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Organisationseinheit der BAM
A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated, quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist’s experiments, while more than half have even failed to reproduce their own experiments1. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique2,3. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g., DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE4), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common Standards and guidelines for quality assessment and reproducibility5.
In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative6 was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models7,8, and tools9,10, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research.
This White Paper 1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; 2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of Stakeholders including, researchers, imaging scientists11, bioimage analysts, bioimage informatics developers, corporate partners, Funding agencies, standards organizations, scientific publishers, and observers of such; 3) outlines the current actions of the QUAREPLiMi initiative, and 4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC.
To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics.
Objectives: Using a murine model of multiple sclerosis, we previously showed that repeated administration of gadopentetate dimeglumine led to retention of gadolinium (Gd) within cerebellar structures and that this process was enhanced with inflammation. This study aimed to compare the kinetics and retention profiles of Gd in inflamed and healthy brains after application of the macrocyclic Gd-based contrast agent (GBCA) gadobutrol or the linear GBCA gadopentetate. Moreover, potential Gd-induced neurotoxicity was investigated in living hippocampal slices ex vivo.
Materials and Methods: Mice at peak of experimental autoimmune encephalomyelitis (EAE; n = 29) and healthy control mice (HC; n = 24) were exposed to a cumulative dose of 20 mmol/kg bodyweight of either gadopentetate dimeglumine or gadobutrol (8 injections of 2.5 mmol/kg over 10 days). Magnetic resonance imaging (7 T) was performed at baseline as well as at day 1, 10, and 40 post final injection (pfi) of GBCAs. Mice were sacrificed after magnetic resonance imaging and brain and blood Gd content was assessed by laser ablation-inductively coupled plasma (ICP)-mass spectrometry (MS) and ICP-MS, respectively. In addition, using chronic organotypic hippocampal slice cultures, Gd-induced neurotoxicity was addressed in living brain tissue ex vivo, both under control or inflammatory (tumor necrosis factor α [TNF-α] at 50 ng/μL) conditions.
Results: Neuroinflammation promoted a significant decrease in T1 relaxation times after multiple injections of both GBCAs as shown by quantitative T1 mapping of EAE brains compared with HC. This corresponded to higher Gd retention within the EAE brains at 1, 10, and 40 days pfi as determined by laser ablation-ICP-MS. In inflamed cerebellum, in particular in the deep cerebellar nuclei (CN), elevated Gd retention was observed until day 40 after last gadopentetate application (CN: EAE vs HC, 55.06 ± 0.16 μM vs 30.44 ± 4.43 μM). In contrast, gadobutrol application led to a rather diffuse Gd content in the inflamed brains, which strongly diminished until day 40 (CN: EAE vs HC, 0.38 ± 0.08 μM vs 0.17 ± 0.03 μM). The analysis of cytotoxic effects of both GBCAs using living brain tissue revealed an elevated cell death rate after incubation with gadopentetate but not gadobutrol at 50 mM. The cytotoxic effect due to gadopentetate increased in the presence of the inflammatory mediator TNF-α (with vs without TNF-α, 3.15% ± 1.18% vs 2.17% ± 1.14%; P = 0.0345).
Conclusions: In the EAE model, neuroinflammation promoted increased Gd retention in the brain for both GBCAs. Whereas in the inflamed brains, efficient clearance of macrocyclic gadobutrol during the investigated time period was observed, the Gd retention after application of linear gadopentetate persisted over the entire observational period. Gadopentetate but not gadubutrol appeared to be neurotoxic in an ex vivo paradigm of neuronal inflammation.
The community-driven initiative Quality Assessment and Reproducibility for Instruments & Images in Light Microscopy (QUAREP-LiMi) wants to improve reproducibility for light microscopy image data through Quality control (QC) management of instruments and images. It aims for a common set of QC guidelines for Hardware calibration and image acquisition, management and analysis.
Inflammatory bowel diseases (IBD) comprise mainly ulcerative colitis (UC) and Crohn´s disease (CD). Both forms present with a chronic inflammation of the (gastro) intestinal tract, which induces excessive changes in the composition of the associated extracellular matrix (ECM). In UC, the inflammation is limited to the colon, whereas it can occur throughout the entire gastrointestinal tract in CD. Tools for early diagnosis of IBD are still very limited and highly invasive and measures for standardized evaluation of structural changes are scarce. To investigate an efficient non-invasive way of diagnosing intestinal inflammation and early changes of the ECM, very small superparamagnetic iron oxide nanoparticles (VSOPs) in magnetic resonance imaging (MRI) were applied in two mouse models of experimental colitis: the dextran sulfate sodium (DSS)-induced colitis and the transfer model of colitis. For further validation of ECM changes and inflammation, tissue sections were analyzed by immunohistochemistry. For in depth ex-vivo investigation of VSOPs localization within the tissue, Europium-doped VSOPs served to visualize the contrast agent by imaging mass cytometry (IMC). VSOPs accumulation in the inflamed colon wall of DSS-induced colitis mice was visualized in T2* weighted MRI scans. Components of the ECM, especially the hyaluronic acid content, were found to influence VSOPs binding. Using IMC, colocalization of VSOPs with macrophages and endothelial cells in colon tissue was shown. In contrast to the DSS model, colonic inflammation could not be visualized with VSOP-enhanced MRI in transfer colitis. VSOPs present a potential contrast agent for contrast-enhanced MRI to detect intestinal inflammation in mice at an early stage and in a less invasive manner depending on hyaluronic acid content.
The formation and properties of laser-induced periodic surface structures (LIPSS) were investigated on carbon fibers under irradiation of fs-laser pulses characterized by a pulse duration τ = 300 fs and a laser wavelength λ = 1025 nm. The LIPSS were fabricated in an air environment at normal incidence with different values of the laser peak fluence and number of pulses per spot. The morphology of the generated structures was characterized by using scanning electron microscopy, atomic force microscopy and Fast-Fourier transform analyses. Moreover, the material structure and the surface chemistry of the carbon fibers before and after laser irradiation was analyzed by micro Raman spectroscopy and X-ray photoelectron spectroscopy. Large areas in the cm2 range of carbon fiber arrangements were successfully processed with homogenously distributed high- and low-spatial frequency LIPSS. Beyond those distinct nanostructures, hybrid structures were realized for the very first time by a superposition of both types of LIPSS in a two-step process. The findings facilitate the fabrication of tailored LIPSS-based surface structures on carbon fibers that could be of particular interest for e.g. fiber reinforced polymers and concretes.
The present study reports on results of analysis of the elemental composition of thin films by electron probe microanalysis with energy dispersive (ED-EPMA) X-ray spectrometry in conjunction with the dedicated thin-film analysis software package Stratagem and by X-ray fluorescence in its version with a micro-focus X-ray fluorescence (μ-XRF) source attached to a scanning electron microscope (SEM). Two thin-film systems have been analyzed: Fe1-xNix on silicon wafer and Si1-xGex on Al2O3 substrate, in both cases the layers being grown to a thickness of about 200 nm by ion beam sputter deposition. Samples of five different atomic fractions have been produced and analyzed for each thin-film system. Moreover, reference samples with certified elemental composition and thickness have been also available. This study is part of an interlaboratory comparison organized in the frame of standardization technical committee ISO/TC 201 “Surface chemical analysis.” Two laboratories have been analyzed by ED-EPMA (one laboratory standardless and one laboratory using both standardless and with standards variants) and one laboratory by μ-XRF (standardless and with standards). All the elemental compositions obtained with different methods are in very good agreement for the complete two sets of five samples each.
Applications of fibre reinforced plastic (FRP) composites in modern industries are increasing due to their considerable advantages such as light weight and excellent mechanical properties. Accordingly, importance of operational safety of modern structures made of advanced composites by ensuring the material quality has led to increasing demands for development of non-destructive evaluation (NDE) systems. In the context of a European project entitled “Validated Inspection Techniques for Composites in Energy Applications” (VITCEA), the aim is to develop and validate traceable procedures for novel NDE techniques with contrasting damage detection capabilities in energy related applications such as wind and marine turbine blades, nacelles, oil and gas flexible risers. Accordingly, VITCEA focuses on optimization of ultrasonic tests (UTs) for quantitative defect detection and quality characterization of FRP structures. In this context, the present study describes the ultrasound field in heterogeneous composite materials. The theoretical predictions are compared with simulation results obtained from CIVA a software package dedicated to NDT simulations based on the asymptotic ray theory.
Analysis of Elemental Composition of Fe1-xNix and Si1-xGex Alloy Thin Films by EPMA and μ-XRF
(2019)
The present study reports on measurements on thin Fe-Ni films on silicon and first-time results of analysis on Si-Ge thin films deposited on a non-conductive aluminium oxide Substrate by electron probe microanalysis (EPMA). Standard-based and standardless EPMA (with EDS) results were used in combination with the thin film analysis software Stratagem for the quantification.
Further, X-ray fluorescence analysis (XRF) can be used for the determination of elemental composition and thickness of such films as well. In this case, XRF with a μ-focus X-ray source (μ-XRF) attached to a SEM was applied. For quantification, a fundamental parameter (FP) approach has been used to calculate standard-based and standardless results.
Both thin film systems have been chosen as samples of an international round robin test (RRT) organised in the frame of standardisation technical committee ISO/TC 201 ‘Surface chemical analysis’, under the lead of KRISS. The main objective of the RRT is to compare the results of atomic fractions of Fe1-xNix and Si1-xGex alloy films obtained by different surface Analysis techniques, such as X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), and secondary ion mass spectrometry (SIMS) applied in the depth-profiling operation mode.
Five samples of different atomic fractions of each thin film system, i.e., Fe1-xNix and Si1-xGex, have been grown by ion beam sputter deposition on silicon and Al2O3 wafers, respectively. Reference FeNi and SiGe films with well-known elemental composition and thickness have been also supplied for standard-based analysis. An excellent agreement has been obtained between the atomic fractions determined by EPMA and µ-XRF with the KRISS certified values.zeige mehr
Analysis of elemental composition of Fe1-xNix and Si1-xGex alloy thin films by EPMA and µ-XRF
(2019)
The present study reports on measurements on thin Fe-Ni films on silicon and first-time results of analysis on Si-Ge thin films deposited on a non-conductive aluminium oxide Substrate by electron probe microanalysis (EPMA). Standard-based and standardless EPMA (with EDS) results were used in combination with the thin film analysis software Stratagem for the quantification.
Further, X-ray fluorescence analysis (XRF) can be used for the determination of elemental composition and thickness of such films as well. In this case, XRF with a μ-focus X-ray source (μ-XRF) attached to a SEM was applied. For quantification, a fundamental parameter (FP) approach has been used to calculate standard-based and standardless results.
Both thin film systems have been chosen as samples of an international round robin test (RRT) organised in the frame of standardisation technical committee ISO/TC 201 ‘Surface chemical analysis’, under the lead of KRISS. The main objective of the RRT is to compare the results of atomic fractions of Fe1-xNix and Si1-xGex alloy films obtained by different surface Analysis techniques, such as X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), and secondary ion mass spectrometry (SIMS) applied in the depth-profiling operation mode.
Five samples of different atomic fractions of each thin film system, i.e., Fe1-xNix and Si1-xGex, have been grown by ion beam sputter deposition on silicon and Al2O3 wafers, respectively. Reference FeNi and SiGe films with well-known elemental composition and thickness have been also supplied for standard-based analysis. An excellent agreement has been obtained between the atomic fractions determined by EPMA and µ-XRF with the KRISS certified values.