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1. A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex

Author

Yao, Shenqin, Wang, Quanxin, Hirokawa, Karla E., Ouellette, Benjamin, Ahmed, Ruweida, Bomben, Jasmin, Brouner, Krissy, Casal, Linzy, Caldejon, Shiella, Cho, Andy, Dotson, Nadezhda I., Daigle, Tanya L., Egdorf, Tom, Enstrom, Rachel, Gary, Amanda, Gelfand, Emily, Gorham, Melissa, Griffin, Fiona, Gu, Hong, Hancock, Nicole, Howard, Robert, Kuan, Leonard, Lambert, Sophie, Lee, Eric Kenji, Luviano, Jennifer, Mace, Kyla, Maxwell, Michelle, Mortrud, Marty T., Naeemi, Maitham, Nayan, Chelsea, Ngo, Nhan-Kiet, Nguyen, Thuyanh, North, Kat, Ransford, Shea, Ruiz, Augustin, Seid, Sam, Swapp, Jackie, Taormina, Michael J., Wakeman, Wayne, Zhou, Thomas, Nicovich, Philip R., Williford, Ali, Potekhina, Lydia, McGraw, Medea, Ng, Lydia, Groblewski, Peter A., Tasic, Bosiljka, Mihalas, Stefan, Harris, Julie A., Cetin, Ali, and Zeng, Hongkui

Published
2023
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2. A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex

Author

de Vries, Saskia E. J., Lecoq, Jerome A., Buice, Michael A., Groblewski, Peter A., Ocker, Gabriel K., Oliver, Michael, Feng, David, Cain, Nicholas, Ledochowitsch, Peter, Millman, Daniel, Roll, Kate, Garrett, Marina, Keenan, Tom, Kuan, Leonard, Mihalas, Stefan, Olsen, Shawn, Thompson, Carol, Wakeman, Wayne, Waters, Jack, Williams, Derric, Barber, Chris, Berbesque, Nathan, Blanchard, Brandon, Bowles, Nicholas, Caldejon, Shiella D., Casal, Linzy, Cho, Andrew, Cross, Sissy, Dang, Chinh, Dolbeare, Tim, Edwards, Melise, Galbraith, John, Gaudreault, Nathalie, Gilbert, Terri L., Griffin, Fiona, Hargrave, Perry, Howard, Robert, Huang, Lawrence, Jewell, Sean, Keller, Nika, Knoblich, Ulf, Larkin, Josh D., Larsen, Rachael, Lau, Chris, Lee, Eric, Lee, Felix, Leon, Arielle, Li, Lu, Long, Fuhui, Luviano, Jennifer, Mace, Kyla, Nguyen, Thuyanh, Perkins, Jed, Robertson, Miranda, Seid, Sam, Shea-Brown, Eric, Shi, Jianghong, Sjoquist, Nathan, Slaughterbeck, Cliff, Sullivan, David, Valenza, Ryan, White, Casey, Williford, Ali, Witten, Daniela M., Zhuang, Jun, Zeng, Hongkui, Farrell, Colin, Ng, Lydia, Bernard, Amy, Phillips, John W., Reid, R. Clay, and Koch, Christof

Published
2020
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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. A High-Resolution Spatiotemporal Atlas of Gene Expression of the Developing Mouse Brain

Author

Thompson, Carol L, Ng, Lydia, Menon, Vilas, Martinez, Salvador, Lee, Chang-Kyu, Glattfelder, Katie, Sunkin, Susan M, Henry, Alex, Lau, Christopher, Dang, Chinh, Garcia-Lopez, Raquel, Martinez-Ferre, Almudena, Pombero, Ana, Rubenstein, John LR, Wakeman, Wayne B, Hohmann, John, Dee, Nick, Sodt, Andrew J, Young, Rob, Smith, Kimberly, Nguyen, Thuc-Nghi, Kidney, Jolene, Kuan, Leonard, Jeromin, Andreas, Kaykas, Ajamete, Miller, Jeremy, Page, Damon, Orta, Geri, Bernard, Amy, Riley, Zackery, Smith, Simon, Wohnoutka, Paul, Hawrylycz, Michael J, Puelles, Luis, and Jones, Allan R

Subjects
Neurosciences, Biotechnology, Genetics, Pediatric, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Animals, Brain, Brain Mapping, Gene Expression, Gene Expression Profiling, Gene Expression Regulation, Developmental, Mice, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for ∼2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

Published
2014

5. An anatomic transcriptional atlas of human glioblastoma

Author

Puchalski, Ralph B., Shah, Nameeta, Miller, Jeremy, Dalley, Rachel, Nomura, Steve R., Yoon, Jae-Guen, Smith, Kimberly A., Lankerovich, Michael, Bertagnolli, Darren, Bickley, Kris, Boe, Andrew F., Brouner, Krissy, Butler, Stephanie, Caldejon, Shiella, Chapin, Mike, Datta, Suvro, Dee, Nick, Desta, Tsega, Dolbeare, Tim, Dotson, Nadezhda, Ebbert, Amanda, Feng, David, Feng, Xu, Fisher, Michael, Gee, Garrett, Goldy, Jeff, Gourley, Lindsey, Gregor, Benjamin W., Gu, Guangyu, Hejazinia, Nika, Hohmann, John, Hothi, Parvinder, Howard, Robert, Joines, Kevin, Kriedberg, Ali, Kuan, Leonard, Lau, Chris, Lee, Felix, Lee, Hwahyung, Lemon, Tracy, Long, Fuhui, Mastan, Naveed, Mott, Erika, Murthy, Chantal, Ngo, Kiet, Olson, Eric, Reding, Melissa, Riley, Zack, Rosen, David, Sandman, David, Shapovalova, Nadiya, Slaughterbeck, Clifford R., Sodt, Andrew, Stockdale, Graham, Szafer, Aaron, Wakeman, Wayne, Wohnoutka, Paul E., White, Steven J., Marsh, Don, Rostomily, Robert C., Ng, Lydia, Dang, Chinh, Jones, Allan, Keogh, Bart, Gittleman, Haley R., Barnholtz-Sloan, Jill S., Cimino, Patrick J., Uppin, Megha S., Keene, C. Dirk, Farrokhi, Farrokh R., Lathia, Justin D., Berens, Michael E., Iavarone, Antonio, Bernard, Amy, Lein, Ed, Phillips, John W., Rostad, Steven W., Cobbs, Charles, Hawrylycz, Michael J., and Foltz, Greg D.

Published
2018

6. Stimulus novelty uncovers coding diversity in visual cortical circuits

Author

Garrett, Marina, primary, Groblewski, Peter, additional, Piet, Alex, additional, Ollerenshaw, Doug, additional, Najafi, Farzaneh, additional, Yavorska, Iryna, additional, Amster, Adam, additional, Bennett, Corbett, additional, Buice, Michael, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, D’Orazi, Florence, additional, Daniel, Scott, additional, de Vries, Saskia EJ, additional, Kapner, Daniel, additional, Kiggins, Justin, additional, Lecoq, Jerome, additional, Ledochowitsch, Peter, additional, Manavi, Sahar, additional, Mei, Nicholas, additional, Morrison, Christopher B., additional, Naylor, Sarah, additional, Orlova, Natalia, additional, Perkins, Jed, additional, Ponvert, Nick, additional, Roll, Clark, additional, Seid, Sam, additional, Williams, Derric, additional, Williford, Allison, additional, Ahmed, Ruweida, additional, Amine, Daniel, additional, Billeh, Yazan, additional, Bowman, Chris, additional, Cain, Nicholas, additional, Cho, Andrew, additional, Dawe, Tim, additional, Departee, Max, additional, Desoto, Marie, additional, Feng, David, additional, Gale, Sam, additional, Gelfand, Emily, additional, Gradis, Nile, additional, Grasso, Conor, additional, Hancock, Nicole, additional, Hu, Brian, additional, Hytnen, Ross, additional, Jia, Xiaoxuan, additional, Johnson, Tye, additional, Kato, India, additional, Kivikas, Sara, additional, Kuan, Leonard, additional, L’Heureux, Quinn, additional, Lambert, Sophie, additional, Leon, Arielle, additional, Liang, Elizabeth, additional, Long, Fuhui, additional, Mace, Kyla, additional, Magrans de Abril, Ildefons, additional, Mochizuki, Chris, additional, Nayan, Chelsea, additional, North, Katherine, additional, Ng, Lydia, additional, Ocker, Gabriel Koch, additional, Oliver, Michael, additional, Rhoads, Paul, additional, Ronellenfitch, Kara, additional, Schelonka, Kathryn, additional, Sevigny, Josh, additional, Sullivan, David, additional, Sutton, Ben, additional, Swapp, Jackie, additional, Nguyen, Thuyanh K, additional, Waughman, Xana, additional, Wilkes, Joshua, additional, Wang, Michael, additional, Farrell, Colin, additional, Wakeman, Wayne, additional, Zeng, Hongkui, additional, Phillips, John, additional, Mihalas, Stefan, additional, Arkhipov, Anton, additional, Koch, Christof, additional, and Olsen, Shawn R, additional

Published
2023
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7. A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex

Author

Yao, Shenqin, primary, Wang, Quanxin, additional, Hirokawa, Karla E., additional, Ouellette, Benjamin, additional, Ahmed, Ruweida, additional, Bomben, Jasmin, additional, Brouner, Krissy, additional, Casal, Linzy, additional, Caldejon, Shiella, additional, Cho, Andy, additional, Dotson, Nadezhda I., additional, Daigle, Tanya L., additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Gary, Amanda, additional, Gelfand, Emily, additional, Gorham, Melissa, additional, Griffin, Fiona, additional, Gu, Hong, additional, Hancock, Nicole, additional, Howard, Robert, additional, Kuan, Leonard, additional, Lambert, Sophie, additional, Lee, Eric Kenji, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Maxwell, Michelle, additional, Mortrud, Marty T., additional, Naeemi, Maitham, additional, Nayan, Chelsea, additional, Ngo, Nhan-Kiet, additional, Nguyen, Thuyanh, additional, North, Kat, additional, Ransford, Shea, additional, Ruiz, Augustin, additional, Seid, Sam, additional, Swapp, Jackie, additional, Taormina, Michael J., additional, Wakeman, Wayne, additional, Zhou, Thomas, additional, Nicovich, Philip R., additional, Williford, Ali, additional, Potekhina, Lydia, additional, McGraw, Medea, additional, Ng, Lydia, additional, Groblewski, Peter A., additional, Tasic, Bosiljka, additional, Mihalas, Stefan, additional, Harris, Julie A., additional, Cetin, Ali, additional, and Zeng, Hongkui, additional

Published
2022
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9. A mesoscale connectome of the mouse brain

Author

Oh, Seung Wook, Harris, Julie A., Ng, Lydia, Winslow, Brent, Cain, Nicholas, Mihalas, Stefan, Wang, Quanxin, Lau, Chris, Kuan, Leonard, Henry, Alex M., Mortrud, Marty T., Ouellette, Benjamin, Nguyen, Thuc Nghi, Sorensen, Staci A., Slaughterbeck, Clifford R., Wakeman, Wayne, Li, Yang, Feng, David, Ho, Anh, Nicholas, Eric, Hirokawa, Karla E., Bohn, Phillip, Joines, Kevin M., Peng, Hanchuan, Hawrylycz, Michael J., Phillips, John W., Hohmann, John G., Wohnoutka, Paul, Gerfen, Charles R., Koch, Christof, Bernard, Amy, Dang, Chinh, Jones, Allan R., and Zeng, Hongkui

Subjects
Brain -- Research -- Physiological aspects, Neural circuitry -- Research -- Physiological aspects, Enhanced green fluorescent protein -- Research -- Physiological aspects, Computer simulation -- Usage, Computer-generated environments -- Usage, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Comprehensive knowledge of the brain's wiring diagram is fundamental for understanding how the nervous system processes information at both local and global scales. However, with the singular exception of the C. elegans microscale connectome, there are no complete connectivity data sets in other species. Here we report a brain-wide, cellular-level, mesoscale connectome for the mouse. The Allen Mouse Brain Connectivity Atlas uses enhanced green fluorescent protein (EGFP)-expressing adeno-associated viral vectors to trace axonal projections from defined regions and cell types, and high-throughput serial two-photon tomography to image the EGFP-labelled axons throughout the brain. This systematic and standardized approach allows spatial registration of individual experiments into a common three dimensional (3D) reference space, resulting in a whole-brain connectivity matrix. A computational model yields insights into connectional strength distribution, symmetry and other network properties. Virtual tractography illustrates 3D topography among interconnected regions. Cortico-thalamic pathway analysis demonstrates segregation and integration of parallel pathways. The Allen Mouse Brain Connectivity Atlas is a freely available, foundational resource for structural and functional investigations into the neural circuits that support behavioural and cognitive processes in health and disease., A central principle of neuroscience is that the nervous system is a network of diverse types of neurons and supporting cells communicating with each other mainly through synaptic connections. This [...]

Published
2014
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10. A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex

Author

Yao, Shenqin, primary, Wang, Quanxin, additional, Hirokawa, Karla, additional, Ouellette, Benjamin, additional, Ahmed, Ruweida, additional, Bomben, Jasmin, additional, Brouner, Krissy, additional, Casal, Linzy, additional, Caldejon, Shiella, additional, Cho, Andy, additional, Dotson, Nadezhda, additional, Daigle, Tanya, additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Gary, Amanda, additional, Gelfand, Emily, additional, Gorham, Melissa, additional, Griffin, Fiona, additional, Gu, Hong, additional, Hancock, Nicole, additional, Howard, Robert, additional, Kuan, Leonard, additional, Lambert, Sophie, additional, Lee, Eric, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Maxwell, Michelle, additional, Mortrud, Marty, additional, Naeemi, Maitham, additional, Nayan, Chelsea, additional, Ngo, Nhan-Kiet, additional, Nguyen, Thuyanh, additional, North, Kat, additional, Ransford, Shea, additional, Ruiz, Augustin, additional, Seid, Sam, additional, Swapp, Jackie, additional, Taormina, Michael, additional, Wakeman, Wayne, additional, Zhou, Thomas, additional, Nicovich, Philip, additional, Williford, Ali, additional, Potekhina, Lydia, additional, McGraw, Medea, additional, Ng, Lydia, additional, Groblewski, Peter, additional, Tasic, Bosiljka, additional, Mihalas, Stefan, additional, Harris, Julie, additional, Cetin, Ali, additional, and Zeng, Hongkui, additional

Published
2021
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11. A mesoscale connectome of the mouse brain

Author

Wook Oh, Seung, Harris, Julie A., Ng, Lydia, Winslow, Brent, Cain, Nicholas, Mihalas, Stefan, Wang, Quanxin, Lau, Chris, Kuan, Leonard, Henry, Alex M., Mortrud, Marty T., Ouellette, Benjamin, Nghi Nguyen, Thuc, Sorensen, Staci A., Slaughterbeck, Clifford R., Wakeman, Wayne, Li, Yang, Feng, David, Ho, Anh, Nicholas, Eric, Hirokawa, Karla E., Bohn, Phillip, Joines, Kevin M., Peng, Hanchuan, Hawrylycz, Michael J., Phillips, John W., Hohmann, John G., Wohnoutka, Paul, Gerfen, Charles R., Koch, Christof, Bernard, Amy, Dang, Chinh, Jones, Allan R., and Zeng, Hongkui

Published
2014
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12. 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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13. 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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14. A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex

Author

de Vries, Saskia E. J., primary, Lecoq, Jerome A., additional, Buice, Michael A., additional, Groblewski, Peter A., additional, Ocker, Gabriel K., additional, Oliver, Michael, additional, Feng, David, additional, Cain, Nicholas, additional, Ledochowitsch, Peter, additional, Millman, Daniel, additional, Roll, Kate, additional, Garrett, Marina, additional, Keenan, Tom, additional, Kuan, Leonard, additional, Mihalas, Stefan, additional, Olsen, Shawn, additional, Thompson, Carol, additional, Wakeman, Wayne, additional, Waters, Jack, additional, Williams, Derric, additional, Barber, Chris, additional, Berbesque, Nathan, additional, Blanchard, Brandon, additional, Bowles, Nicholas, additional, Caldejon, Shiella D., additional, Casal, Linzy, additional, Cho, Andrew, additional, Cross, Sissy, additional, Dang, Chinh, additional, Dolbeare, Tim, additional, Edwards, Melise, additional, Galbraith, John, additional, Gaudreault, Nathalie, additional, Gilbert, Terri L., additional, Griffin, Fiona, additional, Hargrave, Perry, additional, Howard, Robert, additional, Huang, Lawrence, additional, Jewell, Sean, additional, Keller, Nika, additional, Knoblich, Ulf, additional, Larkin, Josh D., additional, Larsen, Rachael, additional, Lau, Chris, additional, Lee, Eric, additional, Lee, Felix, additional, Leon, Arielle, additional, Li, Lu, additional, Long, Fuhui, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nguyen, Thuyanh, additional, Perkins, Jed, additional, Robertson, Miranda, additional, Seid, Sam, additional, Shea-Brown, Eric, additional, Shi, Jianghong, additional, Sjoquist, Nathan, additional, Slaughterbeck, Cliff, additional, Sullivan, David, additional, Valenza, Ryan, additional, White, Casey, additional, Williford, Ali, additional, Witten, Daniela M., additional, Zhuang, Jun, additional, Zeng, Hongkui, additional, Farrell, Colin, additional, Ng, Lydia, additional, Bernard, Amy, additional, Phillips, John W., additional, Reid, R. Clay, additional, and Koch, Christof, additional

Published
2019
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15. Aberration-free multi-plane imaging of neural activity from the mammalian brain using a fast-switching liquid crystal spatial light modulator

Author

Liu, Rui, primary, Ball, Neil, additional, Brockill, James, additional, Kuan, Leonard, additional, Millman, Daniel, additional, White, Cassandra, additional, Leon, Arielle, additional, Williams, Derric, additional, Nishiwaki, Shig, additional, de Vries, Saskia, additional, Larkin, Josh, additional, Sullivan, David, additional, Slaughterbeck, Cliff, additional, Farrell, Colin, additional, and Saggau, Peter, additional

Published
2019
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16. Multi-plane Imaging of Neural Activity From the Mammalian Brain Using a Fast-switching Liquid Crystal Spatial Light Modulator

Author

Liu, Rui, primary, Ball, Neil, additional, Brockill, James, additional, Kuan, Leonard, additional, Millman, Daniel, additional, White, Cassandra, additional, Leon, Arielle, additional, Williams, Derric, additional, Nishiwaki, Shig, additional, de Vries, Saskia, additional, Larkin, Josh, additional, Sullivan, David, additional, Slaughterbeck, Cliff, additional, Farrell, Colin, additional, and Saggau, Peter, additional

Published
2018
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17. 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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18. Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain

Author

Pathak Sayan, Thompson Carol, Ng Lydia, Lau Christopher, Kuan Leonard, Jones Allan, and Hawrylycz Mike

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Spatially mapped large scale gene expression databases enable quantitative comparison of data measurements across genes, anatomy, and phenotype. In most ongoing efforts to study gene expression in the mammalian brain, significant resources are applied to the mapping and visualization of data. This paper describes the implementation and utility of Brain Explorer, a 3D visualization tool for studying in situ hybridization-based (ISH) expression patterns in the Allen Brain Atlas, a genome-wide survey of 21,000 expression patterns in the C57BL6J adult mouse brain. Results Brain Explorer enables users to visualize gene expression data from the C57Bl/6J mouse brain in 3D at a resolution of 100 μm3, allowing co-display of several experiments as well as 179 reference neuro-anatomical structures. Brain Explorer also allows viewing of the original ISH images referenced from any point in a 3D data set. Anatomic and spatial homology searches can be performed from the application to find data sets with expression in specific structures and with similar expression patterns. This latter feature allows for anatomy independent queries and genome wide expression correlation studies. Conclusion These tools offer convenient access to detailed expression information in the adult mouse brain and the ability to perform data mining and visualization of gene expression and neuroanatomy in an integrated manner.

Published
2008
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19. A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

Author

de Vries, Saskia E. J., primary, Lecoq, Jerome, additional, Buice, Michael A., additional, Groblewski, Peter A., additional, Ocker, Gabriel K., additional, Oliver, Michael, additional, Feng, David, additional, Cain, Nicholas, additional, Ledochowitsch, Peter, additional, Millman, Daniel, additional, Roll, Kate, additional, Garrett, Marina, additional, Keenan, Tom, additional, Kuan, Leonard, additional, Mihalas, Stefan, additional, Olsen, Shawn, additional, Thompson, Carol, additional, Wakeman, Wayne, additional, Waters, Jack, additional, Williams, Derric, additional, Barber, Chris, additional, Berbesque, Nathan, additional, Blanchard, Brandon, additional, Bowles, Nicholas, additional, Caldejon, Shiella, additional, Casal, Linzy, additional, Cho, Andrew, additional, Cross, Sissy, additional, Dang, Chinh, additional, Dolbeare, Tim, additional, Edwards, Melise, additional, Galbraith, John, additional, Gaudreault, Nathalie, additional, Griffin, Fiona, additional, Hargrave, Perry, additional, Howard, Robert, additional, Huang, Lawrence, additional, Jewell, Sean, additional, Keller, Nika, additional, Knoblich, Ulf, additional, Larkin, Josh, additional, Larsen, Rachael, additional, Lau, Chris, additional, Lee, Eric, additional, Lee, Felix, additional, Leon, Arielle, additional, Li, Lu, additional, Long, Fuhui, additional, Luviano, Jennifer, additional, Mace, Kyla, additional, Nguyen, Thuyanh, additional, Perkins, Jed, additional, Robertson, Miranda, additional, Seid, Sam, additional, Shea-Brown, Eric, additional, Shi, Jianghong, additional, Sjoquist, Nathan, additional, Slaughterbeck, Cliff, additional, Sullivan, David, additional, Valenza, Ryan, additional, White, Casey, additional, Williford, Ali, additional, Witten, Daniela, additional, Zhuang, Jun, additional, Zeng, Hongkui, additional, Farrell, Colin, additional, Ng, Lydia, additional, Bernard, Amy, additional, Phillips, John W., additional, Reid, R. Clay, additional, and Koch, Christof, additional

Published
2018
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20. 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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21. 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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26. Large-Scale Cellular-Resolution Gene Profiling in Human Neocortex Reveals Species-Specific Molecular Signatures

Author

Zeng, Hongkui, primary, Shen, Elaine H., additional, Hohmann, John G., additional, Oh, Seung Wook, additional, Bernard, Amy, additional, Royall, Joshua J., additional, Glattfelder, Katie J., additional, Sunkin, Susan M., additional, Morris, John A., additional, Guillozet-Bongaarts, Angela L., additional, Smith, Kimberly A., additional, Ebbert, Amanda J., additional, Swanson, Beryl, additional, Kuan, Leonard, additional, Page, Damon T., additional, Overly, Caroline C., additional, Lein, Ed S., additional, Hawrylycz, Michael J., additional, Hof, Patrick R., additional, Hyde, Thomas M., additional, Kleinman, Joel E., additional, and Jones, Allan R., additional

Published
2012
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30. The Allen Brain Atlas: Delivering Neuroscience to the Web on a Genome Wide Scale.

Author

Istrail, Sorin, Pevzner, Pavel, Waterman, Michael S., Cohen-Boulakia, Sarah, Tannen, Val, Chinh Dang, Sodt, Andrew, Lau, Chris, Youngstrom, Brian, Ng, Lydia, Kuan, Leonard, Pathak, Sayan, Jones, Allan, and Hawrylycz, Mike

Abstract

The Allen Brain Atlas (ABA), publicly available at http:// www.brain-map.org, presents the expression patterns of more than 21,500 genes in the adult mouse brain. The project has produced more than 600 Terabytes of cellular level in situ hybridization data whose images have been reconstructed and mapped into whole brain 3D volumes for search and viewing. In this application paper we outline the bioinformatics, data integration, and presentation approach to the ABA and the creation a fully automated high-throughput pipeline to deliver this data set to the Web. [ABSTRACT FROM AUTHOR]

Published
2007
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