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PyTorch: An Imperative Style, High-Performance Deep Learning Library

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Functional connectomics spanning multiple areas of mouse visual cortex

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Functional connectomics spanning multiple areas of mouse visual cortex

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Neuronal wiring diagram of an adult brain

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Oligodendrocyte precursor cells ingest axons in the mouse neocortex

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Hippocampal GABAergic interneurons and memory

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Network statistics of the whole-brain connectome of Drosophila

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Binary and analog variation of synapses between cortical pyramidal neurons

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Instance segmentation of mitochondria in electron microscopy images with a generalist deep learning model trained on a diverse dataset

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Aβ42 oligomers trigger synaptic loss through CAMKK2-AMPK-dependent effectors coordinating mitochondrial fission and mitophagy

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Axonal energy metabolism, and the effects in aging and neurodegenerative diseases

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Synaptic wiring motifs in posterior parietal cortex support decision-making

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CAVE: Connectome Annotation Versioning Engine

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Structural neural plasticity evoked by rapid-acting antidepressant interventions

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Atlas-based data integration for mapping the connections and architecture of the brain

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Mitochondrial plasticity and synaptic plasticity crosstalk; in health and Alzheimer's disease

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Ultrastructural differences impact cilia shape and external exposure across cell classes in the visual cortex

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Activity-dependent compartmentalization of dendritic mitochondria morphology through local regulation of fusion-fission balance in neurons in vivo

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Synaptic architecture of a memory engram in the mouse hippocampus

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Astrocytes as master modulators of neural networks: Synaptic functions and disease‐associated dysfunction of astrocytes

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Dense 4D nanoscale reconstruction of living brain tissue

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A deep learning strategy to identify cell types across species from high-density extracellular recordings

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Directed and acyclic synaptic connectivity in the human layer 2-3 cortical microcircuit

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

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Formation and computational implications of assemblies in neural circuits

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CAVE: Connectome Annotation Versioning Engine

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Multi-layered maps of neuropil with segmentation-guided contrastive learning

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Probing neural circuit mechanisms in Alzheimer’s disease using novel technologies

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Proximity proteomics of synaptopodin provides insight into the molecular composition of the spine apparatus of dendritic spines

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Isochronic development of cortical synapses in primates and mice

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Parvalbumin basket cell myelination accumulates axonal mitochondria to internodes

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MorphoFeatures for unsupervised exploration of cell types, tissues, and organs in volume electron microscopy

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Immersion Fixation and Staining of Multicubic Millimeter Volumes for Electron Microscopy–Based Connectomics of Human Brain Biopsies

Karlupia, N., Schalek, R. L., Wu, Y., Meirovitch, Y., Wei, D., Charney, A. W., Kopell, B. H., & Lichtman, J. W. (2023) · Biological Psychiatry · doi:10.1016/j.biopsych.2023.01.025 · Cited by 33

Tackling the subsampling problem to infer collective properties from limited data

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Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level

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Large-Scale Mechanistic Models of Brain Circuits with Biophysically and Morphologically Detailed Neurons

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Perisomatic ultrastructure efficiently classifies cells in mouse cortex

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Neuronal mitochondrial morphology is significantly affected by both fixative and oxygen level during perfusion

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Connectivity of single neurons classifies cell subtypes in mouse brains

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Igneous: Distributed dense 3D segmentation meshing, neuron skeletonization, and hierarchical downsampling

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SyConn2: dense synaptic connectivity inference for volume electron microscopy

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A conditional strategy for cell-type-specific labeling of endogenous excitatory synapses in Drosophila

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Postsynaptic mitochondria are positioned to support functional diversity of dendritic spines

Thomas, C. I., Ryan, M. A., Kamasawa, N., & Scholl, B. (2023) · eLife · doi:10.7554/elife.89682.3 · Cited by 19

Enabling electric field model of microscopically realistic brain

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Perisomatic Features Enable Efficient and Dataset Wide Cell-Type Classifications Across Large-Scale Electron Microscopy VolumesPreprint

Elabbady, L., Seshamani, S., Mu, S., Mahalingam, G., Schneider-Mizell, C. M., Bodor, Á. L., Bae, J. A., Brittain, D., Buchanan, J., Bumbarger, D. J., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.20.499976 · Cited by 19

mEMbrain: an interactive deep learning MATLAB tool for connectomic segmentation on commodity desktops

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SYNAPTIC AND DENDRITIC ARCHITECTURE OF TWO TYPES OF HIPPOCAMPAL SOMATOSTATIN INTERNEURONS

Takács, V., Bardóczi, Z., Orosz, Á., Major, Á., Tar, L., Berki, P., Papp, P., Mayer, M. I., Sebők, H., Zsolt, L., et al. (2023) · PLoS Biology · doi:10.1016/j.ibneur.2023.08.600 · Cited by 20

Integration across biophysical scales identifies molecular and cellular correlates of person-to-person variability in human brain connectivity

Ng, B., Tasaki, S., Greathouse, K. M., Walker, C. K., Zhang, A., Covitz, S. C., Cieslak, M., Weber, A. J., Adamson, A. B., Andrade, J. P., et al. (2024) · Nature Neuroscience · doi:10.1038/s41593-024-01788-z · Cited by 21

Unambiguous identification of asymmetric and symmetric synapses using volume electron microscopy

Cano-Astorga, N., Plaza-Alonso, S., Turegano-Lopez, M., Rodrigo-Rodríguez, J., Merchan-Perez, A., & DeFelipe, J. (2024) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2024.1348032 · Cited by 17

The synaptic architecture of layer 5 thick tufted excitatory neurons in mouse visual cortex

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Volume electron microscopy reveals human retinal mitochondria that align with reflective bands in optical coherence tomography [Invited]

Kar, D., Kim, Y. J., PACKER, O. S., Clark, M. E., Cao, D., Owsley, C. J., Dacey, D. M., & Curcio, C. A. (2023) · Biomedical Optics Express · doi:10.1364/boe.501228 · Cited by 17

A circuit motif for color in the human foveal retina

Kim, Y. J., PACKER, O. S., & Dacey, D. M. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2405138121 · Cited by 16

Visual information is broadcast among cortical areas in discrete channelsPreprint

Yu, Y., Stirman, J. N., Dorsett, C. R., & Smith, S. L. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/469114 · Cited by 21

Infrequent strong connections constrain connectomic predictions of neuronal function

Currier, T. A., & Clandinin, T. R. (2025) · Cell · doi:10.1016/j.cell.2025.05.007 · Cited by 15

Synaptic-resolution connectomics: towards large brains and connectomic screening

Helmstaedter, M. N. (2025) · Nature reviews. Neuroscience · doi:10.1038/s41583-025-00998-z · Cited by 25

Cytosolic DNA sensing pathway in senescence and aging: Underlying mechanisms and targeted interventions

Alipour-Khezri, E., Moqadami, A., Vahed, S. Z., & Barzegari, A. (2025) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2025.118790 · Cited by 17

High-resolution volumetric imaging constrains compartmental models to explore synaptic integration and temporal processing by cochlear nucleus globular bushy cells

Spirou, G. A., Kersting, M., Carr, S., Razzaq, B., Pinto, C. Y. A., Dawson, M., Ellisman, M. H., & Manis, P. B. (2023) · eLife · doi:10.7554/elife.83393 · Cited by 17

Dendrite architecture determines mitochondrial distribution patterns in vivo

Donovan, E. J., Agrawal, A., Liberman, N., Kalai, J. I., Adler, A. J., Lamper, A. M., Wang, H. Q., Chua, N. J., Koslover, E. F., & Barnhart, E. L. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114190 · Cited by 13

How to incorporate biological insights into network models and why it matters

Timón, L. B., Ekelmans, P., Kraynyukova, N., Rose, T., Busse, L., & Tchumatchenko, T. (2022) · The Journal of Physiology · doi:10.1113/jp282755 · Cited by 17

The majority of axonal mitochondria in mammalian neurons lack mitochondrial DNA and do not produce ATPPreprint

Hirabayashi, Y., Lewis, T. L., Du, Y., Zamponi, E., Kneis, P., Jones, J. U., Decker, A., Coceano, G., Alvelid, J., Kikuchi, M., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.12.579972 · Cited by 18

Postsynaptic mitochondria are positioned to support functional diversity of dendritic spines

Thomas, C. I., Ryan, M. A., Kamasawa, N., & Scholl, B. (2023) · eLife · doi:10.7554/elife.89682 · Cited by 26

Simulation-based inference for efficient identification of generative models in computational connectomics

Boelts, J., Harth, P., Gao, R., Udvary, D., Yáñez, F., Baum, D., Hege, H., Oberlaender, M., & Macke, J. H. (2023) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1011406 · Cited by 13

ViMO - Visual Analysis of Neuronal Connectivity Motifs

Troidl, J., Warchol, S., Choi, J., Matelsky, J., Dhanyasi, N., Wang, X., Wester, B. A., Wei, D., Lichtman, J. W., Pfister, H., et al. (2023) · IEEE Transactions on Visualization and Computer Graphics · doi:10.1109/tvcg.2023.3327388 · Cited by 15

Distinct dendritic integration strategies control dynamics of inhibition in the neocortex

Morabito, A., Zerlaut, Y., Dhanasobhon, D., Berthaux, E., Pinho, C. M., Tzilivaki, A., Moneron, G., Cathala, L., Poirazi, P., Bacci, A., et al. (2025) · Neuron · doi:10.1016/j.neuron.2025.05.029 · Cited by 20

Simulations of cortical networks using spatially extended conductance‐based neuronal models

Haufler, D., Ito, S., Koch, C., & Arkhipov, A. S. (2022) · The Journal of Physiology · doi:10.1113/jp284030 · Cited by 13

Hierarchical Modular Structure of the Drosophila Connectome

Kunin, A. B., Guo, J., Bassler, K. E., Pitkow, X., & Josić́, K. (2023) · Journal of Neuroscience · doi:10.1523/jneurosci.0134-23.2023 · Cited by 13

New Synapse Detection in the Whole-Brain Connectome of DrosophilaPreprint

Yu, S.-C., Bae, J. A., Matsliah, A., Dorkenwald, S., Gager, J., Hebditch, J., Silverman, B., Willie, K. P., Willie, R., Burke, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.11.664377 · Cited by 14

The inferred functional connectome underlying circadian synchronization in the mouse suprachiasmatic nucleus

Nikhil, K. L., Singhal, B., Granados‐Fuentes, D., Li, J.-S., Kiss, I. Z., & Herzog, E. D. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2520674122 · Cited by 11

Dynamics of synaptic damage in severe traumatic brain injury revealed by cerebrospinal fluid SNAP-25 and VILIP-1

Heuvel, F. O., Li, Z., Riedel, D., Halbgebauer, S., Oeckl, P., Mayer, B., Gotzman, N., Shultz, S. R., Semple, B. D., Tumani, H., et al. (2024) · Journal of Neurology Neurosurgery & Psychiatry · doi:10.1136/jnnp-2024-333413 · Cited by 14

Unveiling universal aspects of the cellular anatomy of the brain

Ansell, H. S., & Kovács, I. A. (2024) · Communications Physics · doi:10.1038/s42005-024-01665-y · Cited by 13

Spatial and morphological organization of mitochondria in neurons across a connectome

Sager, G., Pfeiffer, P., Wu, H., Pallasdies, F., Gowers, R. P., Ravikumar, S., Wu, E., Colón‐Ramos, D. A., Schreiber, S., & Clark, D. A. (2025) · Science · doi:10.1126/science.ads6674 · Cited by 18

Connectomic Analysis of Mitochondria in the Central Brain of DrosophilaPreprint

Longden, K. D., Rivlin, P. K., Januszewski, M., Neace, E. R., Scheffer, L. K., Ordish, C., Clements, J., Phillips, E., Smith, N. L., Takemura, S., et al. (2024) · eLife · doi:10.1101/2024.04.21.590464 · Cited by 14

Cyclic structure with cellular precision in a vertebrate sensorimotor neural circuit

Yang, R., Vishwanathan, A., Wu, J., Kemnitz, N., Ih, D., Turner, N., Lee, K., Tartavull, I., Silversmith, W. M., Jordan, C. S., et al. (2023) · Current Biology · doi:10.1016/j.cub.2023.05.010 · Cited by 11

Statistical method accounts for microscopic electric field distortions around neurons when simulating activation thresholds

Weise, K., Makaroff, S. N., Numssen, O., Bikson, M., & Knösche, T. R. (2025) · Brain stimulation · doi:10.1016/j.brs.2025.02.007 · Cited by 11

Reconstruction of a connectome of single neurons in mouse brains by cross-validating multi-scale multi-modality data

Xiong, F., Liu, L., & Peng, H. (2025) · Nature Methods · doi:10.1038/s41592-025-02784-2 · Cited by 15

NeuVue: A scalable and customizable framework for electron microscopy proofreadingPreprint

Xenes, D., Kitchell, L. M., Rivlin, P. K., Martinez, H., Rose, V. A., Bishop, C., Brodsky, R., Celii, B., Joyce, J., Luna, D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.18.500521 · Cited by 11

Most Axonal Mitochondria in Cortical Pyramidal Neurons Lack Mitochondrial DNA and Consume ATPPreprint

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Linking brain activity across scales with simultaneous opto- and electrophysiology

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