Investigation of materials for catalysis with electron tomography

Elektronentomographie mit dem Transmissionselektronenmikroskop (TEM) ermöglicht die Erstellung dreidimensionaler Darstellungen (Tomogramme) von Proben in der Größenordnung von einigen Nanometern bis hin zu einigen Mikrometern. Im Rahmen dieser Arbeit wurden verschiedene auf Ruthenium basierende Werkstoffe für die Katalyse in Brennstoffzellen untersucht. Die Tomographie liefert, im Gegensatz zu gewöhnlichen TEM Bildern (Projektionen), Aufschluss über die Verteilung und Erreichbarkeit der Katalysatorpartikel auf bzw. in dem Trägermaterial. Es konnte gezeigt werden, dass neben qualitativen Vergleichen der Verteilung der Rutheniumpartikel auf/in dem Kohleträgermaterial verschieden hergestellter Proben auch detaillierte quantitative Analysen möglich sind. Da die Katalyse an heterogenen Katalysatoren an der Oberfläche des Katalysators stattfindet, spielen neben der Größe der Oberfläche auch die unterschiedlichen Koordinationszahlen verschieden orientierter Facetten der Katalysatorpartikel eine Rolle. Dazu wurde erstmalig ein Algorithmus entwickelt, der es erlaubt, viele verschiedene Partikel in dreidimensionalen Datensätzen automatisch hinsichtlich Facettierung zu analysieren. Durch die teilweise Einbettung der Katalysatorpartikel in das Trägermaterial ist eine Unterscheidung der bedeckten und unbedeckten Oberfläche nötig, da nur der unbedeckte Teil der Katalysatoroberfläche von den Reaktanten erreicht werden kann. Neben dieser unbedeckten Oberfläche ist durch die teilweise Einbettung auch die Ausrichtung der Katalysatorpartikel in Bezug zur lokalen Oberfläche des Trägers bedeutsam, da so statistische Untersuchungen der unbedeckten Facettentypen möglich werden. Zu den durchgeführten Charakterisierungen wie: Partikelverteilung innerhalb des Trägers, Größenverteilung, Oberflächen, Volumina, Formanalyse und der lokalen Ausrichtung, wurden Erkenntnisse gewonnen, die es erlauben, den untersuchten Katalysatortyp während der Herstellung weiter zu optimieren. Es konnte zudem gezeigt werden, dass die entwickelten Bildanalysemethoden sich auch auf tomographische Datensätze anderer Messmethoden wie z.B. Neutronen- und Focused Ion Beam-Tomographie anwenden lassen.Electron tomography with a transmission electron microscope (TEM) enables creation of three-dimensional representations (tomograms) of samples in the range of a few nanometres to a few micrometres. In the frame of this thesis different ruthenium-based materials for catalysis in fuel cells were investigated. Tomography, in contrast to common TEM images (projections), yields information about the distribution and accessibility of the catalyst particles on or in the support material. It was shown that in addition to qualitative comparisons of the distribution of ruthenium particles on/in the carbon support material of differently manufactured samples, quantitative analyses are also possible. Since catalysis on heterogeneous catalysts takes place at the surface of the catalyst, the amount of surface area matters as do the coordination numbers of differently oriented facets of the catalyst particles. For this purpose a new algorithm was developed that allows to automatically analyse faceting of many different particles in a three-dimensional dataset. Due to the partial embedding of the catalyst particles into the support material only the uncovered fraction of the catalyst surface is accessible to the reactants and therefore a differentiation between the covered and uncovered catalyst surface is necessary. Apart from this uncovered surface, the orientation of the catalyst particles relative to the local support surface is also important since this allows statistical investigation of the uncovered facet types. In addition to the conducted characterizations such as: particle distribution within the support, size distribution, surface areas, volumes, shape analysis and the local orientation, new insights were gained which allow optimization of the examined catalyst during production. Furthermore, it could be shown that the developed image analysis methods can be applied to tomographic datasets from other measurement techniques such as neutron and focused ion beam tomography

Registration of serial sections: An evaluation method based on distortions of the ground truths

Registration of histological serial sections is a challenging task. Serial sections exhibit distortions and damage from sectioning. Missing information on how the tissue looked before cutting makes a realistic validation of 2D registrations extremely difficult. This work proposes methods for ground-truth-based evaluation of registrations. Firstly, we present a methodology to generate test data for registrations. We distort an innately registered image stack in the manner similar to the cutting distortion of serial sections. Test cases are generated from existing 3D data sets, thus the ground truth is known. Secondly, our test case generation premises evaluation of the registrations with known ground truths. Our methodology for such an evaluation technique distinguishes this work from other approaches. Both under- and over-registration become evident in our evaluations. We also survey existing validation efforts. We present a full-series evaluation across six different registration methods applied to our distorted 3D data sets of animal lungs. Our distorted and ground truth data sets are made publicly available.Comment: Supplemental data available under https://zenodo.org/record/428244

mattools/matImage: MatImage 1.2.4

MatImage is an image processing library for Matlab. It is build as a complement of the Image Processing Toolbox. The matImage library is divided into several modules: imFilters - Image filtering (smooth, enhance, gradient...) imMeasures - Measurement of various parameters in digital images imStacks - Functions for manipulation and display of 3D images imMinkowski - Geometric measures (Surface, Perimeter...) in 2D or 3D imGeodesics - Propagation of geodesic distances in images imGranulometry - Compute granulometry curves on grayscale images imShapes - Generation of images representing geometric shapes Improvements Version 1.2.4 fixes several bugs and introduces some new features. added imCropOrientedBox function to extract a rotated portion within an image added imTangentCrop and imTangentCrop3d.m to automatically evaluate orientation of rotated crop added gradientKernels and gradientKernels3d to factorize computation of gradients within 2D/3D images imFeretDimater: added support for 3D diameter several refactoring in "imGranulometry" module. updated the user manua

AlvAnimation.mp4

Short animation of a rotating 3D alveolar model. It depicts the alveolar surface. Flat areas of the surface are colored arbitrarily, curved regions are colored in grey.</p

Method for 3D Airway Topology Extraction

In lungs the number of conducting airway generations as well as bifurcation patterns varies across species and shows specific characteristics relating to illnesses or gene variations. A method to characterize the topology of the mouse airway tree using scanning laser optical tomography (SLOT) tomograms is presented in this paper. It is used to test discrimination between two types of mice based on detected differences in their conducting airway pattern. Based on segmentations of the airways in these tomograms, the main spanning tree of the volume skeleton is computed. The resulting graph structure is used to distinguish between wild type and surfactant protein (SP-D) deficient knock-out mice

Combination of µCT and light microscopy for generation-specific stereological analysis of pulmonary arterial branches: a proof-of-concept study.

Various lung diseases, including pulmonary hypertension, chronic obstructive pulmonary disease or bronchopulmonary dysplasia, are associated with structural and architectural alterations of the pulmonary vasculature. The light microscopic (LM) analysis of the blood vessels is limited by the fact that it is impossible to identify which generation of the arterial tree an arterial profile within a LM microscopic section belongs to. Therefore, we established a workflow that allows for the generation-specific quantitative (stereological) analysis of pulmonary blood vessels. A whole left rabbit lung was fixed by vascular perfusion, embedded in glycol methacrylate and imaged by micro-computed tomography (µCT). The lung was then exhaustively sectioned and 20 consecutive sections were collected every 100 µm to obtain a systematic uniform random sample of the whole lung. The digital processing involved segmentation of the arterial tree, generation analysis, registration of LM sections with the µCT data as well as registration of the segmentation and the LM images. The present study demonstrates that it is feasible to identify arterial profiles according to their generation based on a generation-specific color code. Stereological analysis for the first three arterial generations of the monopodial branching of the vasculature included volume fraction, total volume, lumen-to-wall ratio and wall thickness for each arterial generation. In conclusion, the correlative image analysis of µCT and LM-based datasets is an innovative method to assess the pulmonary vasculature quantitatively

A combined method for correlative 3D imaging of biological samples from macro to nano scale

Correlative analysis requires examination of a specimen from macro to nano scale as well as applicability of analytical methods ranging from morphological to molecular. Accomplishing this with one and the same sample is laborious at best, due to deformation and biodegradation during measurements or intermediary preparation steps. Furthermore, data alignment using differing imaging techniques turns out to be a complex task, which considerably complicates the interconnection of results. We present correlative imaging of the accessory rat lung lobe by combining a modified Scanning Laser Optical Tomography (SLOT) setup with a specially developed sample preparation method (CRISTAL). CRISTAL is a resin-based embedding method that optically clears the specimen while allowing sectioning and preventing degradation. We applied and correlated SLOT with Multi Photon Microscopy, histological and immunofluorescence analysis as well as Transmission Electron Microscopy, all in the same sample. Thus, combining CRISTAL with SLOT enables the correlative utilization of a vast variety of imaging techniques