RR
R. Clay Reid
neuroscienceConnectomeModels, NeurologicalmouseNeuronsVisual CortexBrain MappingAlgorithmsSynapseselectron microscopy
On Valency
published · living versionsW_qwe58ep4·v1 · currentpublished
The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience
with Randal Burns, William Gray Roncal, Dean Kleissas, Kunal Lillaney +15
1 version
Preprints & journals
143 papers in the corpus · 1985–2026Functionally identified neuronal assemblies robustly encode stimuli and are structurally delineated by inhibition.42664054 · Wagner-Carena, Julian, Kate, Sai, Riordan, Trevor et al.2026 · 0 citationsCell reports. 2026;45(9):117900
Scaling up polarization-sensitive optical coherence tomography to image the whole macaque brain10.64898/2026.06.11.731509v1 · Yeatts, M., Chinthalapati, N., Baradaran, B. et al.2026 · 0 citationsbioRxiv
Author Correction: Foundation model of neural activity predicts response to new stimulus types.41951748 · Wang, Eric Y, Fahey, Paul G, Ding, Zhuokun et al.2026 · 0 citationsNature. 2026;652(8111):E10
Heterogeneity of White Matter Structure in the Human Brain.42040959 · Reid, R Clay, Turschak, Emily, Yu, Wan-Qing et al.2026 · 0 citationsResearch square. 2026
NEURD offers automated proofreading and feature extraction for connectomics.36993282 · Celii, Brendan, Papadopoulos, Stelios, Ding, Zhuokun et al.2026 · 15 citationsbioRxiv : the preprint server for biology. 2024
Functional connectomics reveals general wiring rule in mouse visual cortex.36993398 · Ding, Zhuokun, Fahey, Paul G, Papadopoulos, Stelios et al.2026 · 44 citationsbioRxiv : the preprint server for biology. 2024
Author Correction: Inhibitory specificity from a connectomic census of mouse visual cortex.40389750 · Schneider-Mizell, Casey M, Bodor, Agnes L, Brittain, Derrick et al.2026 · 0 citationsNature. 2025;642(8066):E9
Heterogeneity of white matter structure in the human brain10.64898/2026.03.31.714863v1 · Reid, R. C., Turschak, E. E., Yu, W.-Q. et al.2026 · 0 citationsbioRxiv
Reconstructing the human brain's wiring diagram from axons up.41330839 · Heilbronner, Sarah R, Reid, R Clay, Casta, Tanya K et al.2026 · 4 citationsTrends in neurosciences. 2026;49(1):8-19
The past and future of functional connectomics.41360959 · Reid, R Clay2025 · 0 citationsNature methods. 2025;22(12):2479-2480
The synaptic architecture of layer 5 thick tufted excitatory neurons in mouse visual cortex.40721677 · Bodor, Agnes L, Schneider-Mizell, Casey M, Zhang, Chi et al.2025 · 14 citationsNature neuroscience. 2025;28(8):1704-1715
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues.40586775 · Glaser, Adam, Chandrashekar, Jayaram, Vasquez, Sonya et al.2025 · 24 citationseLife. 2025;12
Hebb's Vision: The Structural Underpinnings of Hebbian Assemblies10.1101/2025.04.24.649900v2 · Wagner-Carena, J. A., Kate, S., Riordan, T. et al.2025 · 1 citationbioRxiv
CAVE: Connectome Annotation Versioning Engine.40205066 · Dorkenwald, Sven, Schneider-Mizell, Casey M, Brittain, Derrick et al.2025 · 47 citationsNature methods. 2025;22(5):1112-1120
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues10.1101/2023.06.08.544277v5 · Glaser, A., Chandrashekar, J., Vasquez, S. et al.2023 · 47 citationsbioRxiv
An unsupervised map of excitatory neuron dendritic morphology in the mouse visual cortex.40204760 · Weis, Marissa A, Papadopoulos, Stelios, Hansel, Laura et al.2025 · 17 citationsNature communications. 2025;16(1):3361
NEURD offers automated proofreading and feature extraction for connectomics.40205208 · Celii, Brendan, Papadopoulos, Stelios, Ding, Zhuokun et al.2025 · 28 citationsNature. 2025;640(8058):487-496
Inhibitory specificity from a connectomic census of mouse visual cortex.40205209 · Schneider-Mizell, Casey M, Bodor, Agnes L, Brittain, Derrick et al.2025 · 70 citationsNature. 2025;640(8058):448-458
Connectomics of predicted Sst transcriptomic types in mouse visual cortex.40205210 · Gamlin, Clare R, Schneider-Mizell, Casey M, Mallory, Matthew et al.2025 · 23 citationsNature. 2025;640(8058):497-505
Functional connectomics reveals general wiring rule in mouse visual cortex.40205211 · Ding, Zhuokun, Fahey, Paul G, Papadopoulos, Stelios et al.2025 · 62 citationsNature. 2025;640(8058):459-469
Foundation model of neural activity predicts response to new stimulus types.40205215 · Wang, Eric Y, Fahey, Paul G, Ding, Zhuokun et al.2025 · 78 citationsNature. 2025;640(8058):470-477
Perisomatic ultrastructure efficiently classifies cells in mouse cortex.40205216 · Elabbady, Leila, Seshamani, Sharmishtaa, Mu, Shang et al.2025 · 23 citationsNature. 2025;640(8058):478-486
Foundation model of neural activity predicts response to new stimulus types and anatomy10.1101/2023.03.21.533548v4 · Wang, E. Y., Fahey, P. G., Ding, Z. et al.2023 · 22 citationsbioRxiv
A scalable and modular computational pipeline for axonal connectomics: automated tracing and assembly of axons across serial sections.38915568 · Torres, Russel, Takasaki, Kevin, Gliko, Olga et al.2024 · 4 citationsbioRxiv : the preprint server for biology. 2024
An unsupervised map of excitatory neurons' dendritic morphology in the mouse visual cortex10.1101/2022.12.22.521541v3 · Weis, M. A., Papadopoulos, S., Hansel, L. et al.2022 · 9 citationsbioRxiv
Perisomatic Features Enable Efficient and Dataset Wide Cell-Type Classifications Across Large-Scale Electron Microscopy Volumes10.1101/2022.07.20.499976v2 · Elabbady, L., Seshamani, S., Mu, S. et al.2022 · 23 citationsbioRxiv
Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex10.1101/2023.01.23.525290v3 · Schneider-Mizell, C. M., Bodor, A., Brittain, D. et al.2023 · 76 citationsbioRxiv
The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience.24401992 · Burns, Randal, Roncal, William Gray, Kleissas, Dean et al.2023 · 57 citationsScientific and statistical database management : International Conference, SSDBM ... : proceedings. International Conference on Scientific and Statistical Database Management. 2013
CAVE: Connectome Annotation Versioning Engine10.1101/2023.07.26.550598v1 · Dorkenwald, S., Schneider-Mizell, C. M., Brittain, D. et al.2023 · 81 citationsbioRxiv
Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types10.1101/2023.03.22.533857v1 · Gamlin, C. R., Schneider-Mizell, C. M., Mallory, M. et al.2023 · 12 citationsbioRxiv
Binary and analog variation of synapses between cortical pyramidal neurons.36382887 · Dorkenwald, Sven, Turner, Nicholas L, Macrina, Thomas et al.2022 · 155 citationseLife. 2022;11
Oligodendrocyte precursor cells ingest axons in the mouse neocortex.36417438 · Buchanan, JoAnn, Elabbady, Leila, Collman, Forrest et al.2022 · 152 citationsProceedings of the National Academy of Sciences of the United States of America. 2022;119(48):e2202580119
A scalable and modular automated pipeline for stitching of large electron microscopy datasets.35880860 · Mahalingam, Gayathri, Torres, Russel, Kapner, Daniel et al.2022 · 68 citationseLife. 2022;11
A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues.35545715 · Glaser, Adam K, Bishop, Kevin W, Barner, Lindsey A et al.2022 · 186 citationsNature methods. 2022;19(5):613-619
Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity.35216674 · Turner, Nicholas L, Macrina, Thomas, Bae, J Alexander et al.2022 · 238 citationsCell. 2022;185(6):1082-1100.e24
Laminar distribution and arbor density of two functional classes of thalamic inputs to primary visual cortex.34644562 · Zhuang, Jun, Wang, Yun, Ouellette, Naveen D et al.2022 · 15 citationsCell reports. 2021;37(2):109826
Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice.33683198 · Huang, Lawrence, Ledochowitsch, Peter, Knoblich, Ulf et al.2022 · 192 citationseLife. 2021;10
Binary and analog variation of synapses between cortical pyramidal neurons10.1101/2019.12.29.890319v2 · Dorkenwald, S., Turner, N. L., Macrina, T. et al.2019 · 155 citationsbioRxiv
Autoencoder networks extract latent variables and encode these variables in their connectomes.33957382 · Farrell, Matthew, Recanatesi, Stefano, Reid, R Clay et al.2021 · 9 citationsNeural networks : the official journal of the International Neural Network Society. 2021;141:330-343
A hybrid open-top light-sheet microscope for multi-scale imaging of cleared tissues10.1101/2020.05.06.081745v2 · Glaser, A. K., Bishop, K. W., Barner, L. A. et al.2020 · 13 citationsbioRxiv
Petascale neural circuit reconstruction: automated methods10.1101/2021.08.04.455162v1 · Macrina, T., Lee, K., Lu, R. et al.2021 · 64 citationsbioRxiv
Motion/direction-sensitive thalamic neurons project extensively to the middle layers of primary visual cortex10.1101/2021.07.07.451534v1 · Zhuang, J., Wang, Y., Ouellette, N. D. et al.2021 · 0 citationsbioRxiv
Capillary-Based and Stokes-Based Trapping of Serial Sections for Scalable 3D-EM Connectomics.32094293 · Lee, Timothy J, Yip, Mighten C, Kumar, Aditi et al.2021 · 1 citationeNeuro. 2020;7(2)
Oligodendrocyte precursor cells prune axons in the mouse neocortex10.1101/2021.05.29.446047v1 · Buchanan, J., Elabaddy, L., Collman, F. et al.2021 · 30 citationsbioRxiv
The Mind of a Mouse.32946777 · Abbott, Larry F, Bock, Davi D, Callaway, Edward M et al.2021 · 196 citationsCell. 2020;182(6):1372-1376
Chromatic micromaps in primary visual cortex.33875667 · Chatterjee, Soumya, Ohki, Kenichi, Reid, R Clay2021 · 30 citationsNature communications. 2021;12(1):2315
Survey of spiking in the mouse visual system reveals functional hierarchy.33473216 · Siegle, Joshua H, Jia, Xiaoxuan, Durand, Séverine et al.2021 · 678 citationsNature. 2021;592(7852):86-92
Multiscale and multimodal reconstruction of cortical structure and function10.1101/2020.10.14.338681v3 · Turner, N. L., Macrina, T., Bae, J. A. et al.2020 · 42 citationsbioRxiv
A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy.33009388 · Yin, Wenjing, Brittain, Derrick, Borseth, Jay et al.2020 · 172 citationsNature communications. 2020;11(1):4949
Relationship between simultaneously recorded spiking activity and fluorescence signal in GCaMP6 transgenic mice10.1101/788802v2 · Huang, L., Knoblich, U., Ledochowitsch, P. et al.2019 · 192 citationsbioRxiv
Career total: 197 works. 143 are in this corpus.Showing the 50 most recent.
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