# NeuroRefiner: Morphology-Aware Multi-Agent Refinement for 3D Fluorescence Microscopy Neuron Segmentation

arXiv: https://arxiv.org/abs/2608.09636 · HTML: https://mlsanity.com/paper/2608.09636/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 30 of its 57 references that are in the map.
- First posted on arXiv 10 Aug 2026.

## Builds on (most cited first, 30 of 30)

- [High-Resolution Image Synthesis with Latent Diffusion Models](https://mlsanity.com/paper/2112.10752/) (2021)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Qwen2.5-VL Technical Report](https://mlsanity.com/paper/2502.13923/) (2025)
- [Adding Conditional Control to Text-to-Image Diffusion Models](https://mlsanity.com/paper/2302.05543/) (2023)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [Qwen3-VL Technical Report](https://mlsanity.com/paper/2511.21631/) (2025)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [InternVL3: Exploring Advanced Training and Test-Time Recipes for Open-Source Multimodal Models](https://mlsanity.com/paper/2504.10479/) (2025)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Qwen3 Embedding: Advancing Text Embedding and Reranking Through Foundation Models](https://mlsanity.com/paper/2506.05176/) (2025)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images](https://mlsanity.com/paper/2201.01266/) (2022)
- [DiffEdit: Diffusion-based semantic image editing with mask guidance](https://mlsanity.com/paper/2210.11427/) (2022)
- [nnFormer: Interleaved Transformer for Volumetric Segmentation](https://mlsanity.com/paper/2109.03201/) (2021)
- [SegFix: Model-Agnostic Boundary Refinement for Segmentation](https://mlsanity.com/paper/2007.04269/) (2020)
- [MedSAM2: Segment Anything in 3D Medical Images and Videos](https://mlsanity.com/paper/2504.03600/) (2025)
- [Mask Transfiner for High-Quality Instance Segmentation](https://mlsanity.com/paper/2111.13673/) (2021)
- [Iteratively-Refined Interactive 3D Medical Image Segmentation with Multi-Agent Reinforcement Learning](https://mlsanity.com/paper/1911.10334/) (2019)
- [SegRefiner: Towards Model-Agnostic Segmentation Refinement with Discrete Diffusion Process](https://mlsanity.com/paper/2312.12425/) (2023)
- [Towards Segment Anything Model (SAM) for Medical Image Segmentation: A Survey](https://mlsanity.com/paper/2305.03678/) (2023)
- [Self-Supervised Neuron Segmentation with Multi-Agent Reinforcement Learning](https://mlsanity.com/paper/2310.04148/) (2023)
- [VoxTell: Free-Text Promptable Universal 3D Medical Image Segmentation](https://mlsanity.com/paper/2511.11450/) (2025)
- [Boundary-aware Supervoxel-level Iteratively Refined Interactive 3D Image Segmentation with Multi-agent Reinforcement Learning](https://mlsanity.com/paper/2303.10692/) (2023)
- [IBISAgent: Reinforcing Pixel-Level Visual Reasoning in MLLMs for Universal Biomedical Object Referring and Segmentation](https://mlsanity.com/paper/2601.03054/) (2026)
- [Single Neuron Segmentation using Graph-based Global Reasoning with Auxiliary Skeleton Loss from 3D Optical Microscope Images](https://mlsanity.com/paper/2101.08910/) (2021)
- [Learning Shape Representation on Sparse Point Clouds for Volumetric Image Segmentation](https://mlsanity.com/paper/1906.02281/) (2019)
- [PointNeuron: 3D Neuron Reconstruction via Geometry and Topology Learning of Point Clouds](https://mlsanity.com/paper/2210.08305/) (2022)
- [NRTR: Neuron Reconstruction with Transformer from 3D Optical Microscopy Images](https://mlsanity.com/paper/2212.04163/) (2022)
- [FGNet: Leveraging Feature-Guided Attention to Refine SAM2 for 3D EM Neuron Segmentation](https://mlsanity.com/paper/2511.13063/) (2025)
- [NeuroMamba: Multi-Perspective Feature Interaction with Visual Mamba for Neuron Segmentation](https://mlsanity.com/paper/2601.15929/) (2026)

## Abstract (arXiv)

Accurate 3D neuron segmentation in fluorescence microscopy is critical for neuroscience. However, the sparse and elongated morphology of neurons poses significant challenges to existing segmentation methods. These methods struggle to preserve both local details and global topology, leading to fragmented results. To address this, we propose NeuroRefiner, a multi-agent system that formalizes the human expert workflow involving iterative global observation and local editing. Specifically, NeuroRefiner comprises three collaborative agents dedicated to diagnosing topological errors, generating correction instructions, and validating refinement quality. To facilitate agent instruction-guided segmentation refinement, we propose TopoRefineNet, a dedicated 3D U-Net-based tool that leverages cross-modality feature fusion to generate refined masks. Through multi-round agent reasoning and voxel-level editing, NeuroRefiner produces topologically more accurate segmentations with enhanced interpretability. Experiments on the BigNeuron, CWMBS, and ZBFWB datasets demonstrate that NeuroRefiner outperforms state-of-the-art methods, notably achieving a 3.02% improvement in F1 score on the challenging ZBFWB dataset.