Anna Vilanova

Kirsten W. H. Maas, Danny Ruijters, Anna Vilanova et al.

Dynamic three-dimensional (4D) reconstruction from two-dimensional X-ray coronary angiography (CA) remains a significant clinical problem. Existing CA reconstruction methods often require extensive user interaction or large training datasets. Recently, Neural Radiance Field (NeRF) has successfully reconstructed high-fidelity scenes in natural and medical contexts without these requirements. However, challenges such as sparse-views, intra-scan motion, and complex vessel morphology hinder its direct application to CA data. We introduce NeRF-CA, a first step toward a fully automatic 4D CA reconstruction that achieves reconstructions from sparse coronary angiograms. To the best of our knowledge, we are the first to address the challenges of sparse-views and cardiac motion by decoupling the scene into the moving coronary artery and the static background, effectively translating the problem of motion into a strength. NeRF-CA serves as a first stepping stone for solving the 4D CA reconstruction problem, achieving adequate 4D reconstructions from as few as four angiograms, as required by clinical practice, while significantly outperforming state-of-the-art sparse-view X-ray NeRF. We validate our approach quantitatively and qualitatively using representative 4D phantom datasets and ablation studies. To accelerate research in this domain, we made our codebase public: https://github.com/kirstenmaas/NeRF-CA.

Linhao Meng, Stef van den Elzen, Nicola Pezzotti et al.

Data features and class probabilities are two main perspectives when, e.g., evaluating model results and identifying problematic items. Class probabilities represent the likelihood that each instance belongs to a particular class, which can be produced by probabilistic classifiers or even human labeling with uncertainty. Since both perspectives are multi-dimensional data, dimensionality reduction (DR) techniques are commonly used to extract informative characteristics from them. However, existing methods either focus solely on the data feature perspective or rely on class probability estimates to guide the DR process. In contrast to previous work where separate views are linked to conduct the analysis, we propose a novel approach, class-constrained t-SNE, that combines data features and class probabilities in the same DR result. Specifically, we combine them by balancing two corresponding components in a cost function to optimize the positions of data points and iconic representation of classes -- class landmarks. Furthermore, an interactive user-adjustable parameter balances these two components so that users can focus on the weighted perspectives of interest and also empowers a smooth visual transition between varying perspectives to preserve the mental map. We illustrate its application potential in model evaluation and visual-interactive labeling. A comparative analysis is performed to evaluate the DR results.

Tom Hendriks, Anna Vilanova, Maxime Chamberland

We present a novel way to model diffusion magnetic resonance imaging (dMRI) datasets, that benefits from the structural coherence of the human brain while only using data from a single subject. Current methods model the dMRI signal in individual voxels, disregarding the intervoxel coherence that is present. We use a neural network to parameterize a spherical harmonics series (NeSH) to represent the dMRI signal of a single subject from the Human Connectome Project dataset, continuous in both the angular and spatial domain. The reconstructed dMRI signal using this method shows a more structurally coherent representation of the data. Noise in gradient images is removed and the fiber orientation distribution functions show a smooth change in direction along a fiber tract. We showcase how the reconstruction can be used to calculate mean diffusivity, fractional anisotropy, and total apparent fiber density. These results can be achieved with a single model architecture, tuning only one hyperparameter. In this paper we also demonstrate how upsampling in both the angular and spatial domain yields reconstructions that are on par or better than existing methods.

Ruben Vink, Anna Vilanova, Maxime Chamberland

One of the unspoken challenges of tractography is choosing the right parameters for a given dataset or bundle. In order to tackle this challenge, we explore the multi-dimensional parameter space of tractography using streamline-specific parameters (SSP). We 1) validate a state-of-the-art probabilistic tracking method using per-streamline parameters on synthetic data, and 2) show how we can gain insights into the parameter space by focusing on streamline acceptance using real-world data. We demonstrate the potential added value of SSP to the current state of tractography by showing how SSP can be used to reveal patterns in the parameter space.

Vidya Prasad, Chen Zhu-Tian, Anna Vilanova et al.

Diffusion models have garnered significant attention since they can effectively learn complex multivariate Gaussian distributions, resulting in diverse, high-quality outcomes. They introduce Gaussian noise into training data and reconstruct the original data iteratively. Central to this iterative process is a single Unet, adapting across time steps to facilitate generation. Recent work revealed the presence of composition and denoising phases in this generation process, raising questions about the Unets' varying roles. Our study dives into the dynamic behavior of Unets within denoising diffusion probabilistic models (DDPM), focusing on (de)convolutional blocks and skip connections across time steps. We propose an analytical method to systematically assess the impact of time steps and core Unet components on the final output. This method eliminates components to study causal relations and investigate their influence on output changes. The main purpose is to understand the temporal dynamics and identify potential shortcuts during inference. Our findings provide valuable insights into the various generation phases during inference and shed light on the Unets' usage patterns across these phases. Leveraging these insights, we identify redundancies in GLIDE (an improved DDPM) and improve inference time by ~27% with minimal degradation in output quality. Our ultimate goal is to guide more informed optimization strategies for inference and influence new model designs.

Nancy R. Newlin, Kurt Schilling, Serge Koudoro et al.

White matter alterations are increasingly implicated in neurological diseases and their progression. International-scale studies use diffusion-weighted magnetic resonance imaging (DW-MRI) to qualitatively identify changes in white matter microstructure and connectivity. Yet, quantitative analysis of DW-MRI data is hindered by inconsistencies stemming from varying acquisition protocols. There is a pressing need to harmonize the preprocessing of DW-MRI datasets to ensure the derivation of robust quantitative diffusion metrics across acquisitions. In the MICCAI-CDMRI 2023 QuantConn challenge, participants were provided raw data from the same individuals collected on the same scanner but with two different acquisitions and tasked with preprocessing the DW-MRI to minimize acquisition differences while retaining biological variation. Submissions are evaluated on the reproducibility and comparability of cross-acquisition bundle-wise microstructure measures, bundle shape features, and connectomics. The key innovations of the QuantConn challenge are that (1) we assess bundles and tractography in the context of harmonization for the first time, (2) we assess connectomics in the context of harmonization for the first time, and (3) we have 10x additional subjects over prior harmonization challenge, MUSHAC and 100x over SuperMUDI. We find that bundle surface area, fractional anisotropy, connectome assortativity, betweenness centrality, edge count, modularity, nodal strength, and participation coefficient measures are most biased by acquisition and that machine learning voxel-wise correction, RISH mapping, and NeSH methods effectively reduce these biases. In addition, microstructure measures AD, MD, RD, bundle length, connectome density, efficiency, and path length are least biased by these acquisition differences.

Kirsten W. H. Maas, Danny Ruijters, Nicola Pezzotti et al.

Three-dimensional (3D) and dynamic 3D+time (4D) reconstruction of coronary arteries from X-ray coronary angiography (CA) has the potential to improve clinical procedures. However, there are multiple challenges to be addressed, most notably, blood-vessel structure sparsity, poor background and blood vessel distinction, sparse-views, and intra-scan motion. State-of-the-art reconstruction approaches rely on time-consuming manual or error-prone automatic segmentations, limiting clinical usability. Recently, approaches based on Neural Radiance Fields (NeRF) have shown promise for automatic reconstructions in the sparse-view setting. However, they suffer from long training times due to their dependence on MLP-based representations. We propose NerT-CA, a hybrid approach of Neural and Tensorial representations for accelerated 4D reconstructions with sparse-view CA. Building on top of the previous NeRF-based work, we model the CA scene as a decomposition of low-rank and sparse components, utilizing fast tensorial fields for low-rank static reconstruction and neural fields for dynamic sparse reconstruction. Our approach outperforms previous works in both training time and reconstruction accuracy, yielding reasonable reconstructions from as few as three angiogram views. We validate our approach quantitatively and qualitatively on representative 4D phantom datasets.

Tom Hendriks, Gerrit Arends, Edwin Versteeg et al.

Diffusion magnetic resonance imaging (dMRI) enables non-invasive investigation of tissue microstructure. The Standard Model (SM) of white matter aims to disentangle dMRI signal contributions from intra- and extra-axonal water compartments. However, due to the model its high-dimensional nature, accurately estimating its parameters poses a complex problem and remains an active field of research, in which different (machine learning) strategies have been proposed. This work introduces an estimation framework based on implicit neural representations (INRs), which incorporate spatial regularization through the sinusoidal encoding of the input coordinates. The INR method is evaluated on both synthetic and in vivo datasets and compared to existing methods. Results demonstrate superior accuracy of the INR method in estimating SM parameters, particularly in low signal-to-noise conditions. Additionally, spatial upsampling of the INR can represent the underlying dataset anatomically plausibly in a continuous way. The INR is self-supervised, eliminating the need for labeled training data. It achieves fast inference, is robust to noise, supports joint estimation of SM kernel parameters and the fiber orientation distribution function with spherical harmonics orders up to at least 8, and accommodates gradient non-uniformity corrections. The combination of these properties positions INRs as a potentially important tool for analyzing and interpreting diffusion MRI data.

Vidya Prasad, Anna Vilanova, Nicola Pezzotti

While deep generative models (DGMs) have gained popularity, their susceptibility to biases and other inefficiencies that lead to undesirable outcomes remains an issue. With their growing complexity, there is a critical need for early detection of issues to achieve desired results and optimize resources. Hence, we introduce a progressive analysis framework to monitor the training process of DGMs. Our method utilizes dimensionality reduction techniques to facilitate the inspection of latent representations, the generated and real distributions, and their evolution across training iterations. This monitoring allows us to pause and fix the training method if the representations or distributions progress undesirably. This approach allows for the analysis of a models' training dynamics and the timely identification of biases and failures, minimizing computational loads. We demonstrate how our method supports identifying and mitigating biases early in training a Generative Adversarial Network (GAN) and improving the quality of the generated data distribution.

Vidya Prasad, Hans van Gorp, Christina Humer et al.

Diffusion models, widely used in image generation, rely on iterative refinement to generate images from noise. Understanding this data evolution is important for model development and interpretability, yet challenging due to its high-dimensional, iterative nature. Prior works often focus on static or instance-level analyses, missing the iterative and holistic aspects of the generative path. While dimensionality reduction can visualize image evolution for few instances, it does preserve the iterative structure. To address these gaps, we introduce EvolvED, a method that presents a holistic view of the iterative generative process in diffusion models. EvolvED goes beyond instance exploration by leveraging predefined research questions to streamline generative space exploration. Tailored prompts aligned with these questions are used to extract intermediate images, preserving iterative context. Targeted feature extractors trace the evolution of key image attribute evolution, addressing the complexity of high-dimensional outputs. Central to EvolvED is a novel evolutionary embedding algorithm that encodes iterative steps while maintaining semantic relations. It enhances the visualization of data evolution by clustering semantically similar elements within each iteration with t-SNE, grouping elements by iteration, and aligning an instance's elements across iterations. We present rectilinear and radial layouts to represent iterations and support exploration. We apply EvolvED to diffusion models like GLIDE and Stable Diffusion, demonstrating its ability to provide valuable insights into the generative process.

Alexander Vieth, Anna Vilanova, Boudewijn Lelieveldt et al.

High-dimensional imaging is becoming increasingly relevant in many fields from astronomy and cultural heritage to systems biology. Visual exploration of such high-dimensional data is commonly facilitated by dimensionality reduction. However, common dimensionality reduction methods do not include spatial information present in images, such as local texture features, into the construction of low-dimensional embeddings. Consequently, exploration of such data is typically split into a step focusing on the attribute space followed by a step focusing on spatial information, or vice versa. In this paper, we present a method for incorporating spatial neighborhood information into distance-based dimensionality reduction methods, such as t-Distributed Stochastic Neighbor Embedding (t-SNE). We achieve this by modifying the distance measure between high-dimensional attribute vectors associated with each pixel such that it takes the pixel's spatial neighborhood into account. Based on a classification of different methods for comparing image patches, we explore a number of different approaches. We compare these approaches from a theoretical and experimental point of view. Finally, we illustrate the value of the proposed methods by qualitative and quantitative evaluation on synthetic data and two real-world use cases.

Nicola Pezzotti, Julian Thijssen, Alexander Mordvintsev et al.

The t-distributed Stochastic Neighbor Embedding (tSNE) algorithm has become in recent years one of the most used and insightful techniques for the exploratory data analysis of high-dimensional data. tSNE reveals clusters of high-dimensional data points at different scales while it requires only minimal tuning of its parameters. Despite these advantages, the computational complexity of the algorithm limits its application to relatively small datasets. To address this problem, several evolutions of tSNE have been developed in recent years, mainly focusing on the scalability of the similarity computations between data points. However, these contributions are insufficient to achieve interactive rates when visualizing the evolution of the tSNE embedding for large datasets. In this work, we present a novel approach to the minimization of the tSNE objective function that heavily relies on modern graphics hardware and has linear computational complexity. Our technique does not only beat the state of the art, but can even be executed on the client side in a browser. We propose to approximate the repulsion forces between data points using adaptive-resolution textures that are drawn at every iteration with WebGL. This approximation allows us to reformulate the tSNE minimization problem as a series of tensor operation that are computed with TensorFlow.js, a JavaScript library for scalable tensor computations.

Nicola Pezzotti, Boudewijn P. F. Lelieveldt, Laurens van der Maaten et al.

Progressive Visual Analytics aims at improving the interactivity in existing analytics techniques by means of visualization as well as interaction with intermediate results. One key method for data analysis is dimensionality reduction, for example, to produce 2D embeddings that can be visualized and analyzed efficiently. t-Distributed Stochastic Neighbor Embedding (tSNE) is a well-suited technique for the visualization of several high-dimensional data. tSNE can create meaningful intermediate results but suffers from a slow initialization that constrains its application in Progressive Visual Analytics. We introduce a controllable tSNE approximation (A-tSNE), which trades off speed and accuracy, to enable interactive data exploration. We offer real-time visualization techniques, including a density-based solution and a Magic Lens to inspect the degree of approximation. With this feedback, the user can decide on local refinements and steer the approximation level during the analysis. We demonstrate our technique with several datasets, in a real-world research scenario and for the real-time analysis of high-dimensional streams to illustrate its effectiveness for interactive data analysis.

Thomas Schultz, Anna Vilanova, Ralph Brecheisen et al.

Fiber tracking based on diffusion weighted Magnetic Resonance Imaging (dMRI) allows for noninvasive reconstruction of fiber bundles in the human brain. In this chapter, we discuss sources of error and uncertainty in this technique, and review strategies that afford a more reliable interpretation of the results. This includes methods for computing and rendering probabilistic tractograms, which estimate precision in the face of measurement noise and artifacts. However, we also address aspects that have received less attention so far, such as model selection, partial voluming, and the impact of parameters, both in preprocessing and in fiber tracking itself. We conclude by giving impulses for future research.

Anna Vilanova, Bernhard Preim, Roy van Pelt et al.

Morphology of cardiovascular tissue is influenced by the unsteady behavior of the blood flow and vice versa. Therefore, the pathogenesis of several cardiovascular diseases is directly affected by the blood-flow dynamics. Understanding flow behavior is of vital importance to understand the cardiovascular system and potentially harbors a considerable value for both diagnosis and risk assessment. The analysis of hemodynamic characteristics involves qualitative and quantitative inspection of the blood-flow field. Visualization plays an important role in the qualitative exploration, as well as the definition of relevant quantitative measures and its validation. There are two main approaches to obtain information about the blood flow: simulation by computational fluid dynamics, and in-vivo measurements. Although research on blood flow simulation has been performed for decades, many open problems remain concerning accuracy and patient-specific solutions. Possibilities for real measurement of blood flow have recently increased considerably by new developments in magnetic resonance imaging which enable the acquisition of 3D quantitative measurements of blood-flow velocity fields. This chapter presents the visualization challenges for both simulation and real measurements of unsteady blood-flow fields.