Items where Subject is "brain atlas"

Paper

BRAIN Initiative Cell Census Network (BICCN) (October 2021) A multimodal cell census and atlas of the mammalian primary motor cortex. Nature, 598 (7879). pp. 86-102. ISSN 0028-0836

BRAIN Initiative Cell Census Network (BICCN), Adkins, Ricky, Aldridge, Andrew, Allen, Shona, Ament, Seth, An, Xu, Armand, Ethan, Ascoli, Giorgio, Bakken, Trygve, Bandrowski, Anita, Banerjee, Samik, Barkas, Nikolaos, Bartlett, Anna, Bateup, Helen, Behrens, Margarita, Berens, Philipp, Berg, Jim, Bernabucci, Matteo, Bernaerts, Yves, Bertagnolli, Darren, Biancalani, Tommaso, Boggeman, Lara, Booeshaghi, Sina, Bowman, Ian, Bravo, Héctor Corrada, Cadwell, Cathryn René, Callaway, Edward, Carlin, Benjamin, O'Connor, Carolyn, Carter, Robert, Casper, Tamara, Castanon, Rosa, Castro, Jesus Ramon, Chance, Rebecca, Chatterjee, Apaala, Chen, Huaming, Chun, Jerold, Colantuoni, Carlo, Crabtree, Jonathan, Creasy, Heather, Crichton, Kirsten, Crow, Megan, D'Orazi, Florence, Daigle, Tanya, Dalley, Rachel, Dee, Nick, Degatano, Kylee, Dichter, Benjamin, Diep, Dinh, Ding, Liya, Ding, Song-Lin, Dominguez, Bertha, Dong, Hong-Wei, Dong, Weixiu, Dougherty, Elizabeth, Dudoit, Sandrine, Ecker, Joseph, Eichhorn, Stephen, Fang, Rongxin, Felix, Victor, Feng, Guoping, Feng, Zhao, Fischer, Stephan, Fitzpatrick, Conor, Fong, Olivia, Foster, Nicholas, Galbavy, William, Gee, James, Ghosh, Satrajit, Giglio, Michelle, Gillespie, Thomas, Gillis, Jesse, Goldman, Melissa, Goldy, Jeff, Gong, Hui, Gou, Lin, Grauer, Michael, Halchenko, Yaroslav, Harris, Julie, Hartmanis, Leonard, Hatfield, Joshua, Hawrylycz, Mike, Helba, Brian, Herb, Brian, Hertzano, Ronna, Hintiryan, Houri, Hirokawa, Karla, Hockemeyer, Dirk, Hodge, Rebecca, Hood, Greg, Horwitz, Gregory, Hou, Xiaomeng, Hu, Lijuan, Hu, Qiwen, Huang, Josh, Huo, Bingxing, Ito-Cole, Tony, Jacobs, Matthew, Jia, Xueyan, Jiang, Shengdian, Jiang, Tao, Jiang, Xiaolong, Jin, Xin, Jorstad, Nikolas, Kalmbach, Brian, Kancherla, Jayaram, Keene, Dirk, Kelly, Kathleen, Khajouei, Farzaneh, Kharchenko, Peter, Kim, Gukhan, Ko, Andrew, Kobak, Dmitry, Konwar, Kishori, Kramer, Daniel, Krienen, Fenna, Kroll, Matthew, Kuang, Xiuli, Kuo, Hsien-Chi, Lake, Blue, Larsen, Rachael, Lathia, Kanan, Laturnus, Sophie, Lee, Angus, Lee, Cheng-Ta, Lee, Kuo-Fen, Lein, Ed, Lesnar, Phil, Li, Anan, Li, Xiangning, Li, Xu, Li, Yang Eric, Li, Yaoyao, Li, Yuanyuan, Lim, Byungkook, Linnarsson, Sten, Liu, Christine, Liu, Hanqing, Liu, Lijuan, Lucero, Jacinta, Luo, Chongyuan, Luo, Qingming, Macosko, Evan, Mahurkar, Anup, Martone, Maryann, Matho, Katherine, McCarroll, Steven, McCracken, Carrie, McMillen, Delissa, Miranda, Elanine, Mitra, Partha, Miyazaki, Paula Assakura, Mizrachi, Judith, Mok, Stephanie, Mukamel, Eran, Mulherkar, Shalaka, Nadaf, Naeem, Naeemi, Maitham, Narasimhan, Arun, Nery, Joseph, Ng, Lydia, Ngai, John, Nguyen, Thuc Nghi, Nickel, Lance, Nicovich, Philip, Niu, Sheng-Yong, Ntranos, Vasilis, Nunn, Michael, Olley, Dustin, Orvis, Joshua, Osteen, Julia, Osten, Pavel, Owen, Scott, Pachter, Lior, Palaniswamy, Ramesh, Palmer, Carter, Pang, Yan, Peng, Hanchuan, Pham, Thanh, Pinto-Duarte, Antonio, Plongthongkum, Nongluk, Poirion, Olivier, Preissl, Sebastian, Purdom, Elizabeth, Qu, Lei, Rashid, Mohammad, Reed, Nora, Regev, Aviv, Ren, Bing, Ren, Miao, Rimorin, Christine, Risso, Davide, Rivkin, Angeline, Muñoz-Castañeda, Rodrigo, Romanow, William, Ropelewski, Alexander, Roux de Bézieux, Hector, Ruan, Zongcai, Sandberg, Rickard, Savoia, Steven, Scala, Federico, Schor, Michael, Shen, Elise, Siletti, Kimberly, Smith, Jared, Smith, Kimberly, Somasundaram, Saroja, Song, Yuanyuan, Sorensen, Staci, Stafford, David, Street, Kelly, Sulc, Josef, Sunkin, Susan, Svensson, Valentine, Tan, Pengcheng, Tan, Zheng Huan, Tasic, Bosiljka, Thompson, Carol, Tian, Wei, Tickle, Timothy, Tieu, Michael, Ting, Jonathan, Tolias, Andreas Savas, Torkelson, Amy, Tung, Herman, Vaishnav, Eeshit Dhaval, Van den Berge, Koen, van Velthoven, Cindy TJ, Vanderburg, Charles, Veldman, Matthew, Vu, Minh, Wakeman, Wayne, Wang, Peng, Wang, Quanxin, Wang, Xinxin, Wang, Yimin, Wang, Yun, Welch, Joshua, White, Owen, Williams, Elora, Xie, Fangming, Xie, Peng, Xiong, Feng, Yang, William, Yanny, Anna Marie, Yao, Zizhen, Yin, Lulu, Yu, Yang, Yuan, Jing, Z, Hongkui (October 2020) A multimodal cell census and atlas of the mammalian primary motor cortex. BioRxiv. (Unpublished)

Chen, Yuncong, McElvain, Lauren, Tolpygo, Alex, Ferrante, Daniel, Karten, Harvey, Mitra, Partha, Kleinfeld, David, Freund, Yoav (February 2017) The Active Atlas: Combining 3D Anatomical Models with Texture Detectors. arXiv. (Submitted)

Chen, Y., McElvain, L., Tolpygo, A., Ferrante, D., Karten, H., Mitra, P., Kleinfeld, D., Freund, Y. (2017) The active atlas: Combining 3D anatomical models with texture detectors. Lecture Notes in Computer Science, 10433. pp. 3-11. ISSN 978-331966181-0

Chen, Y., McElvain, L. E., Tolpygo, A. S., Ferrante, D., Friedman, B., Mitra, P. P., Karten, H. J., Freund, Y., Kleinfeld, D. (March 2019) An active texture-based digital atlas enables automated mapping of structures and markers across brains. Nat Methods, 16 (4). pp. 341-350. ISSN 1548-7091

Ecker, Joseph R., Geschwind, Daniel H., Kriegstein, Arnold R., Ngai, John, Osten, Pavel, Polioudakis, Damon, Regev, Aviv, Sestan, Nenad, Wickersham, Ian R., Zeng, Hongkui (November 2017) The BRAIN Initiative Cell Census Consortium: Lessons Learned toward Generating a Comprehensive Brain Cell Atlas. Neuron, 96 (3). pp. 542-557. ISSN 0896-6273

Ellegood, J., Anagnostou, E., Babineau, B. A., Crawley, J. N., Lin, L., Genestine, M., DiCicco-Bloom, E., Lai, J. K., Foster, J. A., Penagarikano, O., Geschwind, D. H., Pacey, L. K., Hampson, D. R., Laliberte, C. L., Mills, A. A., Tam, E., Osborne, L. R., Kouser, M., Espinosa-Becerra, F., Xuan, Z., Powell, C. M., Raznahan, A., Robins, D. M., Nakai, N., Nakatani, J., Takumi, T., van Eede, M. C., Kerr, T. M., Muller, C., Blakely, R. D., Veenstra-VanderWeele, J., Henkelman, R. M., Lerch, J. P. (February 2015) 3D visualization of the regional differences. Mol Psychiatry, 20 (1). p. 1. ISSN 1359-4184

Fischer, Stephan, Gillis, Jesse (November 2021) How many markers are needed to robustly determine a cell's type? iScience, 24 (11). p. 103292. ISSN 2589-0042

Grange, Pascal, Bohland, Jason, Bokil, Hemant, Nelson, Sacha, Okaty, Benjamin, Sugino, Ken, Ng, Lydia, Hawrylycz, Michael, Mitra, Partha P (November 2011) A cell-type based model explaining co-expression patterns of genes in the brain. (Submitted)

Grange, Pascal, Hawrylycz, Michael, Mitra, Partha P (February 2013) Cell-type-specific microarray data and the Allen atlas: quantitative analysis of brain-wide patterns of correlation and density. (Submitted)

Grange, Pascal, Hawrylycz, Michael, Mitra, Partha P (January 2013) Computational neuroanatomy and co-expression of genes in the adult mouse brain, analysis tools for the Allen Brain Atlas. (Submitted)

Grange, Pascal, Mitra, Partha P (April 2011) Algorithmic choice of coordinates for injections into the brain: encoding a neuroanatomical atlas on a grid. (Submitted)

Grange, Pascal, Mitra, Partha P (May 2012) Computational neuroanatomy and gene expression: optimal sets of marker genes for brain regions. (Submitted)

Grange, Pascal, Hawrylycz, Michael, Mitra, Partha P. (2013) Computational neuroanatomy and co-expression of genes in the adult mouse brain, analysis tools for the Allen Brain Atlas. Quantitative Biology, 1 (1). pp. 91-100. ISSN 2095-4689

Huang, Longwen, Kebschull, Justus, Furth, Daniel, Musall, Simon, Kaufman, Matthew T., Churchland, Anne K., Zador, Anthony (September 2018) High-throughput mapping of mesoscale connectomes in individual mice. bioRxiv.

Kim, Yongsoo, Yang, Guangyu Robert, Pradhan, Kith, Venkataraju, Kannan Umadevi, Bota, Mihail, García del Molino, Luis Carlos, Fitzgerald, Greg, Ram, Keerthi, He, Miao, Levine, Jesse Maurica, Mitra, Partha, Huang, Z. Josh, Wang, Xiao-Jing, Osten, Pavel (2017) Brain-wide Maps Reveal Stereotyped Cell-Type-Based Cortical Architecture and Subcortical Sexual Dimorphism. Cell, 171 (2). 456-469.e22. ISSN 0092-8674

Lee, B. C., Tward, D. J., Mitra, P. P., Miller, M. I. (December 2018) On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model. PLoS Comput Biol, 14 (12). e1006610. ISSN 1553-734x

Lovell, P. V., Wirthlin, M., Kaser, T., Buckner, A. A., Carleton, J. B., Snider, B. R., McHugh, A. K., Tolpygo, A., Mitra, P. P., Mello, C. V. (February 2020) ZEBrA - Zebra finch Expression Brain Atlas: a resource for comparative molecular neuroanatomy and brain evolution studies. J Comp Neurol. ISSN 0021-9967 (Public Dataset)

Lu, Shaina, Ortiz, Cantin, Fürth, Daniel, Fischer, Stephan, Meletis, Konstantinos, Zador, Anthony, Gillis, Jesse (July 2021) Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain. PLoS Biology, 19 (7). e3001341. ISSN 1545-7885

Lu, Shaina, Ortiz, Cantin, Fürth, Daniel, Fischer, Stephan, Meletis, Konstantinos, Zador, Anthony, Gillis, Jesse (October 2020) Replicability of spatial gene expression atlas data from the adult mouse brain. bioRxiv. (Unpublished)

Majka, P., Chaplin, T. A., Yu, H. H., Tolpygo, A., Mitra, P. P., Wojcik, D. K., Rosa, M. G. (August 2016) Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template. J Comp Neurol, 524 (11). pp. 2161-2181. ISSN 1096-9861 (Electronic)0021-9967 (Linking)

Muñoz-Castañeda, Rodrigo, Zingg, Brian, Matho, Katherine, Wang, Quanxin, Chen, Xiaoyin, Foster, Nicholas, Narasimhan, Arun, Li, Anan, Hirokawa, Karla, Huo, Bingxing, Bannerjee, Samik, Korobkova, Laura, Park, Chris Sin, Park, Young-Gyun, Bienkowski, Michael, Chon, Uree, Wheeler, Diek, Li, Xiangning, Wang, Yun, Kelly, Kathleen, An, Xu, Attili, Sarojini, Bowman, Ian, Bludova, Anastasiia, Cetin, Ali, Ding, Liya, Drewes, Rhonda, D’Orazi, Florence, Elowsky, Corey, Fischer, Stephan, Galbavy, William, Gao, Lei, Gillis, Jesse, Groblewski, Peter, Gou, Lin, Hahn, Joel, Hatfield, Joshua, Hintiryan, Houri, Huang, Jason, Kondo, Hideki, Kuang, Xiuli, Lesnar, Philip, Li, Xu, Li, Yaoyao, Lin, Mengkuan, Liu, Lijuan, Lo, Darrick, Mizrachi, Judith, Mok, Stephanie, Naeemi, Maitham, Nicovich, Philip, Palaniswamy, Ramesh, Palmer, Jason, Qi, Xiaoli, Shen, Elise, Sun, Yu-Chi, Tao, Huizhong, Wakemen, Wayne, Wang, Yimin, Xie, Peng, Yao, Shenqin, Yuan, Jin, Zhu, Muye, Ng, Lydia, Zhang, Li, Lim, Byung Kook, Hawrylycz, Michael, Gong, Hui, Gee, James, Kim, Yongsoo, Peng, Hanchuan, Chuang, Kwanghun, Yang, William, Luo, Qingming, Mitra, Partha, Zador, Anthony, Zeng, Hongkui, Ascoli, Giorgio, Huang, Josh, Osten, Pavel, Harris, Julie, Dong, Hong-Wei (October 2020) Cellular Anatomy of the Mouse Primary Motor Cortex. BioRxiv. (Unpublished)

Okano, Hideyuki, Mitra, Partha (April 2015) Brain-mapping projects using the common marmoset. Neuroscience Research, 93. pp. 3-7. ISSN 0168-0102

Pinskiy, V., Jones, J., Tolpygo, A. S., Franciotti, N., Weber, K., Mitra, P. P. (July 2015) High-Throughput Method of Whole-Brain Sectioning, Using the Tape-Transfer Technique. PLoS One, 10 (7). e0102363. ISSN 1932-6203 (Electronic)1932-6203 (Linking)

Striedter, G. F., Belgard, T. G., Chen, C. C., Davis, F. P., Finlay, B. L., Gunturkun, O., Hale, M. E., Harris, J. A., Hecht, E. E., Hof, P. R., Hofmann, H. A., Holland, L. Z., Iwaniuk, A. N., Jarvis, E. D., Karten, H. J., Katz, P. S., Kristan, W. B., Macagno, E. R., Mitra, P. P., Moroz, L. L., Preuss, T. M., Ragsdale, C. W., Sherwood, C. C., Stevens, C. F., Stuttgen, M. C., Tsumoto, T., Wilczynski, W. (2014) NSF Workshop Report: Discovering General Principles of Nervous System Organization by Comparing Brain Maps across Species. Brain, Behavior and Evolution, 83 (1). pp. 1-8. ISSN 00068977 (ISSN)

Urai, Anne E, Doiron, Brent, Leifer, Andrew M, Churchland, Anne K (January 2022) Large-scale neural recordings call for new insights to link brain and behavior. Nature Neuroscience. ISSN 1097-6256

Conference or Workshop Item

Rosa, M, Majka, P, Chaplin, T, Yu, H-H, Wojcik, D, Mitra, P (August 2015) Mapping neural connections in primates - an expanding role for cortical connectivity atlases. In: 25th Biennial Meeting of the International-Society-for-Neurochemistry Jointly with the 13th Meeting of the Asian-Pacific-Society-for-Neurochemistry in Conjunction with the 35th Meeting of the Australasian-Neuroscience-Society.

Tward, D, Li, X, Huo, B, Lee, B, Mitra, P, Miller, M (January 2019) 3D Mapping of Serial Histology Sections with Anomalies Using a Novel Robust Deformable Registration Algorithm. In: Multimodal Brain Image Analysis and Mathematical Foundations of Computational Anatomy.

Venkataraju, K. U., Gornet, J., Murugaiyan, G., Wu, Z., Osten, P. (February 2019) Development of brain templates for whole brain atlases. In: Neural Imaging and Sensing 2019, San Francisco, CA.