Zero-Shot Brain MRI Inpainting with 2.5D Unconditional Flow Priors

Arnela Hadzic; Franz Thaler; Simon Johannes Joham; Martin Urschler

Home/Archive/arXiv

arXiv · 2610.08983

Zero-Shot Brain MRI Inpainting with 2.5D Unconditional Flow Priors

Arnela Hadzic·Franz Thaler·Simon Johannes Joham·Martin Urschler

View original source ↗Read source document ↗Export metadata ↓

Abstract

Generative inpainting of brain MRI volumes is essential for synthesizing healthy tissue in pathological regions, improving the accuracy and reliability of automated downstream brain analysis applications such as image registration, brain extraction, and segmentation. However, standard 3D approaches are computationally prohibitive, while efficient 2D slice-wise methods suffer from severe inter-slice discontinuities. Furthermore, traditional models rely on conditional training, requiring task-specific learning of masked inputs. We propose a zero-shot brain MRI inpainting framework utilizing 2.5D unconditional flow priors to capture spatial context along the superior-inferior axis without the overhead of full 3D convolutions. During training, our flow matching model learns the joint distribution of adjacent axial slice triplets, modeling the manifold of healthy brain anatomy while explicitly excluding pathological regions from the loss function. At inference, the model processes the input triplets autoregressively along the depth axis. We employ the Restora-Flow solver to constrain the unconditional prior using the input mask, achieving accurate zero-shot inpainting. Evaluations show our 2.5D strategy resolves the structural discontinuities of 2D baselines, synthesizing plausible healthy tissue while maintaining volumetric consistency across the axial, sagittal, and coronal planes. As a final step, we generate and average an ensemble of multiple stochastic reconstructions to form the final prediction. Quantitative results benchmarked on the official BraTS 2026 Inpainting Challenge validation set demonstrate the effectiveness of our proposed approach, yielding an SSIM of 0.816 $\pm$ 0.112, MSE of 0.007 $\pm$ 0.005, and PSNR of 22.923 $\pm$ 4.343. Code is available at https://github.com/imigraz/brats2026-inpainting.

Explore related subjects

cs.CV

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Arnela Hadzic, Franz Thaler, Simon Johannes Joham, Martin Urschler. 2026-10-06. Zero-Shot Brain MRI Inpainting with 2.5D Unconditional Flow Priors. https://arxiv.org/abs/2610.08983

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

DetoxAI: a Python Toolkit for Debiasing Deep Learning Models in Computer Vision

While machine learning fairness has made significant progress in recent years, most existing solutions focus on tabular data and are poorly suited for vision-based classification tasks, which rely heavily on deep learning. To bridge this gap, we introduce DetoxAI, an open-source Python library for improving fairness in deep learning vision classifiers through post-hoc debiasing. DetoxAI implements state-of-the-art debiasing algorithms, fairness metrics, and visualization tools. It supports debiasing via interventions in internal representations and includes attribution-based visualization tools and quantitative algorithmic fairness metrics to show how bias is mitigated. This paper presents the motivation, design, and use cases of DetoxAI, demonstrating its tangible value to engineers and researchers.

cs.CV↗

arXiv2026

AutoExpert: Automating 3D LiDAR Annotation from Expert-Crafted Guidelines

The contemporary paradigm of scaling data annotation, crucial for developing machine learning solutions, is to hire ordinary human annotators and instruct them with expert-crafted guidelines to label data. This paradigm is laborious, tedious, and costly, motivating us to study an open problem, auto-annotation with expert-crafted guidelines (dubbed AutoExpert). We develop benchmarks by redesigning the evaluation protocol and re-annotating data with nuScenes and PandaSet, two 3D detection datasets for autonomous driving research that provide expert-crafted annotation guidelines. Their guidelines define 18 and 25 object classes, respectively, using nuanced language descriptions and a few visual examples. Following the guidelines that require using 3D cuboids to label LiDAR data, AutoExpert requires algorithms to learn on few-shot labeled images and texts to perform the task of 3D detection on LiDAR data. Apparently, the challenges of AutoExpert lie in the data-modality and task discrepancy. Nevertheless, public foundation models (FMs) serve as promising tools to tackle these challenges. To address AutoExpert, we adopt a conceptually simple pipeline consisting of three components: (1) 2D object detection and segmentation in RGB images, (2) lifting 2D detections into 3D using known sensor poses, and (3) 3D cuboids generation for the 2D detections. Within this pipeline, we enhance and evaluate a variety of methods such as open-vocabulary detectors, few-shot detectors, and self-supervised learned detectors. We also develop novel techniques, leading to refined components that boost 3D detection mAP from 12.1 to 25.4 on the AutoExpert-nuScenes benchmark.

cs.CV↗

arXiv2026

Few-shot Classification as Multi-instance Verification: Effective Backbone-agnostic Transfer across Domains

We investigate cross-domain few-shot learning under the constraint that fine-tuning of backbones (i.e., feature extractors) is impossible or infeasible---a scenario that is increasingly common in practical use cases---and show how representing few-shot classification as a series of multiple instance verification (MIV) tasks enables competitive classification performance using the static embeddings produced by frozen, "black-box" backbones. More specifically, based on this novel representation, we introduce a new approach to few-shot domain adaptation named the "MIV-head": a classification head that is backbone-agnostic and computationally efficient. We show that the core components of the MIV-head, when trained on few-shot data from a target domain, collectively yield strong performance on test data from that domain. Importantly, they do so without fine-tuning the backbone, requiring only the "meta-testing" phase. In experiments under various settings on an extension of the Meta-Dataset benchmark for cross-domain few-shot image classification, using representative off-the-shelf convolutional neural network and vision transformer backbones pretrained on ImageNet1K, we demonstrate that the MIV-head achieves highly competitive accuracy when compared to state-of-the-art "adapter" (or "partial fine-tuning") methods applied to the same backbones, while incurring substantially lower adaptation cost. Moreover, compared to our approach, well-known "classification head" approaches achieve a substantially lower level of accuracy. We share our code at: https://github.com/xxweka/MIV-head.

cs.CV↗