John Kalkhof

Amin Ranem, John Kalkhof, Caner Özer et al.

While machine learning approaches perform well on their training domain, they generally tend to fail in a real-world application. In cardiovascular magnetic resonance imaging (CMR), respiratory motion represents a major challenge in terms of acquisition quality and therefore subsequent analysis and final diagnosis. We present a workflow which predicts a severity score for respiratory motion in CMR for the CMRxMotion challenge 2022. This is an important tool for technicians to immediately provide feedback on the CMR quality during acquisition, as poor-quality images can directly be re-acquired while the patient is still available in the vicinity. Thus, our method ensures that the acquired CMR holds up to a specific quality standard before it is used for further diagnosis. Therefore, it enables an efficient base for proper diagnosis without having time and cost-intensive re-acquisitions in cases of severe motion artefacts. Combined with our segmentation model, this can help cardiologists and technicians in their daily routine by providing a complete pipeline to guarantee proper quality assessment and genuine segmentations for cardiovascular scans. The code base is available at https://github.com/MECLabTUDA/QA_med_data/tree/dev_QA_CMRxMotion.

John Kalkhof, Anirban Mukhopadhyay

Medical image segmentation relies heavily on large-scale deep learning models, such as UNet-based architectures. However, the real-world utility of such models is limited by their high computational requirements, which makes them impractical for resource-constrained environments such as primary care facilities and conflict zones. Furthermore, shifts in the imaging domain can render these models ineffective and even compromise patient safety if such errors go undetected. To address these challenges, we propose M3D-NCA, a novel methodology that leverages Neural Cellular Automata (NCA) segmentation for 3D medical images using n-level patchification. Moreover, we exploit the variance in M3D-NCA to develop a novel quality metric which can automatically detect errors in the segmentation process of NCAs. M3D-NCA outperforms the two magnitudes larger UNet models in hippocampus and prostate segmentation by 2% Dice and can be run on a Raspberry Pi 4 Model B (2GB RAM). This highlights the potential of M3D-NCA as an effective and efficient alternative for medical image segmentation in resource-constrained environments.

Amin Ranem, John Kalkhof, Anirban Mukhopadhyay

Continual learning (CL) in medical imaging presents a unique challenge, requiring models to adapt to new domains while retaining previously acquired knowledge. We introduce NCAdapt, a Neural Cellular Automata (NCA) based method designed to address this challenge. NCAdapt features a domain-specific multi-head structure, integrating adaptable convolutional layers into the NCA backbone for each new domain encountered. After initial training, the NCA backbone is frozen, and only the newly added adaptable convolutional layers, consisting of 384 parameters, are trained along with domain-specific NCA convolutions. We evaluate NCAdapt on hippocampus segmentation tasks, benchmarking its performance against Lifelong nnU-Net and U-Net models with state-of-the-art (SOTA) CL methods. Our lightweight approach achieves SOTA performance, underscoring its effectiveness in addressing CL challenges in medical imaging. Upon acceptance, we will make our code base publicly accessible to support reproducibility and foster further advancements in medical CL.

John Kalkhof, Arlene Kühn, Yannik Frisch et al.

Despite considerable success, large Denoising Diffusion Models (DDMs) with UNet backbone pose practical challenges, particularly on limited hardware and in processing gigapixel images. To address these limitations, we introduce two Neural Cellular Automata (NCA)-based DDMs: Diff-NCA and FourierDiff-NCA. Capitalizing on the local communication capabilities of NCA, Diff-NCA significantly reduces the parameter counts of NCA-based DDMs. Integrating Fourier-based diffusion enables global communication early in the diffusion process. This feature is particularly valuable in synthesizing complex images with important global features, such as the CelebA dataset. We demonstrate that even a 331k parameter Diff-NCA can generate 512x512 pathology slices, while FourierDiff-NCA (1.1m parameters) reaches a three times lower FID score of 43.86, compared to the four times bigger UNet (3.94m parameters) with a score of 128.2. Additionally, FourierDiff-NCA can perform diverse tasks such as super-resolution, out-of-distribution image synthesis, and inpainting without explicit training.

Kang Wang, Chen Qin, Zhang Shi et al.

Deep learning models have achieved state-of-the-art performance in automated Cardiac Magnetic Resonance (CMR) analysis. However, the efficacy of these models is highly dependent on the availability of high-quality, artifact-free images. In clinical practice, CMR acquisitions are frequently degraded by respiratory motion, yet the robustness of deep learning models against such artifacts remains an underexplored problem. To promote research in this domain, we organized the MICCAI CMRxMotion challenge. We curated and publicly released a dataset of 320 CMR cine series from 40 healthy volunteers who performed specific breathing protocols to induce a controlled spectrum of motion artifacts. The challenge comprised two tasks: 1) automated image quality assessment to classify images based on motion severity, and 2) robust myocardial segmentation in the presence of motion artifacts. A total of 22 algorithms were submitted and evaluated on the two designated tasks. This paper presents a comprehensive overview of the challenge design and dataset, reports the evaluation results for the top-performing methods, and further investigates the impact of motion artifacts on five clinically relevant biomarkers. All resources and code are publicly available at: https://github.com/CMRxMotion

Avni Mittal, John Kalkhof, Anirban Mukhopadhyay et al.

Denoising Diffusion Models (DDMs) are widely used for high-quality image generation and medical image segmentation but often rely on Unet-based architectures, leading to high computational overhead, especially with high-resolution images. This work proposes three NCA-based improvements for diffusion-based medical image segmentation. First, Multi-MedSegDiffNCA uses a multilevel NCA framework to refine rough noise estimates generated by lower level NCA models. Second, CBAM-MedSegDiffNCA incorporates channel and spatial attention for improved segmentation. Third, MultiCBAM-MedSegDiffNCA combines these methods with a new RGB channel loss for semantic guidance. Evaluations on Lesion segmentation show that MultiCBAM-MedSegDiffNCA matches Unet-based model performance with dice score of 87.84% while using 60-110 times fewer parameters, offering a more efficient solution for low resource medical settings.

Amin Ranem, John Kalkhof, Anirban Mukhopadhyay

Medical image registration is a critical process that aligns various patient scans, facilitating tasks like diagnosis, surgical planning, and tracking. Traditional optimization based methods are slow, prompting the use of Deep Learning (DL) techniques, such as VoxelMorph and Transformer-based strategies, for faster results. However, these DL methods often impose significant resource demands. In response to these challenges, we present NCA-Morph, an innovative approach that seamlessly blends DL with a bio-inspired communication and networking approach, enabled by Neural Cellular Automata (NCAs). NCA-Morph not only harnesses the power of DL for efficient image registration but also builds a network of local communications between cells and respective voxels over time, mimicking the interaction observed in living systems. In our extensive experiments, we subject NCA-Morph to evaluations across three distinct 3D registration tasks, encompassing Brain, Prostate and Hippocampus images from both healthy and diseased patients. The results showcase NCA-Morph's ability to achieve state-of-the-art performance. Notably, NCA-Morph distinguishes itself as a lightweight architecture with significantly fewer parameters; 60% and 99.7% less than VoxelMorph and TransMorph. This characteristic positions NCA-Morph as an ideal solution for resource-constrained medical applications, such as primary care settings and operating rooms.

Nick Lemke, John Kalkhof, Niklas Babendererde et al.

Medical applications demand segmentation of large inputs, like prostate MRIs, pathology slices, or videos of surgery. These inputs should ideally be inferred at once to provide the model with proper spatial or temporal context. When segmenting large inputs, the VRAM consumption of the GPU becomes the bottleneck. Architectures like UNets or Vision Transformers scale very poorly in VRAM consumption, resulting in patch- or frame-wise approaches that compromise global consistency and inference speed. The lightweight Neural Cellular Automaton (NCA) is a bio-inspired model that is by construction size-invariant. However, due to its local-only communication rules, it lacks global knowledge. We propose OctreeNCA by generalizing the neighborhood definition using an octree data structure. Our generalized neighborhood definition enables the efficient traversal of global knowledge. Since deep learning frameworks are mainly developed for large multi-layer networks, their implementation does not fully leverage the advantages of NCAs. We implement an NCA inference function in CUDA that further reduces VRAM demands and increases inference speed. Our OctreeNCA segments high-resolution images and videos quickly while occupying 90% less VRAM than a UNet during evaluation. This allows us to segment 184 Megapixel pathology slices or 1-minute surgical videos at once.