The Helmholtz-Zentrum Hereon, 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. Attenuation-contrast and phase-contrast techniques were established to provide an imaging tool for applications in biology, medical science and materials science. In the recent years we rebuilt the data preprocessing pipeline before reconstruction to provide different scanning techniques to investigate samples larger than the field of view of the x-ray beam. Within this paper the hardware requirements and calibration used at the imaging stations will be given. Furthermore, we adjust the preprocessing pipeline to deal with different mechanical accuracies of the translation / rotation stages used for addressing the full volume of the sample. Several examples using low photon energies at P05 and high photon energies at P07 will demonstrate the new stitching pipeline.
This study explores recent developments in quantitative phase-contrast microtomography using Talbot Array Illuminators (TAI) combined with Unified Modulated Pattern Analysis (UMPA). We first compare the performance of the TAI-based method for phase-retrieval with propagation-based imaging (PBI) for analyzing a Mg-10Gd bone implant sample that violates the single-material assumption. Our results demonstrate that the TAI method yields a significantly higher contrast-to-noise ratio (CNR) compared to PBI (101.68 vs. 54.37, an 87% improvement) while maintaining comparable edge sharpness. The TAI method also visualizes a substructure of the degradation layer, which appears comparatively blurred in the PBI images. Additionally, we introduce a hanging-rotation-axis approach for imaging paraffin-embedded samples in an ethanol bath, aiming to reduce edge enhancement artifacts caused by large electron density differences. Preliminary results indicate that the TAI-based images of a paraffin-embedded lymph node show improved uniformity in background intensity, though some additional low-frequency noise is observed. All experiments were conducted at the High Energy Materials Beamline (HEMS), PETRA III, DESY, operated by Hereon. Our findings highlight the potential of TAI-based phase-contrast imaging for complex, multi-material samples and suggest avenues for further optimization of the technique.
The Helmholtz-Zentrum Hereon is operating imaging beamlines for X-ray tomography (P05 IBL, P07 HEMS) for academic and industrial users at the synchrotron-radiation source PETRA III at DESY in Hamburg, Germany. The high flux density and coherence of synchrotron radiation enable high-resolution in situ/operando/in vivo tomography experiments and phase-contrast imaging techniques, respectively. Large amounts of 3D and 4D data are collected that are difficult to process and analyze. Recently, we have explored machine learning approaches for the reconstruction, processing and analysis of synchrotron-radiation tomography data. Here, we report on the application of supervised learning for multimodal data analysis to generate a virtual 3D histology, digital volume correlation of 4D in situ tomography data, and instance segmentation. Furthermore, we present findings related to unsupervised learning in the context of semantic segmentation.
Phase-contrast computed tomography enables the visualization of weakly-absorbing samples with high contrast. Speckle-based imaging (SBI) is a phase-sensitive X-ray imaging technique that requires the use of a wavefront marker (typically a sandpaper) to retrieve multi-modal information: absorption, refraction and scattering. These quantities are derived by analyzing the distortions in a reference pattern generated when the sample is inserted into the beam. The Unified Modulated Pattern Analysis (UMPA) model is a speckle-tracking method capable of processing such datasets. While high-resolution tomographic reconstructions can be achieved at the synchrotron, there is usually a trade-off with sample dimensions. Here, we use UMPA with a multi-frame approach for signal retrieval, enabling the expansion of the reconstructed field-of-view (FOV) by moving the sample instead of the modulator transversely to the beam. We demonstrate this technique on a human placental tissue sample.
The Helmholtz-Zentrum Hereon is operating imaging beamlines for X-ray tomography (P05 IBL, P07 HEMS) for academic and industrial users at the synchrotron radiation source PETRA III at DESY in Hamburg, Germany. The high X-ray flux density and coherence of synchrotron radiation enables high-resolution in situ/operando/vivo tomography experiments and provides phase contrast, respectively. Large amounts of 3D/4D data are collected that are difficult to process and analyze. Here, we report on the application of machine learning for image segmentation including a guided interactive framework, multimodal data analysis (virtual histology), image enhancement (denoising), and self-supervised learning for phase retrieval.
KEYWORDS: Tomography, Image segmentation, Monte Carlo methods, Performance modeling, Bone, Process modeling, Data acquisition, Analytical research, Web services, Synchrotron radiation
The Helmholtz-Zentrum Hereon is operating several tomography end stations at the beamlines P05 and P07 of the synchrotron radiation facility PETRA III at DESY in Hamburg, Germany. Attenuation and phase contrast imaging techniques are provided as well as sample environments for in situ/operando/vivo experiments for applications in biology, medicine, materials science, etc. Very large and diverse data sets with varying spatiotemporal resolution, noise levels and artifacts are acquired which are challenging to process and analyze. Here we report on an active learning approach for the semantic segmentation of tomography data using a guided and interactive framework, and evaluate different acquisition functions for the selection of images to be annotated in the iterative process.
Previously, we designed a new quantitative phase-contrast setup for the microtomography experiments at the hereon beamlines P05 and P07 at PETRA III, DESY. This setup is based on Talbot array illuminators (TAI) as high visibility wavefront markers and can reach a spatial resolution level comparable to propagation-based imaging. In this work, we focus on the progress of bringing this setup into user operation. We collaborated with INI-Research to investigate the vascular system of mouse lymph nodes, exploiting the spatial resolution capabilities and using the quantitative aspect of the data to compare different sample preparation methods. We could successfully visualize and trace the blood supply of the lymph nodes, even with fine capillaries, showing the stability and performance of the setup in user application.
The Helmholtz-Zentrum Hereon, 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. Attenuation-contrast and phase-contrast techniques were established to provide an imaging tool for applications in biology, medical science and materials science. Within the recent years we built an imaging pipeline to optimize the deliverd radiation dose onto the sample with respect to the applied imaging technique. This became possible by the modernisation of the experiment control and the integration of different imaging detectors. In combination with an new concept for a high-speed X-ray shutter the applied radiation dose can be adjusted from high, for optimization of the statistic within the tomogram, to low, for avoiding any radiation based artefact. Within this talk the recent hardware and software developments integrated to the microtomography imaging system at the beamlinew P05/PETRA III and P07/PETRA III will be presented. Furthermore, the optimization of dose will be demonstrated on selected samples.
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. Attenuation-contrast and phase-contrast techniques were established to provide an imaging tool for applications in biology, medical science and materials science. In the recent years we rebuilt the integration of imaging detectors. This allows the user to choose from a set of cameras based on different CMOS and CCD sensors. Here we will present the features of the different camera system together with the advantage for different applications. Furthermore, we rebuilt the data preprocessing before reconstruction to provide different scanning techniques to investigate samples larger than the field of view of the X-ray beam. Multi-scale tomography is realized by using different setups or to integrate a low-resolution together with a high-resolution region-of-interest invest
GEMS is the user platform of Helmholtz-Zentrum Geesthacht with a unique infrastructure for complementary research with photons and neutrons. The instruments using synchrotron radiation are operated at DESY in Hamburg, the instruments using neutrons are located at the research reactor FRM II of the Heinz Maier-Leibnitz Center (MLZ) in Garching near Munich. GEMS provides methods for applied materials research to user groups from both industry and science. At the PETRA III synchrotron storage ring of the German Electron Synchrotron (DESY), GEMS operates instruments for tomographic analyses from the micro- to the nanoscale. The high-energy tomography station of the beamline HEMS/P07 uses photon energies from 50 to 200 keV. A robot sample changer enables automated high-throughput measurements. The beamline is therefore of special interest for industrial users, especially from the metal industry sector. In this contribution we introduce the tomography set-up at HEMS and the possibilities for industrial access, together with examples for tomography of challenging highly-absorbing samples.
Phase-contrast imaging is one of the standard X-ray imaging methods at synchrotron beamlines and has already proven to be beneficial for soft-tissue visualization. However, most implementations use single-distance inline phase-contrast techniques, and are thus not able to provide quantitative information. To access these, grating-based imaging (GBI) setups or, rather recently, speckle-based imaging (SBI) methods can be used. We built a new grating-based setup at the beamline P05 operated by HZG at the storage ring PETRA III / DESY. This new setup overcomes the previously reported limitations in spatial resolution compared to inline phase-contrast imaging. Furthermore, it allows for accurate quantitative phase contrast micro computed tomography of biological soft tissue. We replaced the typically used sandpaper by a 2D phase-grating as a wavefront marker, which increased the visibility and allowed for using fewer phase steps. Combined with an existing SBI phase-retrieval algorithm, the so-called Unified Modulated Pattern Analysis (UMPA) and an optimized scan protocol, we reached a resolution below 4 microns in scan times less than two hours. We investigated stained and unstained tissue samples, to quantify the staining process of different tissue types and were able to observe an increase in electron density, dependent on the stain and tissue type. By this, we could show the successful operation of our setup to quantitatively investigate samples on a micro meter scale at the beamline P05.
Microtomography using synchrotron radiation has proven to be a valuable tool for characterizing samples within biology, medical science, paleontology and materials science. A variety of attenuation contrast and phase-contrast imaging techniques were established to focus on spatial resolution, density resolution, and temporal resolution. In this paper, we focus on the recent developments at beamline P07 at PETRA III, Hamburg, Germany, for high-energy microtomography to provide high-density resolution for the study of a fossil tooth sample. Due to the integration of two independent CCDs for alternating use within the X-ray detector the imaging throughput was doubled. The concept, the alignment process, and first results are presented.
A load frame for in situ mechanical testing is developed for the microtomography end stations at the imaging beamline P05 and the high-energy material science beamline P07 of PETRA III at DESY, both operated by the Helmholtz- Zentrum Geesthacht. The load frame is fully integrated into the beamline control system and can be controlled via a feedback loop. All relevant parameters (load, displacement, temperature, etc.) are continuously logged. It can be operated in compression or tensile mode applying forces of up to 1 kN and is compatible with all contrast modalities available at IBL and HEMS i.e. conventional attenuation contrast, propagation based phase contrast and differential phase contrast using a grating interferometer. The modularity and flexibility of the load frame allows conducting a wide range of experiments. E.g. compression tests to understand the failure mechanisms in biodegradable implants in rat bone or to investigate the mechanics and kinematics of the tessellated cartilage skeleton of sharks and rays, or tensile tests to illuminate the structure-property relationship in poplar tension wood or to visualize the 3D deformation of the tendonbone insertion. We present recent results from the experiments described including machine-learning driven volume segmentation and digital volume correlation of load tomography sequences.
The three-dimensional (3D) architecture of organs, tissues and cells together with the spatial distribution of specific molecules, both enables and drives the close interactions between hosts and microbes. To image the 3D anatomy and molecular composition of an animal-microbe system at a single cell scale we developed a correlative workflow combining phase-contrast synchrotron radiation based micro-computed tomography (PC-SRμCT) and mass spectrometry imaging (MSI). The key challenge in combining both techniques was the synchronization of sample preparation and imaging conditions. We used PC-SRμCT for high-resolution 3D imaging, which is the most suitable x-ray tomographic technique to image soft tissue samples without contrast enhancing agents at a single-cell level. For method development, we used small invertebrates that live in symbiosis with bacteria. For PC-SRμCT samples were paraformaldehyde-fixed and submersed in a buffer-filled capillary. We tested sample preparation for Matrix-assisted laser desorption ionization (MALDI)-MSI after PC-SRμCT and achieved the best results for PFA-fixed samples, processed under cryogenic conditions. The resulting molecular composition permitted imaging of hundreds of different molecule distributions from single tissue sections on a micrometer resolution. Image analysis revealed organ- and cell-specific metabolite distributions, which we could match to corresponding structures in the anatomical 3D PC-SRμCT model.
Our PC-SRμCT-MSI sample preparation- and imaging workflow results in a detailed 3D scenario, which provides an atlas to guide other microscopy or omics approaches towards specific organs and cells. Particularly, for animal-microbe systems this approach presents a powerful tool to visualize anatomical and chemical processes at a microscale, linking structure and function in the symbiosis.
Water transport from roots to shoots is a vital necessity in trees in order to sustain their photosynthetic activity and, hence, their physiological activity. The vascular tissue in charge is the woody body of root, stem and branches. In gymnosperm trees, like spruce trees (Picea abies (L.) Karst.), vascular tissue consists of tracheids: elongated, protoplast- free cells with a rigid cell wall that allow for axial water transport via their lumina. In order to analyze the over-all water transport capacity within one growth ring, time-consuming light microscopy analysis of the woody sample still is the conventional approach for calculating tracheid lumen area. In our investigations at the Imaging Beamline (IBL) operated by the Helmholtz-Zentrum Geesthacht (HZG) at PETRA III storage ring of the Deutsches Elektronen-Synchrotron DESY, Hamburg, we applied SRμCT on small wood samples of spruce trees in order to visualize and analyze size and formation of xylem elements and their respective lumina. The selected high-resolution phase-contrast technique makes full use of the novel 20 MPixel CMOS area detector developed within the cooperation of HZG and the Karlsruhe data by light microscopy analysis and, hence, prove, that μCT is a most appropriate method to gain valid information on xylem cell structure and tree water transport capacity.
Permanent implants made of titanium or its alloys are the gold standard in many orthopedic and traumatological
applications due to their good biocompatibility and mechanical properties. However, a second surgical intervention is
required for this kind of implants as they have to be removed in the case of children that are still growing or on patient’s
demand. Therefore, magnesium-based implants are considered for medical applications as they are degraded under
physiological conditions. The major challenge is tailoring the degradation in a manner that is suitable for a biological
environment and such that stabilization of the bone is provided for a controlled period. In order to understand failure
mechanisms of magnesium-based implants in orthopedic applications and, further, to better understand the
osseointegration, screw implants in bone are studied under mechanical load by means of a push-out device installed at
the imaging beamline P05 of PETRA III at DESY. Conventional absorption contrast microtomography and phasecontrast
techniques are applied in order to monitor the bone-to-implant interface under increasing load conditions. In this
proof-of-concept study, first results from an in situ push-out experiment are presented.
Sebastian Schmelzle, Michael Heethoff, Vincent Heuveline, Philipp Lösel, Jürgen Becker, Felix Beckmann, Frank Schluenzen, Jörg Hammel, Andreas Kopmann, Wolfgang Mexner, Matthias Vogelgesang, Nicholas Tan Jerome, Oliver Betz, Rolf Beutel, Benjamin Wipfler, Alexander Blanke, Steffen Harzsch, Marie Hörnig, Tilo Baumbach, Thomas van de Kamp
Beamtime and resulting SRμCT data are a valuable resource for researchers of a broad scientific community in life sciences. Most research groups, however, are only interested in a specific organ and use only a fraction of their data. The rest of the data usually remains untapped. By using a new collaborative approach, the NOVA project (Network for Online Visualization and synergistic Analysis of tomographic data) aims to demonstrate, that more efficient use of the valuable beam time is possible by coordinated research on different organ systems. The biological partners in the project cover different scientific aspects and thus serve as model community for the collaborative approach. As proof of principle, different aspects of insect head morphology will be investigated (e.g., biomechanics of the mouthparts, and neurobiology with the topology of sensory areas). This effort is accomplished by development of advanced analysis tools for the ever-increasing quantity of tomographic datasets. In the preceding project ASTOR, we already successfully demonstrated considerable progress in semi-automatic segmentation and classification of internal structures. Further improvement of these methods is essential for an efficient use of beam time and will be refined in the current NOVAproject. Significant enhancements are also planned at PETRA III beamline p05 to provide all possible contrast modalities in x-ray imaging optimized to biological samples, on the reconstruction algorithms, and the tools for subsequent analyses and management of the data. All improvements made on key technologies within this project will in the long-term be equally beneficial for all users of tomography instrumentations.
Phase-contrast imaging has proven to be a valuable tool when investigating weak absorbing materials like soft tissue, due to its increased contrast compared to conventional absorption-contrast imaging. While propagation-based phase-contrast is an ideal tool to achieve highest resolution at a good contrast for almost not-absorbing material, it quickly comes to its limitations on applications demanding for a high dynamic range in contrast. For those applications grating-based phase-contrast is the tool of choice, although it lacks of spatial resolution compared to inline phase-contrast or attenuation-based microCT. To reduce this gap in spatial resolution we equipped the two PETRA III beamlines P05 and P07 with a customized set of mechanics to maximize the performance of the interferometer. After latest optimization steps our system allows for phase-contrast measurements in a continuous energy range between 10 keV and 80 keV . Dependent on investigated material and energy the setup is capable to achieve a spatial resolution of 5 μm on a field of view of 6.5 mm. We will present our implementation of grating-based phase-contrast computed tomography for fast and high-resolution measurements at the PETRA III along with its recent optimization, and demonstrate its performance based on different kinds of applications.
The use of degradable magnesium based implants is becoming clinically relevant, e.g. for the use as bone screws. Still
there is a lack of analyzing techniques to characterize the in vitro degradation behavior of implant prototypes. The aim of
this study was to design an in situ environment to continuously monitor the degradation processes under physiological
conditions by time-lapse SRμCT. The use of physiological conditions was chosen to get a better approach to the in vivo
situation, as it could be shown by many studies, that these conditions change on the one hand the degradation rate and on
the other hand also the formed degradation products. The resulting in situ environment contains a closed bioreactor
system to control and monitor the relevant parameters (37°C, 5 % O2, 20 % CO2) and to grant sterility of the setup. A
flow cell was designed and manufactured from polyether etherketone (PEEK), which was chosen because of the good
mechanical properties, high thermal and chemical resistance and radiographic translucency. Sterilization of the system
including the sample was reached by a transient flush with 70 % ethanol and subsequent replacement by physiological
medium (Modified Eagle Medium alpha). As proof of principle it could be shown that the system remained sterile during
a beamtime of several days and that the continuous SRμCT imaging was feasible.
Magnesium(Mg)-alloys are promising candidates as temporary implants for orthopedic and cranio-facial applications.
They can sustain tissues during healing, thanks to favorable mechanical properties, and then they slowly degrade into
biocompatible products, avoiding the need of a second surgery for implant removal. They have the potential to benefit a
vast number of patients, especially children and elderly patients. However, to be able to tailor their degradation to match
the speed of tissue regeneration it is crucial to understand how they actually degrade in the living organism. We utilized
high-resolution synchrotron-based tomography at the beamline P05 operated by HZG at the storage ring PETRA III at
DESY to study the degradation of 3 novel Mg-alloys in rat bone and the consequent bone response. On threedimensional
reconstructions of the bone-implant explants we were able to follow the dynamic transformation that the
materials underwent at different healing times and on the basis of absorption coefficients we could distinguish and
quantify the amount of remaining implants, the corrosion layers and the new bone. This was a great advantage compared
to laboratory CT, for which the limitation in contrast and in resolution made impossible to discriminate between original
alloy, degradation products and bone, leading to inaccurate determination of the materials degradation rates. The same
samples imaged by tomography were used for non-decalcified histology. The combination of histological and
tomographical images provided new insight on the nature of the bone-to-implant interface and of the degradation
products, which appeared to have great similarities to the host bone.
Synchrotron X-ray imaging is constantly achieving higher spatial resolution. In the field of grating-based phase- contrast imaging, these developments allow to directly resolve the interference patterns created by a phase grating without need for a analyzer grating. In this study we analyzed the performance of a single-grating interferometer and compared it to a conventional double-grating interferometer. Based on simulations and measurements of a test phantom we evaluated the sensitivity, resolution and signal to noise ratios of different setup configurations.
Imke Greving, Fabian Wilde, Malte Ogurreck, Julia Herzen, Jörg Hammel, Alexander Hipp, Frank Friedrich, Lars Lottermoser, Thomas Dose, Hilmar Burmester, Martin Müller, Felix Beckmann
The imaging beamline (IBL/P05) operated by Helmholtz Zentrum Geesthacht (HZG) at the DESY PETRA III storage ring consists of two experimental stations: A micro tomography and a nano tomography end station. Here an overview of the experimental setups and the data acquisition will be given. In addition some first results out of the wide range of applications using the micro tomography station at P05 will be shown. Furthermore, we present first results of the nano tomography end station. These were obtained with an x–ray microscopy setup, which currently operates at energies of 17.4 and 30 keV using polymer compound refractive lenses (CRLs) and rolled prism lenses. Taken together these results clearly show the high potential of the newly built imaging beamline IBL.
Zoological sciences widely rely on morphological data to reconstruct and understand body structures of animals. The best suitable methods like tomography allow for a direct representation of 3D-structures. In recent years, synchrotron radiation based x-ray microtomography (SR μCT) placed high resolutions to the disposal of morphologists. With the development of highly brilliant and collimated third generation synchrotron sources, phase contrast SR μCT became
widely available. A number of scientific contributions stressed the superiority of phase contrast over absorption contrast. However, here we demonstrate the power of high density resolution methods based on absorption-contrast SRμCT for quantitative 3D-measurements of tissues and other delicate bio-structures in zoological sciences. We used beamline BW2 at DORIS III (DESY, Hamburg, Germany) to perform microtomography on tissue and mineral skeletons of marine sponges (Porifera) which were shock frozen and/or fixed in a glutamate osmium tetroxide solution, followed by critical point drying. High density resolution tomographic reconstructions allowed running quantitative 3D-image analyses in Matlab and ImageJ. By applying contrast and shape rule based algorithms we semi-automatically extracted and measured sponge body structures like mineral spicules, elements of the canal system or tissue structures. This lead to a better understanding of sponge biology: from skeleton functional morphology and internal water flow regimes to body contractility. Our high density resolution based quantitative approach can be applied to a wide variety of biological structures. However, two prerequisites apply: (1) maximum density resolution is necessary; (2) edge effects as seen for example in phase outline contrast SR μCT must not be present. As a consequence, to allow biological sciences to fully
exploit the power of SR μCT further increase of density resolution in absorption contrast methods is desirable.
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