SS
Stephen J. Smith
neurosciencearray tomographymousesynapseelectron microscopyq-bio.NCneuromodulationSynapsesBrain Mappingcorrelative 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
144 papers in the corpus · 1979–2026Optic disc drusen-associated neovascularization: A systematic review.40441443 · Alkhabaz, Anas, Pujari, Rishita, Ren, Yulan et al.2025 · 4 citationsSurvey of ophthalmology. 2025;70(6):1191-1196
Data-driven synapse classification reveals a logic of glutamate receptor diversity10.1101/2024.12.11.628056v2 · Micheva, K. D., Simhal, A. K., Schardt, J. et al.2024 · 1 citationbioRxiv
Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses.37945352 · Micheva, Kristina D, Gong, Belvin, Collman, Forrest et al.2023 · 8 citationseNeuro. 2023;10(12)
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
Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses10.1101/2023.06.28.546920v2 · Micheva, K. D., Gong, B., Collman, F. C. et al.2023 · 9 citationsbioRxiv
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 Molecular Landscape of Mouse Hippocampal Neuromodulation.35601530 · Smith, Stephen J, von Zastrow, Mark2022 · 13 citationsFrontiers in neural circuits. 2022;16:836930
Transcriptomic evidence for dense peptidergic networks within forebrains of four widely divergent tetrapods.34775262 · Smith, Stephen J2022 · 14 citationsCurrent opinion in neurobiology. 2021;71:100-109
Cell-type-specific neuromodulation guides synaptic credit assignment in a spiking neural network.34916291 · Liu, Yuhan Helena, Smith, Stephen, Mihalas, Stefan et al.2022 · 32 citationsProceedings of the National Academy of Sciences of the United States of America. 2021;118(51)
A Scalable and Modular Automated Pipeline for Stitching of Large Electron Microscopy Datasets10.1101/2021.11.24.469932v2 · Mahalingam, G., Torres, R., Kapner, D. et al.2021 · 68 citationsbioRxiv
Automatic Identification of Referral-Warranted Diabetic Retinopathy Using Deep Learning on Mobile Phone Images.33294301 · Ludwig, Cassie A, Perera, Chandrashan, Myung, David et al.2021 · 35 citationsTranslational vision science & technology. 2020;9(2):60
A solution to temporal credit assignment using cell-type-specific modulatory signals10.1101/2020.11.22.393504v3 · Liu, Y. H., Smith, S. J., Mihalas, S. et al.2020 · 6 citationsbioRxiv
New light on cortical neuropeptides and synaptic network plasticity.32679509 · Smith, Stephen J, Hawrylycz, Michael, Rossier, Jean et al.2020 · 35 citationsCurrent opinion in neurobiology. 2020;63:176-188
A Computational Synaptic Antibody Characterization Tool for Array Tomography.30065633 · Simhal, Anish K, Gong, Belvin, Trimmer, James S et al.2020 · 10 citationsFrontiers in neuroanatomy. 2018;12:51
A synapse census for the ages.32675362 · Micheva, Kristina D, Weinberg, Richard J, Smith, Stephen J2020 · 5 citationsScience (New York, N.Y.). 2020;369(6501):253-254
Single-cell transcriptomic evidence for dense intracortical neuropeptide networks.31710287 · Smith, Stephen J, Sümbül, Uygar, Graybuck, Lucas T et al.2020 · 178 citationseLife. 2019;8
New Light on Cortical Neuropeptides and Synaptic Network Plasticity2004.07975v1 · Stephen J. Smith, Michael Hawrylycz, Jean Rossier et al.2020 · 35 citationsarXiv
Optical Coherence Tomography Angiography Highlights Chorioretinal Lesions in Ocular Coccidioidomycosis.30893459 · Shields, Ryan A, Tang, Peter H, Bodnar, Zachary M et al.2019 · 4 citationsOphthalmic surgery, lasers & imaging retina. 2019;50(3):e71-e73
Single-Cell Transcriptomic Evidence for Dense Intracortical Neuropeptide Networks10.1101/519694v3 · Smith, S. J., Sumbul, U., Graybuck, L. T. et al.2019 · 178 citationsbioRxiv
A community-developed open-source computational ecosystem for big neuro data.30377345 · Vogelstein, Joshua T, Perlman, Eric, Falk, Benjamin et al.2019 · 71 citationsNature methods. 2018;15(11):846-847
Q&A: Array tomography.30189863 · Smith, Stephen J2019 · 92 citationsBMC biology. 2018;16(1):98
Distinctive Structural and Molecular Features of Myelinated Inhibitory Axons in Human Neocortex.30406183 · Micheva, Kristina D, Chang, Edward F, Nana, Alissa L et al.2019 · 44 citationseNeuro. 2018;5(5)
Testing the X-IFU calibration requirements: an example for quantum efficiency and energy resolution1807.01582v1 · Edoardo Cucchetti, Francois Pajot, Etienne Pointecouteau et al.2018 · 3 citationsarXiv
Myelinated inhibitory axons in human neocortex10.1101/306480v1 · Micheva, K. D., Chang, E. F., Nana, A. L. et al.2018 · 5 citationsbioRxiv
A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data1804.02835v2 · Randal Burns, Eric Perlman, Alex Baden et al.2018 · 71 citationsarXiv
A Computational Synaptic Antibody Characterization and Screening Framework for Array Tomography10.1101/258756v2 · Simhal, A. K., Gong, B., Trimmer, J. S. et al.2018 · 2 citationsbioRxiv
A large fraction of neocortical myelin ensheathes axons of local inhibitory neurons.27383052 · Micheva, Kristina D, Wolman, Dylan, Mensh, Brett D et al.2017 · 312 citationseLife. 2016;5
Sub-synaptic, multiplexed analysis of proteins reveals Fragile X related protein 2 is mislocalized in Fmr1 KO synapses.27770568 · Wang, Gordon X, Smith, Stephen J, Mourrain, Philippe2017 · 11 citationseLife. 2016;5
Probabilistic Fluorescence-Based Synapse Detection1611.05479v1 · Anish K. Simhal, Cecilia Aguerrebere, Forrest Collman et al.2016 · 18 citationsarXiv
Enhanced phasic GABA inhibition during the repair phase of stroke: a novel therapeutic target.26685158 · Hiu, Takeshi, Farzampour, Zoya, Paz, Jeanne T et al.2016 · 133 citationsBrain : a journal of neurology. 2016;139(Pt 2):468-80
Increased cortical synaptic activation of TrkB and downstream signaling markers in a mouse model of Down Syndrome.25753471 · Nosheny, R L, Belichenko, P V, Busse, B L et al.2016 · 19 citationsNeurobiology of disease. 2015;77:173-90
Synaptic molecular imaging in spared and deprived columns of mouse barrel cortex with array tomography.25977797 · Weiler, Nicholas C, Collman, Forrest, Vogelstein, Joshua T et al.2015 · 15 citationsScientific data. 2014;1:140046
Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture.26005811 · Paşca, Anca M, Sloan, Steven A, Clarke, Laura E et al.2015 · 1,670 citationsNature methods. 2015;12(7):671-8
Knowing a synapse when you see one.26283929 · Burette, Alain, Collman, Forrest, Micheva, Kristina D et al.2015 · 35 citationsFrontiers in neuroanatomy. 2015;9:100
Mapping synapses by conjugate light-electron array tomography.25855189 · Collman, Forrest, Buchanan, JoAnn, Phend, Kristen D et al.2015 · 130 citationsThe Journal of neuroscience : the official journal of the Society for Neuroscience. 2015;35(14):5792-807
Fmr1 KO and fenobam treatment differentially impact distinct synapse populations of mouse neocortex.25521380 · Wang, Gordon X, Smith, Stephen J, Mourrain, Philippe2015 · 38 citationsNeuron. 2014;84(6):1273-86
Astrocytes mediate synapse elimination through MEGF10 and MERTK pathways.24270812 · Chung, Won-Suk, Clarke, Laura E, Wang, Gordon X et al.2014 · 1,452 citationsNature. 2013;504(7480):394-400
Accelerated experience-dependent pruning of cortical synapses in ephrin-A2 knockout mice.24094103 · Yu, Xinzhu, Wang, Gordon, Gilmore, Anthony et al.2013 · 49 citationsNeuron. 2013;80(1):64-71
Automated analysis of a diverse synapse population.23555213 · Busse, Brad, Smith, Stephen2013 · 27 citationsPLoS computational biology. 2013;9(3):e1002976
The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience1306.3543v2 · Randal Burns, William Gray Roncal, Dean Kleissas et al.2013 · 30 citationsarXivon Valency
Sub-diffraction limit localization of proteins in volumetric space using Bayesian restoration of fluorescence images from ultrathin specimens.22956902 · Wang, Gordon, Smith, Stephen J2012 · 27 citationsPLoS computational biology. 2012;8(8):e1002671
High-contrast en bloc staining of neuronal tissue for field emission scanning electron microscopy.22240582 · Tapia, Juan Carlos, Kasthuri, Narayanan, Hayworth, Kenneth J et al.2012 · 316 citationsNature protocols. 2012;7(2):193-206
Astrocyte glypicans 4 and 6 promote formation of excitatory synapses via GluA1 AMPA receptors.22722203 · Allen, Nicola J, Bennett, Mariko L, Foo, Lynette C et al.2012 · 790 citationsNature. 2012;486(7403):410-4
Deep molecular diversity of mammalian synapses: why it matters and how to measure it.22573027 · O'Rourke, Nancy A, Weiler, Nicholas C, Micheva, Kristina D et al.2012 · 230 citationsNature reviews. Neuroscience. 2012;13(6):365-79
Three-dimensional microstructural changes in murine abdominal aortic aneurysms quantified using immunofluorescent array tomography.22140132 · Saatchi, Sanaz, Azuma, Junya, Wanchoo, Nishey et al.2012 · 12 citationsThe journal of histochemistry and cytochemistry : official journal of the Histochemistry Society. 2012;60(2):97-109
Bidirectional regulation of dendritic voltage-gated potassium channels by the fragile X mental retardation protein.22099464 · Lee, Hye Young, Ge, Woo-Ping, Huang, Wendy et al.2012 · 155 citationsNeuron. 2011;72(4):630-42
Large-scale automated histology in the pursuit of connectomes.22072665 · Kleinfeld, David, Bharioke, Arjun, Blinder, Pablo et al.2012 · 167 citationsThe Journal of neuroscience : the official journal of the Society for Neuroscience. 2011;31(45):16125-38
Characterization of genetically targeted neuron types in the zebrafish optic tectum.21390291 · Robles, Estuardo, Smith, Stephen J, Baier, Herwig2011 · 120 citationsFrontiers in neural circuits. 2011;5:1
Array tomography: rodent brain fixation and embedding.21041396 · Micheva, Kristina D, O'Rourke, Nancy, Busse, Brad et al.2011 · 8 citationsCold Spring Harbor protocols. 2010;2010(11):pdb.prot5523
Array tomography: production of arrays.21041397 · Micheva, Kristina D, O'Rourke, Nancy, Busse, Brad et al.2011 · 18 citationsCold Spring Harbor protocols. 2010;2010(11):pdb.prot5524
Career total: 451 works. 144 are in this corpus.Showing the 50 most recent.
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