Dense connectomic reconstruction in layer 4 of the somatosensory cortex

Statistical significance for genomewide studies

Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692

Additive logistic regression: a statistical view of boosting (with discussion and a rejoinder by the authors)

Friedman, J., Hastie, T., & Tibshirani, R. (2000) · The Annals of Statistics · doi:10.1214/aos/1016218223 · Cited by 6,884

Regulation of Synaptic Efficacy by Coincidence of Postsynaptic APs and EPSPs

Markram, H., Lübke, J., Frotscher, M., & Sakmann, B. (1997) · Science · doi:10.1126/science.275.5297.213 · Cited by 3,832

Structural basis of long-term potentiation in single dendritic spines

Matsuzaki, M., Honkura, N., Ellis-Davies, G. C. R., & Kasai, H. (2004) · Nature · doi:10.1038/nature02617 · Cited by 2,483

Globally optimal stitching of tiled 3D microscopic image acquisitions

Preibisch, S., Saalfeld, S., & Tomancak, P. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp184 · Cited by 2,452

Long-term in vivo imaging of experience-dependent synaptic plasticity in adult cortex

Trachtenberg, J. T., Chen, B. E., Knott, G. W., Feng, G., Sanes, J. R., Welker, E., & Svoboda, K. (2002) · Nature · doi:10.1038/nature01273 · Cited by 1,927

Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure

Denk, W., & Horstmann, H. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020329 · Cited by 1,644

Reconstruction and Simulation of Neocortical Microcircuitry

Markram, H., Muller, E., Ramaswamy, S., Reimann, M. W., Abdellah, M., Sanchez, C. A., Ailamaki, A., Alonso-Nanclares, L., Antille, N., Arsever, S., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.029 · Cited by 1,557

Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex

The Petilla Interneuron Nomenclature Group (PING) (2008) · Nature Reviews Neuroscience · doi:10.1038/nrn2402 · Cited by 1,491

A place theory of sound localization.

Jeffress, L. A. (1948) · Journal of Comparative and Physiological Psychology · doi:10.1037/h0061495 · Cited by 1,484

Synaptic environment and extrasynaptic glutamate signals: The quest continues

Rusakov, D. A., & Stewart, M. G. (2021) · Neuropharmacology · doi:10.1016/j.neuropharm.2021.108688 · Cited by 23

Unique properties of dually innervated dendritic spines in pyramidal neurons of the somatosensory cortex uncovered by 3D correlative light and electron microscopy

Gemin, O., Serna, P., Zamith, J., Assendorp, N., Fossati, M., Rostaing, P., Triller, A., & Charrier, C. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001375 · Cited by 25

Synaptic recognition molecules in development and disease

Chowdhury, D., Watters, K. E., & Biederer, T. (2021) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2020.12.009 · Cited by 26

Automatic Detection of Synaptic Partners in a Whole-Brain Drosophila EM Dataset

Buhmann, J., Sheridan, A., Gerhard, S., Krause, R., Nguyen, T., Heinrich, L., Schlegel, P., Lee, W.-C. A., Wilson, R., Saalfeld, S., et al. (2019) · doi:10.1101/2019.12.12.874172 · Cited by 21

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Müller, A., Schmidt, D., Albrecht, J. P., Rieckert, L., Otto, M., Garcia, L. E. G., Fabig, G., Solimena, M., & WEIGERT, M. G. (2024) · Nature Protocols · doi:10.1038/s41596-024-00957-5 · Cited by 21

Illuminating the Brain With X-Rays: Contributions and Future Perspectives of High-Resolution Microtomography to Neuroscience

Rodrigues, P. V., Tostes, K., Bosque, B. P., de Godoy, J. V. P., Neto, D. P. A., Dias, C. S. B., & Fonseca, M. D. C. (2021) · Frontiers in Neuroscience · doi:10.3389/fnins.2021.627994 · Cited by 21

Big data in nanoscale connectomics, and the greed for training labels

Motta, A., Sievers, M., Staffler, B., & Helmstaedter, M. N. (2019) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2019.03.012 · Cited by 21

InShaDe: Invariant Shape Descriptors for visual 2D and 3D cellular and nuclear shape analysis and classification

Al-Thelaya, K., Agus, M., Gilal, N. U., Yang, Y., Pintore, G., Gobbetti, E., Calì, C., Magistretti, P. J., Mifsud, W., & Schneider, J. (2021) · Computers & Graphics · doi:10.1016/j.cag.2021.04.037 · Cited by 20

Three-Dimensional Structure of Dendritic Spines Revealed by Volume Electron Microscopy Techniques

Parajuli, L. K., & Koike, M. (2021) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2021.627368 · Cited by 23

Between neurons and networks: investigating mesoscale brain connectivity in neurological and psychiatric disorders

Silveira, A. C. C., Antunes, A. S. L. M., Athié, M. C. P., da Silva, B. F., dos Santos, J. V. R., Canateli, C., Fontoura, M. A., Pinto, A. D. S., Pimentel‐Silva, L. R., Avansini, S. H., et al. (2024) · Frontiers in Neuroscience · doi:10.3389/fnins.2024.1340345 · Cited by 20

An Implantable Biohybrid Neural Interface Toward Synaptic Deep Brain Stimulation

Sifringer, L., Fratzl, A., Clément, B., Chansoria, P., Mönkemöller, L. S., Duru, J., Ihle, S. J., Steffens, S., Beltraminelli, A., Ceylan, E., et al. (2025) · Advanced Functional Materials · doi:10.1002/adfm.202416557 · Cited by 23

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

Automatic segmentation and reconstruction of intracellular compartments in volumetric electron microscopy data

Mekuč, M. Ž., Bohak, C., Boneš, E., Hudoklin, S., Romih, R., & Marolt, M. (2022) · Computer Methods and Programs in Biomedicine · doi:10.1016/j.cmpb.2022.106959 · Cited by 19

AxonEM Dataset: 3D Axon Instance Segmentation of Brain Cortical Regions

Wei, D., Lee, K., Li, H., Lu, R., Bae, J. A., Liu, Z., Zhang, L., dos Santos, M., Lin, Z., Uram, T. D., et al. (2021) · Lecture notes in computer science · doi:10.1007/978-3-030-87193-2_17 · Cited by 24

EASE: EM-Assisted Source Extraction from calcium imaging dataPreprint

Zhou, P., Reimer, J., Zhou, D. X., Pasarkar, A., Kinsella, I., Froudarakis, E., Yatsenko, D., Fahey, P. G., Bodor, Á. L., Buchanan, J., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.25.007468 · Cited by 16

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

Graph partitioning algorithms with biological connectivity decisions for neuron reconstruction in electron microscope volumes

Hong, B., Liu, J., Shen, L., Xie, Q., Yuan, J., Emrouznejad, A., & Han, H. (2023) · Expert Systems with Applications · doi:10.1016/j.eswa.2023.119776 · Cited by 17

Neuronal Subcompartment Classification and Merge Error Correction

Li, H., Januszewski, M., Jain, V., & Li, P. H. (2020) · Lecture notes in computer science · doi:10.1007/978-3-030-59722-1_9 · Cited by 18

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

Specific inhibition and disinhibition in the higher-order structure of a cortical connectome

Reimann, M., Santander, D. E., Ecker, A., & Muller, E. B. (2024) · Cerebral Cortex · doi:10.1093/cercor/bhae433 · Cited by 20

Expansion tomography for large volume tissue imaging with nanoscale resolution

Chen, R., Cheng, X., Zhang, Y., Yang, X., Wang, Y., Liu, X., & Zeng, S. (2021) · Biomedical Optics Express · doi:10.1364/boe.431696 · Cited by 17

Joint reconstruction of neuron and ultrastructure via connectivity consensus in electron microscope volumes

Hong, B., Liu, J., Zhai, H., Liu, J., Shen, L., Chen, X., Xie, Q., & Han, H. (2022) · BMC Bioinformatics · doi:10.1186/s12859-022-04991-6 · Cited by 15

Towards a Comprehensive Optical Connectome at Single Synapse Resolution via Expansion Microscopy

Sneve, M. A., & Piatkevich, K. D. (2022) · Frontiers in Synaptic Neuroscience · doi:10.3389/fnsyn.2021.754814 · Cited by 15

Dynamics of phase oscillator networks with synaptic weight and structural plasticity

Chauhan, K., Khaledi‐Nasab, A., NEIMAN, A. B., & Tass, P. A. (2022) · Scientific Reports · doi:10.1038/s41598-022-19417-9 · Cited by 16

Generative and discriminative model-based approaches to microscopic image restoration and segmentation

Ishii, S., Lee, S., Urakubo, H., Kume, H., & Kasai, H. (2020) · Microscopy · doi:10.1093/jmicro/dfaa007 · Cited by 15

Volume electron microscopy analysis of synapses in primary regions of the human cerebral cortex

Cano‐Astorga, N., Plaza‐Alonso, S., DeFelipe, J., & Alonso‐Nanclares, L. (2024) · Cerebral Cortex · doi:10.1093/cercor/bhae312 · Cited by 15

The gradient clusteron: A model neuron that learns to solve classification tasks via dendritic nonlinearities, structural plasticity, and gradient descent

Moldwin, T., Kalmenson, M., & Segev, I. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009015 · Cited by 16

Structural Analysis of the Caenorhabditis elegans Dauer Larval Anterior Sensilla by Focused Ion Beam-Scanning Electron Microscopy

Britz, S., Markert, S. M., Witvliet, D. K., Steyer, A. M., Tröger, S., Mulcahy, B., Kollmannsberger, P., Schwab, Y., Zhen, M., & Stigloher, C. (2021) · Frontiers in Neuroanatomy · doi:10.3389/fnana.2021.732520 · Cited by 13

Regimes and mechanisms of transient amplification in abstract and biological neural networks

Christodoulou, G., Vogels, T. P., & Agnes, E. J. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010365 · Cited by 15

Predicting modular functions and neural coding of behavior from a synaptic wiring diagramPreprint

Vishwanathan, A., Ramirez, A. D., Wu, J., Sood, A., Yang, R., Kemnitz, N., Ih, D., Turner, N. L., Lee, K., Tartavull, I., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.10.28.359620 · Cited by 14

Femtosecond laser preparation of resin embedded samples for correlative microscopy workflows in life sciences

Bosch, C., Lindenau, J., Pacureanu, A., Peddie, C. J., Majkut, M., Douglas, A. C., Carzaniga, R., Rack, A., Collinson, L., Schaefer, A. T., et al. (2023) · Applied Physics Letters · doi:10.1063/5.0142405 · Cited by 13

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

High‐throughput morphometric and transcriptomic profiling uncovers composition of naïve and sensory‐deprived cortical cholinergic VIP/CHAT neurons

Yayon, N., Amsalem, O., Zorbaz, T., Yakov, O., Dubnov, S., Winek, K., Dudai, A., Adam, G., Schmidtner, A. K., Tessier‐Lavigne, M., et al. (2022) · The EMBO Journal · doi:10.15252/embj.2021110565 · Cited by 12

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

Shared and divergent principles of synaptic transmission between cortical excitatory neurons in rodent and human brain

de Kock, C. P. J., & Feldmeyer, D. (2023) · Frontiers in Synaptic Neuroscience · doi:10.3389/fnsyn.2023.1274383 · Cited by 13

Republished: Dynamics of Stochastic Integrate-and-Fire Networks

Ocker, G. K. (2023) · Physical Review X · doi:10.1103/physrevx.13.041047 · Cited by 13

Morphomics via next-generation electron microscopy

Son, R., Yamazawa, K., Oguchi, A., Suga, M., Tamura, M., Yanagita, M., Murakawa, Y., & Kume, S. (2023) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjad081 · Cited by 13

Biophysical Modeling of Synaptic Plasticity

Lee, C. T., Bell, M. K., Bonilla-Quintana, M., & Rangamani, P. (2024) · Annual Review of Biophysics · doi:10.1146/annurev-biophys-072123-124954 · Cited by 16

Combined topological and spatial constraints are required to capture the structure of neural connectomes

Salova, A., & Kovács, I. A. (2024) · Network Neuroscience · doi:10.1162/netn_a_00428 · Cited by 14

Quantifying axonal features of human superficial white matter from three-dimensional multibeam serial electron microscopy data assisted by deep learning

Tian, Q., Ngamsombat, C., Lee, H., Berger, D. R., Wu, Y., Fan, Q., Bilgiç, B., Li, Z., Novikov, D. S., Fieremans, E., et al. (2025) · NeuroImage · doi:10.1016/j.neuroimage.2025.121212 · Cited by 12

Dendritic Spine Density Scales with Microtubule Number in Rat Hippocampal Dendrites

Harris, K. M., Hubbard, D. D., Kuwajima, M., Abraham, W. C., Bourne, J. N., Bowden, J. B., Haessly, A., Mendenhall, J. M., Parker, P. H., Shi, B., et al. (2022) · Neuroscience · doi:10.1016/j.neuroscience.2022.02.021 · Cited by 12

Toward an Automated HPC Pipeline for Processing Large Scale Electron Microscopy Data

Vescovi, R., Li, H., Kinnison, J., Keçeli, M., Salim, M., Kasthuri, N., Uram, T. D., & Ferrier, N. (2020) · doi:10.1109/xloop51963.2020.00008 · Cited by 12

A theory for the emergence of neocortical network architecturePreprint

Udvary, D., Harth, P., Macke, J. H., Hege, H., de Kock, C. P. J., Sakmann, B. J., & Oberlaender, M. (2020) · MPG.PuRe (Max Planck Society) · Cited by 12

Vision-dependent specification of cell types and function in the developing cortexPreprint

Cheng, S., Butrus, S., Tan, L., Xu, R., Sagireddy, S., Trachtenberg, J. T., Shekhar, K., & Zipursky, S. L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.10.455824 · Cited by 12

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: AnatomyPreprint

Reimann, M., Bolaños‐Puchet, S., Courcol, J.-D., Santander, D. E., Arnaudon, A., Coste, B., Delalondre, F., Delemontex, T., Devresse, A., Dictus, H., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.11.503144 · Cited by 15

High-order rotor Hopfield neural networks for associative memory

Chen, B., & Zhang, H. (2024) · Neurocomputing · doi:10.1016/j.neucom.2024.128893 · Cited by 12

Cellular connectomes as arbiters of local circuit models in the cerebral cortex

Klinger, E., Motta, A., Marr, C., Theis, F. J., & Helmstaedter, M. N. (2021) · Nature Communications · doi:10.1038/s41467-021-22856-z · Cited by 11

Nervous system-wide single-cell morphology atlas of excitatory and inhibitory neurons in larval zebrafishPreprint

Du, X.-F., Yue, Z.-F., Chen, M.-Q., Li, W.-L., Chen, T.-L., Hu, H.-Y., Wan, H.-L., Zhao, T.-T., Zhong, Y., Ning, X., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.06.658008 · Cited by 18

Scalable Approximation and Solvers for Ionic Electrodiffusion in Cellular Geometries

Benedusi, P., Ellingsrud, A. J., Herlyng, H., & Rognes, M. E. (2024) · SIAM Journal on Scientific Computing · doi:10.1137/24m1644717 · Cited by 10

nGauge: Integrated and Extensible Neuron Morphology Analysis in Python

Walker, L. A., Williams, J. S., Li, Y., Roossien, D. H., Lee, W. J., Michki, S. N., & Cai, D. (2022) · Neuroinformatics · doi:10.1007/s12021-022-09573-8 · Cited by 10

A Scalable Staining Strategy for Whole-Brain ConnectomicsPreprint

Lu, X., Wu, Y., Schalek, R. L., Meirovitch, Y., Berger, D. R., & Lichtman, J. W. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.26.558265 · Cited by 10

ShapeMamba-EM: Fine-Tuning Foundation Model with Local Shape Descriptors and Mamba Blocks for 3D EM Image Segmentation

Shi, R., Pang, Q., Ма, Л., Duan, L., Huang, T., & Jiang, T. (2024) · Lecture notes in computer science · doi:10.1007/978-3-031-72390-2_68 · Cited by 9

Volume electron microscopy reveals unique laminar synaptic characteristics in the human entorhinal cortex

Plaza‐Alonso, S., Cano‐Astorga, N., DeFelipe, J., & Alonso‐Nanclares, L. (2025) · eLife · doi:10.7554/elife.96144 · Cited by 10

Quantitative evaluation of embedding resins for volume electron microscopy

Tegethoff, L., & Briggman, K. L. (2024) · Frontiers in Neuroscience · doi:10.3389/fnins.2024.1286991 · Cited by 9

MCMC sampling of directed flag complexes with fixed undirected graphs

Unger, F., & Krebs, J. (2024) · Journal of Applied and Computational Topology · doi:10.1007/s41468-024-00178-5 · Cited by 10

Tracing nerve fibers with volume electron microscopy to quantitatively analyze brain connectivity

Turégano-López, M., Pozas, F. D. L., Santuy, A., Rodríguez, J., DeFelipe, J., & Merchán-Pérez, Á. (2024) · Communications Biology · doi:10.1038/s42003-024-06491-0 · Cited by 11

Local Connections of Pyramidal Neurons to Parvalbumin-Producing Interneurons in Motor-Associated Cortical Areas of Mice

Kuramoto, E., Tanaka, Y. R., Hioki, H., Goto, T., & Kaneko, T. (2021) · eNeuro · doi:10.1523/eneuro.0567-20.2021 · Cited by 9

Frozen algorithms: how the brain's wiring facilitates learning

Raman, D. V., & O’Leary, T. (2021) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2020.12.017 · Cited by 9

A detailed mathematical theory of thalamic and cortical microcircuits based on inference in a generative vision modelPreprint

George, D., Lázaro-Gredilla, M., Lehrach, W. P., Dedieu, A., & Zhou, G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.09.09.290601 · Cited by 9

The structure and function of neural connectomes are shaped by a small number of design principlesPreprint

Haber, A., Wanner, A. A., Friedrich, R. W., & Schneidman, E. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.15.532611 · Cited by 12

Cell–cell junctions in focus – imaging junctional architectures and dynamics at high resolution

Janssen, V., & Huveneers, S. (2024) · Journal of Cell Science · doi:10.1242/jcs.262041 · Cited by 11

Decoding gray matter, large-scale analysis of brain cell morphometry to inform microstructural modeling of diffusion MR signals

Aird-Rossiter, C., Zhang, H. G., Alexander, D. C., Jones, D. K., & Palombo, M. (2026) · Communications Biology · doi:10.1038/s42003-025-09353-5 · Cited by 11

Vertically Integrated Monolithic Neuromorphic Nanowire Device for Physiological Information Processing

Liu, J., Jiang, C., Wei, H., Wang, Z., Sun, L., Zhang, S., Ni, Y., Qu, S., Yang, L., & Xu, W. (2024) · Nano Letters · doi:10.1021/acs.nanolett.3c04391 · Cited by 8

A Picture Worth a Thousand Molecules—Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits

Minehart, J. A., & Speer, C. M. (2021) · Frontiers in Synaptic Neuroscience · doi:10.3389/fnsyn.2020.615059 · Cited by 9

Mechanisms Underlying Target Selectivity for Cell Types and Subcellular Domains in Developing Neocortical Circuits

Gutman-Wei, A. Y., & Brown, S. P. (2021) · Frontiers in Neural Circuits · doi:10.3389/fncir.2021.728832 · Cited by 9

How the world’s biggest brain maps could transform neuroscience

Abbott, A. (2021) · Nature · doi:10.1038/d41586-021-02661-w · Cited by 8

Synaptic degeneration in the prefrontal cortex of a rat AD model revealed by volume electron microscopy

Jiang, Y. H., Li, L., Pang, K., Liu, J., Chen, B., Yuan, J., Shen, L., Chen, X., Lu, B., & Han, H. (2022) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjac012 · Cited by 8

Connecting Connectomes to Physiology

Borst, A., & Leibold, C. (2023) · Journal of Neuroscience · doi:10.1523/jneurosci.2208-22.2023 · Cited by 8

An adhesion signaling axis involving Dystroglycan, β1-Integrin, and Cas adaptor proteins regulates the establishment of the cortical glial scaffold

Wong, W., Estep, J. A., Treptow, A. M., Rajabli, N., Jahncke, J. N., Ubina, T., Wright, K. M., & Riccomagno, M. M. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002212 · Cited by 8

PUPIL enables mapping and stamping of transient electrical connectivity in developing nervous systems

Xie, S., Li, H., Yao, F., Huang, J., Yang, X., Chen, X., Liu, Q., Zhuang, M., & He, S. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109853 · Cited by 8

High-contrast en-bloc staining of mouse whole-brain samples for EM-based connectomicsPreprint

Song, K., Feng, Z., & Helmstaedter, M. N. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.30.486341 · Cited by 8

Modeling and simulation of neocortical micro- and mesocircuitry (Part I, anatomy)Preprint

Reimann, M., Bolaños‐Puchet, S., Courcol, J.-D., Santander, D. E., Arnaudon, A., Coste, B., Delalondre, F., Delemontex, T., Devresse, A., Dictus, H., et al. (2024) · eLife · doi:10.7554/elife.99688 · Cited by 9

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: AnatomyPreprint

Reimann, M., Bolaños‐Puchet, S., Courcol, J.-D., Santander, D. E., Arnaudon, A., Coste, B., Delalondre, F., Delemontex, T., Devresse, A., Dictus, H., et al. (2024) · eLife · doi:10.7554/elife.99688.2 · Cited by 9

Connectome-seq: high-throughput mapping of neuronal connectivity at single-synapse resolution via barcode sequencing

Chen, D., Isakova, A., Wan, Z., Wagner, M. J., Wu, Y., & Zhao, B. S. (2026) · Nature Methods · doi:10.1038/s41592-026-03026-9 · Cited by 8

A Splitting, Discontinuous Galerkin Solver for the Cell-by-Cell Electroneutral Nernst–Planck Framework

Ellingsrud, A. J., Benedusi, P., & Kuchta, M. (2025) · SIAM Journal on Scientific Computing · doi:10.1137/24m1653367 · Cited by 7

Computational Concepts for Reconstructing and Simulating Brain Tissue

Schürmann, F., Courcol, J.-D., & Ramaswamy, S. (2022) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-89439-9_10 · Cited by 7

Increased Extrasynaptic Glutamate Escape in Stochastically Shaped Probabilistic Synaptic Environment

Savtchenko, L. P., & Rusakov, D. A. (2022) · Biomedicines · doi:10.3390/biomedicines10102406 · Cited by 7

DeepMulticut: Deep Learning of Multicut Problem for Neuron Segmentation From Electron Microscopy Volume

Li, Z., Yang, X., Liu, J., Hong, B., Zhang, Y., Zhai, H., Shen, L., Chen, X., Liu, Z., & Han, H. (2024) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2024.3409634 · Cited by 7

Cut Finite Element Discretizations of Cell-by-Cell EMI Electrophysiology Models

Berre, N., Rognes, M. E., & Massing, A. (2024) · SIAM Journal on Scientific Computing · doi:10.1137/23m1580632 · Cited by 7

Increased Callosal Connectivity in Reeler Mice Revealed by Brain-Wide Input Mapping of VIP Neurons in Barrel Cortex

Hafner, G., Guy, J., Witte, M., Truschow, P., Rüppel, A., Sirmpilatze, N., Dadarwal, R., Boretius, S., & Staiger, J. F. (2020) · Cerebral Cortex · doi:10.1093/cercor/bhaa280 · Cited by 10

Beyond the connectome: A map of a brain architecture derived from whole-brain volumetric reconstructionsPreprint

Brittin, C. A., Cook, S. J., Hall, D. H., Emmons, S. W., & Cohen, N. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.24.112870 · Cited by 7

Decoding the Mouse Spinal Cord Locomotor Neural Network Using Tissue Clearing, Tissue Expansion and Tiling Light Sheet Microscopy TechniquesPreprint

Feng, R., Xie, J., Lü, J., Hu, H., Chen, Y., Wang, D., & Gao, L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.04.498760 · Cited by 5

Evaluating traces of Hebbian plasticity in the Drosophila antennal lobe

Castro, A. F., Wilson, S. R., & Cardona, A. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2315790120 · Cited by 9

The retina’s neurovascular unit: Müller glial sheaths and neuronal contactsPreprint

Grimes, W. N., Berson, D. M., Sabnis, A., Hoon, M., Sinha, R., Tian, H., & Diamond, J. S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.30.591885 · Cited by 7

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: AnatomyPreprint

Reimann, M., Bolaños‐Puchet, S., Courcol, J.-D., Santander, D. E., Arnaudon, A., Coste, B., Delalondre, F., Delemontex, T., Devresse, A., Dictus, H., et al. (2024) · eLife · doi:10.7554/elife.99688.1 · Cited by 7

Long-range axon branching: contributions to brain network plasticity and repair

Richards, L. J., Huang, C., Bauer, A. Q., & Lee, J. (2026) · Nature reviews. Neuroscience · doi:10.1038/s41583-025-01008-y · Cited by 9

Volume electron microscopy reveals age-related circuit remodeling in the auditory brainstem

Charan, D. C., Hua, Y., Wang, H., Huang, W.-Q., Wang, F., Elgoyhen, A. B., Boergens, K. M., & Guilmi, M. N. D. (2022) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2022.1070438 · Cited by 6

Morphology and ultrastructure of external sense organs of Drosophila larvae

Richter, V., Rist, A., Kislinger, G., Laumann, M., Schoofs, A., Miroschnikow, A., Pankratz, M. J., Cardona, A., & Thum, A. S. (2023) · eLife · doi:10.7554/elife.91155.3 · Cited by 19

Convergence Circuit Mapping: Genetic Approaches From Structure to Function

Yook, J. S., Kim, J., & Kim, J. (2021) · Frontiers in Systems Neuroscience · doi:10.3389/fnsys.2021.688673 · Cited by 6

An effective AI integrated system for neuron tracing on anisotropic electron microscopy volume

Liu, J., Hong, B., Chen, X., Xie, Q., Tang, Y., & Han, H. (2021) · Biomedical Signal Processing and Control · doi:10.1016/j.bspc.2021.102829 · Cited by 6

A Soma Segmentation Benchmark in Full Adult Fly Brain

Liu, X., Hu, B., Li, M., Huang, W., Zhang, Y., & Xiong, Z. (2023) · IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings - IEEE Computer Society Conference on Computer Vision and Pattern Recognition/Proceedings · doi:10.1109/cvpr52729.2023.00715 · Cited by 6

An intelligent workflow for sub-nanoscale 3D reconstruction of intact synapses from serial section electron tomography

Chang, S., Li, L., Hong, B., Liu, J., Xu, Y., Pang, K., Zhang, L., Han, H., & Chen, X. (2023) · BMC Biology · doi:10.1186/s12915-023-01696-x · Cited by 6

SegNeuron: 3D Neuron Instance Segmentation in Any EM Volume with a Generalist Model

Zhang, Y.-C. S. L.-G., Guo, J., Zhai, H., Liu, J., & Han, H. (2024) · Lecture notes in computer science · doi:10.1007/978-3-031-72111-3_55 · Cited by 5

Afferent convergence to a shared population of interneuron AMPA receptors

Pennock, R. L., Coddington, L. T., Yan, X. E., Overstreet‐Wadiche, L., & Wadiche, J. I. (2023) · Nature Communications · doi:10.1038/s41467-023-38854-2 · Cited by 5

A guide to CNN-based dense segmentation of neuronal EM images

Urakubo, H. (2025) · Microscopy · doi:10.1093/jmicro/dfaf002 · Cited by 5

Efficient cell-wide mapping of mitochondria in electron microscopic volumes using webKnossos

Jiang, Y., Wang, H., Boergens, K. M., Rzepka, N., Wang, F., & Hua, Y. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2025.100989 · Cited by 6

Dual Networks for High-Precision and High-Speed Registration of Brain Electron Microscopy Images

Shu, C., Tong, X., Zhou, F., Chen, X., & Han, H. (2020) · Brain Sciences · doi:10.3390/brainsci10020086 · Cited by 5

Boosting Multilabel Semantic Segmentation for Somata and Vessels in Mouse Brain

Wu, X., Tao, Y., He, G., Liu, D., Meiling, F., Yang, S., Gong, H., Xiao, R., Chen, S., & Huang, J. (2021) · Frontiers in Neuroscience · doi:10.3389/fnins.2021.610122 · Cited by 4

Denoising of scanning electron microscope images for biological ultrastructure enhancement

Chang, S., Shen, L., Li, L., Chen, X., & Han, H. (2022) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s021972002250007x · Cited by 5

Connectomic reconstruction of a cortical columnPreprint

Sievers, M., Motta, A., Schmidt, M., Yener, Y., Loomba, S., Song, K., Bruett, J., & Helmstaedter, M. N. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.03.22.586254 · Cited by 32

Connectomics: The dense reconstruction of neuronal circuits

Helmstaedter, M. N. (2013) · Frontiers in Neuroinformatics · doi:10.3389/conf.fninf.2013.10.00016 · Cited by 2

Brain anatomy revealed in startling detail

Stern, P. (2019) · Science · doi:10.1126/science.366.6469.1090-i

Dissecting origins of wiring specificity in dense reconstructions of neural tissuePreprint

Harth, P., Udvary, D., Boelts, J., Macke, J. H., Baum, D., Hege, H., & Oberlaender, M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.14.628490 · Cited by 6

Sparse reconstruction of brain circuits: Or, how to survive without a microscopic connectome

da Costa, N. M., & Martin, K. A. C. (2013) · NeuroImage · doi:10.1016/j.neuroimage.2013.04.054 · Cited by 30