# FleXray: Universal Clinical X-ray Segmentation

arXiv: https://arxiv.org/abs/2609.26756 · HTML: https://mlsanity.com/paper/2609.26756/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 29 of its 100 references that are in the map.
- First posted on arXiv 22 Sep 2026.

## Builds on (most cited first, 29 of 29)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Microsoft COCO: Common Objects in Context](https://mlsanity.com/paper/1405.0312/) (2014)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [LVIS: A Dataset for Large Vocabulary Instance Segmentation](https://mlsanity.com/paper/1908.03195/) (2019)
- [TotalSegmentator: robust segmentation of 104 anatomical structures in CT images](https://mlsanity.com/paper/2208.05868/) (2022)
- [Exploring the Limits of Weakly Supervised Pretraining](https://mlsanity.com/paper/1805.00932/) (2018)
- [SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining](https://mlsanity.com/paper/2107.09559/) (2021)
- [Kornia: an Open Source Differentiable Computer Vision Library for PyTorch](https://mlsanity.com/paper/1910.02190/) (2019)
- [Better Aggregation in Test-Time Augmentation](https://mlsanity.com/paper/2011.11156/) (2020)
- [RoentGen: Vision-Language Foundation Model for Chest X-ray Generation](https://mlsanity.com/paper/2211.12737/) (2022)
- [TotalSegmentator MRI: Robust Sequence-independent Segmentation of Multiple Anatomic Structures in MRI](https://mlsanity.com/paper/2405.19492/) (2024)
- [DeepDRR -- A Catalyst for Machine Learning in Fluoroscopy-guided Procedures](https://mlsanity.com/paper/1803.08606/) (2018)
- [Fast Auto-Differentiable Digitally Reconstructed Radiographs for Solving Inverse Problems in Intraoperative Imaging](https://mlsanity.com/paper/2208.12737/) (2022)
- [Reference-guided Pseudo-Label Generation for Medical Semantic Segmentation](https://mlsanity.com/paper/2112.00735/) (2021)
- [CheXmask: a large-scale dataset of anatomical segmentation masks for multi-center chest x-ray images](https://mlsanity.com/paper/2307.03293/) (2023)
- [Automatic Annotation of Hip Anatomy in Fluoroscopy for Robust and Efficient 2D/3D Registration](https://mlsanity.com/paper/1911.07042/) (2019)
- [Learning General-Purpose Biomedical Volume Representations using Randomized Synthesis](https://mlsanity.com/paper/2411.02372/) (2024)
- [Accurate Fine-Grained Segmentation of Human Anatomy in Radiographs via Volumetric Pseudo-Labeling](https://mlsanity.com/paper/2306.03934/) (2023)
- [VinDr-RibCXR: A Benchmark Dataset for Automatic Segmentation and Labeling of Individual Ribs on Chest X-rays](https://mlsanity.com/paper/2107.01327/) (2021)
- [The Impact of Machine Learning on 2D/3D Registration for Image-guided Interventions: A Systematic Review and Perspective](https://mlsanity.com/paper/2108.02238/) (2021)
- [GAN-based Data Augmentation for Chest X-ray Classification](https://mlsanity.com/paper/2107.02970/) (2021)
- [Deep Learning Based Rib Centerline Extraction and Labeling](https://mlsanity.com/paper/1809.07082/) (2018)
- [Pose Estimation of Periacetabular Osteotomy Fragments with Intraoperative X-Ray Navigation](https://mlsanity.com/paper/1903.09339/) (2019)
- [FluoroSAM: A Language-promptable Foundation Model for Flexible X-ray Image Segmentation](https://mlsanity.com/paper/2403.08059/) (2024)
- [RayEmb: Arbitrary Landmark Detection in X-Ray Images Using Ray Embedding Subspace](https://mlsanity.com/paper/2410.08152/) (2024)
- [RAM-W600: A Multi-Task Wrist Dataset and Benchmark for Rheumatoid Arthritis](https://mlsanity.com/paper/2507.05193/) (2025)
- [AnyCXR: Human Anatomy Segmentation of Chest X-ray at Any Acquisition Position using Multi-stage Domain Randomized Synthetic Data with Imperfect Annotations and Conditional Joint Annotation Regularization Learning](https://mlsanity.com/paper/2512.17263/) (2025)
- [Scaling Generative Foundation Models for Chest Radiography with Rectified Flow Transformers](https://mlsanity.com/paper/2606.19460/) (2026)

## Abstract (arXiv)

X-ray is medicine's most widely used imaging modality, yet remains among its least quantitative. Unlike volumetric modalities like CT or MRI, X-ray collapses 3D anatomy into a 2D projection, causing structures to overlap and anatomical boundaries to be ambiguous, even to experts. As a result, labeling X-ray databases for training general-purpose segmentation systems is impractical, leaving morphometric and functional X-ray analysis confined to narrow anatomical regions and applications. To this end, we present FleXray, a generalist model for anatomical segmentation across the entire body in clinical X-rays. Instead of curating large, manually annotated X-ray datasets, we build a scalable, physics-based generative X-ray data engine. Using existing 3D whole-body CT segmentation datasets and generative image-editing models, we simulate fully-annotated 2D X-rays with diverse appearances, physiological properties, and imaging geometries. Trained on these simulations, FleXray accurately segments 60 anatomical structures across unseen research datasets and in-the-wild X-rays. We further show that FleXray makes X-rays directly amenable to quantitative analysis, enabling automated measurements for disease grading, robust navigation during X-ray-guided interventions, and data-efficient learning of pathological targets. We release the model, code, a full-body X-ray segmentation dataset, and a local, easy-to-use browser-based tool at https://flexray.csail.mit.edu .