MedROI: Codec-Agnostic Region of Interest-Centric Compression for Medical Images

Large-scale multi-modal MRI datasets impose substantial storage and I/O costs, limiting the training of 3D generative models on commodity infrastructure. While lossy compression is known to preserve accuracy for discriminative segmentation networks, its effect on generative models, which must learn the full data distribution rather than a decision boundary, is unexplored. We study whether standard image codecs can effectively compress semantically rich brain tumor MRI while preserving the fidelity required to train and deploy a 3D MRI generative model. Each 3D volume is compressed with JPEG2000 or a near-lossless JPEG-LS pipeline. Next, a Wavelet Flow Matching model, conditioned on BraTS image sequences (T1n, T1c, T2, T2f), is trained on compressed data, and the resulting models are evaluated on the validation set. At a 20:1 compression ratio, synthesis quality is statistically equivalent to a model trained on uncompressed data within a pre-specified margin ($Δ$PSNR $<1$,dB, $Δ$SSIM $<0.02$; paired TOST $p=[[p]]$): mean PSNR is 27.3,dB vs. 27.0,dB and mean SSIM is 0.95 vs. 0.96 across modalities. Our results indicate that JPEG2000 compression is a practical step toward scalable 3D MRI generative modeling without degrading synthesis quality. The codebase is available at https://github.com/lisafis/MRIComp4Flow .

Convolutional neural networks (CNNs) have become increasingly difficult to deploy in resource-constrained environments due to their large memory and computational requirements. Although low-rank compression methods can reduce this burden, most existing approaches compress spatial and channel redundancy independently and therefore do not fully exploit the localised structure within convolutional feature maps. This paper proposes a hierarchical spatio-channel low-rank compression framework for CNNs that exploits redundancy across spatial regions and channel activations. Unlike conventional methods, which apply a uniform decomposition across an entire layer, the proposed approach first partitions feature maps into spatial regions, then groups channels according to their co-activation patterns within each region, and finally applies rank-adaptive SVD to each resulting spatio-channel cluster. The method is evaluated on an AlexNet-based brain tumour MRI classification model and compared with Global SVD and Tucker decomposition under $3\times$ and $6\times$ compression budgets. Our method outperforms both baselines, reducing FLOPs from $8.21\,\mathrm{G}$ to $1.55\,\mathrm{G}$ ($81.1\%$ reduction), achieving a $1.38\times$ inference speed-up, and increasing classification accuracy from $87.76\%$ to $89.80\%$. The method also improves the macro $F_1$-score and performance on challenging classes such as meningioma. A hyper-parameter trade-off analysis demonstrates that the framework provides Pareto-optimal configurations, enabling control over the balance between compression and predictive performance. Moderate clustering with adaptive rank selection yields strong results. Bootstrap standard errors are reported for all classification metrics.

Lossless compression of volumetric medical images is of paramount importance for clinical and research applications where data fidelity is essential. Traditional compression methods are often limited in efficiency due to rigid, handcrafted models. Conversely, deep neural network (DNN)-based compression methods, while effective, demand substantial computational resources, hindering deployment in resource-constrained settings. To address these challenges, we propose a novel tri-plane context tree (TCT)-based method for lossless volumetric medical image compression that delivers high performance without relying on DNNs or external training data. To exploit intra-slice and inter-slice redundancies, we introduce a compact tri-plane context representation that decomposes complex 3D context modeling into efficient 2D modeling on three orthogonal planes. By integrating this representation with a context tree framework, we develop an input-specific TCT model employing an adaptive binary tree structure. At each tree node, the model dynamically selects from a suite of tri-plane based predictors and contextual feature extractors, enabling data-adaptive context modeling tailored to local structural characteristics. Instead of offline training, we sample a subset of the input volume to learn the TCT model by optimizing the minimum description length (MDL) through iterative construction and pruning. With the learned TCT model, each pixel retrieves its corresponding context, computes the prediction residual using the predictor dictated by the context, and performs entropy encoding based on the associated histograms. Experimental results demonstrate that the proposed method achieves compression performance on par with recent DNN-based methods on multiple datasets, while maintaining low computational cost and fast coding speeds, making it highly applicable in practice.