# FGNet: Leveraging Feature-Guided Attention to Refine SAM2 for 3D EM Neuron Segmentation

arXiv: https://arxiv.org/abs/2511.13063 · HTML: https://mlsanity.com/paper/2511.13063/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 35 references that are in the map.
- First posted on arXiv 17 Nov 2025.

## Builds on (most cited first, 15 of 15)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [CBAM: Convolutional Block Attention Module](https://mlsanity.com/paper/1807.06521/) (2018)
- [Masked-attention Mask Transformer for Universal Image Segmentation](https://mlsanity.com/paper/2112.01527/) (2021)
- [Non-local Neural Networks](https://mlsanity.com/paper/1711.07971/) (2017)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Dual Attention Network for Scene Segmentation](https://mlsanity.com/paper/1809.02983/) (2018)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [ECA-Net: Efficient Channel Attention for Deep Convolutional Neural Networks](https://mlsanity.com/paper/1910.03151/) (2019)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [Superhuman Accuracy on the SNEMI3D Connectomics Challenge](https://mlsanity.com/paper/1706.00120/) (2017)
- [Look Closer to Segment Better: Boundary Patch Refinement for Instance Segmentation](https://mlsanity.com/paper/2104.05239/) (2021)
- [SemiSAM: Enhancing Semi-Supervised Medical Image Segmentation via SAM-Assisted Consistency Regularization](https://mlsanity.com/paper/2312.06316/) (2023)
- [TokenUnify: Scaling Up Autoregressive Pretraining for Neuron Segmentation](https://mlsanity.com/paper/2405.16847/) (2024)
- [PyTorch Connectomics: A Scalable and Flexible Segmentation Framework for EM Connectomics](https://mlsanity.com/paper/2112.05754/) (2021)

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

- [NeuroRefiner: Morphology-Aware Multi-Agent Refinement for 3D Fluorescence Microscopy Neuron Segmentation](https://mlsanity.com/paper/2608.09636/) (2026)

## Abstract (arXiv)

Accurate segmentation of neural structures in Electron Microscopy (EM) images is paramount for neuroscience. However, this task is challenged by intricate morphologies, low signal-to-noise ratios, and scarce annotations, limiting the accuracy and generalization of existing methods. To address these challenges, we seek to leverage the priors learned by visual foundation models on a vast amount of natural images to better tackle this task. Specifically, we propose a novel framework that can effectively transfer knowledge from Segment Anything 2 (SAM2), which is pre-trained on natural images, to the EM domain. We first use SAM2 to extract powerful, general-purpose features. To bridge the domain gap, we introduce a Feature-Guided Attention module that leverages semantic cues from SAM2 to guide a lightweight encoder, the Fine-Grained Encoder (FGE), in focusing on these challenging regions. Finally, a dual-affinity decoder generates both coarse and refined affinity maps. Experimental results demonstrate that our method achieves performance comparable to state-of-the-art (SOTA) approaches with the SAM2 weights frozen. Upon further fine-tuning on EM data, our method significantly outperforms existing SOTA methods. This study validates that transferring representations pre-trained on natural images, when combined with targeted domain-adaptive guidance, can effectively address the specific challenges in neuron segmentation.