# Probe-EM: Targeted Neuron Tracing via Training-Free Semantic Verification

arXiv: https://arxiv.org/abs/2607.04696 · HTML: https://mlsanity.com/paper/2607.04696/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 22 references that are in the map.
- First posted on arXiv 6 Jul 2026.

## Builds on (most cited first, 4 of 4)

- [PointNet: Deep Learning on Point Sets for 3D Classification and Segmentation](https://mlsanity.com/paper/1612.00593/) (2016)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [Superhuman Accuracy on the SNEMI3D Connectomics Challenge](https://mlsanity.com/paper/1706.00120/) (2017)
- [Learning Multimodal Volumetric Features for Large-Scale Neuron Tracing](https://mlsanity.com/paper/2401.03043/) (2024)

## Abstract (arXiv)

Establishing large-scale, high-resolution neural connectivity maps is fundamental to elucidating the structural basis of brain function. However, when processing terabyte- or petabyte-scale electron microscopy data, over-segmentation inherent in automated reconstruction algorithms remains a critical bottleneck, requiring extensive manual proofreading spanning person-years. To alleviate the heavy reliance on annotated data and the limited flexibility of conventional tracing methods, we propose a training-free, targeted neuron tracing framework. Specifically, we introduce a skeleton-guided Heuristic Spatial Search paradigm that leverages geometric priors to iteratively reconstruct neuronal morphologies through a probing-verification cycle. To achieve robust zero-shot semantic verification, we further develop a Dimension-Aware Semantic Verification strategy built upon the foundation model NeuroSAM 2. This strategy resolves intra-slice splits via Planar Ensemble Consensus and inter-slice splits via Axial Spatio-Temporal Propagation. Notably, we integrate the proposed workflow into the Neuroglancer visualization platform, enabling an interactive human-in-the-loop proofreading system. Experimental results demonstrate that the proposed method outperforms supervised baselines and reduces manual proofreading time by 33.4%. The source code is publicly available at https://github.com/HeadLiuYun/Probe-EM.