Image-based Control and Automation of High-speed X-ray Imaging Experiments

Moderne Röntgenbildgebung gibt Aufschluss über die innere Struktur von Objekten aus den verschiedensten Materialien. Der Erfolg solcher Messungen hängt dabei entscheidend von einer geeigneten Wahl der Aufnahmebedingungen ab, von der mechanischen Instrumentierung und von den Eigenschaften der Probe oder des untersuchten Prozesses selbst. Bisher gibt es kein bekanntes Verfahren für autonome Datenakquise, welches auch für sehr verschiedene Röntgenbildgebungsexperimenten die Steuerung über bildbasiertes Feedback erlaubt. Die vorliegende Arbeit setzt sich als Ziel, diese Lücke zu schließen, indem gezielt die hierbei auftretenden Probleme angegangen und gelöst werden: die Auswahl der experimentellen Startparameter, eine schnelle Verarbeitung der aufgenommenen Daten und ein automatisches Feedback zur Korrektur der laufenden Messprozedur. Um die am besten geeigneten experimentellen Bedingungen zu bestimmen, gehen wir von den Grundlagen der Bildentstehung aus und entwickeln ein Framework für dessen Simulation. Dieses ermöglicht uns eine große Bandbreite an virtuellen Röntgenbildgebungsexperimenten durchzuführen, wobei die entscheidenden physikalischen Prozesse auf dem Weg der Röntgenstrahlung von der Quelle bis zum Detektor berücksichtigt werden. Darüber hinaus betrachten wir verschiedene Probenformen und bewegungen, was uns die Simulation von Experimenten wie etwa 4D (zeitaufgelöster) Tomographie ermöglicht. Außerdem entwickeln wir eine autonome Prozedur für die Datenakquise, welches die Startbedingungen des Versuchs dann während der schon laufenden Messung auf Basis schneller Bildanalyse das nachjustiert und auch andere Parameter des Experiments steuern kann. Besonderes Augenmerk legen wir hier auf Hochgeschwindigkeitsexperimente, welche hohen Anforderungen an die Geschwindigkeit der Datenverarbeitung stellen, vor allem wenn die Steuerung auf rechenintensiven Algorithmen wie etwa für die tomographische 3D Rekonstruktion der Probe basiert. Um hierzu einen effizienten Algorithmus zu implementieren, verwenden wir ein hochgradig parallelisiertes Framework. Dessen Ausgabe kann dann zur Berechnung verschiedener Bildmetriken verwendet werden, um quantitative Information über die aufgenommenen Daten zu erhalten. Diese bilden die Grundlage zur Entscheidungsfindung in einem geschlossenen Regelkreis, in dem die Hardware für die Datenakquise betrieben wird. Die Genauigkeit des entwickelten Simulationsframeworks zeigen wir, indem wir virtuelle und reale Experimente vergleichen, die auf Gitterinterferometrie basieren und damit spezielle optische Elemente für die Kontrastbildung einsetzen. Außerdem untersuchen wir im Detail den Einfluss der Bildgebungsbedingungen auf die Genauigkeit des implementierten Algorithmus für gefilterte Rückprojektion, und inwiefern unter dessen Berücksichtigung eine Optimierung der experimentellen Bedingungen möglich ist. Wir demonstrieren die Fähigkeiten des von uns entwickelten Systems zur autonomen Datenakquise anhand eines in-situ Tomographieexperiments, bei dem es basierend auf 3D-Rekonstruktion die Framerate der Kamera optimiert und damit sicherstellt, dass die aufgezeichneten Datensätze ohne Artefakte rekonstruiert werden können. Außerdem nutzen wir unser System, um ein Tomographieexperiment mit hohem Probendurchsatz durchzuführen, bei dem viele ähnliche biologische Proben gescannt werde: Für jede davon wird automatisch die tomographische Rotationsachse bestimmt und schließlich zur Sicherstellung der Qualität schon während der Messung ein komplettes 3D Volumen rekonstruiert. Darüber hinaus führen wir ein in-situ Laminographieexperiment durch, welches die Rissbildung in einer Materialprobe untersucht. Hierbei führt unser System die Datenakquise durch und rekonstruiert einen zentral gelegenen Querschnitt durch die Probe, um dessen korrekte Ausrichtung und die Qualität der Daten sicherzustellen. Unsere Arbeit ermöglicht - basierend auf hochgenauen Simulationen - die Wahl der am besten geeigneten Startbedingungen eines Experiments, deren Feinabstimmung während eines realen Experiments und schließlich dessen automatische Steuerung basierend auf schneller Analyse der gerade aufgezeichneten Daten. Ein solches Vorgehen bei der Datenakquise ermöglicht neuartige in-vivo und in-situ Hochgeschwindigkeitsexperimente, die bedingt durch die hohen Datenraten nicht mehr von einer menschlichen Bedienperson gehandhabt werden könnten

Morphology of powerful suction organs from blepharicerid larvae living in raging torrents

Background: Suction organs provide powerful yet dynamic attachments for many aquatic animals, including octopus, squid, remora, and clingfish. While the functional morphology of suction organs from some cephalopods and fishes has been investigated in detail, there are only few studies on such attachment devices in insects. Here we characterise the morphology and ultrastructure of the suction attachment organs of net-winged midge larvae (genus Liponeura; Diptera: Blephariceridae) – aquatic insects that live on rocks in rapid alpine waterways where flow speeds can reach 3ms⁻¹– using scanning electron microscopy, confocal laser scanning microscopy, and X-ray computed micro-tomography (micro-CT). Furthermore, we study the function of these organs in vivo using interference reflection microscopy. Results: We identified structural adaptations important for the function of the suction attachment organs in L. cinerascens and L. cordata. First, a dense array of spine-like microtrichia covering each suction disc comes into contact with the substrate upon attachment, analogous to hairy structures on suction organs from octopus, clingfish, and remora fish. These spine-like microtrichia may contribute to the seal and provide increased shear force resistance in high-drag environments. Second, specialised rim microtrichia at the suction disc periphery were found to form a continuous ring in close contact and may serve as a seal on a variety of surfaces. Third, a V-shaped cut on the suction disc (“V-notch“) is actively opened via two cuticular apodemes inserting on its flanks. The apodemes are attached to dedicated V-notch opening muscles, thereby providing a unique detachment mechanism. The complex cuticular design of the suction organs, along with specialized muscles that attach to them, allows blepharicerid larvae to generate powerful attachments which can withstand strong hydrodynamic forces and quickly detach for locomotion. Conclusion: The suction organs from Liponeura are underwater attachment devices specialised for resisting extremely fast flows. Structural adaptations from these suction organs could translate into future bioinspired attachment systems that perform well on a wide range of surfaces

Tofu : a fast, versatile and user-friendly image processing toolkit for computed tomography

Tofu is a toolkit for processing large amounts of images and for tomographic reconstruction. Complex image processing tasks are organized as workflows of individual processing steps. The toolkit is able to reconstruct parallel and cone beam as well as tomographic and laminographic geometries. Many pre- and post-processing algorithms needed for high-quality 3D reconstruction are available, e.g. phase retrieval, ring removal and de-noising. Tofu is optimized for stand-alone GPU workstations on which it achieves reconstruction speed comparable with costly CPU clusters. It automatically utilizes all GPUs in the system and generates 3D reconstruction code with minimal number of instructions given the input geometry (parallel/cone beam, tomography/laminography), hence yielding optimal run-time performance. In order to improve accessibility for researchers with no previous knowledge of programming, tofu contains graphical user interfaces for both optimization of 3D reconstruction parameters and batch processing of data with pre-configured workflows for typical computed tomography reconstruction. The toolkit is open source and extensive documentation is available for both end-users and developers. Thanks to the mentioned features, tofu is suitable for both expert users with specialized image processing needs (e.g. when dealing with data from custom-built computed tomography scanners) and for application-specific end-users who just need to reconstruct their data on off-the-shelf hardware

Morphology of powerful suction organs from blepharicerid larvae living in raging torrents

Abstract: Background: Suction organs provide powerful yet dynamic attachments for many aquatic animals, including octopus, squid, remora, and clingfish. While the functional morphology of suction organs from some cephalopods and fishes has been investigated in detail, there are only few studies on such attachment devices in insects. Here we characterise the morphology and ultrastructure of the suction attachment organs of net-winged midge larvae (genus Liponeura; Diptera: Blephariceridae) – aquatic insects that live on rocks in rapid alpine waterways where flow speeds can reach 3 m s− 1 – using scanning electron microscopy, confocal laser scanning microscopy, and X-ray computed micro-tomography (micro-CT). Furthermore, we study the function of these organs in vivo using interference reflection microscopy. Results: We identified structural adaptations important for the function of the suction attachment organs in L. cinerascens and L. cordata. First, a dense array of spine-like microtrichia covering each suction disc comes into contact with the substrate upon attachment, analogous to hairy structures on suction organs from octopus, clingfish, and remora fish. These spine-like microtrichia may contribute to the seal and provide increased shear force resistance in high-drag environments. Second, specialised rim microtrichia at the suction disc periphery were found to form a continuous ring in close contact and may serve as a seal on a variety of surfaces. Third, a V-shaped cut on the suction disc (“V-notch“) is actively opened via two cuticular apodemes inserting on its flanks. The apodemes are attached to dedicated V-notch opening muscles, thereby providing a unique detachment mechanism. The complex cuticular design of the suction organs, along with specialised muscles that attach to them, allows blepharicerid larvae to generate powerful attachments which can withstand strong hydrodynamic forces and quickly detach for locomotion. Conclusion: The suction organs from Liponeura are underwater attachment devices specialised for resisting extremely fast flows. Structural adaptations from these suction organs could translate into future bioinspired attachment systems that perform well on a wide range of surfaces

Juvenile ecology drives adult morphology in two insect orders

Most animals undergo ecological niche shifts between distinct life phases,but such shifts can result in adaptive conflicts of phenotypic traits. Metamor-phosis can reduce these conflicts by breaking up trait correlations, allowingeach life phase to independently adapt to its ecological niche. This process iscalled adaptive decoupling. It is, however, yet unknown to what extentadaptive decoupling is realized on a macroevolutionary scale in hemimeta-bolous insects and if the degree of adaptive decoupling is correlated with thestrength of ontogenetic niche shifts. It is also unclear whether the degree ofadaptive decoupling is correlated with phenotypic disparity. Here, we quan-tify nymphal and adult trait correlations in 219 species across the wholephylogeny of earwigs and stoneflies to test whether juvenile and adulttraits are decoupled from each other. We demonstrate that adult head mor-phology is largely driven by nymphal ecology, and that adult head shapedisparity has increased with stronger ontogenetic niche shifts in some stone-fly lineages. Our findings implicate that the hemimetabolan metamorphosisin earwigs and stoneflies does not allow for high degrees of adaptive decou-pling, and that high phenotypic disparity can even be realized when theevolution of distinct life phases is coupled

Evolution of flexible biting in hyperdiverse parasitoid wasps

One key event in insect evolution was the development of mandibles with two joints, which allowed powerful biting but restricted their movement to a single degree of freedom. These mandibles define the Dicondylia, which constitute over 99% of all extant insect species. It was common doctrine that the dicondylic articulation of chewing mandibles remained unaltered for more than 400 million years. We report highly modified mandibles overcoming the restrictions of a single degree of freedom and hypothesize their major role in insect diversification. These mandibles are defining features of parasitoid chalcid wasps, one of the most species-rich lineages of insects. The shift from powerful chewing to precise cutting likely facilitated adaptations to parasitize hosts hidden in hard substrates, which pose challenges to the emerging wasps. We reveal a crucial step in insect evolution and highlight the importance of comprehensive studies even of putatively well-known systems

Zu den Wurzeln der Modernen Architektur, Teil I

Modern emerging technologies, such as additive manufacturing, bioprinting, and new material production, require novel metrology tools to probe fundamental high-speed dynamics happening in such systems. Here we demonstrate the application of the megahertz (MHz) European X-ray Free-Electron Laser (EuXFEL) to image the fast stochastic processes induced by a laser on water-filled capillaries with micrometer-scale spatial resolution. The EuXFEL provides superior contrast and spatial resolution compared to equivalent state-of-the-art synchrotron experiments. This work opens up new possibilities for the characterization of MHz stochastic processes on the nanosecond to microsecond time scales with object velocities up to a few kilometers per second using XFEL sources

Simulation framework SYRIS tested for microtomography applications at the imaging beamline P05/PETRA III

The Helmholtz-Zentrum Geesthacht, Germany, is operating the user experiments for microtomography at the beamlines P05 and P07 using synchrotron radiation produced in the storage ring PETRA III at DESY, Hamburg, Germany. In recent years the software pipeline and sample changing hardware for performing high throughput experiments were developed. To test and optimize the different measurement techniques together with quantification of the quality of different reconstruction algorithms a software framework to simulate experiments was implemented. Results from simulated microtomography experiments using the photon source characteristics of P05 will be shown