Search

Your search keyword '"Macrina, Thomas"' showing total 45 results
Start Over Author "Macrina, Thomas"
45 results on '"Macrina, Thomas"'

1. Connectomic reconstruction of a female Drosophila ventral nerve cord

Author

Azevedo, Anthony, Lesser, Ellen, Phelps, Jasper S., Mark, Brandon, Elabbady, Leila, Kuroda, Sumiya, Sustar, Anne, Moussa, Anthony, Khandelwal, Avinash, Dallmann, Chris J., Agrawal, Sweta, Lee, Su-Yee J., Pratt, Brandon, Cook, Andrew, Skutt-Kakaria, Kyobi, Gerhard, Stephan, Lu, Ran, Kemnitz, Nico, Lee, Kisuk, Halageri, Akhilesh, Castro, Manuel, Ih, Dodam, Gager, Jay, Tammam, Marwan, Dorkenwald, Sven, Collman, Forrest, Schneider-Mizell, Casey, Brittain, Derrick, Jordan, Chris S., Dickinson, Michael, Pacureanu, Alexandra, Seung, H. Sebastian, Macrina, Thomas, Lee, Wei-Chung Allen, and Tuthill, John C.

Published
2024
Full Text
View/download PDF

2. Synaptic architecture of leg and wing premotor control networks in Drosophila

Author

Lesser, Ellen, Azevedo, Anthony W., Phelps, Jasper S., Elabbady, Leila, Cook, Andrew, Syed, Durafshan Sakeena, Mark, Brandon, Kuroda, Sumiya, Sustar, Anne, Moussa, Anthony, Dallmann, Chris J., Agrawal, Sweta, Lee, Su-Yee J., Pratt, Brandon, Skutt-Kakaria, Kyobi, Gerhard, Stephan, Lu, Ran, Kemnitz, Nico, Lee, Kisuk, Halageri, Akhilesh, Castro, Manuel, Ih, Dodam, Gager, Jay, Tammam, Marwan, Dorkenwald, Sven, Collman, Forrest, Schneider-Mizell, Casey, Brittain, Derrick, Jordan, Chris S., Macrina, Thomas, Dickinson, Michael, Lee, Wei-Chung Allen, and Tuthill, John C.

Published
2024
Full Text
View/download PDF

3. Automated Neuron Shape Analysis from Electron Microscopy

Author

Seshamani, Sharmishtaa, Elabbady, Leila, Schneider-Mizell, Casey, Mahalingam, Gayathri, Dorkenwald, Sven, Bodor, Agnes, Macrina, Thomas, Bumbarger, Daniel, Buchanan, JoAnn, Takeno, Marc, Yin, Wenjing, Brittain, Derrick, Torres, Russel, Kapner, Daniel, lee, Kisuk, Lu, Ran, Wu, Jinpeng, daCosta, Nuno, Reid, Clay, and Collman, Forrest

Subjects
Computer Science - Computer Vision and Pattern Recognition, I.4.9, I.5.3, J.3
Abstract

Morphology based analysis of cell types has been an area of great interest to the neuroscience community for several decades. Recently, high resolution electron microscopy (EM) datasets of the mouse brain have opened up opportunities for data analysis at a level of detail that was previously impossible. These datasets are very large in nature and thus, manual analysis is not a practical solution. Of particular interest are details to the level of post synaptic structures. This paper proposes a fully automated framework for analysis of post-synaptic structure based neuron analysis from EM data. The processing framework involves shape extraction, representation with an autoencoder, and whole cell modeling and analysis based on shape distributions. We apply our novel framework on a dataset of 1031 neurons obtained from imaging a 1mm x 1mm x 40 micrometer volume of the mouse visual cortex and show the strength of our method in clustering and classification of neuronal shapes., Comment: 9 pages, 4 figures

Published
2020

5. Convolutional nets for reconstructing neural circuits from brain images acquired by serial section electron microscopy

Author

Lee, Kisuk, Turner, Nicholas, Macrina, Thomas, Wu, Jingpeng, Lu, Ran, and Seung, H. Sebastian

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Neural circuits can be reconstructed from brain images acquired by serial section electron microscopy. Image analysis has been performed by manual labor for half a century, and efforts at automation date back almost as far. Convolutional nets were first applied to neuronal boundary detection a dozen years ago, and have now achieved impressive accuracy on clean images. Robust handling of image defects is a major outstanding challenge. Convolutional nets are also being employed for other tasks in neural circuit reconstruction: finding synapses and identifying synaptic partners, extending or pruning neuronal reconstructions, and aligning serial section images to create a 3D image stack. Computational systems are being engineered to handle petavoxel images of cubic millimeter brain volumes.

Published
2019

6. FlyWire: online community for whole-brain connectomics

Author

Dorkenwald, Sven, McKellar, Claire E., Macrina, Thomas, Kemnitz, Nico, Lee, Kisuk, Lu, Ran, Wu, Jingpeng, Popovych, Sergiy, Mitchell, Eric, Nehoran, Barak, Jia, Zhen, Bae, J. Alexander, Mu, Shang, Ih, Dodam, Castro, Manuel, Ogedengbe, Oluwaseun, Halageri, Akhilesh, Kuehner, Kai, Sterling, Amy R., Ashwood, Zoe, Zung, Jonathan, Brittain, Derrick, Collman, Forrest, Schneider-Mizell, Casey, Jordan, Chris, Silversmith, William, Baker, Christa, Deutsch, David, Encarnacion-Rivera, Lucas, Kumar, Sandeep, Burke, Austin, Bland, Doug, Gager, Jay, Hebditch, James, Koolman, Selden, Moore, Merlin, Morejohn, Sarah, Silverman, Ben, Willie, Kyle, Willie, Ryan, Yu, Szi-chieh, Murthy, Mala, and Seung, H. Sebastian

Published
2022
Full Text
View/download PDF

7. Deep Learning Improves Template Matching by Normalized Cross Correlation

Author

Buniatyan, Davit, Macrina, Thomas, Ih, Dodam, Zung, Jonathan, and Seung, H. Sebastian

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Template matching by normalized cross correlation (NCC) is widely used for finding image correspondences. We improve the robustness of this algorithm by preprocessing images with "siamese" convolutional networks trained to maximize the contrast between NCC values of true and false matches. The improvement is quantified using patches of brain images from serial section electron microscopy. Relative to a parameter-tuned bandpass filter, siamese convolutional networks significantly reduce false matches. Furthermore, all false matches can be eliminated by removing a tiny fraction of all matches based on NCC values. The improved accuracy of our method could be essential for connectomics, because emerging petascale datasets may require billions of template matches to assemble 2D images of serial sections into a 3D image stack. Our method is also expected to generalize to many other computer vision applications that use NCC template matching to find image correspondences.

Published
2017

8. Weakly Supervised Deep Metric Learning for Template Matching

Author

Buniatyan, Davit, Popovych, Sergiy, Ih, Dodam, Macrina, Thomas, Zung, Jonathan, Seung, H. Sebastian, Kacprzyk, Janusz, Series Editor, Pal, Nikhil R., Advisory Editor, Bello Perez, Rafael, Advisory Editor, Corchado, Emilio S., Advisory Editor, Hagras, Hani, Advisory Editor, Kóczy, László T., Advisory Editor, Kreinovich, Vladik, Advisory Editor, Lin, Chin-Teng, Advisory Editor, Lu, Jie, Advisory Editor, Melin, Patricia, Advisory Editor, Nedjah, Nadia, Advisory Editor, Nguyen, Ngoc Thanh, Advisory Editor, Wang, Jun, Advisory Editor, Arai, Kohei, editor, and Kapoor, Supriya, editor

Published
2020
Full Text
View/download PDF

9. Connectomic reconstruction of a female Drosophilaventral nerve cord

Author

Azevedo, Anthony, Lesser, Ellen, Phelps, Jasper S., Mark, Brandon, Elabbady, Leila, Kuroda, Sumiya, Sustar, Anne, Moussa, Anthony, Khandelwal, Avinash, Dallmann, Chris J., Agrawal, Sweta, Lee, Su-Yee J., Pratt, Brandon, Cook, Andrew, Skutt-Kakaria, Kyobi, Gerhard, Stephan, Lu, Ran, Kemnitz, Nico, Lee, Kisuk, Halageri, Akhilesh, Castro, Manuel, Ih, Dodam, Gager, Jay, Tammam, Marwan, Dorkenwald, Sven, Collman, Forrest, Schneider-Mizell, Casey, Brittain, Derrick, Jordan, Chris S., Dickinson, Michael, Pacureanu, Alexandra, Seung, H. Sebastian, Macrina, Thomas, Lee, Wei-Chung Allen, and Tuthill, John C.

Abstract

A deep understanding of how the brain controls behaviour requires mapping neural circuits down to the muscles that they control. Here, we apply automated tools to segment neurons and identify synapses in an electron microscopy dataset of an adult female Drosophila melanogasterventral nerve cord (VNC)1, which functions like the vertebrate spinal cord to sense and control the body. We find that the fly VNC contains roughly 45 million synapses and 14,600 neuronal cell bodies. To interpret the output of the connectome, we mapped the muscle targets of leg and wing motor neurons using genetic driver lines2and X-ray holographic nanotomography3. With this motor neuron atlas, we identified neural circuits that coordinate leg and wing movements during take-off. We provide the reconstruction of VNC circuits, the motor neuron atlas and tools for programmatic and interactive access as resources to support experimental and theoretical studies of how the nervous system controls behaviour.

Published
2024
Full Text
View/download PDF

10. CAVE: Connectome Annotation Versioning Engine

Author

Dorkenwald, Sven, primary, Schneider-Mizell, Casey M., additional, Brittain, Derrick, additional, Halageri, Akhilesh, additional, Jordan, Chris, additional, Kemnitz, Nico, additional, Castro, Manual A., additional, Silversmith, William, additional, Maitin-Shephard, Jeremy, additional, Troidl, Jakob, additional, Pfister, Hanspeter, additional, Gillet, Valentin, additional, Xenes, Daniel, additional, Bae, J. Alexander, additional, Bodor, Agnes L., additional, Buchanan, JoAnn, additional, Bumbarger, Daniel J., additional, Elabbady, Leila, additional, Jia, Zhen, additional, Kapner, Daniel, additional, Kinn, Sam, additional, Lee, Kisuk, additional, Li, Kai, additional, Lu, Ran, additional, Macrina, Thomas, additional, Mahalingam, Gayathri, additional, Mitchell, Eric, additional, Mondal, Shanka Subhra, additional, Mu, Shang, additional, Nehoran, Barak, additional, Popovych, Sergiy, additional, Takeno, Marc, additional, Torres, Russel, additional, Turner, Nicholas L., additional, Wong, William, additional, Wu, Jingpeng, additional, Yin, Wenjing, additional, Yu, Szi-chieh, additional, Reid, R. Clay, additional, da Costa, Nuno Maçarico, additional, Seung, H. Sebastian, additional, and Collman, Forrest, additional

Published
2023
Full Text
View/download PDF

11. Synaptic architecture of leg and wing motor control networks inDrosophila

Author

Lesser, Ellen, primary, Azevedo, Anthony W., additional, Phelps, Jasper S., additional, Elabbady, Leila, additional, Cook, Andrew P., additional, Mark, Brandon, additional, Kuroda, Sumiya, additional, Sustar, Anne, additional, Moussa, Anthony J., additional, Dallmann, Chris J., additional, Agrawal, Sweta, additional, Lee, Su-Yee J., additional, Pratt, Brandon G., additional, Skutt-Kakari, Kyobi, additional, Gerhard, Stephan, additional, Lu, Ran, additional, Kemnitz, Nico, additional, Lee, Kisuk, additional, Halageri, Akhilesh, additional, Castro, Manuel, additional, Ih, Dodam, additional, Gager, Jay, additional, Tammam, Marwan, additional, Dorkenwald, Sven, additional, Collman, Forrest C., additional, Schneider-Mizell, Casey M, additional, Brittain, Derrick, additional, Jordan, Chris S, additional, Seung, H Sebastian, additional, Macrina, Thomas, additional, Dickinson, Michael H, additional, Lee, Wei-Chung Allen, additional, and Tuthill, John C., additional

Published
2023
Full Text
View/download PDF

12. NEURD: A mesh decomposition framework for automated proofreading and morphological analysis of neuronal EM reconstructions

Author

Celii, Brendan, primary, Papadopoulos, Stelios, additional, Ding, Zhuokun, additional, Fahey, Paul G., additional, Wang, Eric, additional, Papadopoulos, Christos, additional, Kunin, Alexander, additional, Patel, Saumil, additional, Bae, J. Alexander, additional, Bodor, Agnes L., additional, Brittain, Derrick, additional, Buchanan, JoAnn, additional, Bumbarger, Daniel J., additional, Castro, Manuel A., additional, Cobos, Erick, additional, Dorkenwald, Sven, additional, Elabbady, Leila, additional, Halageri, Akhilesh, additional, Jia, Zhen, additional, Jordan, Chris, additional, Kapner, Dan, additional, Kemnitz, Nico, additional, Kinn, Sam, additional, Lee, Kisuk, additional, Li, Kai, additional, Lu, Ran, additional, Macrina, Thomas, additional, Mahalingam, Gayathri, additional, Mitchell, Eric, additional, Mondal, Shanka Subhra, additional, Mu, Shang, additional, Nehoran, Barak, additional, Popovych, Sergiy, additional, Schneider-Mizell, Casey M., additional, Silversmith, William, additional, Takeno, Marc, additional, Torres, Russel, additional, Turner, Nicholas L., additional, Wong, William, additional, Wu, Jingpeng, additional, Yu, Szi-chieh, additional, Yin, Wenjing, additional, Xenes, Daniel, additional, Kitchell, Lindsey M., additional, Rivlin, Patricia K., additional, Rose, Victoria A., additional, Bishop, Caitlyn A., additional, Wester, Brock, additional, Froudarakis, Emmanouil, additional, Walker, Edgar Y., additional, Sinz, Fabian H., additional, Seung, H. Sebastian, additional, Collman, Forrest, additional, da Costa, Nuno Maçarico, additional, Reid, R. Clay, additional, Pitkow, Xaq, additional, Tolias, Andreas S., additional, and Reimer, Jacob, additional

Published
2023
Full Text
View/download PDF

13. Functional connectomics reveals general wiring rule in mouse visual cortex

Author

Ding, Zhuokun, primary, Fahey, Paul G., additional, Papadopoulos, Stelios, additional, Wang, Eric, additional, Celii, Brendan, additional, Papadopoulos, Christos, additional, Kunin, Alexander B., additional, Chang, Andersen, additional, Fu, Jiakun, additional, Ding, Zhiwei, additional, Patel, Saumil, additional, Ponder, Kayla, additional, Bae, J. Alexander, additional, Bodor, Agnes L., additional, Brittain, Derrick, additional, Buchanan, JoAnn, additional, Bumbarger, Daniel J., additional, Castro, Manuel A., additional, Cobos, Erick, additional, Dorkenwald, Sven, additional, Elabbady, Leila, additional, Halageri, Akhilesh, additional, Jia, Zhen, additional, Jordan, Chris, additional, Kapner, Dan, additional, Kemnitz, Nico, additional, Kinn, Sam, additional, Lee, Kisuk, additional, Li, Kai, additional, Lu, Ran, additional, Macrina, Thomas, additional, Mahalingam, Gayathri, additional, Mitchell, Eric, additional, Mondal, Shanka Subhra, additional, Mu, Shang, additional, Nehoran, Barak, additional, Popovych, Sergiy, additional, Schneider-Mizell, Casey M., additional, Silversmith, William, additional, Takeno, Marc, additional, Torres, Russel, additional, Turner, Nicholas L., additional, Wong, William, additional, Wu, Jingpeng, additional, Yin, Wenjing, additional, Yu, Szi-chieh, additional, Froudarakis, Emmanouil, additional, Sinz, Fabian, additional, Seung, H. Sebastian, additional, Collman, Forrest, additional, da Costa, Nuno Maçarico, additional, Reid, R. Clay, additional, Walker, Edgar Y., additional, Pitkow, Xaq, additional, Reimer, Jacob, additional, and Tolias, Andreas S., additional

Published
2023
Full Text
View/download PDF

15. Large-scale unsupervised discovery of excitatory morphological cell types in mouse visual cortex

Author

Weis, Marissa A., primary, Papadopoulos, Stelios, additional, Hansel, Laura, additional, Lüddecke, Timo, additional, Celii, Brendan, additional, Fahey, Paul G., additional, Bae, J. Alexander, additional, Bodor, Agnes L., additional, Brittain, Derrick, additional, Buchanan, JoAnn, additional, Bumbarger, Daniel J., additional, Castro, Manuel A., additional, Cobos, Erick, additional, Collman, Forrest, additional, da Costa, Nuno Maçarico, additional, Dorkenwald, Sven, additional, Elabbady, Leila, additional, Froudarakis, Emmanouil, additional, Halageri, Akhilesh, additional, Jia, Zhen, additional, Jordan, Chris, additional, Kapner, Dan, additional, Kemnitz, Nico, additional, Kinn, Sam, additional, Lee, Kisuk, additional, Li, Kai, additional, Lu, Ran, additional, Macrina, Thomas, additional, Mahalingam, Gayathri, additional, Mitchell, Eric, additional, Mondal, Shanka Subhra, additional, Mu, Shang, additional, Nehoran, Barak, additional, Patel, Saumil, additional, Pitkow, Xaq, additional, Popovych, Sergiy, additional, Reid, R. Clay, additional, Schneider-Mizell, Casey M., additional, Seung, H. Sebastian, additional, Silversmith, William, additional, Sinz, Fabian H., additional, Takeno, Marc, additional, Torres, Russel, additional, Turner, Nicholas L., additional, Wong, William, additional, Wu, Jingpeng, additional, Yin, Wenjing, additional, Yu, Szi-chieh, additional, Reimer, Jacob, additional, Tolias, Andreas S., additional, and Ecker, Alexander S., additional

Published
2022
Full Text
View/download PDF

16. Tools for comprehensive reconstruction and analysis ofDrosophilamotor circuits

Author

Azevedo, Anthony, primary, Lesser, Ellen, additional, Mark, Brandon, additional, Phelps, Jasper, additional, Elabbady, Leila, additional, Kuroda, Sumiya, additional, Sustar, Anne, additional, Moussa, Anthony, additional, Kandelwal, Avinash, additional, Dallmann, Chris J., additional, Agrawal, Sweta, additional, Lee, Su-Yee J., additional, Pratt, Brandon, additional, Cook, Andrew, additional, Skutt-Kakaria, Kyobi, additional, Gerhard, Stephan, additional, Lu, Ran, additional, Kemnitz, Nico, additional, Lee, Kisuk, additional, Halageri, Akhilesh, additional, Castro, Manuel, additional, Ih, Dodam, additional, Gager, Jay, additional, Tammam, Marwan, additional, Dorkenwald, Sven, additional, Collman, Forrest, additional, Schneider-Mizell, Casey, additional, Brittain, Derrick, additional, Jordan, Chris S., additional, Dickinson, Michael, additional, Pacureanu, Alexandra, additional, Seung, H. Sebastian, additional, Macrina, Thomas, additional, Lee, Wei-Chung Allen, additional, and Tuthill, John C., additional

Published
2022
Full Text
View/download PDF

17. Oligodendrocyte precursor cells ingest axons in the mouse neocortex

Author

Buchanan, JoAnn, primary, Elabbady, Leila, additional, Collman, Forrest, additional, Jorstad, Nikolas L., additional, Bakken, Trygve E., additional, Ott, Carolyn, additional, Glatzer, Jenna, additional, Bleckert, Adam A., additional, Bodor, Agnes L., additional, Brittain, Derrick, additional, Bumbarger, Daniel J., additional, Mahalingam, Gayathri, additional, Seshamani, Sharmishtaa, additional, Schneider-Mizell, Casey, additional, Takeno, Marc M., additional, Torres, Russel, additional, Yin, Wenjing, additional, Hodge, Rebecca D., additional, Castro, Manuel, additional, Dorkenwald, Sven, additional, Ih, Dodam, additional, Jordan, Chris S., additional, Kemnitz, Nico, additional, Lee, Kisuk, additional, Lu, Ran, additional, Macrina, Thomas, additional, Mu, Shang, additional, Popovych, Sergiy, additional, Silversmith, William M., additional, Tartavull, Ignacio, additional, Turner, Nicholas L., additional, Wilson, Alyssa M., additional, Wong, William, additional, Wu, Jingpeng, additional, Zlateski, Aleksandar, additional, Zung, Jonathan, additional, Lippincott-Schwartz, Jennifer, additional, Lein, Ed S., additional, Seung, H. Sebastian, additional, Bergles, Dwight E., additional, Reid, R. Clay, additional, and da Costa, Nuno Maçarico, additional

Published
2022
Full Text
View/download PDF

18. Binary and analog variation of synapses between cortical pyramidal neurons

Author

Dorkenwald, Sven, primary, Turner, Nicholas L, primary, Macrina, Thomas, primary, Lee, Kisuk, primary, Lu, Ran, primary, Wu, Jingpeng, primary, Bodor, Agnes L, primary, Bleckert, Adam A, primary, Brittain, Derrick, primary, Kemnitz, Nico, additional, Silversmith, William M, additional, Ih, Dodam, additional, Zung, Jonathan, additional, Zlateski, Aleksandar, additional, Tartavull, Ignacio, additional, Yu, Szi-Chieh, additional, Popovych, Sergiy, additional, Wong, William, additional, Castro, Manuel, additional, Jordan, Chris S, additional, Wilson, Alyssa M, additional, Froudarakis, Emmanouil, additional, Buchanan, JoAnn, additional, Takeno, Marc M, additional, Torres, Russel, additional, Mahalingam, Gayathri, additional, Collman, Forrest, additional, Schneider-Mizell, Casey M, additional, Bumbarger, Daniel J, additional, Li, Yang, additional, Becker, Lynne, additional, Suckow, Shelby, additional, Reimer, Jacob, additional, Tolias, Andreas S, additional, Macarico da Costa, Nuno, additional, Reid, R Clay, additional, and Seung, H Sebastian, additional

Published
2022
Full Text
View/download PDF

19. Author response: Binary and analog variation of synapses between cortical pyramidal neurons

Author

Dorkenwald, Sven, primary, Turner, Nicholas L, primary, Macrina, Thomas, primary, Lee, Kisuk, primary, Lu, Ran, primary, Wu, Jingpeng, primary, Bodor, Agnes L, primary, Bleckert, Adam A, primary, Brittain, Derrick, primary, Kemnitz, Nico, additional, Silversmith, William M, additional, Ih, Dodam, additional, Zung, Jonathan, additional, Zlateski, Aleksandar, additional, Tartavull, Ignacio, additional, Yu, Szi-Chieh, additional, Popovych, Sergiy, additional, Wong, William, additional, Castro, Manuel, additional, Jordan, Chris S, additional, Wilson, Alyssa M, additional, Froudarakis, Emmanouil, additional, Buchanan, JoAnn, additional, Takeno, Marc M, additional, Torres, Russel, additional, Mahalingam, Gayathri, additional, Collman, Forrest, additional, Schneider-Mizell, Casey M, additional, Bumbarger, Daniel J, additional, Li, Yang, additional, Becker, Lynne, additional, Suckow, Shelby, additional, Reimer, Jacob, additional, Tolias, Andreas S, additional, Macarico da Costa, Nuno, additional, Reid, R Clay, additional, and Seung, H Sebastian, additional

Published
2022
Full Text
View/download PDF

20. Quantitative Census of Local Somatic Features in Mouse Visual Cortex

Author

Elabbady, Leila, primary, Seshamani, Sharmishtaa, additional, Mu, Shang, additional, Mahalingam, Gayathri, additional, Schneider-Mizell, Casey, additional, Bodor, Agnes, additional, Bae, J. Alexander, additional, Brittain, Derrick, additional, Buchanan, JoAnn, additional, Bumbarger, Daniel J., additional, Castro, Manuel A., additional, Cobos, Erick, additional, Dorkenwald, Sven, additional, Fahey, Paul G., additional, Froudarakis, Emmanouil, additional, Halageri, Akhilesh, additional, Jia, Zhen, additional, Jordan, Chris, additional, Kapner, Dan, additional, Kemnitz, Nico, additional, Kinn, Sam, additional, Lee, Kisuk, additional, Li, Kai, additional, Lu, Ran, additional, Macrina, Thomas, additional, Mitchell, Eric, additional, Mondal, Shanka Subhra, additional, Nehoran, Barak, additional, Papadopoulos, Stelios, additional, Patel, Saumil, additional, Pitkow, Xaq, additional, Popovych, Sergiy, additional, Reimer, Jacob, additional, Silversmith, William, additional, Sinz, Fabian H., additional, Takeno, Marc, additional, Torres, Russel, additional, Turner, Nicholas, additional, Wong, William, additional, Wu, Jingpeng, additional, Yin, Wenjing, additional, Yu, Szi-chieh, additional, Tolias, Andreas, additional, Seung, H. Sebastian, additional, Reid, R. Clay, additional, Maçarico Da Costa, Nuno, additional, and Collman, Forrest, additional

Published
2022
Full Text
View/download PDF

21. Petascale pipeline for precise alignment of images from serial section electron microscopy

Author

Popovych, Sergiy, primary, Macrina, Thomas, additional, Kemnitz, Nico, additional, Castro, Manuel, additional, Nehoran, Barak, additional, Jia, Zhen, additional, Bae, J. Alexander, additional, Mitchell, Eric, additional, Mu, Shang, additional, Trautman, Eric T., additional, Saalfeld, Stephan, additional, Li, Kai, additional, and Seung, Sebastian, additional

Published
2022
Full Text
View/download PDF

22. Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity

Author

Turner, Nicholas L., primary, Macrina, Thomas, additional, Bae, J. Alexander, additional, Yang, Runzhe, additional, Wilson, Alyssa M., additional, Schneider-Mizell, Casey, additional, Lee, Kisuk, additional, Lu, Ran, additional, Wu, Jingpeng, additional, Bodor, Agnes L., additional, Bleckert, Adam A., additional, Brittain, Derrick, additional, Froudarakis, Emmanouil, additional, Dorkenwald, Sven, additional, Collman, Forrest, additional, Kemnitz, Nico, additional, Ih, Dodam, additional, Silversmith, William M., additional, Zung, Jonathan, additional, Zlateski, Aleksandar, additional, Tartavull, Ignacio, additional, Yu, Szi-chieh, additional, Popovych, Sergiy, additional, Mu, Shang, additional, Wong, William, additional, Jordan, Chris S., additional, Castro, Manuel, additional, Buchanan, JoAnn, additional, Bumbarger, Daniel J., additional, Takeno, Marc, additional, Torres, Russel, additional, Mahalingam, Gayathri, additional, Elabbady, Leila, additional, Li, Yang, additional, Cobos, Erick, additional, Zhou, Pengcheng, additional, Suckow, Shelby, additional, Becker, Lynne, additional, Paninski, Liam, additional, Polleux, Franck, additional, Reimer, Jacob, additional, Tolias, Andreas S., additional, Reid, R. Clay, additional, da Costa, Nuno Maçarico, additional, and Seung, H. Sebastian, additional

Published
2022
Full Text
View/download PDF

23. FlyWire: online community for whole-brain connectomics

Author

Dorkenwald, Sven, primary, McKellar, Claire E., additional, Macrina, Thomas, additional, Kemnitz, Nico, additional, Lee, Kisuk, additional, Lu, Ran, additional, Wu, Jingpeng, additional, Popovych, Sergiy, additional, Mitchell, Eric, additional, Nehoran, Barak, additional, Jia, Zhen, additional, Bae, J. Alexander, additional, Mu, Shang, additional, Ih, Dodam, additional, Castro, Manuel, additional, Ogedengbe, Oluwaseun, additional, Halageri, Akhilesh, additional, Kuehner, Kai, additional, Sterling, Amy R., additional, Ashwood, Zoe, additional, Zung, Jonathan, additional, Brittain, Derrick, additional, Collman, Forrest, additional, Schneider-Mizell, Casey, additional, Jordan, Chris, additional, Silversmith, William, additional, Baker, Christa, additional, Deutsch, David, additional, Encarnacion-Rivera, Lucas, additional, Kumar, Sandeep, additional, Burke, Austin, additional, Bland, Doug, additional, Gager, Jay, additional, Hebditch, James, additional, Koolman, Selden, additional, Moore, Merlin, additional, Morejohn, Sarah, additional, Silverman, Ben, additional, Willie, Kyle, additional, Willie, Ryan, additional, Yu, Szi-chieh, additional, Murthy, Mala, additional, and Seung, H. Sebastian, additional

Published
2021
Full Text
View/download PDF

24. Structure and function of axo-axonic inhibition

Author

Schneider-Mizell, Casey M, primary, Bodor, Agnes L, additional, Collman, Forrest, additional, Brittain, Derrick, additional, Bleckert, Adam, additional, Dorkenwald, Sven, additional, Turner, Nicholas L, additional, Macrina, Thomas, additional, Lee, Kisuk, additional, Lu, Ran, additional, Wu, Jingpeng, additional, Zhuang, Jun, additional, Nandi, Anirban, additional, Hu, Brian, additional, Buchanan, JoAnn, additional, Takeno, Marc M, additional, Torres, Russel, additional, Mahalingam, Gayathri, additional, Bumbarger, Daniel J, additional, Li, Yang, additional, Chartrand, Thomas, additional, Kemnitz, Nico, additional, Silversmith, William M, additional, Ih, Dodam, additional, Zung, Jonathan, additional, Zlateski, Aleksandar, additional, Tartavull, Ignacio, additional, Popovych, Sergiy, additional, Wong, William, additional, Castro, Manuel, additional, Jordan, Chris S, additional, Froudarakis, Emmanouil, additional, Becker, Lynne, additional, Suckow, Shelby, additional, Reimer, Jacob, additional, Tolias, Andreas S, additional, Anastassiou, Costas A, additional, Seung, H Sebastian, additional, Reid, R Clay, additional, and Costa, Nuno Maçarico da, additional

Published
2021
Full Text
View/download PDF

25. Author response: Structure and function of axo-axonic inhibition

Author

Schneider-Mizell, Casey M, primary, Bodor, Agnes L, additional, Collman, Forrest, additional, Brittain, Derrick, additional, Bleckert, Adam, additional, Dorkenwald, Sven, additional, Turner, Nicholas L, additional, Macrina, Thomas, additional, Lee, Kisuk, additional, Lu, Ran, additional, Wu, Jingpeng, additional, Zhuang, Jun, additional, Nandi, Anirban, additional, Hu, Brian, additional, Buchanan, JoAnn, additional, Takeno, Marc M, additional, Torres, Russel, additional, Mahalingam, Gayathri, additional, Bumbarger, Daniel J, additional, Li, Yang, additional, Chartrand, Thomas, additional, Kemnitz, Nico, additional, Silversmith, William M, additional, Ih, Dodam, additional, Zung, Jonathan, additional, Zlateski, Aleksandar, additional, Tartavull, Ignacio, additional, Popovych, Sergiy, additional, Wong, William, additional, Castro, Manuel, additional, Jordan, Chris S, additional, Froudarakis, Emmanouil, additional, Becker, Lynne, additional, Suckow, Shelby, additional, Reimer, Jacob, additional, Tolias, Andreas S, additional, Anastassiou, Costas A, additional, Seung, H Sebastian, additional, Reid, R Clay, additional, and Costa, Nuno Maçarico da, additional

Published
2021
Full Text
View/download PDF

26. 3D reconstruction of cell nuclei in a full Drosophila brain

Author

Mu, Shang, primary, Yu, Szi-chieh, additional, Turner, Nicholas L., additional, McKellar, Claire E., additional, Dorkenwald, Sven, additional, Collman, Forrest, additional, Koolman, Selden, additional, Moore, Merlin, additional, Morejohn, Sarah, additional, Silverman, Ben, additional, Willie, Kyle, additional, Willie, Ryan, additional, Bland, Doug, additional, Burke, Austin, additional, Ashwood, Zoe, additional, Luther, Kyle, additional, Castro, Manuel, additional, Ogedengbe, Oluwaseun, additional, Silversmith, William, additional, Wu, Jingpeng, additional, Halageri, Akhilesh, additional, Macrina, Thomas, additional, Kemnitz, Nico, additional, Murthy, Mala, additional, and Seung, H. Sebastian, additional

Published
2021
Full Text
View/download PDF

27. Petascale neural circuit reconstruction: automated methods

Author

Macrina, Thomas, primary, Lee, Kisuk, additional, Lu, Ran, additional, Turner, Nicholas L., additional, Wu, Jingpeng, additional, Popovych, Sergiy, additional, Silversmith, William, additional, Kemnitz, Nico, additional, Bae, J. Alexander, additional, Castro, Manuel A., additional, Dorkenwald, Sven, additional, Halageri, Akhilesh, additional, Jia, Zhen, additional, Jordan, Chris, additional, Li, Kai, additional, Mitchell, Eric, additional, Mondal, Shanka Subhra, additional, Mu, Shang, additional, Nehoran, Barak, additional, Wong, William, additional, Yu, Szi-chieh, additional, Bodor, Agnes L., additional, Brittain, Derrick, additional, Buchanan, JoAnn, additional, Bumbarger, Daniel J., additional, Cobos, Erick, additional, Collman, Forrest, additional, Elabbady, Leila, additional, Fahey, Paul G., additional, Froudarakis, Emmanouil, additional, Kapner, Daniel, additional, Kinn, Sam, additional, Mahalingam, Gayathri, additional, Papadopoulos, Stelios, additional, Patel, Saumil, additional, Schneider-Mizell, Casey M., additional, Sinz, Fabian H., additional, Takeno, Marc, additional, Torres, Russel, additional, Yin, Wenjing, additional, Pitkow, Xaq, additional, Reimer, Jacob, additional, Tolias, Andreas S., additional, Reid, R. Clay, additional, Costa, Nuno Maçarico da, additional, and Seung, H. Sebastian, additional

Published
2021
Full Text
View/download PDF

28. Oligodendrocyte precursor cells prune axons in the mouse neocortex

Author

Buchanan, JoAnn, primary, Elabbady, Leila, additional, Collman, Forrest, additional, Jorstad, Nicholas, additional, Bakken, Trygve, additional, Ott, Carolyn, additional, Glazer, Jenna, additional, Bleckert, Adam, additional, Bodor, Agnes, additional, Brittain, Derrick, additional, Bumbarger, Dan, additional, Mahalingam, Gayathri, additional, Seshamani, Sharmishtaa, additional, Schneider-Mizell, Casey, additional, Takeno, Marc, additional, Torres, Russel, additional, Yin, Wenjing, additional, Hodge, Rebecca, additional, Castro, Manuel, additional, Dorkenwald, Sven, additional, Ih, Dodam, additional, Jordan, Chris, additional, Kemnitz, Nico, additional, Lee, Kisuk, additional, Lu, Ran, additional, Macrina, Thomas, additional, Mu, Shang, additional, Popovych, Sergiy, additional, Silversmith, William, additional, Tartavull, Ignacio, additional, Turner, Nicholas, additional, Wilson, Alyssa, additional, Wong, William, additional, Wu, Jingpeng, additional, Zlateski, Aleksandar, additional, Zung, Jonathan, additional, Lippincott-Schwartz, Jennifer, additional, Lein, Ed S., additional, Seung, H. Sebastian, additional, Bergles, Dwight, additional, Reid, R. Clay, additional, and Costa, Nuno da, additional

Published
2021
Full Text
View/download PDF

29. The neural basis for a persistent internal state in Drosophila females

Author

Deutsch, David, primary, Pacheco, Diego, additional, Encarnacion-Rivera, Lucas, additional, Pereira, Talmo, additional, Fathy, Ramie, additional, Clemens, Jan, additional, Girardin, Cyrille, additional, Calhoun, Adam, additional, Ireland, Elise, additional, Burke, Austin, additional, Dorkenwald, Sven, additional, McKellar, Claire, additional, Macrina, Thomas, additional, Lu, Ran, additional, Lee, Kisuk, additional, Kemnitz, Nico, additional, Ih, Dodam, additional, Castro, Manuel, additional, Halageri, Akhilesh, additional, Jordan, Chris, additional, Silversmith, William, additional, Wu, Jingpeng, additional, Seung, H Sebastian, additional, and Murthy, Mala, additional

Published
2020
Full Text
View/download PDF

30. Author response: The neural basis for a persistent internal state in Drosophila females

Author

Deutsch, David, primary, Pacheco, Diego, additional, Encarnacion-Rivera, Lucas, additional, Pereira, Talmo, additional, Fathy, Ramie, additional, Clemens, Jan, additional, Girardin, Cyrille, additional, Calhoun, Adam, additional, Ireland, Elise, additional, Burke, Austin, additional, Dorkenwald, Sven, additional, McKellar, Claire, additional, Macrina, Thomas, additional, Lu, Ran, additional, Lee, Kisuk, additional, Kemnitz, Nico, additional, Ih, Dodham, additional, Castro, Manuel, additional, Halageri, Akhilesh, additional, Jordan, Chris, additional, Silversmith, William, additional, Wu, Jingpeng, additional, Seung, H Sebastian, additional, and Murthy, Mala, additional

Published
2020
Full Text
View/download PDF

31. Multiscale and multimodal reconstruction of cortical structure and function

Author

Turner, Nicholas L., primary, Macrina, Thomas, additional, Bae, J. Alexander, additional, Yang, Runzhe, additional, Wilson, Alyssa M., additional, Schneider-Mizell, Casey, additional, Lee, Kisuk, additional, Lu, Ran, additional, Wu, Jingpeng, additional, Bodor, Agnes L., additional, Bleckert, Adam A., additional, Brittain, Derrick, additional, Froudarakis, Emmanouil, additional, Dorkenwald, Sven, additional, Collman, Forrest, additional, Kemnitz, Nico, additional, Ih, Dodam, additional, Silversmith, William M., additional, Zung, Jonathan, additional, Zlateski, Aleksandar, additional, Tartavull, Ignacio, additional, Yu, Szi-chieh, additional, Popovych, Sergiy, additional, Mu, Shang, additional, Wong, William, additional, Jordan, Chris S., additional, Castro, Manuel, additional, Buchanan, JoAnn, additional, Bumbarger, Daniel J., additional, Takeno, Marc, additional, Torres, Russel, additional, Mahalingam, Gayathri, additional, Elabbady, Leila, additional, Li, Yang, additional, Cobos, Erick, additional, Zhou, Pengcheng, additional, Suckow, Shelby, additional, Becker, Lynne, additional, Paninski, Liam, additional, Polleux, Franck, additional, Reimer, Jacob, additional, Tolias, Andreas S., additional, Reid, R. Clay, additional, da Costa, Nuno Maçarico, additional, and Seung, H. Sebastian, additional

Published
2020
Full Text
View/download PDF

32. FlyWire: Online community for whole-brain connectomics

Author

Dorkenwald, Sven, primary, McKellar, Claire, additional, Macrina, Thomas, additional, Kemnitz, Nico, additional, Lee, Kisuk, additional, Lu, Ran, additional, Wu, Jingpeng, additional, Popovych, Sergiy, additional, Mitchell, Eric, additional, Nehoran, Barak, additional, Jia, Zhen, additional, Bae, J. Alexander, additional, Mu, Shang, additional, Ih, Dodam, additional, Castro, Manuel, additional, Ogedengbe, Oluwaseun, additional, Halageri, Akhilesh, additional, Ashwood, Zoe, additional, Zung, Jonathan, additional, Brittain, Derrick, additional, Collman, Forrest, additional, Schneider-Mizell, Casey, additional, Jordan, Chris, additional, Silversmith, William, additional, Baker, Christa, additional, Deutsch, David, additional, Encarnacion-Rivera, Lucas, additional, Kumar, Sandeep, additional, Burke, Austin, additional, Gager, Jay, additional, Hebditch, James, additional, Koolman, Selden, additional, Moore, Merlin, additional, Morejohn, Sarah, additional, Silverman, Ben, additional, Willie, Kyle, additional, Willie, Ryan, additional, Yu, Szi-chieh, additional, Murthy, Mala, additional, and Seung, H. Sebastian, additional

Published
2020
Full Text
View/download PDF

33. Structure and function of axo-axonic inhibition.

Author

Schneider-MizellAgnes, Casey M., Bodor, L., Collman, Forrest, Brittain, Derrick, Bleckert, Adam, Dorkenwald, Sven, Turner, Nicholas L., Macrina, Thomas, Kisuk Lee, Ran Lu, Jingpeng Wu, Zhuang, Jun, Nandi, Anirban, Hu, Brian, Buchanan, JoAnn, Takeno, Marc M., Torres, Russel, Mahalingam, Gayathri, Bumbarger, Daniel J., and Yang Li

Published
2022
Full Text
View/download PDF

34. Chandelier cell anatomy and function reveal a variably distributed but common signal

Author

Schneider-Mizell, Casey M., primary, Bodor, Agnes L., additional, Collman, Forrest, additional, Brittain, Derrick, additional, Bleckert, Adam A., additional, Dorkenwald, Sven, additional, Turner, Nicholas L., additional, Macrina, Thomas, additional, Lee, Kisuk, additional, Lu, Ran, additional, Wu, Jingpeng, additional, Zhuang, Jun, additional, Nandi, Anirban, additional, Hu, Brian, additional, Buchanan, JoAnn, additional, Takeno, Marc M., additional, Torres, Russel, additional, Mahalingam, Gayathri, additional, Bumbarger, Daniel J., additional, Li, Yang, additional, Chartrand, Tom, additional, Kemnitz, Nico, additional, Silversmith, William M., additional, Ih, Dodam, additional, Zung, Jonathan, additional, Zlateski, Aleksandar, additional, Tartavull, Ignacio, additional, Popovych, Sergiy, additional, Wong, William, additional, Castro, Manuel, additional, Jordan, Chris S., additional, Froudarakis, Emmanouil, additional, Becker, Lynne, additional, Suckow, Shelby, additional, Reimer, Jacob, additional, Tolias, Andreas S., additional, Anastassiou, Costas, additional, Seung, H. Sebastian, additional, Reid, R. Clay, additional, and Maçarico da Costa, Nuno, additional

Published
2020
Full Text
View/download PDF

35. EASE: EM-Assisted Source Extraction from calcium imaging data

Author

Zhou, Pengcheng, primary, Reimer, Jacob, additional, Zhou, Ding, additional, Pasarkar, Amol, additional, Kinsella, Ian, additional, Froudarakis, Emmanouil, additional, Yatsenko, Dimitri V, additional, Fahey, Paul G, additional, Bodor, Agnes, additional, Buchanan, JoAnn, additional, Bumbarger, Dan, additional, Mahalingam, Gayathri, additional, Torres, Russel, additional, Dorkenwald, Sven, additional, Ih, Dodam, additional, Lee, Kisuk, additional, Lu, Ran, additional, Macrina, Thomas, additional, Wu, Jingpeng, additional, da Costa, Nuno, additional, Reid, R. Clay, additional, Tolias, Andreas S, additional, and Paninski, Liam, additional

Published
2020
Full Text
View/download PDF

36. The Neural Basis for a Persistent Internal State inDrosophilaFemales

Author

Deutsch, David, primary, Pacheco, Diego A., additional, Encarnacion-Rivera, Lucas J., additional, Pereira, Talmo, additional, Fathy, Ramie, additional, Calhoun, Adam, additional, Ireland, Elise C., additional, Burke, Austin T., additional, Dorkenwald, Sven, additional, McKellar, Claire, additional, Macrina, Thomas, additional, Lu, Ran, additional, Lee, Kisuk, additional, Kemnitz, Nico, additional, Ih, Dodam, additional, Castro, Manuel, additional, Halageri, Akhilesh, additional, Jordan, Chris, additional, Silversmith, William, additional, Wu, Jingpeng, additional, Seung, H. Sebastian, additional, and Murthy, Mala, additional

Published
2020
Full Text
View/download PDF

37. Binary and analog variation of synapses between cortical pyramidal neurons

Author

Dorkenwald, Sven, primary, Turner, Nicholas L., additional, Macrina, Thomas, additional, Lee, Kisuk, additional, Lu, Ran, additional, Wu, Jingpeng, additional, Bodor, Agnes L., additional, Bleckert, Adam A., additional, Brittain, Derrick, additional, Kemnitz, Nico, additional, Silversmith, William M., additional, Ih, Dodam, additional, Zung, Jonathan, additional, Zlateski, Aleksandar, additional, Tartavull, Ignacio, additional, Yu, Szi-Chieh, additional, Popovych, Sergiy, additional, Wong, William, additional, Castro, Manuel, additional, Jordan, Chris S., additional, Wilson, Alyssa M., additional, Froudarakis, Emmanouil, additional, Buchanan, JoAnn, additional, Takeno, Marc, additional, Torres, Russel, additional, Mahalingam, Gayathri, additional, Collman, Forrest, additional, Schneider-Mizell, Casey, additional, Bumbarger, Daniel J., additional, Li, Yang, additional, Becker, Lynne, additional, Suckow, Shelby, additional, Reimer, Jacob, additional, Tolias, Andreas S., additional, Maçarico da Costa, Nuno, additional, Reid, R. Clay, additional, and Seung, H. Sebastian, additional

Published
2019
Full Text
View/download PDF

39. The neural basis for a persistent internal state in Drosophila females.

Author

Deutsch, David, Pacheco, Diego, Encarnacion-Rivera, Lucas, Pereira, Talmo, Fathy, Ramie, Clemens, Jan, Girardin, Cyrille, Calhoun, Adam, Ireland, Elise, Burke, Austin, Dorkenwald, Sven, McKellar, Claire, Macrina, Thomas, Lu, Ran, Lee, Kisuk, Kemnitz, Nico, Ih, Dodham, Castro, Manuel, Halageri, Akhilesh, and Jordan, Chris

Published
2021
Full Text
View/download PDF

40. Synaptic architecture of leg and wing premotor control networks in Drosophila .

Author

Lesser E, Azevedo AW, Phelps JS, Elabbady L, Cook A, Sakeena Syed D, Mark B, Kuroda S, Sustar A, Moussa A, Dallmann CJ, Agrawal S, Lee SJ, Pratt B, Skutt-Kakaria K, Gerhard S, Lu R, Kemnitz N, Lee K, Halageri A, Castro M, Ih D, Gager J, Tammam M, Dorkenwald S, Collman F, Schneider-Mizell C, Brittain D, Jordan CS, Macrina T, Dickinson M, Lee WA, and Tuthill JC

Abstract

Animal movement is controlled by motor neurons (MNs), which project out of the central nervous system to activate muscles. MN activity is coordinated by complex premotor networks that allow individual muscles to contribute to many different behaviors. Here, we use connectomics to analyze the wiring logic of premotor circuits controlling the Drosophila leg and wing. We find that both premotor networks cluster into modules that link MNs innervating muscles with related functions. Within most leg motor modules, the synaptic weights of each premotor neuron are proportional to the size of their target MNs, establishing a circuit basis for hierarchical MN recruitment. In contrast, wing premotor networks lack proportional synaptic connectivity, which may allow wing steering muscles to be recruited with different relative timing. By comparing the architecture of distinct limb motor control systems within the same animal, we identify common principles of premotor network organization and specializations that reflect the unique biomechanical constraints and evolutionary origins of leg and wing motor control.

Published
2024
Full Text
View/download PDF

41. NEURD: automated proofreading and feature extraction for connectomics.

Author

Celii B, Papadopoulos S, Ding Z, Fahey PG, Wang E, Papadopoulos C, Kunin AB, Patel S, Bae JA, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Castro MA, Cobos E, Dorkenwald S, Elabbady L, Halageri A, Jia Z, Jordan C, Kapner D, Kemnitz N, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Schneider-Mizell CM, Silversmith W, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yu SC, Yin W, Xenes D, Kitchell LM, Rivlin PK, Rose VA, Bishop CA, Wester B, Froudarakis E, Walker EY, Sinz F, Seung HS, Collman F, da Costa NM, Reid RC, Pitkow X, Tolias AS, and Reimer J

Abstract

We are now in the era of millimeter-scale electron microscopy (EM) volumes collected at nanometer resolution (Shapson-Coe et al., 2021; Consortium et al., 2021). Dense reconstruction of cellular compartments in these EM volumes has been enabled by recent advances in Machine Learning (ML) (Lee et al., 2017; Wu et al., 2021; Lu et al., 2021; Macrina et al., 2021). Automated segmentation methods can now yield exceptionally accurate reconstructions of cells, but despite this accuracy, laborious post-hoc proofreading is still required to generate large connectomes free of merge and split errors. The elaborate 3-D meshes of neurons produced by these segmentations contain detailed morphological information, from the diameter, shape, and branching patterns of axons and dendrites, down to the fine-scale structure of dendritic spines. However, extracting information about these features can require substantial effort to piece together existing tools into custom workflows. Building on existing open-source software for mesh manipulation, here we present "NEURD", a software package that decomposes each meshed neuron into a compact and extensively-annotated graph representation. With these feature-rich graphs, we implement workflows to automate a variety of tasks that would otherwise require extensive manual effort, such as state of the art automated post-hoc proofreading of merge errors, cell classification, spine detection, axon-dendritic proximities, and computation of other features. These features enable many downstream analyses of neural morphology and connectivity, making these new massive and complex datasets more accessible to neuroscience researchers focused on a variety of scientific questions.

Published
2024
Full Text
View/download PDF

42. Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex.

Author

Schneider-Mizell CM, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Elabbady L, Gamlin C, Kapner D, Kinn S, Mahalingam G, Seshamani S, Suckow S, Takeno M, Torres R, Yin W, Dorkenwald S, Bae JA, Castro MA, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Turner NL, Wong W, Wu J, Reimer J, Tolias AS, Seung HS, Reid RC, Collman F, and Maçarico da Costa N

Abstract

Mammalian cortex features a vast diversity of neuronal cell types, each with characteristic anatomical, molecular and functional properties. Synaptic connectivity powerfully shapes how each cell type participates in the cortical circuit, but mapping connectivity rules at the resolution of distinct cell types remains difficult. Here, we used millimeter-scale volumetric electron microscopy 1 to investigate the connectivity of all inhibitory neurons across a densely-segmented neuronal population of 1352 cells spanning all layers of mouse visual cortex, producing a wiring diagram of inhibitory connections with more than 70,000 synapses. Taking a data-driven approach inspired by classical neuroanatomy, we classified inhibitory neurons based on the relative targeting of dendritic compartments and other inhibitory cells and developed a novel classification of excitatory neurons based on the morphological and synaptic input properties. The synaptic connectivity between inhibitory cells revealed a novel class of disinhibitory specialist targeting basket cells, in addition to familiar subclasses. Analysis of the inhibitory connectivity onto excitatory neurons found widespread specificity, with many interneurons exhibiting differential targeting of certain subpopulations spatially intermingled with other potential targets. Inhibitory targeting was organized into "motif groups," diverse sets of cells that collectively target both perisomatic and dendritic compartments of the same excitatory targets. Collectively, our analysis identified new organizing principles for cortical inhibition and will serve as a foundation for linking modern multimodal neuronal atlases with the cortical wiring diagram.

Published
2024
Full Text
View/download PDF

43. CAVE: Connectome Annotation Versioning Engine.

Author

Dorkenwald S, Schneider-Mizell CM, Brittain D, Halageri A, Jordan C, Kemnitz N, Castro MA, Silversmith W, Maitin-Shephard J, Troidl J, Pfister H, Gillet V, Xenes D, Bae JA, Bodor AL, Buchanan J, Bumbarger DJ, Elabbady L, Jia Z, Kapner D, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yin W, Yu SC, Reid RC, da Costa NM, Seung HS, and Collman F

Abstract

Advances in Electron Microscopy, image segmentation and computational infrastructure have given rise to large-scale and richly annotated connectomic datasets which are increasingly shared across communities. To enable collaboration, users need to be able to concurrently create new annotations and correct errors in the automated segmentation by proofreading. In large datasets, every proofreading edit relabels cell identities of millions of voxels and thousands of annotations like synapses. For analysis, users require immediate and reproducible access to this constantly changing and expanding data landscape. Here, we present the Connectome Annotation Versioning Engine (CAVE), a computational infrastructure for immediate and reproducible connectome analysis in up-to petascale datasets (~1mm 3 ) while proofreading and annotating is ongoing. For segmentation, CAVE provides a distributed proofreading infrastructure for continuous versioning of large reconstructions. Annotations in CAVE are defined by locations such that they can be quickly assigned to the underlying segment which enables fast analysis queries of CAVE's data for arbitrary time points. CAVE supports schematized, extensible annotations, so that researchers can readily design novel annotation types. CAVE is already used for many connectomics datasets, including the largest datasets available to date., Competing Interests: Competing interests T. Macrina, K. Lee, S. Popovych, D. Ih, N. Kemnitz, and H. S. Seung declare financial interests in Zetta AI.

Published
2023
Full Text
View/download PDF

44. Neuronal wiring diagram of an adult brain.

Author

Dorkenwald S, Matsliah A, Sterling AR, Schlegel P, Yu SC, McKellar CE, Lin A, Costa M, Eichler K, Yin Y, Silversmith W, Schneider-Mizell C, Jordan CS, Brittain D, Halageri A, Kuehner K, Ogedengbe O, Morey R, Gager J, Kruk K, Perlman E, Yang R, Deutsch D, Bland D, Sorek M, Lu R, Macrina T, Lee K, Bae JA, Mu S, Nehoran B, Mitchell E, Popovych S, Wu J, Jia Z, Castro M, Kemnitz N, Ih D, Bates AS, Eckstein N, Funke J, Collman F, Bock DD, Jefferis GSXE, Seung HS, and Murthy M

Abstract

Connections between neurons can be mapped by acquiring and analyzing electron microscopic (EM) brain images. In recent years, this approach has been applied to chunks of brains to reconstruct local connectivity maps that are highly informative, yet inadequate for understanding brain function more globally. Here, we present the first neuronal wiring diagram of a whole adult brain, containing 5×10 7 chemical synapses between ~130,000 neurons reconstructed from a female Drosophila melanogaster . The resource also incorporates annotations of cell classes and types, nerves, hemilineages, and predictions of neurotransmitter identities. Data products are available by download, programmatic access, and interactive browsing and made interoperable with other fly data resources. We show how to derive a projectome, a map of projections between regions, from the connectome. We demonstrate the tracing of synaptic pathways and the analysis of information flow from inputs (sensory and ascending neurons) to outputs (motor, endocrine, and descending neurons), across both hemispheres, and between the central brain and the optic lobes. Tracing from a subset of photoreceptors all the way to descending motor pathways illustrates how structure can uncover putative circuit mechanisms underlying sensorimotor behaviors. The technologies and open ecosystem of the FlyWire Consortium set the stage for future large-scale connectome projects in other species., Competing Interests: Competing interests T. Macrina, K. Lee, S. Popovych, D. Ih, N. Kemnitz, and H. S. Seung declare financial interests in Zetta AI.

Published
2023
Full Text
View/download PDF

45. Functional connectomics reveals general wiring rule in mouse visual cortex.

Author

Ding Z, Fahey PG, Papadopoulos S, Wang EY, Celii B, Papadopoulos C, Kunin AB, Chang A, Fu J, Ding Z, Patel S, Ponder K, Muhammad T, Bae JA, Bodor AL, Brittain D, Buchanan J, Bumbarger DJ, Castro MA, Cobos E, Dorkenwald S, Elabbady L, Halageri A, Jia Z, Jordan C, Kapner D, Kemnitz N, Kinn S, Lee K, Li K, Lu R, Macrina T, Mahalingam G, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Schneider-Mizell CM, Silversmith W, Takeno M, Torres R, Turner NL, Wong W, Wu J, Yin W, Yu SC, Froudarakis E, Sinz F, Seung HS, Collman F, da Costa NM, Reid RC, Walker EY, Pitkow X, Reimer J, and Tolias AS

Abstract

To understand how the brain computes, it is important to unravel the relationship between circuit connectivity and function. Previous research has shown that excitatory neurons in layer 2/3 of the primary visual cortex of mice with similar response properties are more likely to form connections. However, technical challenges of combining synaptic connectivity and functional measurements have limited these studies to few, highly local connections. Utilizing the millimeter scale and nanometer resolution of the MICrONS dataset, we studied the connectivity-function relationship in excitatory neurons of the mouse visual cortex across interlaminar and interarea projections, assessing connection selectivity at the coarse axon trajectory and fine synaptic formation levels. A digital twin model of this mouse, that accurately predicted responses to arbitrary video stimuli, enabled a comprehensive characterization of the function of neurons. We found that neurons with highly correlated responses to natural videos tended to be connected with each other, not only within the same cortical area but also across multiple layers and visual areas, including feedforward and feedback connections, whereas we did not find that orientation preference predicted connectivity. The digital twin model separated each neuron's tuning into a feature component (what the neuron responds to) and a spatial component (where the neuron's receptive field is located). We show that the feature, but not the spatial component, predicted which neurons were connected at the fine synaptic scale. Together, our results demonstrate the "like-to-like" connectivity rule generalizes to multiple connection types, and the rich MICrONS dataset is suitable to further refine a mechanistic understanding of circuit structure and function., Competing Interests: COMPETING FINANCIAL INTERESTS XP is a co-founder of Upload AI, LLC, a company in which he has financial interests. AST is co-founder of Vathes Inc., and UploadAI LLC companies in which he has financial interests. JR is co-founder of Vathes Inc., and UploadAI LLC companies in which he has financial interests.

Published
2023
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results