Stitching and dimensionality effects on large artificially generated volume datasets
Authors: Lucas von Chamier, Jan Philipp Albrecht, Dagmar Kainmüller
Organizations: 1GFZ Helmholtz-Zentrum für Geoforschung · 2Max Delbrück Center for Molecular Medicine in the Helmholtz Association · 3Helmholtz Imaging · 4Humboldt-Universität zu Berlin · University of Potsdam
Generating large images via deep learning requires patching input data to accommodate hardware memory limitations, then assembling output patches, a process that can introduce stitching artifacts when neighboring patches do not align at borders. While these artifacts are known to affect segmentation tasks, their impact on generative models for style-transfer remains poorly understood. We investigated three stitching approaches and two patch dimensionalities (2D vs 3D) using cycleGAN models trained on cryo-electron microscopy datasets. We evaluated both perceptual quality and performance on downstream mitochondria segmentation. Our key findings reveal that: (1) FID scores fail to detect subtle stitching artifacts that significantly impact downstream segmentation performance, (2) 3D models with artifact-free stitching marginally outperform 2D models on downstream tasks, though the improvement barely justifies the computational cost, and (3) 2D models train more stably due to larger batch sizes. Additionally, we demonstrate that ensembling predictions from three orthogonal directions can improve low-quality volumes but provides no benefit for high-quality outputs. These results demonstrate that maximizing generative model performance on large scientific datasets requires careful consideration and mitigation of stitching artifacts, and that perceptual metrics alone are insufficient for evaluating domain adaptation quality in biomedical imaging.
We consider the problem of generating images whose internal structure -- defined by the distribution of patches across multiple scales -- matches that of a single reference image. Recent approaches address this problem by training a diffusion model on a single image. But even in this setting, training is computationally expensive and requires hours of optimization. Instead, we model the image using a dataset of its patches at different scales. As this dataset is finite and the dimensionality of its patches is small, the score function for a noisy patch can be computed tractably using an optimal, closed-form denoiser, eliminating the need for neural network training. We integrate this patch-based denoiser into an efficient, training-free image diffusion model, and we describe how our method connects to classical patch-based image restoration techniques. Our approach achieves state-of-the-art generation quality and diversity compared to trained single-image diffusion models, and we demonstrate applications, including unconditional image generation, text-guided stylization, image symmetrization, and retargeting. Further, we show that our approach is compatible with latent space diffusion, and we show multiple additional acceleration techniques to achieve megapixel single-image generation in one second, and gigapixel generation in minutes.
Haojun Qiu, Kiriakos N. Kutulakos, David B. Lindell
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 (ΔPSNR <1,dB, ΔSSIM <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 .
Lisa K. Fischer, Mykhailo Riabets, Daniel Rueckert +3
Characterizing the physical properties of clay and cementitious materials matters across many fields, from materials science to geological waste disposal. Property simulation typically calls for 3D imaging, which is expensive, not always accessible, and technically limited for certain materials. Recent progress in deep generative models offers a way around this, reconstructing 3D volumes from the more easily acquired 2D images. Among GAN-based methods for 3D microstructure generation, SliceGAN has shown strong results for homogeneous isotropic and anisotropic systems. It struggles, however, to capture the finer detail of more complex heterogeneous microstructures, which motivates alternative generative frameworks. We introduce a hybrid approach that draws on the stability and generation quality of denoising diffusion models. Since no 3D ground truth is available, we replace the standard denoising loss with an adversarial loss, which yields a stable training process in our experiments. We show that the resulting model generates microstructures of varying complexity with minimal slice artefacts and close agreement with ground-truth phase fractions and structural descriptors.