NK
Narayanan Kasthuri
neurosciencecs.CVq-bio.NCelectron microscopyComputer GraphicsConnectomeconnectomicscs.DCeess.IVMicroscopy, Electron
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
82 papers in the corpus · 2001–2026DRIFT-EM enables direct wafer retrieval of ultrathin serial sections for large-volume electron microscopy.42086049 · Medina, Nelson, Gogola, Joseph V, Boergens, Kevin et al.2026 · 1 citationCell reports methods. 2026;6(6):101429
From sample to knowledge: Towards an integrated approach for neuroscience discovery1604.03199v2 · William Gray Roncal, Eva L Dyer, Doga Gursoy et al.2016 · 0 citationsarXiv
Compiling molecular ultrastructure into neural dynamics2603.25713v1 · Konrad P. Kording, Anton Arkhipov, Davy Deng et al.2026 · 0 citationsarXiv
Photoemission electron microscopy for connectomics.41284880 · Wildenberg, Gregg, Boergens, Kevin M, Lambert, Lola et al.2025 · 2 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(48):e2521349122
Local Dendritic Landscape of Mouse V110.1101/2025.07.10.664234v1 · Medina, N. D., Sorokina, A., Kasthuri, N.2025 · 0 citationsbioRxiv
Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues.39939319 · Shin, Tay Won, Wang, Hao, Zhang, Chi et al.2025 · 19 citationsNature communications. 2025;16(1):1579
Synchrotron-source micro-x-ray computed tomography for examining butterfly eyes.38571794 · Paukner, Dawn, Wildenberg, Gregg A, Badalamente, Griffin S et al.2024 · 5 citationsEcology and evolution. 2024;14(4):e11137
OsO2 as the Contrast-Generating Chemical Species of Osmium-Stained Biological Tissues in Electron Microscopy.39037826 · Li, Ruiyu, Wildenberg, Gregg, Boergens, Kevin et al.2024 · 11 citationsChembiochem : a European journal of chemical biology. 2024;25(20):e202400311
Synaptic integration of somatosensory and motor cortical inputs onto spiny projection neurons of mice caudoputamen.39315531 · Sampathkumar, Vandana, Koster, Kevin P, Carroll, Briana J et al.2024 · 0 citationsThe European journal of neuroscience. 2024;60(8):6107-6122
Photoemission electron microscopy for connectomics10.1101/2023.09.05.556423v3 · Boergens, K. M., Wildenberg, G., Li, R. et al.2023 · 5 citationsbioRxiv
Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues10.1101/2024.03.07.583776v2 · Shin, T. W., Wang, H., Zhang, C. et al.2024 · 25 citationsbioRxiv
Synchrotron-source micro-x-ray computed tomography for examining butterfly eyes10.1101/2023.12.08.570583v1 · Paukner, D., Wildenberg, G. A., Badalamente, G. S. et al.2023 · 5 citationsbioRxiv
Isochronic development of cortical synapses in primates and mice.38049416 · Wildenberg, Gregg, Li, Hanyu, Sampathkumar, Vandana et al.2023 · 33 citationsNature communications. 2023;14(1):8018
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
A Pipeline for a Primate Projectome: mapping every individual myelinated axon across the whole brain10.1101/2023.10.23.563679v1 · Wildenberg, G. A., Boergens, K. M., Nikitin, V. et al.2023 · 1 citationbioRxiv
The Development of Synapses in Mouse and Macaque Primary Sensory Cortices10.1101/2023.02.15.528564v1 · Wildenberg, G. A., Li, H., Kasthuri, N.2023 · 10 citationsbioRxiv
Regional cytoarchitecture of the adult and developing mouse enteric nervous system.36070775 · Hamnett, Ryan, Dershowitz, Lori B, Sampathkumar, Vandana et al.2022 · 45 citationsCurrent biology : CB. 2022;32(20):4483-4492.e5
Layer 5 of cortex innervates the thalamic reticular nucleus in mice.36095204 · Carroll, Briana J, Sampathkumar, Vandana, Kasthuri, Narayanan et al.2022 · 34 citationsProceedings of the National Academy of Sciences of the United States of America. 2022;119(38):e2205209119
Performance Characteristics of a Novel 3D-Printed Bubble Intermittent Mandatory Ventilator (B-IMV) for Adult Pulmonary Support.35447711 · Poli, Jonathan A, Howard, Christopher, Garcia, Alfredo J et al.2022 · 5 citationsBioengineering (Basel, Switzerland). 2022;9(4)
Ultrastructural analysis of dendritic spine necks reveals a continuum of spine morphologies.33977655 · Ofer, Netanel, Berger, Daniel R, Kasthuri, Narayanan et al.2022 · 71 citationsDevelopmental neurobiology. 2021;81(5):746-757
Model-free analysis in the spectral domain of postmortem mouse brain EPSI reveals inconsistencies with model-based analyses of the free induction decay10.1101/2022.02.24.481824v1 · Trinkle, S., Wildenberg, G., Kasthuri, N. et al.2022 · 0 citationsbioRxiv
Primate neuronal connections are sparse in cortex as compared to mouse.34525373 · Wildenberg, Gregg A, Rosen, Matt R, Lundell, Jack et al.2022 · 51 citationsCell reports. 2021;36(11):109709
The role of spatial embedding in mouse brain networks constructed from diffusion tractography and tracer injections.34520833 · Trinkle, Scott, Foxley, Sean, Wildenberg, Gregg et al.2022 · 9 citationsNeuroImage. 2021;244:118576
Integration of signals from different cortical areas in higher order thalamic neurons.34282018 · Sampathkumar, Vandana, Miller-Hansen, Andrew, Sherman, S Murray et al.2021 · 56 citationsProceedings of the National Academy of Sciences of the United States of America. 2021;118(30)
Internal Feedback in Biological Control: Architectures and Examples2110.05029v3 · Anish A. Sarma, Jing Shuang Li, Josefin Stenberg et al.2021 · 9 citationsarXiv
Multi-modal imaging of a single mouse brain over five orders of magnitude of resolution.34116154 · Foxley, Sean, Sampathkumar, Vandana, De Andrade, Vincent et al.2021 · 34 citationsNeuroImage. 2021;238:118250
Large-scale dendritic spine extraction and analysis through petascale computing10.1101/2021.07.29.454371v1 · Wildenberg, G., Li, H., Badalamente, G. A. et al.2021 · 0 citationsbioRxiv
Regional cytoarchitecture of the adult and developing mouse enteric nervous system10.1101/2021.07.16.452735v1 · Hamnett, R., Dershowitz, L. B., Sampathkumar, V. et al.2021 · 45 citationsbioRxiv
AxonEM Dataset: 3D Axon Instance Segmentation of Brain Cortical Regions2107.05451v1 · Donglai Wei, Kisuk Lee, Hanyu Li et al.2021 · 18 citationsarXiv
Cell type specific labeling and partial connectomes of dopaminergic circuits reveal non-synaptic communication and large-scale axonal remodeling after exposure to cocaine10.1101/2020.09.29.318881v3 · Wildenberg, G. A., Sorokina, A. M., Koranda, J. et al.2020 · 1 citationbioRxiv
An ultrastructural connectomic analysis of a higher-order thalamocortical circuit in the mouse.33368722 · Sampathkumar, Vandana, Miller-Hansen, Andrew, Murray Sherman, S et al.2021 · 28 citationsThe European journal of neuroscience. 2021;53(3):750-762
Synchrotron X-ray micro-CT as a validation dataset for diffusion MRI in whole mouse brain.33768633 · Trinkle, Scott, Foxley, Sean, Kasthuri, Narayanan et al.2021 · 13 citationsMagnetic resonance in medicine. 2021;86(2):1067-1076
ZO-1 Regulates Intercalated Disc Composition and Atrioventricular Node Conduction.32347164 · Dai, Wenli, Nadadur, Rangarajan D, Brennan, Jaclyn A et al.2021 · 29 citationsCirculation research. 2020;127(2):e28-e43
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
Sensitivity to myelin using model-free analysis of the water resonance line-shape in postmortem mouse brain.32783262 · Foxley, Sean, Wildenberg, Gregg, Sampathkumar, Vandana et al.2021 · 2 citationsMagnetic resonance in medicine. 2021;85(2):667-677
Neuronal BIN1 Regulates Presynaptic Neurotransmitter Release and Memory Consolidation.32160554 · De Rossi, Pierre, Nomura, Toshihiro, Andrew, Robert J et al.2021 · 122 citationsCell reports. 2020;30(10):3520-3535.e7
Distributed optimization for nonrigid nano-tomography2008.03375v2 · Viktor Nikitin, Vincent De Andrade, Azat Slyamov et al.2020 · 28 citationsarXiv
Ultrastructural analysis of dendritic spine necks reveals a continuum of spine morphologies10.1101/2021.02.18.431725v1 · Ofer, N., Berger, D. R., Kasthuri, N. et al.2021 · 71 citationsbioRxiv
A three-dimensional thalamocortical dataset for characterizing brain heterogeneity.33082340 · Prasad, Judy A, Balwani, Aishwarya H, Johnson, Erik C et al.2021 · 20 citationsScientific data. 2020;7(1):358
Primate neuronal connections are sparse as compared to mouse10.1101/2020.09.24.311852v2 · Wildenberg, G. A., Rosen, M. C., Lundell, J. et al.2020 · 1 citationbioRxiv
Multi-modal imaging of a single postmortem mouse brain over five orders of magnitude of resolution10.1101/2020.10.07.329789v3 · Foxley, S., Sampathkumar, V., De Andrade, V. et al.2020 · 3 citationsbioRxiv
Toward an Automated HPC Pipeline for Processing Large Scale Electron Microscopy Data2011.03204v1 · Rafael Vescovi, Hanyu Li, Jeffery Kinnison et al.2020 · 13 citationsarXiv
A three-dimensional thalamocortical dataset for characterizing brain heterogeneity10.1101/2020.05.22.111617v1 · Prasad, J. A., Balwani, A. H., Johnson, E. C. et al.2020 · 20 citationsbioRxiv
Scaling Distributed Training of Flood-Filling Networks on HPC Infrastructure for Brain Mapping1905.06236v4 · Wushi Dong, Murat Keceli, Rafael Vescovi et al.2019 · 8 citationsarXiv
Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.30250218 · Shahbazi, Ali, Kinnison, Jeffery, Vescovi, Rafael et al.2019 · 18 citationsScientific reports. 2018;8(1):14247
Publisher Correction: Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.30498261 · Shahbazi, Ali, Kinnison, Jeffery, Vescovi, Rafael et al.2019 · 0 citationsScientific reports. 2018;8(1):17585
Expansion Microscopy of Lipid Membranes10.1101/829903v1 · Karagiannis, E. D., Kang, J. S., Shin, T. W. et al.2019 · 63 citationsbioRxiv
Low-dose x-ray tomography through a deep convolutional neural network.29416047 · Yang, Xiaogang, De Andrade, Vincent, Scullin, William et al.2019 · 107 citationsScientific reports. 2018;8(1):2575
Contrast enhancement of biological nanoporous materials with zinc oxide infiltration for electron and X-ray nanoscale microscopy.28724918 · Ocola, L E, Sampathkumar, V, Kasthuri, N et al.2019 · 5 citationsScientific reports. 2017;7(1):5879
Flexible Learning-Free Segmentation and Reconstruction for Sparse Neuronal Circuit Tracing10.1101/278515v2 · Shahbazi, A., Kinnison, J., Vescovi, R. et al.2018 · 0 citationsbioRxiv
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