# Denoising Diffusion Models for Inpainting of Healthy Brain Tissue

arXiv: https://arxiv.org/abs/2402.17307 · HTML: https://mlsanity.com/paper/2402.17307/

## Key facts

- Cited by 13 papers in the map (data through 14 Oct 2026).
- Placed in Medical imaging and segmentation, one of 14 directions in Diffusion models.
- Builds on 11 of its 18 references that are in the map.
- First posted on arXiv 27 Feb 2024.

## Placed in

- Diffusion models / [Medical imaging and segmentation](https://mlsanity.com/diffusion/medical-imaging-and-segmentation/)

## Builds on (most cited first, 11 of 11)

- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Improved Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2102.09672/) (2021)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [Consistency Models](https://mlsanity.com/paper/2303.01469/) (2023)
- [Palette: Image-to-Image Diffusion Models](https://mlsanity.com/paper/2111.05826/) (2021)
- [The RSNA-ASNR-MICCAI BraTS 2021 Benchmark on Brain Tumor Segmentation and Radiogenomic Classification](https://mlsanity.com/paper/2107.02314/) (2021)
- [Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge](https://mlsanity.com/paper/1811.02629/) (2018)
- [Diffusion Models for Implicit Image Segmentation Ensembles](https://mlsanity.com/paper/2112.03145/) (2021)
- [MedPerf: Open Benchmarking Platform for Medical Artificial Intelligence using Federated Evaluation](https://mlsanity.com/paper/2110.01406/) (2021)
- [Memory-Efficient 3D Denoising Diffusion Models for Medical Image Processing](https://mlsanity.com/paper/2303.15288/) (2023)
- [Diffusion Models for Contrast Harmonization of Magnetic Resonance Images](https://mlsanity.com/paper/2303.08189/) (2023)

## Built on by (most cited first, 13 of 13)

- [Denoising Diffusion Models for 3D Healthy Brain Tissue Inpainting](https://mlsanity.com/paper/2403.14499/) (2024)
- [fastWDM3D: Fast and Accurate 3D Healthy Tissue Inpainting](https://mlsanity.com/paper/2507.13146/) (2025)
- [Brain Tumour Removing and Missing Modality Generation using 3D WDM](https://mlsanity.com/paper/2411.04630/) (2024)
- [Exploring Robustness of Cortical Morphometry in the presence of white matter lesions, using Diffusion Models for Lesion Filling](https://mlsanity.com/paper/2503.20571/) (2025)
- [CADD: Context aware disease deviations via restoration of brain images using normative conditional diffusion models](https://mlsanity.com/paper/2508.03594/) (2025)
- [Generating healthy counterfactuals with denoising diffusion bridge models](https://mlsanity.com/paper/2510.13684/) (2025)
- [Deep generative priors for 3D brain analysis](https://mlsanity.com/paper/2510.15119/) (2025)
- [Deep Generative Models for Enhanced Vitreous OCT Imaging](https://mlsanity.com/paper/2511.00881/) (2025)
- [KAO: Kernel-Adaptive Optimization in Diffusion for Satellite Image](https://mlsanity.com/paper/2511.02462/) (2025)
- [BrainNormalizer: Anatomy-Informed Pseudo-Healthy Brain Reconstruction from Tumor MRI via Edge-Guided ControlNet](https://mlsanity.com/paper/2511.12853/) (2025)
- [Unified Multi-Site Multi-Sequence Brain MRI Harmonization Enriched by Biomedical Semantic Style](https://mlsanity.com/paper/2601.08193/) (2026)
- [Local Label-Informed Feature Transfer for Generating Ground-Truth Medical Images: A Comparison of GAN- and Diffusion-Based Approaches](https://mlsanity.com/paper/2607.18882/) (2026)
- [Diffusion Models in Medical Image Inpainting: Challenges, Solution Taxonomy, and Future Directions](https://mlsanity.com/paper/2607.21904/) (2026)

## Abstract (arXiv)

This paper is a contribution to the "BraTS 2023 Local Synthesis of Healthy Brain Tissue via Inpainting Challenge". The task of this challenge is to transform tumor tissue into healthy tissue in brain magnetic resonance (MR) images. This idea originates from the problem that MR images can be evaluated using automatic processing tools, however, many of these tools are optimized for the analysis of healthy tissue. By solving the given inpainting task, we enable the automatic analysis of images featuring lesions, and further downstream tasks. Our approach builds on denoising diffusion probabilistic models. We use a 2D model that is trained using slices in which healthy tissue was cropped out and is learned to be inpainted again. This allows us to use the ground truth healthy tissue during training. In the sampling stage, we replace the slices containing diseased tissue in the original 3D volume with the slices containing the healthy tissue inpainting. With our approach, we achieve comparable results to the competing methods. On the validation set our model achieves a mean SSIM of 0.7804, a PSNR of 20.3525 and a MSE of 0.0113. In future we plan to extend our 2D model to a 3D model, allowing to inpaint the region of interest as a whole without losing context information of neighboring slices.