arXiv subjects

Boudewijn Lelieveldt

Publications and source records attributed to Boudewijn Lelieveldt.

5 recordsLinked to original sources

arXiv2026

Manifold-Preserving Superpixel Hierarchies and Embeddings for the Exploration of High-Dimensional Images

High-dimensional images, or images with a high-dimensional attribute vector per pixel, are commonly explored with coordinated views of a low-dimensional embedding of the attribute space and a conventional image representation. Nowadays, such images can easily contain several million pixels. For such large datasets, hierarchical embedding techniques are better suited to represent the high-dimensional attribute space than flat dimensionality reduction methods. However, available hierarchical dimensionality reduction methods construct the hierarchy purely based on the attribute information and ignore the spatial layout of pixels in the images. This impedes the exploration of regions of interest in the image space, since there is no congruence between a region of interest in image space and the associated attribute abstractions in the hierarchy. In this paper, we present a superpixel hierarchy for high-dimensional images that takes the high-dimensional attribute manifold into account during construction. Through this, our method enables consistent exploration of high-dimensional images in both image and attribute space. We show the effectiveness of this new image-guided hierarchy in the context of embedding exploration by comparing it with classical hierarchical embedding-based image exploration in two use cases.

cs.CV↗

arXiv2023

ManiVault: A Flexible and Extensible Visual Analytics Framework for High-Dimensional Data

Exploration and analysis of high-dimensional data are important tasks in many fields that produce large and complex data, like the financial sector, systems biology, or cultural heritage. Tailor-made visual analytics software is developed for each specific application, limiting their applicability in other fields. However, as diverse as these fields are, their characteristics and requirements for data analysis are conceptually similar. Many applications share abstract tasks and data types and are often constructed with similar building blocks. Developing such applications, even when based mostly on existing building blocks, requires significant engineering efforts. We developed ManiVault, a flexible and extensible open-source visual analytics framework for analyzing high-dimensional data. The primary objective of ManiVault is to facilitate rapid prototyping of visual analytics workflows for visualization software developers and practitioners alike. ManiVault is built using a plugin-based architecture that offers easy extensibility. While our architecture deliberately keeps plugins self-contained, to guarantee maximum flexibility and re-usability, we have designed and implemented a messaging API for tight integration and linking of modules to support common visual analytics design patterns. We provide several visualization and analytics plugins, and ManiVault's API makes the integration of new plugins easy for developers. ManiVault facilitates the distribution of visualization and analysis pipelines and results for practitioners through saving and reproducing complete application states. As such, ManiVault can be used as a communication tool among researchers to discuss workflows and results. A copy of this paper and all supplemental material is available at https://osf.io/9k6jw and source code at https://github.com/ManiVaultStudio.

cs.HC↗

arXiv2022

Incorporating Texture Information into Dimensionality Reduction for High-Dimensional Images

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.

cs.CV↗

arXiv2019

Hierarchical stochastic neighbor embedding as a tool for visualizing the encoding capability of magnetic resonance fingerprinting dictionaries

In Magnetic Resonance Fingerprinting (MRF) the quality of the estimated parameter maps depends on the encoding capability of the variable flip angle train. In this work we show how the dimensionality reduction technique Hierarchical Stochastic Neighbor Embedding (HSNE) can be used to obtain insight into the encoding capability of different MRF sequences. Embedding high-dimensional MRF dictionaries into a lower-dimensional space and visualizing them with colors, being a surrogate for location in low-dimensional space, provides a comprehensive overview of particular dictionaries and, in addition, enables comparison of different sequences. Dictionaries for various sequences and sequence lengths were compared to each other, and the effect of transmit field variations on the encoding capability was assessed. Clear differences in encoding capability were observed between different sequences, and HSNE results accurately reflect those obtained from an MRF matching simulation.

eess.IV↗

arXiv2019

A community-based transcriptomics classification and nomenclature of neocortical cell types

To understand the function of cortical circuits it is necessary to classify their underlying cellular diversity. Traditional attempts based on comparing anatomical or physiological features of neurons and glia, while productive, have not resulted in a unified taxonomy of neural cell types. The recent development of single-cell transcriptomics has enabled, for the first time, systematic high-throughput profiling of large numbers of cortical cells and the generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data have revealed the existence of clear clusters, many of which correspond to cell types defined by traditional criteria, and which are conserved across cortical areas and species. To capitalize on these innovations and advance the field, we, the Copenhagen Convention Group, propose the community adopts a transcriptome-based taxonomy of the cell types in the adult mammalian neocortex. This core classification should be ontological, hierarchical and use a standardized nomenclature. It should be configured to flexibly incorporate new data from multiple approaches, developmental stages and a growing number of species, enabling improvement and revision of the classification. This community-based strategy could serve as a common foundation for future detailed analysis and reverse engineering of cortical circuits and serve as an example for cell type classification in other parts of the nervous system and other organs.

q-bio.GN↗