# Anatomical Priors for Image Segmentation via Post-Processing with Denoising Autoencoders

arXiv: https://arxiv.org/abs/1906.02343 · HTML: https://mlsanity.com/paper/1906.02343/

## Key facts

- Cited by 14 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 5 Jun 2019.

## Built on by (most cited first, 14 of 14)

- [Improving anatomical plausibility in medical image segmentation via hybrid graph neural networks: applications to chest x-ray analysis](https://mlsanity.com/paper/2203.10977/) (2022)
- [Medical Image Segmentation with Limited Supervision: A Review of Deep Network Models](https://mlsanity.com/paper/2103.00429/) (2021)
- [Hybrid graph convolutional neural networks for landmark-based anatomical segmentation](https://mlsanity.com/paper/2106.09832/) (2021)
- [Cooperative Training and Latent Space Data Augmentation for Robust Medical Image Segmentation](https://mlsanity.com/paper/2107.01079/) (2021)
- [Temporally Constrained Neural Networks (TCNN): A framework for semi-supervised video semantic segmentation](https://mlsanity.com/paper/2112.13815/) (2021)
- [Synergy Between Semantic Segmentation and Image Denoising via Alternate Boosting](https://mlsanity.com/paper/2102.12095/) (2021)
- [Source-Free Unsupervised Domain Adaptation with Norm and Shape Constraints for Medical Image Segmentation](https://mlsanity.com/paper/2209.01300/) (2022)
- [Striving for Simplicity: Simple Yet Effective Prior-Aware Pseudo-Labeling for Semi-Supervised Ultrasound Image Segmentation](https://mlsanity.com/paper/2503.13987/) (2025)
- [Pay Attention to the Atlas: Atlas-Guided Test-Time Adaptation Method for Robust 3D Medical Image Segmentation](https://mlsanity.com/paper/2307.00676/) (2023)
- [Semi-supervised Instance Segmentation with a Learned Shape Prior](https://mlsanity.com/paper/2309.04888/) (2023)
- [FLODCAST: Flow and Depth Forecasting via Multimodal Recurrent Architectures](https://mlsanity.com/paper/2310.20593/) (2023)
- [REN: Anatomically-Informed Mixture-of-Experts for Interstitial Lung Disease Diagnosis](https://mlsanity.com/paper/2510.04923/) (2025)
- [Mask-HybridGNet: Graph-based segmentation with emergent anatomical correspondence from pixel-level supervision](https://mlsanity.com/paper/2602.21179/) (2026)
- [Deep vessel segmentation with joint multi-prior encoding](https://mlsanity.com/paper/2409.12334/) (2024)

## Abstract (arXiv)

Deep convolutional neural networks (CNN) proved to be highly accurate to perform anatomical segmentation of medical images. However, some of the most popular CNN architectures for image segmentation still rely on post-processing strategies (e.g. Conditional Random Fields) to incorporate connectivity constraints into the resulting masks. These post-processing steps are based on the assumption that objects are usually continuous and therefore nearby pixels should be assigned the same object label. Even if it is a valid assumption in general, these methods do not offer a straightforward way to incorporate more complex priors like convexity or arbitrary shape restrictions. In this work we propose Post-DAE, a post-processing method based on denoising autoencoders (DAE) trained using only segmentation masks. We learn a low-dimensional space of anatomically plausible segmentations, and use it as a post-processing step to impose shape constraints on the resulting masks obtained with arbitrary segmentation methods. Our approach is independent of image modality and intensity information since it employs only segmentation masks for training. This enables the use of anatomical segmentations that do not need to be paired with intensity images, making the approach very flexible. Our experimental results on anatomical segmentation of X-ray images show that Post-DAE can improve the quality of noisy and incorrect segmentation masks obtained with a variety of standard methods, by bringing them back to a feasible space, with almost no extra computational time.