Influence of Morphological Changes in a Source Material on the Growth Interface of 4H-SiC Single Crystals

In this study, the change of mass distribution in a source material is tracked using an in situ computer tomography (CT) setup during the bulk growth of 4H- silicon carbide (SiC) via physical vapor depostion (PVT). The changing properties of the source material due to recrystallization and densification are evaluated. Laser flash measurement showed that the thermal properties of different regions of the source material change significantly before and after the growth run. The Si-depleted area at the bottom of the crucible is thermally insulating, while the residual SiC source showed increased thermal conductivity compared to the initially charged powder. Ex situ CT measurements revealed a needle-like structure with elongated pores causing anisotropic behavior for the heat conductivity. Models to assess the thermal conductivity are applied in order to calculate the changes in the temperature field in the crucible and the changes in growth kinetics are discussed

Comparison of Achievable Contrast Features in Computed Tomography Observing the Growth of a 4H-SiC Bulk Crystal

Today the physical vapor transport process is regularly applied for the growth of bulk SiC crystals. Due to the required high temperature of up to 2400 °C, and low gas pressure of several Mbar inside the crucible, the systems are encapsulated by several layers for heating, cooling and isolation inhibiting the operator from observing the growth. Also, the crucible itself is fully encapsulated to avoid impurities from being inserted into the crystal or disturbing the temperature field distribution. Thus, once the crucible has been set up with SiC powder and the seed crystal, the visible access to the progress of growth is limited. In the past, X-ray radiography has allowed this limitation to be overcome by placing the crucible in between an X-ray source and a radiographic film. Recently these two-dimensional attenuation signals have been extended to three-dimensional density distribution by the technique of computed tomography (CT). Beside the classic X-ray attenuation signal dominated by photoelectric effect, Compton effect and Rayleigh scattering, X-ray diffraction resulting in the crystalline structure of the 4H-SiC superimposes the reconstructed result. In this contribution, the achievable material contrast related to the level of X-ray energy and the absorption effects is analyzed using different CT systems with energies from 125 kV to 9 MeV. Furthermore the X-ray diffraction influence is shown by the comparison between the advanced helical-CT method and the classical 3D-CT

Exploring Flood Filling Networks for Instance Segmentation of XXL-Volumetric and Bulk Material CT Data

XXL-Computed Tomography (XXL-CT) is able to produce large scale volume datasets of scanned objects such as crash tested cars, sea and aircraft containers or cultural heritage objects. The acquired image data consists of volumes of up to and above 10,0003 voxels which can relate up to many terabytes in file size and can contain multiple 10,000 of different entities of depicted objects. In order to extract specific information about these entities from the scanned objects in such vast datasets, segmentation or delineation of these parts is necessary. Due to unknown and varying properties (shapes, densities, materials, compositions) of these objects, as well as interfering acquisition artefacts, classical (automatic) segmentation is usually not feasible. Contrarily, a complete manual delineation is error-prone and time-consuming, and can only be performed by trained and experienced personnel. Hence, an interactive and partial segmentation of so-called “chunks” into tightly coupled assemblies or sub-assemblies may help the assessment, exploration and understanding of such large scale volume data. In order to assist users with such an (possibly interactive) instance segmentation for the data exploration process, we propose to utilize delineation algorithms with an approach derived from flood filling networks. We present primary results of a flood filling network implementation adapted to non-destructive testing applications based on large scale CT from various test objects, as well as real data of an airplane and describe the adaptions to this domain. Furthermore, we address and discuss segmentation challenges due to acquisition artefacts such as scattered radiation or beam hardening resulting in reduced data quality, which can severely impair the interactive segmentation results

3D segmentation of plant root systems using spatial pyramid pooling and locally adaptive field-of-view inference

BackgroundThe non-invasive 3D-imaging and successive 3D-segmentation of plant root systems has gained interest within fundamental plant research and selectively breeding resilient crops. Currently the state of the art consists of computed tomography (CT) scans and reconstruction followed by an adequate 3D-segmentation process.ChallengeGenerating an exact 3D-segmentation of the roots becomes challenging due to inhomogeneous soil composition, as well as high scale variance in the root structures themselves.Approach(1) We address the challenge by combining deep convolutional neural networks (DCNNs) with a weakly supervised learning paradigm. Furthermore, (2) we apply a spatial pyramid pooling (SPP) layer to cope with the scale variance of roots. (3) We generate a fine-tuned training data set with a specialized sub-labeling technique. (4) Finally, to yield fast and high-quality segmentations, we propose a specialized iterative inference algorithm, which locally adapts the field of view (FoV) for the network.ExperimentsWe compare our segmentation results against an analytical reference algorithm for root segmentation (RootForce) on a set of roots from Cassava plants and show qualitatively that an increased amount of root voxels and root branches can be segmented.ResultsOur findings show that with the proposed DCNN approach combined with the dynamic inference, much more, and especially fine, root structures can be detected than with a classical analytical reference method.ConclusionWe show that the application of the proposed DCNN approach leads to better and more robust root segmentation, especially for very small and thin roots

MIFA: Metadata, Incentives, Formats, and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis

Artificial Intelligence methods are powerful tools for biological image analysis and processing. High-quality annotated images are key to training and developing new methods, but access to such data is often hindered by the lack of standards for sharing datasets. We brought together community experts in a workshop to develop guidelines to improve the reuse of bioimages and annotations for AI applications. These include standards on data formats, metadata, data presentation and sharing, and incentives to generate new datasets. We are positive that the MIFA (Metadata, Incentives, Formats, and Accessibility) recommendations will accelerate the development of AI tools for bioimage analysis by facilitating access to high quality training data.Comment: 16 pages, 3 figure

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

Simulationen zur Compton-Kamera und Entwicklung zweier Absorptionsdetektoren auf Halbleiter- und Szintillatorbasis

The Compton-Camera offers a large potential in the future in emission tomography beside PET and SPECT as the third picture-giving procedure due to the efficiency and dose saving. The photons emitted by the patient are scattered in the first detector by a compton interaction and absorbed in a further detector. From the energy deposited in the scatter detector and the two points of interaction the starting point of the photon can be limited to a cone coat. The extension of the connecting line of the points of interaction represents the axis of the cone, the opening angle of the cone is determined by the energy deposited in the scatter detector. By the overlay of many cone coats the distribution of the tracer material in the reconstruction volume (patient) can be determined three-dimensional. A goal of this PHD thesis was to develop the absorption detector for the Compton-Camera. Two solutions, once on basis of a semiconductor detector and once on basis of a scintillation detector, were pursued. As sensor material for the semiconductor detector CdZnTe was selected, since it offers a good resolution of energy at room temperature and a good absorption efficiency. The sensor has an area of 1cm x 1cm and a thickness of 5mm. The anode structure is pixelated by 4 x 4 pixels with a pixel edge length of 2 x 2mm^2. For the 16-p ixel detector a plate for preamplifier electronics, the main amplifier electronics and the trigger logic was developed, with which a simple and flexible measurement without NIM electronics with scatter detector superstructures of the collaboration partners was ensured. The detector module attains at a primary energy of 122keV a mean energy resolution of 3,6% and at 662keV of 1,48% in the photo peak and is somewhat better thereby than the manufacturer data. A crosstalk between the individual pixels could be determined only in very small fraction (0,1%). Thus a detector module is available for the middle energy range up to 700keV with sufficient efficiency and for middle counting rates, which is easily scalable in the size and can be operated at roomtemperature with little effort. The high activities of the tracer applied in clinical applications necessitates an absorption detector with extremely good time resolution, which can be hardly achieved with a semiconductor detector. With scintillation detectors substantially better timing resolutions are possible. However additionally a very good efficiency is demanded at a high primary energy, what leads to an appropriate thickness of the scintillator. To avoid parallax errors with the event reconstruction, a three-dimensional (3D) reconstruction of the point of interaction is necessary. In this work it could be shown that a 3D-reconstruction of the point of interaction is possible in a continuous scintillator block with position-sensitive photomultipliers. For the dimensions selected here a position resolution of less than 1,5mm to 4,0mm in transversal direction and a resolution of depth from less than 1,3mm to 4,5mm could be achieved at a photon energy of 122keV. Thus this kind of 3D-detector is interesting not only for the Compton-Camera but could apply also in PET devices. With Monte Carlo simulations potential absorber materials were examined for the interactions which can be expected. It turned out that with a primary energy of the photons of 511keV also with heavy absorber materials maximally 1/4 are absorbed by photoelectric absorption and a large part of compton and multiple scattering will happen. The investigation of the range of the secondary electrons resulted in no considerable influence on the expected positionresolution of the detectors. Due to the expected large fraction of multiple scattering also the distribution of the energy deposition in the sensormaterials was examined. Despite a high fraction of multiple scattering on the average a relatively compact energy deposition results around the place of the first point of interaction of the photons. For the optimization of the scintillation absorption detector it was copied virtually in the computer with the materials and dimensions. Thus it was easy to investigate the 3d position resolution of the point of interaction depending on different scintillator materials, scintillator thicknesses and at different energies. It could be shown that with lighter scintillator materials (e.g. LaCl_3) due to the higher luminous efficiency and despite the bigger part of multiple scattering a better position resolution can be achieved. Likewise the 3d position resolution can be increased by the reduction of the thickness of the scintillator block due to increasing statistics of the optical photons.Die Compton-Kamera bietet in der Zukunft in der Emissionstomographie neben PET und SPECT als drittes bildgebendes Verfahren aufgrund der Effizienz und der Dosiseinsparung ein großes Potential. Die vom Patienten emittierten Photonen werden in dem ersten Detektor durch eine Comptonwechselwirkung gestreut und in einem weiteren Detektor absorbiert. Aus der in dem Streudetektor deponierten Energie und den beiden Wechselwirkungsorten kann der Startort des Photons auf einen Kegelmantel begrenzt werden. Die Verlängerung der Verbindungslinie der Wechselwirkungsorte stellt die Achse des Kegels dar, der Öffnungswinkel des Kegels kann durch die im Streudetektor deponierte Energie berechnet werden. Durch die Überlagerung vieler Kegelmäntel lässt sich die Verteilung des Tracermaterials im Rekonstruktionsvolumen (Patienten) 3-dimensional bestimmen. Ziel dieser Doktorarbeit war es, den Absorptionsdetektor für die Compton-Kamera zu entwickeln. Dabei wurden zwei Lösungsansätze, einmal auf Basis eines Halbleiterdetektors und einmal auf Basis eines Szintillationsdetektors, verfolgt. Als Sensormaterial für den Halbleiterdetektor wurde CdZnTe gewählt, da es neben einem guten Absorptionsvermögen auch bei Raumtemperatur eine gute Energieauflösung bietet. Der Sensor hat eine Fläche von 1cm x 1 cm und eine Dicke von 5mm. Die Anodenstruktur hat eine Pixelierung von 4 x 4 Pixeln mit einer Pixelkantenlänge von 2 x 2mm^2. Passend zu dem 16-Pixel Detektor wurde eine Platine für die Vorverstärkerelektronik, die Hauptverstärkerelektronik und die Triggerlogik entwickelt, womit eine einfache und flexible Messung ohne NIM-Elektronik mit den Streudetektoraufbauten der Kollaborationspartner gewährleistet war. Das Detektormodul erreicht bei einer Primärenergie von 122keV eine mittlere Energieauflösung von 3,6% und bei 662keV von 1,48% im Photopeak und ist damit etwas besser als die Herstellerangabe. Ein übersprechen zwischen den einzelnen Pixeln konnte nur in sehr geringem Maße festgestellt werden (0,1%). Damit steht ein günstiges Detektormodul für den mittleren Energiebereich bis zu 700keV mit ausreichender Effizienz und für mittlere Zählraten zur Verfügung, das in der Größe leicht skalierbar ist und bei Raumtemperatur mit wenig Aufwand betrieben werden kann. Die im klinischen Bereich applizierten hohen Aktivitäten des Tracers machen einen Absorptionsdetektor mit extrem guter Zeitauflösung notwendig, die mit einem Halbleiterdetektor nur schwer erreicht werden kann. Mit Szintillationsdetektoren sind wesentlich bessere Zeitauflösungen möglich. Allerdings ist zusätzlich eine sehr gute Effizienz bei einer hohen Primärenergie gefordert, was zu einer entsprechenden Dicke des Szintillators führt. Um Parallaxenfehler bei der Ereignisrekonstruktion zu vermeiden ist eine dreidimensionale (3D) Rekonstruktion des Wechselwirkungspunktes notwendig. In dieser Arbeit konnte gezeigt werden, dass eine 3D-Rekonstruktion des Wechselwirkungspunktes in einem kontinuierlichen Szintillatorblock mit positionsempfindlichen Photomultipliern möglich ist. Für die hier gewählten Abmessungen konnte bei einer Photonenenergie von 122keV eine Auflösung von unter 1,5mm bis 4,0mm in transversaler Richtung und eine Tiefenauflösung von unter 1,3mm bis 4,5mm erreicht werden. Damit ist diese Art von 3D-Detektor nicht nur für die Compton-Kamera interessant, sondern könnte auch in PET-Geräten ihre Anwendung finden. Mit Hilfe von Monte-Carlo-Simulationen wurden potentielle Absorbermaterialien auf die zu erwartenden Wechselwirkungen untersucht. Dabei stellte sich heraus, dass bei einer Primärenergie von 511keV auch bei schweren Absorbermaterialien maximal 1/4 der eingestrahlten Photonen durch Photoabsorption absorbiert werden und mit einem großen Anteil an Compton- und Mehrfachstreuung zu rechnen ist. Die Untersuchung der Reichweite der Sekundärelektronen der Wechselwirkungen ergab, keinen nennenswerten Einfluss auf die zu erwartende Ortsauflösung der Detektoren. Aufgrund der Häufigkeit der zu erwartenden Mehrfachstreuung wurde auch die Verteilung der Energiedeposition in den Sensormaterialien untersucht. Trotz eines hohen Anteils an Mehrfachstreuung ergibt sich im Mittel eine relativ kompakte Energiedeposition um den Ort der ersten Wechselwirkung der Photonen. Zur Optimierung des Szintillations-Absorptionsdetektors wurde dieser virtuell im Computer mit den realen Abmessungen nachgebaut. Damit war es möglich verschiedene Szintillatormaterialien und Szintillatordicken bei unterschiedlichen Energien auf die zu erreichenden 3D-Ortsauflösung des Wechselwirkungsortes hin zu untersuchen. Dabei zeigte sich, dass mit leichteren Szintillatormaterialien (z.B. LaCl_3) aufgrund der höheren Lichtausbeute und trotz des höheren Mehrfachstreuanteils eine bessere Ortsauflösung erreicht werden kann. Ebenso lässt sich die 3D-Ortsauflösung durch Reduzierung der Dicke des Szintillatorblocks aufgrund zunehmender Statistik der optischen Photonen deutlich steigern