DB
Daniel R. Berger
neuroscienceConnectomeconnectomicselectron microscopyAxon diameterconnectomeConnectomicscs.CVImage Processing, Computer-AssistedImaging, Three-Dimensional
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
51 papers in the corpus · 2012–2026Multiplexed volumetric CLEM enabled by antibody derivatives provides new insights into the cytology of the mouse cerebellar cortex.37461609 · Han, Xiaomeng, Lu, Xiaotang, Li, Peter H et al.2026 · 0 citationsResearch square. 2023
Connectomic evidence that ordered activity drives neuromuscular network formation.42380673 · Meirovitch, Yaron, Kang, Kai, Draft, Ryan W et al.2026 · 0 citationsNature neuroscience. 2026;29(8):1873-1884
A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain.40661440 · Petkova, Mariela D, Januszewski, Michał, Blakely, Tim et al.2026 · 14 citationsbioRxiv : the preprint server for biology. 2025
Are Synaptic Clefts Directionally Oriented?10.64898/2026.01.30.702623v2 · Tang, D., Deng, Z.-D., Danskin, B. et al.2026 · 0 citationsbioRxiv
SmartEM: machine learning-guided electron microscopy.41461905 · Meirovitch, Yaron, Chandok, Ishaan Singh, Park, Core Francisco et al.2026 · 9 citationsNature methods. 2026;23(1):193-204
Frenet-Serret Frame-Based Decomposition for Part Segmentation of 3-D Curvilinear Structures.40668707 · Leslie Gu, Shixuan, Adhinarta, Jason Ken, Bessmeltsev, Mikhail et al.2025 · 2 citationsIEEE transactions on medical imaging. 2025;44(12):5319-5331
Developmental Connectomics of the Mouse Cerebellum10.1101/2025.09.15.676403v1 · Dhanyasi, N., Meirovitch, Y., Kapoor, V. et al.2025 · 2 citationsbioRxiv
Frenet-Serret Frame-based Decomposition for Part Segmentation of 3D Curvilinear Structures2404.14435v3 · Leslie Gu, Jason Ken Adhinarta, Mikhail Bessmeltsev et al.2024 · 0 citationsIEEE Transactions on Medical Imaging, 2025
Quantifying axonal features of human superficial white matter from three-dimensional multibeam serial electron microscopy data assisted by deep learning.40222502 · Tian, Qiyuan, Ngamsombat, Chanon, Lee, Hong-Hsi et al.2025 · 12 citationsNeuroImage. 2025;313:121212
SmartEM: machine-learning guided electron microscopy10.1101/2023.10.05.561103v4 · Meirovitch, Y., Chandok, I. S., Park, C. F. et al.2023 · 16 citationsbioRxiv
Mapping Alzheimer Disease Molecular Pathologies in Large-Scale Connectomics Data: A Publicly Accessible Correlative Microscopy Resource10.1101/2023.10.24.563674v4 · Han, X., Li, P. H., Wang, S. et al.2023 · 3 citationsbioRxiv
Multiplexed volumetric CLEM enabled by scFvs provides insights into the cytology of cerebellar cortex.39103318 · Han, Xiaomeng, Lu, Xiaotang, Li, Peter H et al.2024 · 9 citationsNature communications. 2024;15(1):6648
EM-Compressor: Electron Microscopy Image Compression in Connectomics with Variational Autoencoders10.1101/2024.07.07.601368v1 · Li, Y., Park, C. F., Xenes, D. et al.2024 · 4 citationsbioRxiv
Extensive soma-soma plate-like contact sites (ephapses) connect suprachiasmatic nucleus neurons.38896499 · Czeisler, Mark É, Shan, Yongli, Schalek, Richard et al.2024 · 6 citationsThe Journal of comparative neurology. 2024;532(6):e25624
A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution.38723085 · Shapson-Coe, Alexander, Januszewski, Michał, Berger, Daniel R et al.2024 · 357 citationsScience (New York, N.Y.). 2024;384(6696):eadk4858
Two Stream Active Query Suggestion for Active Learning in Connectomics.33345257 · Lin, Zudi, Wei, Donglai, Jang, Won-Dong et al.2024 · 16 citationsComputer vision - ECCV ... : ... European Conference on Computer Vision : proceedings. European Conference on Computer Vision. 2020;12363:103-120
Mapping of neuronal and glial primary cilia contactome and connectome in the human cerebral cortex.37898123 · Wu, Jun Yao, Cho, Su-Ji, Descant, Katherine et al.2024 · 95 citationsNeuron. 2024;112(1):41-55.e3
Multi-layered maps of neuropil with segmentation-guided contrastive learning.37985712 · Dorkenwald, Sven, Li, Peter H, Januszewski, Michał et al.2023 · 37 citationsNature methods. 2023;20(12):2011-2020
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 Scalable Staining Strategy for Whole-Brain Connectomics10.1101/2023.09.26.558265v1 · Lu, X., Wu, Y., Schalek, R. L. et al.2023 · 12 citationsbioRxiv
Connectomics of the Octopus vulgaris vertical lobe provides insight into conserved and novel principles of a memory acquisition network.37410519 · Bidel, Flavie, Meirovitch, Yaron, Schalek, Richard Lee et al.2023 · 41 citationseLife. 2023;12
Multiplexed volumetric CLEM enabled by antibody derivatives provides new insights into the cytology of the mouse cerebellar cortex10.1101/2023.05.20.540091v4 · Han, X., Lu, X., Li, P. H. et al.2023 · 5 citationsbioRxiv
Neuromuscular connectomes across development reveal synaptic ordering rules10.1101/2021.09.20.460480v3 · Meirovitch, Y., Kang, K., Draft, R. W. et al.2021 · 9 citationsbioRxiv
Post-embryonic remodeling of the C. elegans motor circuit.36283410 · Mulcahy, Ben, Witvliet, Daniel K, Mitchell, James et al.2022 · 32 citationsCurrent biology : CB. 2022;32(21):4645-4659.e3
Multi-Layered Maps of Neuropil with Segmentation-Guided Contrastive Learning10.1101/2022.03.29.486320v2 · Dorkenwald, S., Li, P., Januszewski, M. et al.2022 · 37 citationsbioRxiv
Connectomics of the Octopus vulgaris vertical lobe provides insight into conserved and novel principles of a memory acquisition network10.1101/2022.10.03.510303v2 · Bidel, F., Meirovitch, Y., Schalek, R. L. et al.2022 · 41 citationsbioRxiv
Extensive Soma-Soma Plate-Like Contact Sites (Ephapses) Connect Suprachiasmatic Nucleus Neurons10.1101/2022.09.09.507192v1 · Czeisler, M. E., Shan, Y., Schalek, R. L. et al.2022 · 6 citationsbioRxiv
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
Post-embryonic maturation of the C. elegans motor circuit10.1101/2022.01.24.477421v1 · Mulcahy, B., Witvliet, D., Mitchell, J. K. et al.2022 · 3 citationsbioRxiv
Connectome 2.0: Developing the next-generation ultra-high gradient strength human MRI scanner for bridging studies of the micro-, meso- and macro-connectome.34464739 · Huang, Susie Y, Witzel, Thomas, Keil, Boris et al.2022 · 195 citationsNeuroImage. 2021;243:118530
A connectomic study of a petascale fragment of human cerebral cortex10.1101/2021.05.29.446289v4 · Shapson-Coe, A., Januszewski, M., Berger, D. R. et al.2021 · 279 citationsbioRxiv
Connectomes across development reveal principles of brain maturation.34349261 · Witvliet, Daniel, Mulcahy, Ben, Mitchell, James K et al.2021 · 462 citationsNature. 2021;596(7871):257-261
Connectomes across development reveal principles of brain maturation10.1101/2020.04.30.066209v3 · Witvliet, D., Mulcahy, B., Mitchell, J. K. et al.2020 · 499 citationsbioRxiv
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
Individual Oligodendrocytes Show Bias for Inhibitory Axons in the Neocortex.31167127 · Zonouzi, Marzieh, Berger, Daniel, Jokhi, Vahbiz et al.2020 · 123 citationsCell reports. 2019;27(10):2799-2808.e3
Nanobody immunostaining for correlated light and electron microscopy with preservation of ultrastructure.30397326 · Fang, Tao, Lu, Xiaotang, Berger, Daniel et al.2019 · 124 citationsNature methods. 2018;15(12):1029-1032
VAST (Volume Annotation and Segmentation Tool): Efficient Manual and Semi-Automatic Labeling of Large 3D Image Stacks.30386216 · Berger, Daniel R, Seung, H Sebastian, Lichtman, Jeff W2019 · 248 citationsFrontiers in neural circuits. 2018;12:88
Cell diversity and network dynamics in photosensitive human brain organoids.28445462 · Quadrato, Giorgia, Nguyen, Tuan, Macosko, Evan Z et al.2017 · 1,390 citationsNature. 2017;545(7652):48-53
RhoanaNet Pipeline: Dense Automatic Neural Annotation1611.06973v1 · Seymour Knowles-Barley, Verena Kaynig, Thouis Ray Jones et al.2016 · 22 citationsarXiv
The Fuzzy Logic of Network Connectivity in Mouse Visual Thalamus.27015312 · Morgan, Josh Lyskowski, Berger, Daniel Raimund, Wetzel, Arthur Willis et al.2016 · 304 citationsCell. 2016;165(1):192-206
Crowdsourcing the creation of image segmentation algorithms for connectomics.26594156 · Arganda-Carreras, Ignacio, Turaga, Srinivas C, Berger, Daniel R et al.2015 · 357 citationsFrontiers in neuroanatomy. 2015;9:142
Saturated Reconstruction of a Volume of Neocortex.26232230 · Kasthuri, Narayanan, Hayworth, Kenneth Jeffrey, Berger, Daniel Raimund et al.2015 · 1,171 citationsCell. 2015;162(3):648-61
Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits.25018701 · Hayworth, Kenneth J, Morgan, Josh L, Schalek, Richard et al.2014 · 308 citationsFrontiers in neural circuits. 2014;8:68
Distinct profiles of myelin distribution along single axons of pyramidal neurons in the neocortex.24744380 · Tomassy, Giulio Srubek, Berger, Daniel R, Chen, Hsu-Hsin et al.2014 · 629 citationsScience (New York, N.Y.). 2014;344(6181):319-24
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
Pervasive synaptic branch removal in the mammalian neuromuscular system at birth.22681687 · Tapia, Juan C, Wylie, John D, Kasthuri, Narayanan et al.2012 · 147 citationsNeuron. 2012;74(5):816-29
Career total: 63 works. 51 are in this corpus.Showing the 46 most recent.
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