Scalable robust graph and feature extraction for arbitrary vessel networks in large volumetric datasets.

Background: Recent advances in 3D imaging technologies provide novel insights to researchers and reveal finer and more detail of examined specimen, especially in the biomedical domain, but also impose huge challenges regarding scalability for automated analysis algorithms due to rapidly increasing dataset sizes. In particular, existing research towards automated vessel network analysis does not always consider memory requirements of proposed algorithms and often generates a large number of spurious branches for structures consisting of many voxels. Additionally, very often these algorithms have further restrictions such as the limitation to tree topologies or relying on the properties of specific image modalities.

Three-Dimensional Visualization of the Lymphatic Vasculature.

Like the circulatory blood vessel system, the dendriform lymphatic vascular system forms a disseminated organ that is virtually indispensible for the function of most other organs. Formation and maintenance of the correct topology are essential for lymph vessel physiology and hence analysis of its three-dimensional architecture provides crucial functional information.Here we describe protocols for whole-mount immunostaining of the vessel systems in various mouse tissues, mouse fetuses, and human skin biopsies.

Automatic non-invasive heartbeat quantification of Drosophila pupae.

The importance of studying model organisms such as Drosophila melanogaster has significantly increased in recent biological research. Amongst others, Drosophila can be used to study heart development and heartbeat related diseases. Here we propose a method for automatic in vivo heartbeat detection of Drosophila melanogaster pupae based on morphological structures which are recorded without any dissection using FIM imaging.

VIPAR, a quantitative approach to 3D histopathology applied to lymphatic malformations.

Background: Lack of investigatory and diagnostic tools has been a major contributing factor to the failure to mechanistically understand lymphedema and other lymphatic disorders in order to develop effective drug and surgical therapies. One difficulty has been understanding the true changes in lymph vessel pathology from standard 2D tissue sections.

Methods: VIPAR (volume information-based histopathological analysis by 3D reconstruction and data extraction), a light-sheet microscopy-based approach for the analysis of tissue biopsies, is based on digital reconstruction and visualization of microscopic image stacks.

Statistical Permutation-based Artery Mapping (SPAM): a novel approach to evaluate imaging signals in the vessel wall.

Background: Cardiovascular diseases are the leading cause of death worldwide. A prominent cause of cardiovascular events is atherosclerosis, a chronic inflammation of the arterial wall that leads to the formation of so called atherosclerotic plaques. There is a strong clinical need to develop new, non-invasive vascular imaging techniques in order to identify high-risk plaques, which might escape detection using conventional methods based on the assessment of the luminal narrowing.

Interactive Exploration of Cosmological Dark-Matter Simulation Data.

The winning entry of the 2015 IEEE Scientific Visualization Contest, this article describes a visualization tool for cosmological data resulting from dark-matter simulations. The proposed system helps users explore all aspects of the data at once and receive more detailed information about structures of interest at any time. Moreover, novel methods for visualizing and interactively exploring dark-matter halo substructures are proposed.