additional, Masquelier, Timothée, additional, Kheradpisheh, Saeed Reza, additional, Kim, Hojeong, additional, Kim, Chang Sub, additional, Marakshina, Julia A., additional, Vartanov, Alexander V., additional, Neklyudova, Anastasia A., additional, Kozlovskiy, Stanislav A., additional, Kiselnikov, Andrey A., additional, Taniguchi, Kanako, additional, Kitano, Katsunori, additional, Schmitt, Oliver, additional, Lessmann, Felix, additional, Schwanke, Sebastian, additional, Eipert, Peter, additional, Meinhardt, Jennifer, additional, Beier, Julia, additional, Kadir, Kanar, additional, Karnitzki, Adrian, additional, Sellner, Linda, additional, Klünker, Ann-Christin, additional, Kuch, Lena, additional, Ruß, Frauke, additional, Jenssen, Jörg, additional, Wree, Andreas, additional, Sanz-Leon, Paula, additional, Knock, Stuart A., additional, Chien, Shih-Cheng, additional, Maess, Burkhard, additional, Knösche, Thomas R., additional, Cohen, Charles C., additional, Popovic, Marko A., additional, Klooster, Jan, additional, Kole, Maarten H.P., additional, Roberts, Erik A., additional, Kopell, Nancy J., additional, Kepple, Daniel, additional, Giaffar, Hamza, additional, Rinberg, Dima, additional, Koulakov, Alex, additional, Forlim, Caroline Garcia, additional, Klock, Leonie, additional, Bächle, Johanna, additional, Stoll, Laura, additional, Giemsa, Patrick, additional, Fuchs, Marie, additional, Schoofs, Nikola, additional, Montag, Christiane, additional, Gallinat, Jürgen, additional, Lee, Ray X., additional, Stephens, Greg J., additional, Kuhn, Bernd, additional, Tauffer, Luiz, additional, Isope, Philippe, additional, Inoue, Katsuma, additional, Ohmura, Yoshiyuki, additional, Yonekura, Shogo, additional, Kuniyoshi, Yasuo, additional, Jang, Hyun Jae, additional, Kwag, Jeehyun, additional, de Kamps, Marc, additional, Lai, Yi Ming, additional, dos Santos, Filipa, additional, Lam, K. P., additional, Andras, Peter, additional, Imperatore, Julia, additional, Helms, Jessica, additional, Tompa, Tamas, additional, Lavin, Antonieta, additional, Inkpen, Felicity H., additional, Ashby, Michael C., additional, Lepora, Nathan F., additional, Shifman, Aaron R., additional, Lewis, John E., additional, Zhang, Zhong, additional, Feng, Yeqian, additional, Tetzlaff, Christian, additional, Kulvicius, Tomas, additional, Li, Yinyun, additional, Pena, Rodrigo F. O., additional, Bernardi, Davide, additional, Roque, Antonio C., additional, Lindner, Benjamin, additional, Vellmer, Sebastian, additional, Saudargiene, Ausra, additional, Maninen, Tiina, additional, Havela, Riikka, additional, Linne, Marja-Leena, additional, Powanwe, Arthur, additional, Longtin, Andre, additional, Garrido, Jesús A., additional, Graham, Joe W., additional, Dura-Bernal, Salvador, additional, Angulo, Sergio L., additional, Neymotin, Samuel A., additional, and Antic, Srdjan D., additional

Published
2017
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25. Three-Dimensional Reconstruction of Brain-wide Wiring Networks in Drosophila at Single-Cell Resolution

Author

Chiang, Ann-Shyn, primary, Lin, Chih-Yung, additional, Chuang, Chao-Chun, additional, Chang, Hsiu-Ming, additional, Hsieh, Chang-Huain, additional, Yeh, Chang-Wei, additional, Shih, Chi-Tin, additional, Wu, Jian-Jheng, additional, Wang, Guo-Tzau, additional, Chen, Yung-Chang, additional, Wu, Cheng-Chi, additional, Chen, Guan-Yu, additional, Ching, Yu-Tai, additional, Lee, Ping-Chang, additional, Lin, Chih-Yang, additional, Lin, Hui-Hao, additional, Wu, Chia-Chou, additional, Hsu, Hao-Wei, additional, Huang, Yun-Ann, additional, Chen, Jing-Yi, additional, Chiang, Hsin-Jung, additional, Lu, Chun-Fang, additional, Ni, Ru-Fen, additional, Yeh, Chao-Yuan, additional, and Hwang, Jenn-Kang, additional

Published
2011
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28. A synchrotron X-ray imaging strategy to map large animal brains

Author

Chin, An-Lun, Yang, Shun-Min, Chen, Hsiang-Hsin, Li, Min-Tsang, Lee, Tsung-Tse, Chen, Ying-Jie, Lee, Ting-Kuo, Petibois, Cyril, Cai, Xiaoqing, Low, Chian-Ming, Tan, Francis Chee Kuan, Teo, Alvin, Tok, Eng Soon, Ong, Edwin B. L., Lin, Yen-Yin, Lin, I-Jin, Tseng, Yi-Chi, Chen, Nan-Yow, Shih, Chi-Tin, Lim, Jae-Hong, Lim, Jun, Je, Jung-Ho, Kohmura, Yoshiki, Ishikawa, Tetsuya, Margaritondo, Giorgio, Chiang, Ann-Shyn, and Hwu, Yeukuang

Subjects
microtomography, nanotomography, neural network, connectome, diffusion, x-ray imaging, microscopy, brain imaging, tomography, light
Abstract

Mapping the large neural networks of animal and human brains is a fundamental but so far elusive task, because of the massive amount of data and the consequent prohibitively long image taking and processing times. We developed an effective strategy called "AXON" (Accelerated X-ray Observation of Neurons) to solve this problem. AXON can achieve comprehensive whole-brain mapping within a reasonable time by combining fast image taking and processing, plus two other critical performances: three-dimensional (3D) imaging with high and isotropic spatial resolution, and multi-scale resolution. We successfully tested this strategy with coordinated experiments at four synchrotron facilities in Japan, Taiwan, Singapore and Korea on two animal models, Drosophila and mouse. Its performances notably allowed full 3D mapping of the Drosophila brain in a few days. With reasonable improvements, AXON can deliver full mapping of large animal and human brains on a realistic time scale of a few years.

29. LYNSU: automated 3D neuropil segmentation of fluorescent images for Drosophila brains.

Author

Hsu KY, Shih CT, Chen NY, and Lo CC

Abstract

The brain atlas, which provides information about the distribution of genes, proteins, neurons, or anatomical regions, plays a crucial role in contemporary neuroscience research. To analyze the spatial distribution of those substances based on images from different brain samples, we often need to warp and register individual brain images to a standard brain template. However, the process of warping and registration may lead to spatial errors, thereby severely reducing the accuracy of the analysis. To address this issue, we develop an automated method for segmenting neuropils in the Drosophila brain for fluorescence images from the FlyCircuit database. This technique allows future brain atlas studies to be conducted accurately at the individual level without warping and aligning to a standard brain template. Our method, LYNSU (Locating by YOLO and Segmenting by U-Net), consists of two stages. In the first stage, we use the YOLOv7 model to quickly locate neuropils and rapidly extract small-scale 3D images as input for the second stage model. This stage achieves a 99.4% accuracy rate in neuropil localization. In the second stage, we employ the 3D U-Net model to segment neuropils. LYNSU can achieve high accuracy in segmentation using a small training set consisting of images from merely 16 brains. We demonstrate LYNSU on six distinct neuropils or structures, achieving a high segmentation accuracy comparable to professional manual annotations with a 3D Intersection-over-Union (IoU) reaching up to 0.869. Our method takes only about 7 s to segment a neuropil while achieving a similar level of performance as the human annotators. To demonstrate a use case of LYNSU, we applied it to all female Drosophila brains from the FlyCircuit database to investigate the asymmetry of the mushroom bodies (MBs), the learning center of fruit flies. We used LYNSU to segment bilateral MBs and compare the volumes between left and right for each individual. Notably, of 8,703 valid brain samples, 10.14% showed bilateral volume differences that exceeded 10%. The study demonstrated the potential of the proposed method in high-throughput anatomical analysis and connectomics construction of the Drosophila brain., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Hsu, Shih, Chen and Lo.)

Published
2024
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