Deep Generative Models for 3D Medical Image Synthesis

Deep generative modeling has emerged as a powerful tool for synthesizing realistic medical images, driving advances in medical image analysis, disease diagnosis, and treatment planning. This chapter explores various deep generative models for 3D medical image synthesis, with a focus on Variational Autoencoders (VAEs), Generative Adversarial Networks (GANs), and Denoising Diffusion Models (DDMs). We discuss the fundamental principles, recent advances, as well as strengths and weaknesses of these models and examine their applications in clinically relevant problems, including unconditional and conditional generation tasks like image-to-image translation and image reconstruction. We additionally review commonly used evaluation metrics for assessing image fidelity, diversity, utility, and privacy and provide an overview of current challenges in the field.

Frequency-Time Diffusion with Neural Cellular Automata

Denoising Diffusion Models (DDMs) have become the leading generative technique for synthesizing high-quality images but are often constrained by their UNet-based architectures that impose certain limitations. In particular, the considerable size of often hundreds of millions of parameters makes them impractical when hardware resources are limited. However, even with powerful hardware, processing images in the gigapixel range is difficult. This is especially true in fields such as microscopy or satellite imaging, where such challenges arise from the limitation to a predefined generative size and the inefficient scaling to larger images. We present two variations of Neural Cellular Automata (NCA)-based DDM methods to address these challenges and jumpstart NCA-based DDMs: Diff-NCA and FourierDiff-NCA. Diff-NCA performs diffusion by using only local features of the underlying distribution, making it suitable for applications where local features are critical. To communicate global knowledge in image space, naive NCA setups require timesteps that increase with the image scale. We solve this bottleneck of current NCA architectures by introducing FourierDiff-NCA, which advances Diff-NCA by adding a Fourier-based diffusion process and combines the frequency-organized Fourier space with the image space. By initiating diffusion in the Fourier domain and finalizing it in the image space, FourierDiff-NCA accelerates global communication. We validate our techniques by using Diff-NCA (208k parameters) to generate high-resolution digital pathology scans at 576x576 resolution and FourierDiff-NCA (887k parameters) to synthesize CelebA images at 64x64, outperforming VNCA and five times bigger UNet-based DDMs. In addition, we demonstrate FourierDiff-NCA's capabilities in super-resolution, OOD image synthesis, and inpainting without additional training.

Synthesising Rare Cataract Surgery Samples with Guided Diffusion Models

Cataract surgery is a frequently performed procedure that demands automation and advanced assistance systems. However, gathering and annotating data for training such systems is resource intensive. The publicly available data also comprises severe imbalances inherent to the surgical process. Motivated by this, we analyse cataract surgery video data for the worst-performing phases of a pre-trained downstream tool classifier. The analysis demonstrates that imbalances deteriorate the classifier's performance on underrepresented cases. To address this challenge, we utilise a conditional generative model based on Denoising Diffusion Implicit Models (DDIM) and Classifier-Free Guidance (CFG). Our model can synthesise diverse, high-quality examples based on complex multi-class multi-label conditions, such as surgical phases and combinations of surgical tools. We affirm that the synthesised samples display tools that the classifier recognises. These samples are hard to differentiate from real images, even for clinical experts with more than five years of experience. Further, our synthetically extended data can improve the data sparsity problem for the downstream task of tool classification. The evaluations demonstrate that the model can generate valuable unseen examples, allowing the tool classifier to improve by up to 10% for rare cases. Overall, our approach can facilitate the development of automated assistance systems for cataract surgery by providing a reliable source of realistic synthetic data, which we make available for everyone.