# NRTR: Neuron Reconstruction with Transformer from 3D Optical Microscopy Images

arXiv: https://arxiv.org/abs/2212.04163 · HTML: https://mlsanity.com/paper/2212.04163/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 13 of its 37 references that are in the map.
- First posted on arXiv 8 Dec 2022.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [Feature Pyramid Networks for Object Detection](https://mlsanity.com/paper/1612.03144/) (2016)
- [Deformable DETR: Deformable Transformers for End-to-End Object Detection](https://mlsanity.com/paper/2010.04159/) (2020)
- [Generalized Intersection over Union: A Metric and A Loss for Bounding Box Regression](https://mlsanity.com/paper/1902.09630/) (2019)
- [Multi-Task Learning Using Uncertainty to Weigh Losses for Scene Geometry and Semantics](https://mlsanity.com/paper/1705.07115/) (2017)
- [Image Transformer](https://mlsanity.com/paper/1802.05751/) (2018)
- [Conditional DETR for Fast Training Convergence](https://mlsanity.com/paper/2108.06152/) (2021)
- [Hidden Markov Modeling for Maximum Likelihood Neuron Reconstruction](https://mlsanity.com/paper/2106.02701/) (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)

The neuron reconstruction from raw Optical Microscopy (OM) image stacks is the basis of neuroscience. Manual annotation and semi-automatic neuron tracing algorithms are time-consuming and inefficient. Existing deep learning neuron reconstruction methods, although demonstrating exemplary performance, greatly demand complex rule-based components. Therefore, a crucial challenge is designing an end-to-end neuron reconstruction method that makes the overall framework simpler and model training easier. We propose a Neuron Reconstruction Transformer (NRTR) that, discarding the complex rule-based components, views neuron reconstruction as a direct set-prediction problem. To the best of our knowledge, NRTR is the first image-to-set deep learning model for end-to-end neuron reconstruction. In experiments using the BigNeuron and VISoR-40 datasets, NRTR achieves excellent neuron reconstruction results for comprehensive benchmarks and outperforms competitive baselines. Results of extensive experiments indicate that NRTR is effective at showing that neuron reconstruction is viewed as a set-prediction problem, which makes end-to-end model training available.