Kevin Mader

A quantitative framework for the 3D characterization of the osteocyte lacunar system

Assessing the role of osteocyte lacunae and the ways in which they communicate with one another is important for determining the function and viability of bone tissue. Osteocytes are able to play a significant role in bone development and remodeling because they can receive nourishment from, interact with, and communicate with other cells. In this sense the immediate environment of an osteocyte is crucial for understanding its function. Modern imaging techniques, ranging from synchrotron radiation-based computed tomography (SR CT) to confocal laser scanning microscopy, produce large volumes of high-quality imaging data of bone tissue on the micrometer scale in rapidly shortening times. These images often contain tens of thousands of osteocytes and their lacunae, void spaces which enclose the osteocytes. While theoretically possible, quantitative analysis of the osteocyte lacunar system is too time consuming to be practical without highly automated tools. Moreover, quantitative morphometry of the osteocyte lacunar system necessitates clearly defined, robust, and three-dimensional (3D) measures. Here, we introduce a framework for the quantitative characterization of millions of osteocyte lacunae and their spatial relationships in 3D. The metrics complement and expand previous works looking at shape and number density while providing novel measures for quantifying spatial distribution and alignment. We developed model, in silico systems to visualize and validate the metrics and provide a concrete example of the attribute being classified with each metric. We then illustrate the applicability to biological samples in a first study comparing two strains of mice and the effect of growth hormone. We found significant differences in shape and distribution between strains for alignment. The proposed quantitative framework can be used in future studies examining differences and treatment effects in bone microstructure at the cell scale. Furthermore, the proposed strategy for quantitative bone cell morphometry will allow investigating structure-function relationships in bone tissue, for example by linking cellular morphometry to bone remodeling.

Assessment of the 3 D Pore Structure and Individual Components of Preshaped Catalyst Bodies by X-Ray Imaging

Porosity in catalyst particles is essential because it enables reactants to reach the active sites and it enables products to leave the catalyst. The engineering of composite‐particle catalysts through the tuning of pore‐size distribution and connectivity is hampered by the inability to visualize structure and porosity at critical‐length scales. Herein, it is shown that the combination of phase‐contrast X‐ray microtomography and high‐resolution ptychographic X‐ray tomography allows the visualization and characterization of the interparticle pores at micro‐ and nanometer‐length scales. Furthermore, individual components in preshaped catalyst bodies used in fluid catalytic cracking, one of the most used catalysts, could be visualized and identified. The distribution of pore sizes, as well as enclosed pores, which cannot be probed by traditional methods, such as nitrogen physisorption and isotherm analysis, were determined.

Quantitative interior x-ray nanotomography by a hybrid imaging technique

Hierarchical structures appear often in life and materials sciences, and their characterization profits greatly from imaging methods that allow seamless probing of various length scales without sacrificing image quality. X-ray tomography is particularly adept at probing 3D structures; however, zooming in on a region of interest results in a loss of quantitativeness of image contrast and suffers from artifacts unless a priori knowledge or assumptions about the sample are used. Here, we demonstrate a hybrid technique that exploits a micrometer-resolution overview to realize ab initio nanoscale interior tomography with quantitative contrast. In a study of avian eggshell, a model for bionanoporous materials, our approach reveals a complex arrangement of vesicles with sizes ranging from hundred nanometers to a few micrometers. We anticipate that such an approach can be widely adopted and benefited from at synchrotron and laboratory sources, for instance, where such zooming capabilities are already present or can be readily realized.

Amelioration of Metabolic Syndrome-Associated Cognitive Impairments in Mice via a Reduction in Dietary Fat Content or Infusion of Non-Diabetic Plasma

Obesity, metabolic syndrome (MetS) and type 2 diabetes (T2D) are associated with decreased cognitive function. While weight loss and T2D remission result in improvements in metabolism and vascular function, it is less clear if these benefits extend to cognitive performance. Here, we highlight the malleable nature of MetS-associated cognitive dysfunction using a mouse model of high fat diet (HFD)-induced MetS. While learning and memory was generally unaffected in mice with type 1 diabetes (T1D), multiple cognitive impairments were associated with MetS, including deficits in novel object recognition, cued fear memory, and spatial learning and memory. However, a brief reduction in dietary fat content in chronic HFD-fed mice led to a complete rescue of cognitive function. Cerebral blood volume (CBV), a measure of vascular perfusion, was decreased during MetS, was associated with long term memory, and recovered following the intervention. Finally, repeated infusion of plasma collected from age-matched, low fat diet-fed mice improved memory in HFD mice, and was associated with a distinct metabolic profile. Thus, the cognitive dysfunction accompanying MetS appears to be amenable to treatment, related to cerebrovascular function, and mitigated by systemic factors.

Three-dimensional foam flow resolved by fast X-ray tomographic microscopy

Thanks to ultra fast and high resolution X-ray tomography, we managed to capture the evolution of the local structure of the bubble network of a 3D foam flowing around a sphere. As for the 2D foam flow around a circular obstacle, we observed an axisymmetric velocity field with a recirculation zone, and indications of a negative wake downstream the obstacle. The bubble deformations, quantified by a shape tensor, are smaller than in 2D, due to a purely 3D feature: the azimuthal bubble shape variation. Moreover, we were able to detect plastic rearrangements, characterized by the neighbor-swapping of four bubbles. Their spatial structure suggest that rearrangements are triggered when films faces get smaller than a characteristic area.

High-throughput phenotyping and genetic linkage of cortical bone microstructure in the mouse.

BackgroundUnderstanding cellular structure and organization, which plays an important role in biological systems ranging from mechanosensation to neural organization, is a complicated multifactorial problem depending on genetics, environmental factors, and stochastic processes. Isolating these factors necessitates the measurement and sensitive quantification of many samples in a reliable, high-throughput, unbiased manner. In this manuscript we present a pipelined approach using a fully automated framework based on Synchrotron-based X-ray Tomographic Microscopy (SRXTM) for performing a full 3D characterization of millions of substructures.ResultsWe demonstrate the framework on a genetic study on the femur bones of in-bred mice. We measured 1300 femurs from a F2 cross experiment in mice without the growth hormone (which can confound many of the smaller structural differences between strains) and characterized more than 50 million osteocyte lacunae (cell-sized hollows in the bone). The results were then correlated with genetic markers in a process called quantitative trait localization (QTL). Our findings provide a mapping between regions of the genome (all 19 autosomes) and observable phenotypes which could explain between 8–40 % of the variance using between 2–10 loci for each trait. This map shows 4 areas of overlap with previous studies looking at bone strength and 3 areas not previously associated with bone.ConclusionsThe mapping of microstructural phenotypes provides a starting point for both structure-function and genetic studies on murine bone structure and the specific loci can be investigated in more detail to identify single gene candidates which can then be translated to human investigations. The flexible infrastructure offers a full spectrum of shape, distribution, and connectivity metrics for cellular networks and can be adapted to a wide variety of materials ranging from plant roots to lung tissue in studies requiring high sample counts and sensitive metrics such as the drug-gene interactions and high-throughput screening.

Identifying layers in random multiphase structures

X-Ray microscopic methods, benefiting from the large penetration depth of X-rays in many materials, enable 3D investigation of a wide variety of samples. This allows for a wide variety of physical, chemical, and biological structures to be seen and explored, in some cases even in real time. Such measurements have lead to insights into paleontology, vulcanology, genetics, and material science. The ability to see and visualize complex systems can provide otherwise unobtainable information on structure, interactions, mechanical behavior, and evolution. The field has, however, led to a massive amount of new, heterogenous, difficult to process data. We present a general, model-free approach for characterizing multiphase 3D systems and show how the method can be applied to experimental X-ray microscopy data to better understand and quantify layer structure in two typical systems: investigation of layered fibers and clay samples.

Moving image analysis to the cloud: A case study with a genome-scale tomographic study

Over the last decade, the time required to measure a terabyte of microscopic imaging data has gone from years to minutes. This shift has moved many of the challenges away from experimental design and measurement to scalable storage, organization, and analysis. As many scientists and scientific institutions lack training and competencies in these areas, major bottlenecks have arisen and led to substantial delays and gaps between measurement, understanding, and dissemination. We present in this paper a framework for analyzing large 3D datasets using cloud-based computational and storage resources. We demonstrate its applicability by showing the setup and costs associated with the analysis of a genome-scale study of bone microstructure. We then evaluate the relative advantages and disadvantages associated with local versus cloud infrastructures.

Coherent X-ray imaging: bridging the gap between atomic and micro-scale investigations.

We present a review of state-of-the art X-ray imaging techniques based on partially coherent synchrotron radiation. Full-field X-ray tomography, X-ray ptychography, scanning small-angle X-ray scattering, and scanning transmission X-ray microscopy are imaging techniques that gather structural information at spatial resolution ranging from several microns to a few tens of nanometers in both real- and reciprocal space. These methods exploit contrast mechanisms based on absorption, phase, and spectroscopic signals. We provide examples of how these techniques can be applied to address scientific questions ranging from imaging of biological samples, to foam rheology, and cement composition.We present a review of state-of-the art X-ray imaging techniques based on partially coherent synchrotron radiation. Full-field X-ray tomography, X-ray ptychography, scanning small-angle X-ray scattering, and scanning transmission X-ray microscopy are imaging techniques that gather structural information at spatial resolution ranging from several microns to a few tens of nanometers in both real- and reciprocal space. These methods exploit contrast mechanisms based on absorption, phase, and spectroscopic signals. We provide examples of how these techniques can be applied to address scientific questions ranging from imaging of biological samples, to foam rheology, and cement composition.