General Vision Encoder Features as Guidance in Medical Image Registration

General vision encoders like DINOv2 and SAM have recently transformed computer vision. Even though they are trained on natural images, such encoder models have excelled in medical imaging, e.g., in classification, segmentation, and registration. However, no in-depth comparison of different state-of-the-art general vision encoders for medical registration is available. In this work, we investigate how well general vision encoder features can be used in the dissimilarity metrics for medical image registration. We explore two encoders that were trained on natural images as well as one that was fine-tuned on medical data. We apply the features within the well-established B-spline FFD registration framework. In extensive experiments on cardiac cine MRI data, we find that using features as additional guidance for conventional metrics improves the registration quality. The code is available at github.com/compai-lab/2024-miccai-koegl.

Data-Driven Tissue- and Subject-Specific Elastic Regularization for Medical Image Registration

Physics-inspired regularization is desired for intra-patient image registration since it can effectively capture the biomechanical characteristics of anatomical structures. However, a major challenge lies in the reliance on physical parameters: Parameter estimations vary widely across the literature, and the physical properties themselves are inherently subject-specific. In this work, we introduce a novel data-driven method that leverages hypernetworks to learn the tissue-dependent elasticity parameters of an elastic regularizer. Notably, our approach facilitates the estimation of patient-specific parameters without the need to retrain the network. We evaluate our method on three publicly available 2D and 3D lung CT and cardiac MR datasets. We find that with our proposed subject-specific tissue-dependent regularization, a higher registration quality is achieved across all datasets compared to using a global regularizer. The code is available at https://github.com/compai-lab/2024-miccai-reithmeir.

Learned Image Compression for HE-stained Histopathological Images via Stain Deconvolution

Processing histopathological Whole Slide Images (WSI) leads to massive storage requirements for clinics worldwide. Even after lossy image compression during image acquisition, additional lossy compression is frequently possible without substantially affecting the performance of deep learning-based (DL) downstream tasks. In this paper, we show that the commonly used JPEG algorithm is not best suited for further compression and we propose Stain Quantized Latent Compression (SQLC ), a novel DL based histopathology data compression approach. SQLC compresses staining and RGB channels before passing it through a compression autoencoder (CAE ) in order to obtain quantized latent representations for maximizing the compression. We show that our approach yields superior performance in a classification downstream task, compared to traditional approaches like JPEG, while image quality metrics like the Multi-Scale Structural Similarity Index (MS-SSIM) is largely preserved. Our method is online available.

Real-World Federated Learning in Radiology: Hurdles to overcome and Benefits to gain

Objective: Federated Learning (FL) enables collaborative model training while keeping data locally. Currently, most FL studies in radiology are conducted in simulated environments due to numerous hurdles impeding its translation into practice. The few existing real-world FL initiatives rarely communicate specific measures taken to overcome these hurdles, leaving behind a significant knowledge gap. Minding efforts to implement real-world FL, there is a notable lack of comprehensive assessment comparing FL to less complex alternatives. Materials & Methods: We extensively reviewed FL literature, categorizing insights along with our findings according to their nature and phase while establishing a FL initiative, summarized to a comprehensive guide. We developed our own FL infrastructure within the German Radiological Cooperative Network (RACOON) and demonstrated its functionality by training FL models on lung pathology segmentation tasks across six university hospitals. We extensively evaluated FL against less complex alternatives in three distinct evaluation scenarios. Results: The proposed guide outlines essential steps, identified hurdles, and proposed solutions for establishing successful FL initiatives conducting real-world experiments. Our experimental results show that FL outperforms less complex alternatives in all evaluation scenarios, justifying the effort required to translate FL into real-world applications. Discussion & Conclusion: Our proposed guide aims to aid future FL researchers in circumventing pitfalls and accelerating translation of FL into radiological applications. Our results underscore the value of efforts needed to translate FL into real-world applications by demonstrating advantageous performance over alternatives, and emphasize the importance of strategic organization, robust management of distributed data and infrastructure in real-world settings.

Reconciling AI Performance and Data Reconstruction Resilience for Medical Imaging

Artificial Intelligence (AI) models are vulnerable to information leakage of their training data, which can be highly sensitive, for example in medical imaging. Privacy Enhancing Technologies (PETs), such as Differential Privacy (DP), aim to circumvent these susceptibilities. DP is the strongest possible protection for training models while bounding the risks of inferring the inclusion of training samples or reconstructing the original data. DP achieves this by setting a quantifiable privacy budget. Although a lower budget decreases the risk of information leakage, it typically also reduces the performance of such models. This imposes a trade-off between robust performance and stringent privacy. Additionally, the interpretation of a privacy budget remains abstract and challenging to contextualize. In this study, we contrast the performance of AI models at various privacy budgets against both, theoretical risk bounds and empirical success of reconstruction attacks. We show that using very large privacy budgets can render reconstruction attacks impossible, while drops in performance are negligible. We thus conclude that not using DP -- at all -- is negligent when applying AI models to sensitive data. We deem those results to lie a foundation for further debates on striking a balance between privacy risks and model performance.

3D Arterial Segmentation via Single 2D Projections and Depth Supervision in Contrast-Enhanced CT Images

Automated segmentation of the blood vessels in 3D volumes is an essential step for the quantitative diagnosis and treatment of many vascular diseases. 3D vessel segmentation is being actively investigated in existing works, mostly in deep learning approaches. However, training 3D deep networks requires large amounts of manual 3D annotations from experts, which are laborious to obtain. This is especially the case for 3D vessel segmentation, as vessels are sparse yet spread out over many slices and disconnected when visualized in 2D slices. In this work, we propose a novel method to segment the 3D peripancreatic arteries solely from one annotated 2D projection per training image with depth supervision. We perform extensive experiments on the segmentation of peripancreatic arteries on 3D contrast-enhanced CT images and demonstrate how well we capture the rich depth information from 2D projections. We demonstrate that by annotating a single, randomly chosen projection for each training sample, we obtain comparable performance to annotating multiple 2D projections, thereby reducing the annotation effort. Furthermore, by mapping the 2D labels to the 3D space using depth information and incorporating this into training, we almost close the performance gap between 3D supervision and 2D supervision. Our code is available at: https://github.com/alinafdima/3Dseg-mip-depth.

Constructing Population-Specific Atlases from Whole Body MRI: Application to the UKBB

Population atlases are commonly utilised in medical imaging to facilitate the investigation of variability across populations. Such atlases enable the mapping of medical images into a common coordinate system, promoting comparability and enabling the study of inter-subject differences. Constructing such atlases becomes particularly challenging when working with highly heterogeneous datasets, such as whole-body images, where subjects show significant anatomical variations. In this work, we propose a pipeline for generating a standardised whole-body atlas for a highly heterogeneous population by partitioning the population into meaningful subgroups. We create six whole-body atlases that represent a healthy population average using magnetic resonance (MR) images from the UK Biobank dataset. We furthermore unbias them, and this way obtain a realistic representation of the population. In addition to the anatomical atlases, we generate probabilistic atlases that capture the distributions of abdominal fat and five abdominal organs across the population. We demonstrate different applications of these atlases, using the differences between subjects with medical conditions such as diabetes and cardiovascular diseases and healthy subjects from the atlas space. With this work, we make the constructed anatomical and label atlases publically available and anticipate them to support medical research conducted on whole-body MR images.

Atlas-Based Interpretable Age Prediction

Age prediction is an important part of medical assessments and research. It can aid in detecting diseases as well as abnormal ageing by highlighting the discrepancy between chronological and biological age. To gain a comprehensive understanding of age-related changes observed in various body parts, we investigate them on a larger scale by using whole-body images. We utilise the Grad-CAM interpretability method to determine the body areas most predictive of a person's age. We expand our analysis beyond individual subjects by employing registration techniques to generate population-wide interpretability maps. Furthermore, we set state-of-the-art whole-body age prediction with a model that achieves a mean absolute error of 2.76 years. Our findings reveal three primary areas of interest: the spine, the autochthonous back muscles, and the cardiac region, which exhibits the highest importance.

Explainable 2D Vision Models for 3D Medical Data

Training Artificial Intelligence (AI) models on three-dimensional image data presents unique challenges compared to the two-dimensional case: Firstly, the computational resources are significantly higher, and secondly, the availability of large pretraining datasets is often limited, impeding training success. In this study, we propose a simple approach of adapting 2D networks with an intermediate feature representation for processing 3D volumes. Our method involves sequentially applying these networks to slices of a 3D volume from all orientations. Subsequently, a feature reduction module combines the extracted slice features into a single representation, which is then used for classification. We evaluate our approach on medical classification benchmarks and a real-world clinical dataset, demonstrating comparable results to existing methods. Furthermore, by employing attention pooling as a feature reduction module we obtain weighted importance values for each slice during the forward pass. We show that slices deemed important by our approach allow the inspection of the basis of a model's prediction.

Body Fat Estimation from Surface Meshes using Graph Neural Networks

Body fat volume and distribution can be a strong indication for a person's overall health and the risk for developing diseases like type 2 diabetes and cardiovascular diseases. Frequently used measures for fat estimation are the body mass index (BMI), waist circumference, or the waist-hip-ratio. However, those are rather imprecise measures that do not allow for a discrimination between different types of fat or between fat and muscle tissue. The estimation of visceral (VAT) and abdominal subcutaneous (ASAT) adipose tissue volume has shown to be a more accurate measure for named risk factors. In this work, we show that triangulated body surface meshes can be used to accurately predict VAT and ASAT volumes using graph neural networks. Our methods achieve high performance while reducing training time and required resources compared to state-of-the-art convolutional neural networks in this area. We furthermore envision this method to be applicable to cheaper and easily accessible medical surface scans instead of expensive medical images.