# Pixel Embedding Method for Tubular Neurite Segmentation

arXiv: https://arxiv.org/abs/2507.23359 · HTML: https://mlsanity.com/paper/2507.23359/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 32 references that are in the map.
- First posted on arXiv 31 Jul 2025.

## Builds on (most cited first, 13 of 13)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [Deformable Convolutional Networks](https://mlsanity.com/paper/1703.06211/) (2017)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [Dilated Residual Networks](https://mlsanity.com/paper/1705.09914/) (2017)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [ResUNet-a: a deep learning framework for semantic segmentation of remotely sensed data](https://mlsanity.com/paper/1904.00592/) (2019)
- [A Topological Loss Function for Deep-Learning based Image Segmentation using Persistent Homology](https://mlsanity.com/paper/1910.01877/) (2019)
- [Semantic Instance Segmentation with a Discriminative Loss Function](https://mlsanity.com/paper/1708.02551/) (2017)
- [DUNet: A deformable network for retinal vessel segmentation](https://mlsanity.com/paper/1811.01206/) (2018)
- [Dynamic Snake Convolution based on Topological Geometric Constraints for Tubular Structure Segmentation](https://mlsanity.com/paper/2307.08388/) (2023)
- [Deep Distance Transform for Tubular Structure Segmentation in CT Scans](https://mlsanity.com/paper/1912.03383/) (2019)

## Abstract (arXiv)

Automatic segmentation of neuronal topology is critical for handling large scale neuroimaging data, as it can greatly accelerate neuron annotation and analysis. However, the intricate morphology of neuronal branches and the occlusions among fibers pose significant challenges for deep learning based segmentation. To address these issues, we propose an improved framework: First, we introduce a deep network that outputs pixel level embedding vectors and design a corresponding loss function, enabling the learned features to effectively distinguish different neuronal connections within occluded regions. Second, building on this model, we develop an end to end pipeline that directly maps raw neuronal images to SWC formatted neuron structure trees. Finally, recognizing that existing evaluation metrics fail to fully capture segmentation accuracy, we propose a novel topological assessment metric to more appropriately quantify the quality of neuron segmentation and reconstruction. Experiments on our fMOST imaging dataset demonstrate that, compared to several classical methods, our approach significantly reduces the error rate in neuronal topology reconstruction.