mlsanityData to 14 Oct 2026

Superhuman Accuracy on the SNEMI3D Connectomics Challenge

arXiv 1706.00120 ↗First posted 31 May 2017cs.CVcited by 64

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Abstract (arXiv)

For the past decade, convolutional networks have been used for 3D reconstruction of neurons from electron microscopic (EM) brain images. Recent years have seen great improvements in accuracy, as evidenced by submissions to the SNEMI3D benchmark challenge. Here we report the first submission to surpass the estimate of human accuracy provided by the SNEMI3D leaderboard. A variant of 3D U-Net is trained on a primary task of predicting affinities between nearest neighbor voxels, and an auxiliary task of predicting long-range affinities. The training data is augmented by simulated image defects. The nearest neighbor affinities are used to create an oversegmentation, and then supervoxels are greedily agglomerated based on mean affinity. The resulting SNEMI3D score exceeds the estimate of human accuracy by a large margin. While one should be cautious about extrapolating from the SNEMI3D benchmark to real-world accuracy of large-scale neural circuit reconstruction, our result inspires optimism that the goal of full automation may be realizable in the future.

Key facts. Cited by 64 papers in the map (data through 14 Oct 2026). First posted on arXiv 31 May 2017.

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Citing papers per year: 2021: 17; 2022: 10; 2023: 8; 2024: 11; 2025: 10; 2026: 8.

64 papers.

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  1. 2022Harmonizing the object recognition strategies of deep neural networks with humanscited by 59
  2. 2021Deep Implicit Statistical Shape Models for 3D Medical Image Delineationcited by 26
  3. 2023Self-Supervised Neuron Segmentation with Multi-Agent Reinforcement Learningcited by 19
  4. 2023Learning Multiscale Consistency for Self-supervised Electron Microscopy Instance Segmentationcited by 16
  5. 2024The 3D-PC: a benchmark for visual perspective taking in humans and machinescited by 16
  6. 2024Understanding Visual Feature Reliance through the Lens of Complexitycited by 15
  7. 2024Deep Rib Fracture Instance Segmentation and Classification from CT on the RibFrac Challengecited by 14
  8. 2022Deep Lake: a Lakehouse for Deep Learningcited by 13
  9. 2021NucMM Dataset: 3D Neuronal Nuclei Instance Segmentation at Sub-Cubic Millimeter Scalecited by 12
  10. 2021AxonEM Dataset: 3D Axon Instance Segmentation of Brain Cortical Regionscited by 11
  11. 2021Sparse Object-level Supervision for Instance Segmentation with Pixel Embeddingscited by 10
  12. 2021Advanced Deep Networks for 3D Mitochondria Instance Segmentationcited by 8
38 more
  1. 2022An Analysis on Ensemble Learning optimized Medical Image Classification with Deep Convolutional Neural Networkscited by 8
  2. 2024GOV-NeSF: Generalizable Open-Vocabulary Neural Semantic Fieldscited by 8
  3. 2021How Shift Equivariance Impacts Metric Learning for Instance Segmentationcited by 7
  4. 2023MTNeuro: A Benchmark for Evaluating Representations of Brain Structure Across Multiple Levels of Abstractioncited by 7
  5. 2024TokenUnify: Scaling Up Autoregressive Pretraining for Neuron Segmentationcited by 7
  6. 2025Does DINOv3 Set a New Medical Vision Standard? Benchmarking 2D and 3D Classification, Segmentation, and Registrationcited by 7
  7. 2022Segmentation in large-scale cellular electron microscopy with deep learning: A literature surveycited by 6
  8. 2023Self-supervised learning via inter-modal reconstruction and feature projection networks for label-efficient 3D-to-2D segmentationcited by 5
  9. 2021Automatic Volumetric Segmentation of Additive Manufacturing Defects with 3D U-Netcited by 4
  10. 2022Asymmetry Disentanglement Network for Interpretable Acute Ischemic Stroke Infarct Segmentation in Non-Contrast CT Scanscited by 4
  11. 2024Learning Multimodal Volumetric Features for Large-Scale Neuron Tracingcited by 4
  12. 2024HResFormer: Hybrid Residual Transformer for Volumetric Medical Image Segmentationcited by 4
  13. 2025H3DE-Net: Efficient and Accurate 3D Landmark Detection in Medical Imagingcited by 4
  14. 2021Consistent Recurrent Neural Networks for 3D Neuron Segmentationcited by 3
  15. 2021Voxel-level Siamese Representation Learning for Abdominal Multi-Organ Segmentationcited by 3
  16. 2021PyTorch Connectomics: A Scalable and Flexible Segmentation Framework for EM Connectomicscited by 3
  17. 2022Instance Segmentation of Unlabeled Modalities via Cyclic Segmentation GANcited by 3
  18. 2022Scan2Part: Fine-grained and Hierarchical Part-level Understanding of Real-World 3D Scanscited by 3
  19. 2022Mixed Supervision of Histopathology Improves Prostate Cancer Classification from MRIcited by 3
  20. 2023AxonCallosumEM Dataset: Axon Semantic Segmentation of Whole Corpus Callosum cross section from EM Imagescited by 3
  21. 2024Deep Multimodal Fusion of Data with Heterogeneous Dimensionality via Projective Networkscited by 3
  22. 2024ShapeMamba-EM: Fine-Tuning Foundation Model with Local Shape Descriptors and Mamba Blocks for 3D EM Image Segmentationcited by 3
  23. 2021Contrastive Learning for Mitochondria Segmentationcited by 2
  24. 2021Sub-cortical structure segmentation database for young populationcited by 2
  25. 2021PATO: Producibility-Aware Topology Optimization using Deep Learning for Metal Additive Manufacturingcited by 2
  26. 2022MISm: A Medical Image Segmentation Metric for Evaluation of weak labeled Datacited by 2
  27. 20233D Mitochondria Instance Segmentation with Spatio-Temporal Transformerscited by 2
  28. 2023Domain Adaptive Synapse Detection with Weak Point Annotationscited by 2
  29. 2021Bridging the Gap: Point Clouds for Merging Neurons in Connectomicscited by 1
  30. 2022DeepSTI: Towards Tensor Reconstruction using Fewer Orientations in Susceptibility Tensor Imagingcited by 1
  31. 2023The XPRESS Challenge: Xray Projectomic Reconstruction -- Extracting Segmentation with Skeletonscited by 1
  32. 2024DaCapo: a modular deep learning framework for scalable 3D image segmentationcited by 1
  33. 2024Efficient Slice Anomaly Detection Network for 3D Brain MRI Volumecited by 1
  34. 2025A Novel Convolutional-Free Method for 3D Medical Imaging Segmentationcited by 1
  35. 2025Dual form Complementary Masking for Domain-Adaptive Image Segmentationcited by 1
  36. 2025Deep Biomechanically-Guided Interpolation for Keypoint-Based Brain Shift Registrationcited by 1
  37. 2025Fast 3D Surrogate Modeling for Data Center Thermal Managementcited by 1
  38. 2025FGNet: Leveraging Feature-Guided Attention to Refine SAM2 for 3D EM Neuron Segmentationcited by 1

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