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19 results on '"Graddis, Nile"'

1. NWB:N 2.0: An Accessible Data Standard for Neurophysiology

Author

Rübel, Oliver, Tritt, Andrew, Dichter, Benjamin, Braun, Thomas, Cain, Nicholas, Clack, Nathan, Davidson, Thomas, Dougherty, Max, Fillion-Robin, Jean-Christophe, Graddis, Nile, Grauer, Michael, Kiggins, Justin, Niu, Lawrence, Ozturk, Doruk, Schroeder, William, Soltesz, Ivan, Sommer, Friedrich, Svoboda, Karel, Lydia, Ng, Frank, Loren, and Bouchard, Kristofer

Subjects
Brain Disorders, Networking and Information Technology R&D
Abstract

ABSTRACT Neurodata Without Borders: Neurophysiology (NWB:N) is a data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build common analysis tools for neurophysiology data. With NWB:N version 2.0 (NWB:N 2.0) we made significant advances towards creating a usable standard, software ecosystem, and vibrant community for standardizing neurophysiology data. In this manuscript we focus in particular on the NWB:N data standard schema and present advances towards creating an accessible data standard for neurophysiology.

Published
2019

2. Survey of spiking in the mouse visual system reveals functional hierarchy

Author

Siegle, Joshua H., Jia, Xiaoxuan, Durand, Séverine, Gale, Sam, Bennett, Corbett, Graddis, Nile, Heller, Greggory, Ramirez, Tamina K., Choi, Hannah, Luviano, Jennifer A., Groblewski, Peter A., Ahmed, Ruweida, Arkhipov, Anton, Bernard, Amy, Billeh, Yazan N., Brown, Dillan, Buice, Michael A., Cain, Nicolas, Caldejon, Shiella, Casal, Linzy, Cho, Andrew, Chvilicek, Maggie, Cox, Timothy C., Dai, Kael, Denman, Daniel J., de Vries, Saskia E. J., Dietzman, Roald, Esposito, Luke, Farrell, Colin, Feng, David, Galbraith, John, Garrett, Marina, Gelfand, Emily C., Hancock, Nicole, Harris, Julie A., Howard, Robert, Hu, Brian, Hytnen, Ross, Iyer, Ramakrishnan, Jessett, Erika, Johnson, Katelyn, Kato, India, Kiggins, Justin, Lambert, Sophie, Lecoq, Jerome, Ledochowitsch, Peter, Lee, Jung Hoon, Leon, Arielle, Li, Yang, Liang, Elizabeth, Long, Fuhui, Mace, Kyla, Melchior, Jose, Millman, Daniel, Mollenkopf, Tyler, Nayan, Chelsea, Ng, Lydia, Ngo, Kiet, Nguyen, Thuyahn, Nicovich, Philip R., North, Kat, Ocker, Gabriel Koch, Ollerenshaw, Doug, Oliver, Michael, Pachitariu, Marius, Perkins, Jed, Reding, Melissa, Reid, David, Robertson, Miranda, Ronellenfitch, Kara, Seid, Sam, Slaughterbeck, Cliff, Stoecklin, Michelle, Sullivan, David, Sutton, Ben, Swapp, Jackie, Thompson, Carol, Turner, Kristen, Wakeman, Wayne, Whitesell, Jennifer D., Williams, Derric, Williford, Ali, Young, Rob, Zeng, Hongkui, Naylor, Sarah, Phillips, John W., Reid, R. Clay, Mihalas, Stefan, Olsen, Shawn R., and Koch, Christof

Published
2021
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3. Hierarchical organization of cortical and thalamic connectivity

Author

Harris, Julie A., Mihalas, Stefan, Hirokawa, Karla E., Whitesell, Jennifer D., Choi, Hannah, Bernard, Amy, Bohn, Phillip, Caldejon, Shiella, Casal, Linzy, Cho, Andrew, Feiner, Aaron, Feng, David, Gaudreault, Nathalie, Gerfen, Charles R., Graddis, Nile, Groblewski, Peter A., Henry, Alex M., Ho, Anh, Howard, Robert, Knox, Joseph E., Kuan, Leonard, Kuang, Xiuli, Lecoq, Jerome, Lesnar, Phil, Li, Yaoyao, Luviano, Jennifer, McConoughey, Stephen, Mortrud, Marty T., Naeemi, Maitham, Ng, Lydia, Oh, Seung Wook, Ouellette, Benjamin, Shen, Elise, Sorensen, Staci A., Wakeman, Wayne, Wang, Quanxin, Wang, Yun, Williford, Ali, Phillips, John W., Jones, Allan R., Koch, Christof, and Zeng, Hongkui

Published
2019
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4. Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network

Author

Whitesell, Jennifer D., primary, Liska, Adam, additional, Coletta, Ludovico, additional, Hirokawa, Karla E., additional, Bohn, Phillip, additional, Williford, Ali, additional, Groblewski, Peter A., additional, Graddis, Nile, additional, Kuan, Leonard, additional, Knox, Joseph E., additional, Ho, Anh, additional, Wakeman, Wayne, additional, Nicovich, Philip R., additional, Nguyen, Thuc Nghi, additional, van Velthoven, Cindy T.J., additional, Garren, Emma, additional, Fong, Olivia, additional, Naeemi, Maitham, additional, Henry, Alex M., additional, Dee, Nick, additional, Smith, Kimberly A., additional, Levi, Boaz, additional, Feng, David, additional, Ng, Lydia, additional, Tasic, Bosiljka, additional, Zeng, Hongkui, additional, Mihalas, Stefan, additional, Gozzi, Alessandro, additional, and Harris, Julie A., additional

Published
2021
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5. Regional, layer, and cell-class specific connectivity of the mouse default mode network

Author

Whitesell, Jennifer D., primary, Liska, Adam, additional, Coletta, Ludovico, additional, Hirokawa, Karla E., additional, Bohn, Phillip, additional, Williford, Ali, additional, Groblewski, Peter A., additional, Graddis, Nile, additional, Kuan, Leonard, additional, Knox, Joseph E., additional, Ho, Anh, additional, Wakeman, Wayne, additional, Nicovich, Philip R., additional, Nguyen, Thuc Nghi, additional, Garren, Emma, additional, van Velthoven, Cindy T. J., additional, Fong, Olivia, additional, Feng, David, additional, Naeemi, Maitham, additional, Henry, Alex M., additional, Dee, Nick, additional, Smith, Kimberly A., additional, Levi, Boaz P., additional, Ng, Lydia, additional, Tasic, Bosiljka, additional, Zeng, Hongkui, additional, Mihalas, Stefan, additional, Gozzi, Alessandro, additional, and Harris, Julie A., additional

Published
2020
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6. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

Author

Wang, Quanxin, primary, Ding, Song-Lin, additional, Li, Yang, additional, Royall, Josh, additional, Feng, David, additional, Lesnar, Phil, additional, Graddis, Nile, additional, Naeemi, Maitham, additional, Facer, Benjamin, additional, Ho, Anh, additional, Dolbeare, Tim, additional, Blanchard, Brandon, additional, Dee, Nick, additional, Wakeman, Wayne, additional, Hirokawa, Karla E., additional, Szafer, Aaron, additional, Sunkin, Susan M., additional, Oh, Seung Wook, additional, Bernard, Amy, additional, Phillips, John W., additional, Hawrylycz, Michael, additional, Koch, Christof, additional, Zeng, Hongkui, additional, Harris, Julie A., additional, and Ng, Lydia, additional

Published
2020
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7. A survey of spiking activity reveals a functional hierarchy of mouse corticothalamic visual areas

Author

Siegle, Joshua H., primary, Jia, Xiaoxuan, additional, Durand, Séverine, additional, Gale, Sam, additional, Bennett, Corbett, additional, Graddis, Nile, additional, Heller, Greggory, additional, Ramirez, Tamina K., additional, Choi, Hannah, additional, Luviano, Jennifer A., additional, Groblewski, Peter A., additional, Ahmed, Ruweida, additional, Arkhipov, Anton, additional, Bernard, Amy, additional, Billeh, Yazan N., additional, Brown, Dillan, additional, Buice, Michael A., additional, Cain, Nicolas, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andrew, additional, Chvilicek, Maggie, additional, Cox, Timothy C., additional, Dai, Kael, additional, Denman, Daniel J., additional, de Vries, Saskia E. J., additional, Dietzman, Roald, additional, Esposito, Luke, additional, Farrell, Colin, additional, Feng, David, additional, Galbraith, John, additional, Garrett, Marina, additional, Gelfand, Emily C., additional, Hancock, Nicole, additional, Harris, Julie A., additional, Howard, Robert, additional, Hu, Brian, additional, Hytnen, Ross, additional, Iyer, Ramakrishnan, additional, Jessett, Erika, additional, Johnson, Katelyn, additional, Kato, India, additional, Kiggins, Justin, additional, Lambert, Sophie, additional, Lecoq, Jerome, additional, Ledochowitsch, Peter, additional, Lee, Jung Hoon, additional, Leon, Arielle, additional, Li, Yang, additional, Liang, Elizabeth, additional, Long, Fuhui, additional, Mace, Kyla, additional, Melchior, Jose, additional, Millman, Daniel, additional, Mollenkopf, Tyler, additional, Nayan, Chelsea, additional, Ng, Lydia, additional, Ngo, Kiet, additional, Nguyen, Thuyahn, additional, Nicovich, Philip R., additional, North, Kat, additional, Ocker, Gabriel Koch, additional, Ollerenshaw, Doug, additional, Oliver, Michael, additional, Pachitariu, Marius, additional, Perkins, Jed, additional, Reding, Melissa, additional, Reid, David, additional, Robertson, Miranda, additional, Ronellenfitch, Kara, additional, Seid, Sam, additional, Slaughterbeck, Cliff, additional, Stoecklin, Michelle, additional, Sullivan, David, additional, Sutton, Ben, additional, Swapp, Jackie, additional, Thompson, Carol, additional, Turner, Kristen, additional, Wakeman, Wayne, additional, Whitesell, Jennifer D., additional, Williams, Derric, additional, Williford, Ali, additional, Young, Rob, additional, Zeng, Hongkui, additional, Naylor, Sarah, additional, Phillips, John W., additional, Reid, R. Clay, additional, Mihalas, Stefan, additional, Olsen, Shawn R., additional, and Koch, Christof, additional

Published
2019
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9. Biological variation in the sizes, shapes and locations of visual cortical areas in the mouse

Author

Waters, Jack, primary, Lee, Eric, additional, Gaudreault, Nathalie, additional, Griffin, Fiona, additional, Lecoq, Jerome, additional, Slaughterbeck, Cliff, additional, Sullivan, David, additional, Farrell, Colin, additional, Perkins, Jed, additional, Reid, David, additional, Feng, David, additional, Graddis, Nile, additional, Garrett, Marina, additional, Li, Yang, additional, Long, Fuhui, additional, Mochizuki, Chris, additional, Roll, Kate, additional, Zhuang, Jun, additional, and Thompson, Carol, additional

Published
2019
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10. NWB:N 2.0: An Accessible Data Standard for Neurophysiology

Author

Rübel, Oliver, primary, Tritt, Andrew, additional, Dichter, Benjamin, additional, Braun, Thomas, additional, Cain, Nicholas, additional, Clack, Nathan, additional, Davidson, Thomas J., additional, Dougherty, Max, additional, Fillion-Robin, Jean-Christophe, additional, Graddis, Nile, additional, Grauer, Michael, additional, Kiggins, Justin T., additional, Niu, Lawrence, additional, Ozturk, Doruk, additional, Schroeder, William, additional, Soltesz, Ivan, additional, Sommer, Friedrich T., additional, Svoboda, Karel, additional, Lydia, Ng, additional, Frank, Loren M., additional, and Bouchard, Kristofer, additional

Published
2019
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12. Whole brain imaging reveals distinct spatial patterns of amyloid beta deposition in three mouse models of Alzheimer's disease

Author

Whitesell, Jennifer D., primary, Buckley, Alex R., additional, Knox, Joseph E., additional, Kuan, Leonard, additional, Graddis, Nile, additional, Pelos, Andrew, additional, Mukora, Alice, additional, Wakeman, Wayne, additional, Bohn, Phillip, additional, Ho, Anh, additional, Hirokawa, Karla E., additional, and Harris, Julie A., additional

Published
2018
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13. Biological variation in the sizes, shapes and locations of visual cortical areas in the mouse

Author

Waters, Jack, primary, Lee, Eric, additional, Gaudreault, Nathalie, additional, Griffin, Fiona, additional, Lecoq, Jerome, additional, Slaughterbeck, Cliff, additional, Sullivan, David, additional, Farrell, Colin, additional, Perkins, Jed, additional, Reid, David, additional, Feng, David, additional, Graddis, Nile, additional, Garrett, Marina, additional, Li, Yang, additional, Long, Fuhui, additional, Mochizuki, Chris, additional, Roll, Kate, additional, Zhuang, Jun, additional, and Thompson, Carol, additional

Published
2018
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14. The organization of intracortical connections by layer and cell class in the mouse brain

Author

Harris, Julie A., primary, Mihalas, Stefan, additional, Hirokawa, Karla E., additional, Whitesell, Jennifer D., additional, Knox, Joseph E., additional, Bernard, Amy, additional, Bohn, Phillip, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andrew, additional, Feng, David, additional, Gaudreault, Nathalie, additional, Gerfen, Charles R., additional, Graddis, Nile, additional, Groblewski, Peter A., additional, Henry, Alex, additional, Ho, Anh, additional, Howard, Robert, additional, Kuan, Leonard, additional, Lecoq, Jerome, additional, Luviano, Jennifer, additional, McConoghy, Stephen, additional, Mortrud, Marty T., additional, Naeemi, Maitham, additional, Ng, Lydia, additional, Oh, Seung W., additional, Ouellette, Benjamin, additional, Sorensen, Staci A., additional, Wakeman, Wayne, additional, Wang, Quanxin, additional, Williford, Ali, additional, Phillips, John W., additional, Jones, Allan, additional, Koch, Christof, additional, and Zeng, Hongkui, additional

Published
2018
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16. Whole brain imaging reveals distinct spatial patterns of amyloid beta deposition in three mouse models of Alzheimer's disease.

Author

Whitesell, Jennifer D., Buckley, Alex R., Knox, Joseph E., Kuan, Leonard, Graddis, Nile, Pelos, Andrew, Mukora, Alice, Wakeman, Wayne, Bohn, Phillip, Ho, Anh, Hirokawa, Karla E., and Harris, Julie A.

Abstract

A variety of Alzheimer's disease (AD) mouse models overexpress mutant forms of human amyloid precursor protein (APP), producing high levels of amyloid β (Aβ) and forming plaques. However, the degree to which these models mimic spatiotemporal patterns of Aβ deposition in brains of AD patients is unknown. Here, we mapped the spatial distribution of Aβ plaques across age in three APP‐overexpression mouse lines (APP/PS1, Tg2576, and hAPP‐J20) using in vivo labeling with methoxy‐X04, high throughput whole brain imaging, and an automated informatics pipeline. Images were acquired with high resolution serial two‐photon tomography and labeled plaques were detected using custom‐built segmentation algorithms. Image series were registered to the Allen Mouse Brain Common Coordinate Framework, a 3D reference atlas, enabling automated brain‐wide quantification of plaque density, number, and location. In both APP/PS1 and Tg2576 mice, plaques were identified first in isocortex, followed by olfactory, hippocampal, and cortical subplate areas. In hAPP‐J20 mice, plaque density was highest in hippocampal areas, followed by isocortex, with little to no involvement of olfactory or cortical subplate areas. Within the major brain divisions, distinct regions were identified with high (or low) plaque accumulation; for example, the lateral visual area within the isocortex of APP/PS1 mice had relatively higher plaque density compared with other cortical areas, while in hAPP‐J20 mice, plaques were densest in the ventral retrosplenial cortex. In summary, we show how whole brain imaging of amyloid pathology in mice reveals the extent to which a given model recapitulates the regional Aβ deposition patterns described in AD. [ABSTRACT FROM AUTHOR]

Published
2019
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19. High-resolution data-driven model of the mouse connectome.

Author

Knox JE, Harris KD, Graddis N, Whitesell JD, Zeng H, Harris JA, Shea-Brown E, and Mihalas S

Abstract

Knowledge of mesoscopic brain connectivity is important for understanding inter- and intraregion information processing. Models of structural connectivity are typically constructed and analyzed with the assumption that regions are homogeneous. We instead use the Allen Mouse Brain Connectivity Atlas to construct a model of whole-brain connectivity at the scale of 100 μm voxels. The data consist of 428 anterograde tracing experiments in wild type C57BL/6J mice, mapping fluorescently labeled neuronal projections brain-wide. Inferring spatial connectivity with this dataset is underdetermined, since the approximately 2 × 10 5 source voxels outnumber the number of experiments. To address this issue, we assume that connection patterns and strengths vary smoothly across major brain divisions. We model the connectivity at each voxel as a radial basis kernel-weighted average of the projection patterns of nearby injections. The voxel model outperforms a previous regional model in predicting held-out experiments and compared with a human-curated dataset. This voxel-scale model of the mouse connectome permits researchers to extend their previous analyses of structural connectivity to much higher levels of resolution, and it allows for comparison with functional imaging and other datasets., Competing Interests: Competing Interests: The authors have declared that no competing interests exist.

Published
2018
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