JL
Jeff Lichtman
neurosciencecs.CVConnectomeconnectomicselectron microscopyq-bio.NCComputer GraphicsImaging, Three-DimensionalMicroscopy, ElectronModels, Neurological
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
297 papers in the corpus · 1973–2026Connectomics Annotation Metadata Standardization for Increased Accessibility and Queryability.35651719 · Sanchez, Morgan, Moore, Dymon, Johnson, Erik C et al.2026 · 6 citationsFrontiers in neuroinformatics. 2022;16:828458
Connectome analysis of a cerebellum-like circuit for sensory prediction.42686902 · Perks, Krista E, Petkova, Mariela D, Muller, Salomon Z et al.2026 · 2 citationsNature. 2026
Vimo - Visual Analysis of Neuronal Connectivity Motifs.37883279 · Troidl, Jakob, Warchol, Simon, Choi, Jinhan et al.2026 · 17 citationsIEEE transactions on visualization and computer graphics. 2023;PP
Multiplexed 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
Human brain organoids record the passage of time over multiple years.42618795 · Faravelli, Irene, Antón-Bolaños, Noelia, Wei, Anqi et al.2026 · 3 citationsNature. 2026;657(8132):713-723
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
RAEM: random-access electron microscopy for revisitable 3D imaging.42395368 · Chandok, Ishaan Singh, Patel, Milan, Wu, Yuelong et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
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
Structured sampling of molecularly classified mossy fiber inputs by cerebellar granule cells.42440829 · Han, Xiaomeng, Meral, Elif Sevde, Lichtman, Jeff W2026 · 1 citationFrontiers in computational neuroscience. 2026;20:1717379
Probing molecular diversity and ultrastructure of brain cells with fluorescent aptamers.42045230 · Lu, Xiaotang, Wu, Yuelong, Li, Peter H et al.2026 · 1 citationNature communications. 2026;17(1)
Lrrn-mediated retinal ganglion cell targeting drives visual circuit assembly for brightness and contrast detection.41576160 · Putti, Elena, Faini, Giulia, Thanh-Mai Dang, Julie et al.2026 · 1 citationScience advances. 2026;12(4):eadz4585
DRIFT-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
FEABAS: A Stitching and Alignment Tool for Serial EM Data10.64898/2026.06.07.730510v1 · Wu, Y., Lichtman, J. W.2026 · 0 citationsbioRxiv
MicroscopyMatching: Towards a Ready-to-use Framework for Microscopy Image Analysis in Diverse Conditions2605.14980v1 · Xiaofei Hui, Haoxuan Qu, Hossein Rahmani et al.2026 · 0 citationsarXiv
Hierarchical X-ray microscopy and mesoscopic diffusion MRI in the same brain reveal the human connectome across scales10.64898/2026.04.02.716198v1 · Chourrout, M., Gong, T., Schalek, R. 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
Sparse Graph Reconstruction and Seriation for Large-Scale Image Stacks2509.23084v2 · Fuming Yang, Yaron Meirovitch, Jeff W. Lichtman2025 · 0 citationsarXiv
TriSAM: Tri-Plane SAM for Zero-Shot Cortical Blood Vessel Segmentation in VEM Images.40489282 · Wan, Jia, Li, Wanhua, Adhinarta, Jason Ken et al.2025 · 14 citationsIEEE journal of biomedical and health informatics. 2025;29(11):8246-8255
Towards 1000-fold Electron Microscopy Image Compression for Connectomics via VQ-VAE with Transformer Prior2511.00231v2 · Fuming Yang, Yicong Li, Hanspeter Pfister et al.2025 · 0 citationsarXiv
Structured Sampling of Molecularly Classified Mossy Fiber Inputs by Cerebellar Granule Cells10.1101/2025.10.02.679866v1 · Han, X., Meral, E. S., Lichtman, J. W.2025 · 1 citationbioRxiv
Budgeted Broadcast: An Activity-Dependent Pruning Rule for Neural Network Efficiency2510.01263v1 · Yaron Meirovitch, Fuming Yang, Jeff Lichtman et al.2025 · 0 citationsarXiv
Human brain organoids record the passage of time over multiple years in culture10.1101/2025.10.01.679721v1 · Faravelli, I., Anton-Bolanos, N., Wei, A. et al.2025 · 11 citationsbioRxiv
Developmental Connectomics of the Mouse Cerebellum10.1101/2025.09.15.676403v1 · Dhanyasi, N., Meirovitch, Y., Kapoor, V. et al.2025 · 2 citationsbioRxiv
Paired and solitary ionocytes in the zebrafish olfactory epithelium.40810206 · Peloggia, Julia, Cheung, King Yee, Petkova, Mariela D et al.2025 · 2 citationsChemical senses. 2025;50
Publisher Correction: Tutorial: avoiding and correcting sample-induced spherical aberration artifacts in 3D fluorescence microscopy.33268884 · Diel, Erin E, Lichtman, Jeff W, Richardson, Douglas S2025 · 3 citationsNature protocols. 2021;16(7):3736
Fishexplorer: A multimodal cellular atlas platform for neuronal circuit dissection in larval zebrafish10.1101/2025.07.14.664689v1 · Vohra, S. K., Eberle, M., Boulanger-Weill, J. 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
Paired and solitary ionocytes in the zebrafish olfactory epithelium10.1101/2024.11.08.620918v3 · Peloggia, J., Cheung, K. Y., Petkova, M. et al.2024 · 4 citationsbioRxiv
Connectome analysis of a cerebellum-like circuit for sensory prediction10.1101/2025.07.03.662989v1 · Perks, K. E., Petkova, M. D., Muller, S. Z. et al.2025 · 2 citationsbioRxiv
Correlative light and electron microscopy reveals the fine circuit structure underlying evidence accumulation in larval zebrafish10.1101/2025.03.14.643363v2 · Boulanger-Weill, J., Kaempf, F., Schuhknecht, G. F. P. et al.2025 · 10 citationsbioRxiv
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
Lrrns define a visual circuit underlying brightness and contrast perception10.1101/2025.05.05.652281v1 · Putti, E., Faini, G., Dang, J. T.-M. et al.2025 · 1 citationbioRxiv
ZAPBench: A Benchmark for Whole-Brain Activity Prediction in Zebrafish2503.02618v1 · Jan-Matthis Lueckmann, Alexander Immer, Alex Bo-Yuan Chen et al.2025 · 1 citationarXiv
Improved tools for the Brainbow toolbox.23817127 · Cai, Dawen, Cohen, Kimberly B, Luo, Tuanlian et al.2025 · 471 citationsNature methods. 2013;10(6):540-7
Forecasting Whole-Brain Neuronal Activity from Volumetric Video2503.00073v1 · Alexander Immer, Jan-Matthis Lueckmann, Alex Bo-Yuan Chen et al.2025 · 0 citationsarXiv
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
Cellular and synaptic organization of the Octopus vertical lobe10.1101/2025.01.29.635406v1 · Bidel, F., Meirovitch, Y., Yang, F. et al.2025 · 1 citationbioRxiv
High-throughput ultrastructural analysis of macular telangiectasia type 2.39140090 · Zucker, Charles L, Bernstein, Paul S, Schalek, Richard L et al.2024 · 4 citationsFrontiers in ophthalmology. 2024;4:1428777
A neural algorithm for computing bipartite matchings.39226341 · Dasgupta, Sanjoy, Meirovitch, Yaron, Zheng, Xingyu et al.2024 · 2 citationsProceedings of the National Academy of Sciences of the United States of America. 2024;121(37):e2321032121
TISSUE CLEARING.35128463 · Richardson, Douglas S, Guan, Webster, Matsumoto, Katsuhiko et al.2024 · 197 citationsNature reviews. Methods primers. 2021;1(1)
TriSAM: Tri-Plane SAM for zero-shot cortical blood vessel segmentation in VEM images2401.13961v4 · Jia Wan, Wanhua Li, Jason Ken Adhinarta et al.2024 · 14 citationsarXiv
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
Two-stage error detection to improve electron microscopy image mosaicking.38909449 · Shi, Jiahao, Ge, Hongyu, Wang, Shuohong et al.2024 · 2 citationsComputers in biology and medicine. 2024;178:108456
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
MitoEM Dataset: Large-scale 3D Mitochondria Instance Segmentation from EM Images.33283212 · Wei, Donglai, Lin, Zudi, Franco-Barranco, Daniel et al.2024 · 118 citationsMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention. 2020;12265:66-76
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
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