Fast pixelated detectors in scanning transmission electron microscopy. Part II: post acquisition data processing, visualisation, and structural characterisation

Fast pixelated detectors incorporating direct electron detection (DED) technology are increasingly being regarded as universal detectors for scanning transmission electron microscopy (STEM), capable of imaging under multiple modes of operation. However, several issues remain around the post acquisition processing and visualisation of the often very large multidimensional STEM datasets produced by them. We discuss these issues and present open source software libraries to enable efficient processing and visualisation of such datasets. Throughout, we provide examples of the analysis methodologies presented, utilising data from a 256×256 pixel Medipix3 hybrid DED detector, with a particular focus on the STEM characterisation of the structural properties of materials. These include the techniques of virtual detector imaging; higher order Laue zone analysis; nanobeam electron diffraction; and scanning precession electron diffraction. In the latter, we demonstrate nanoscale lattice parameter mapping with a fractional precision ≤6×10−4 (0.06%)

Non-pharmacological, non-surgical interventions for urinary incontinence in older persons : A systematic review of systematic reviews. The SENATOR project ONTOP series

This work was supported by the European Union Seventh Framework program (FP7/2007–2013) under grant agreement n° 305930Peer reviewedPostprin

Quantifying the Performance of a Hybrid Pixel Detector with GaAs:Cr Sensor for Transmission Electron Microscopy

Hybrid pixel detectors (HPDs) have been shown to be highly effective for diffraction-based and time-resolved studies in transmission electron microscopy, but their performance is limited by the fact that high-energy electrons scatter over long distances in their thick Si sensors. An advantage of HPDs compared to monolithic active pixel sensors (MAPS) is that their sensor does not need to be fabricated from Si. We have compared the performance of the Medipix3 HPD with a Si sensor and with a GaAs:Cr sensor using primary electrons in the energy range of 60 - 300keV. We describe the measurement and calculation of the detectors' modulation transfer function (MTF) and detective quantum efficiency (DQE), which show that the performance of the GaAs:Cr device is markedly superior to that of the Si device for high-energy electrons.Comment: 15 pages + references, 13 figure

Fast pixelated detectors in scanning transmission electron microscopy. Part I: data acquisition, live processing and storage

The use of fast pixelated detectors and direct electron detection technology is revolutionising many aspects of scanning transmission electron microscopy (STEM). The widespread adoption of these new technologies is impeded by the technical challenges associated them. These include issues related to hardware control, and the acquisition, real-time processing and visualisation, and storage of data from such detectors. We discuss these problems and present software solutions for them, with a view to making the benefits of new detectors in the context of STEM more accessible. Throughout, we provide examples of the application of the technologies presented, using data from a Medipix3 direct electron detector. Most of our software is available under an open source licence, permitting transparency of the implemented algorithms, and allowing the community to freely use and further improve upon them

Individual common variants exert weak effects on the risk for autism spectrum disorders.

While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest

Characterization of iLGADs using soft X-rays

Experiments at synchrotron radiation sources and X-ray Free-Electron Lasers in the soft X-ray energy range ($250$eV--$2$keV) stand to benefit from the adaptation of the hybrid silicon detector technology for low energy photons. Inverse Low Gain Avalanche Diode (iLGAD) sensors provide an internal gain, enhancing the signal-to-noise ratio and allowing single photon detection below $1$keV using hybrid detectors. In addition, an optimization of the entrance window of these sensors enhances their quantum efficiency (QE). In this work, the QE and the gain of a batch of different iLGAD diodes with optimized entrance windows were characterized using soft X-rays at the Surface/Interface:Microscopy beamline of the Swiss Light Source synchrotron. Above $250$eV, the QE is larger than $55\%$ for all sensor variations, while the charge collection efficiency is close to $100\%$. The average gain depends on the gain layer design of the iLGADs and increases with photon energy. A fitting procedure is introduced to extract the multiplication factor as a function of the absorption depth of X-ray photons inside the sensors. In particular, the multiplication factors for electron- and hole-triggered avalanches are estimated, corresponding to photon absorption beyond or before the gain layer, respectively.Comment: 16 pages, 8 figure