# ConnectomeBench2: A Unified Benchmark for Automated Connectomic Proofreading

arXiv: https://arxiv.org/abs/2606.21116 · HTML: https://mlsanity.com/paper/2606.21116/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 47 references that are in the map.
- First posted on arXiv 19 Jun 2026.

## Builds on (most cited first, 18 of 18)

- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [A Simple Unified Framework for Detecting Out-of-Distribution Samples and Adversarial Attacks](https://mlsanity.com/paper/1807.03888/) (2018)
- [How transferable are features in deep neural networks?](https://mlsanity.com/paper/1411.1792/) (2014)
- [Big Transfer (BiT): General Visual Representation Learning](https://mlsanity.com/paper/1912.11370/) (2019)
- [Deep Batch Active Learning by Diverse, Uncertain Gradient Lower Bounds](https://mlsanity.com/paper/1906.03671/) (2019)
- [Measuring Calibration in Deep Learning](https://mlsanity.com/paper/1904.01685/) (2019)
- [Gone Fishing: Neural Active Learning with Fisher Embeddings](https://mlsanity.com/paper/2106.09675/) (2021)
- [Synaptic Cleft Segmentation in Non-Isotropic Volume Electron Microscopy of the Complete Drosophila Brain](https://mlsanity.com/paper/1805.02718/) (2018)
- [Guided Proofreading of Automatic Segmentations for Connectomics](https://mlsanity.com/paper/1704.00848/) (2017)
- [Synaptic Partner Assignment Using Attentional Voxel Association Networks](https://mlsanity.com/paper/1904.09947/) (2019)
- [An Error Detection and Correction Framework for Connectomics](https://mlsanity.com/paper/1708.02599/) (2017)
- [Learning Multimodal Volumetric Features for Large-Scale Neuron Tracing](https://mlsanity.com/paper/2401.03043/) (2024)
- [A Multi-Pass Approach to Large-Scale Connectomics](https://mlsanity.com/paper/1612.02120/) (2016)
- [RLCorrector: Reinforced Proofreading for Cell-level Microscopy Image Segmentation](https://mlsanity.com/paper/2106.05487/) (2021)
- [ConnectomeBench: Can LLMs Proofread the Connectome?](https://mlsanity.com/paper/2511.05542/) (2025)
- [Morphological Error Detection in 3D Segmentations](https://mlsanity.com/paper/1705.10882/) (2017)
- [Bridging the Gap: Point Clouds for Merging Neurons in Connectomics](https://mlsanity.com/paper/2112.02039/) (2021)
- [Autoproof: Automated Segmentation Proofreading for Connectomics](https://mlsanity.com/paper/2509.26585/) (2025)

## Built on by (most cited first, 1 of 1)

- [Benchmarking Vision-Language Models on Synapse Detection and Proofreading in Connectomics](https://mlsanity.com/paper/2609.36492/) (2026)

## Abstract (arXiv)

Proofreading--correcting segmentation errors in 3D brain reconstructions--is the rate-limiting step in synapse-resolution connectomics. We release ConnectomeBench2, a unified multi-species dataset of over 716,485 expert-labeled proofreading decisions with >4,500,000 associated images spanning four major open connectomes (mouse, human, zebrafish, fly), spanning both split and merge error correction. Trained on this dataset, a single Vision Transformer with shared encoders for mesh geometry and electron microscopy reaches human-level accuracy across species for split error correction and merge error identification, with performance scaling with data size and modality. Beyond accuracy, we show that the model is well-calibrated within distribution, that measures of distribution distance predict where calibration and accuracy will degrade on unseen data, and that connectomics-specific pretraining and active learning-based sample selection show potential to substantially reduce the labeling effort needed to extend to new species and brain regions. The benchmark provides the infrastructure to train and evaluate increasingly capable vision models for connectomic proofreading. Data and code availability. The ConnectomeBench2 dataset is released on Hugging Face at https://huggingface.co/datasets/jeffbbrown2/ConnectomeBench2. The accompanying codebase is available on GitHub at https://github.com/timfarkas/ConnectomeBench2.