Coincidence Loss Research Articles

Modeling the impact of coincidence loss on count rate statistics and noise performance in counting detectors for imaging applications

Coincidence loss can have detrimental effects on the image quality provided by pixelated counting detectors, especially in dose-sensitive applications like cryoEM where the information extracted from the recorded signal needs to be maximized. In this work, we investigate the impact of coincidence loss phenomena on the recorded statistics in counting detectors producing sparse binary images. First, we derive exact analytical expressions for the mean and the variance of the recorded counts as a function of the incoming event rate. Second, we address the problem of the mean and variance of the recorded events (i.e., pixel clusters identified as individual incoming events), which also acts as a function of the incoming event rate. In this frame, we review previous studies from different disciplines on approximated two-dimensional models, and we critically reinterpret them in our context and evaluate the suitability of their adoption in the present case. The knowledge of the first two momenta of the recorded statistics allows inferring about the signal-to-noise ratio (SNR) and the detective quantum efficiency at zero frequency (DQE0). Analytical results are validated through comparison with numerical data obtained with a custom-made Monte Carlo code. We chose a realistic case study for cryoEM application consisting of a 25-µm-thick MAPS detector featuring a pixel size of 10 µm and illuminated with electrons of 300 keV energy over a wide range of incoming rate.

Deep Learning Approach for High-accuracy Electron Counting of Monolithic Active Pixel Sensor-type Direct Electron Detectors at Increased Electron Dose.

Electron counting can be performed algorithmically for monolithic active pixel sensor direct electron detectors to eliminate readout noise and Landau noise arising from the variability in the amount of deposited energy for each electron. Errors in existing counting algorithms include mistakenly counting a multielectron strike as a single electron event, and inaccurately locating the incident position of the electron due to lateral spread of deposited energy and dark noise. Here, we report a supervised deep learning (DL) approach based on Faster region-based convolutional neural network (R-CNN) to recognize single electron events at varying electron doses and voltages. The DL approach shows high accuracy according to the near-ideal modulation transfer function (MTF) and detector quantum efficiency for sparse images. It predicts, on average, 0.47 pixel deviation from the incident positions for 200 kV electrons versus 0.59 pixel using the conventional counting method. The DL approach also shows better robustness against coincidence loss as the electron dose increases, maintaining the MTF at half Nyquist frequency above 0.83 as the electron density increases to 0.06 e-/pixel. Thus, the DL model extends the advantages of counting analysis to higher dose rates than conventional methods.

Electron counting with direct electron detectors in MicroED

The combination of high sensitivity and rapid readout makes it possible for electron-counting detectors to record cryogenic electron microscopy data faster and more accurately without increasing the number of electrons used for data collection. This is especially useful for MicroED of macromolecular crystals where the strength of the diffracted signal at high resolution is comparable to the surrounding background. The ability to decrease fluence also alleviates concerns about radiation damage which limits the information that can be recovered from a diffraction measurement. The major concern with electron-counting direct detectors lies at the low end of the resolution spectrum: their limited linear range makes strong low-resolution reflections susceptible to coincidence loss and careful data collection is required to avoid compromising data quality. Nevertheless, these cameras are increasingly deployed in cryo-EM facilities, and several have been successfully used for MicroED. Provided coincidence loss can be minimized, electron-counting detectors bring high potential rewards.

Characterizing the resolution and throughput of the Apollo direct electron detector

Advances in electron detection have been essential to the success of high-resolution cryo-EM structure determination. A new generation of direct electron detector called the Apollo, has been developed by Direct Electron. The Apollo uses a novel event-based MAPS detector custom designed for ultra-fast electron counting. We have evaluated this new camera, finding that it delivers high detective quantum efficiency (DQE) and low coincidence loss, enabling high-quality electron counting data acquisition at up to nearly 80 input electrons per pixel per second. We further characterized the performance of Apollo for single particle cryo-EM on real biological samples. Using mouse apoferritin, Apollo yielded better than 1.9 Å resolution reconstructions at all three tested dose rates from a half-day data collection session each. With longer collection time and improved specimen preparation, mouse apoferritin was reconstructed to 1.66 Å resolution. Applied to a more challenging small protein aldolase, we obtained a 2.24 Å resolution reconstruction. The high quality of the map indicates that the Apollo has sufficiently high DQE to reconstruct smaller proteins and complexes with high-fidelity. Our results demonstrate that the Apollo camera performs well across a broad range of dose rates and is capable of capturing high quality data that produce high-resolution reconstructions for large and small single particle samples.

Electron-counting MicroED data with the K2 and K3 direct electron detectors

Microcrystal electron diffraction (MicroED) uses electron cryo-microscopy (cryo-EM) to collect diffraction data from small crystals during continuous rotation of the sample. As a result of advances in hardware as well as methods development, the data quality has continuously improved over the past decade, to the point where even macromolecular structures can be determined ab initio. Detectors suitable for electron diffraction should ideally have fast readout to record data in movie mode, and high sensitivity at low exposure rates to accurately report the intensities. Direct electron detectors are commonly used in cryo-EM imaging for their sensitivity and speed, but despite their availability are generally not used in diffraction. Primary concerns with diffraction experiments are the dynamic range and coincidence loss, which will corrupt the measurement if the flux exceeds the count rate of the detector. Here, we describe instrument setup and low-exposure MicroED data collection in electron-counting mode using K2 and K3 direct electron detectors and show that the integrated intensities can be effectively used to solve structures of two macromolecules between 1.2 Å and 2.8 Å resolution. Even though a beam stop was not used with the K3 studies we did not observe damage to the camera. As these cameras are already available in many cryo-EM facilities, this provides opportunities for users who do not have access to dedicated facilities for MicroED.

A bilateral comparison of particle number concentration standards via calibration of an optical particle counter for number concentration up to ∼1000 cm−3

The first bilateral comparison of particle number concentration (PNC) standards via calibrating the counting efficiency (CE) of an optical particle counter (OPC) at high concentration of 1000 cm−3 is reported. An OPC (GRIMM 11-D) has been used as the transfer standard between NMC and NMIJ, with its CE being calibrated using monodisperse polystyrene latex (PSL) particles around 0.3 µm by the Faraday Cup Aerosol Electrometers (FCAE) of both metrology institutes. The CE of the OPC has been evaluated for a series of increasing concentrations to determine the highest concentration level which is free from coincidence loss. The OPC was also calibrated at 0.5 µm using an inkjet aerosol generator (IAG) and FCAE to compare its CE at different concentration levels. We have analysed the CE’s stability at decreasing concentration levels from 1228 to 0.5 cm−3 to derive the evidence for the equivalence of CE at different concentration levels. The CE values of the OPC around 0.3 and 0.5 µm measured by two institutes have agreement within 1.5% (normalizederror En < 1), which can serve as evidence of the equivalence of the PNC standards of both metrology institutes for concentrations up to 1000 cm−3. The measurement setup, comparison results and uncertainty analysis for the OPC calibration have been presented.

A data reduction and compression description for high throughput time-resolved electron microscopy

Fast, direct electron detectors have significantly improved the spatio-temporal resolution of electron microscopy movies. Preserving both spatial and temporal resolution in extended observations, however, requires storing prohibitively large amounts of data. Here, we describe an efficient and flexible data reduction and compression scheme (ReCoDe) that retains both spatial and temporal resolution by preserving individual electron events. Running ReCoDe on a workstation we demonstrate on-the-fly reduction and compression of raw data streaming off a detector at 3 GB/s, for hours of uninterrupted data collection. The output was 100-fold smaller than the raw data and saved directly onto network-attached storage drives over a 10 GbE connection. We discuss calibration techniques that support electron detection and counting (e.g., estimate electron backscattering rates, false positive rates, and data compressibility), and novel data analysis methods enabled by ReCoDe (e.g., recalibration of data post acquisition, and accurate estimation of coincidence loss).

The calibration of read-out-streak photometry in theXMM–NewtonOptical Monitor and the construction of a bright-source catalogue

The dynamic range of the XMM–Newton Optical Monitor (XMM-OM) is limited at the bright end by coincidence loss, the superposition of multiple photons in the individual frames recorded from its micro-channel-plate (MCP) intensified charge-coupled device (CCD) detector. One way to overcome this limitation is to use photons that arrive during the frame transfer of the CCD, forming vertical read-out streaks for bright sources. We calibrate these read-out streaks for photometry of bright sources observed with XMM-OM. The bright-source limit for read-out-streak photometry is set by the recharge time of the MCPs. For XMM-OM, we find that the MCP recharge time is 5.5 × 10−4 s. We determine that the effective bright limits for read-out-streak photometry with XMM-OM are approximately 1.5 mag brighter than the bright-source limits for normal aperture photometry in full-frame images. This translates into bright-source limits in Vega magnitudes of UVW2=7.1, UVM2=8.0, UVW1=9.4, U=10.5, B=11.5, V=10.2, and White=12.5 for data taken early in the mission. The limits brighten by up to 0.2 mag, depending on filter, over the course of the mission as the detector ages. The method is demonstrated by deriving UVW1 photometry for the symbiotic nova RR Telescopii, and the new photometry is used to constrain the e-folding time of its decaying ultraviolet (UV) emission. Using the read-out-streak method, we obtain photometry for 50 per cent of the missing UV source measurements in version 2.1 of the XMM–Newton Serendipitous UV Source Survey catalogue.

Calibration of the Swift-UVOT ultraviolet and visible grisms

We present the calibration of the Swift UVOT grisms, of which there are two, providing low-resolution field spectroscopy in the ultraviolet and optical bands respectively. The UV grism covers the range 1700-5000 Angstrom with a spectral resolution of 75 at 2600 Angstrom for source magnitudes of u=10-16 mag, while the visible grism covers the range 2850-6600 Angstrom with a spectral resolution of 100 at 4000 Angstrom for source magnitudes of b=12-17 mag. This calibration extends over all detector positions, for all modes used during operations. The wavelength accuracy (1-sigma) is 9 Angstrom in the UV grism clocked mode, 17 Angstrom in the UV grism nominal mode and 22 Angstrom in the visible grism. The range below 2740 Angstrom in the UV grism and 5200 Angstrom in the visible grism never suffers from overlapping by higher spectral orders. The flux calibration of the grisms includes a correction we developed for coincidence loss in the detector. The error in the coincidence loss correction is less than 20%. The position of the spectrum on the detector only affects the effective area (sensitivity) by a few percent in the nominal modes, but varies substantially in the clocked modes. The error in the effective area is from 9% in the UV grism clocked mode to 15% in the visible grism clocked mode .

The use and calibration of read-out streaks to increase the dynamic range of the Swift Ultraviolet/Optical Telescope

The dynamic range of photon counting micro-channel-plate (MCP) intensified charged-coupled device (CCD) instruments such as the Swift Ultraviolet/Optical Telescope (UVOT) and the XMM-Newton Optical Monitor (XMM-OM) is limited at the bright end by coincidence loss, the superposition of multiple photons in the individual frames recorded by the CCD. Photons which arrive during the brief period in which the image frame is transferred for read out of the CCD are displaced in the transfer direction in the recorded images. For sufficiently bright sources, these displaced counts form read-out streaks. Using UVOT observations of Tycho-2 stars, we investigate the use of these read-out streaks to obtain photometry for sources which are too bright (and hence have too much coincidence loss) for normal aperture photometry to be reliable. For read-out-streak photometry, the bright-source limiting factor is coincidence loss within the MCPs rather than the CCD. We find that photometric measurements can be obtained for stars up to 2.4 magnitudes brighter than the usual full-frame coincidence-loss limit by using the read-out streaks. The resulting bright-limit Vega magnitudes in the UVOT passbands are UVW2=8.80, UVM2=8.27, UVW1=8.86, u=9.76, b=10.53, v=9.31 and White=11.71; these limits are independent of the windowing mode of the camera. We find that a photometric precision of 0.1 mag can be achieved through read-out streak measurements. A suitable method for the measurement of read-out streaks is described and all necessary calibration factors are given.

Influence of electron dose rate on electron counting images recorded with the K2 camera.

A recent technological breakthrough in electron cryomicroscopy (cryoEM) is the development of direct electron detection cameras for data acquisition. By bypassing the traditional phosphor scintillator and fiber optic coupling, these cameras have greatly enhanced sensitivity and detective quantum efficiency (DQE). Of the three currently available commercial cameras, the Gatan K2 Summit was designed specifically for counting individual electron events. Counting further enhances the DQE, allows for practical doubling of detector resolution and eliminates noise arising from the variable deposition of energy by each primary electron. While counting has many advantages, undercounting of electrons happens when more than one electron strikes the same area of the detector within the analog readout period (coincidence loss), which influences image quality. In this work, we characterized the K2 Summit in electron counting mode, and studied the relationship of dose rate and coincidence loss and its influence on the quality of counted images. We found that coincidence loss reduces low frequency amplitudes but has no significant influence on the signal-to-noise ratio of the recorded image. It also has little influence on high frequency signals. Images of frozen hydrated archaeal 20S proteasome (~700 kDa, D7 symmetry) recorded at the optimal dose rate retained both high-resolution signal and low-resolution contrast and enabled calculating a 3.6 Å three-dimensional reconstruction from only 10,000 particles.

A multiwavelength study of the Magellanic-type galaxy NGC 4449 – I. Modelling the spectral energy distribution, the ionization structure and the star formation history

[Abridged] We present an integrated photometric spectral energy distribution (SED) of the Magellanic-type galaxy NGC 4449 from the far-ultraviolet (UV) to the submillimetre, including new observations acquired by the Herschel Space Observatory. We include integrated UV photometry from the Swift Ultraviolet and Optical Telescope using a measurement technique which is appropriate for extended sources with coincidence loss. In this paper, we examine the available multiwavelength data to infer a range of ages, metallicities and star formation rates for the underlying stellar populations, as well as the composition and the total mass of dust in NGC 4449. We present an iterative scheme, which allows us to build an in-depth and multicomponent representation of NGC 4449 `bottom-up', taking advantage of the broad capabilities of the photoionization and radiative transfer code MOCASSIN (MOnte CArlo SimulationS of Ionized Nebulae). We fit the observed SED, the global ionization structure and the emission line intensities, and infer a recent SFR of 0.4 Msolar/yr and a total stellar mass of approximately 1e9 Msolar emitting with a bolometric luminosity of 5.7e9 Lsolar. Our fits yield a total dust mass of 2.9e6 Msolar including 2 per cent attributed to polycyclic aromatic hydrocarbons. We deduce a dust to gas mass ratio of 1/190 within the modelled region. While we do not consider possible additional contributions from even colder dust, we note that including the extended HI envelope and the molecular gas is likely to bring the ratio down to as low as ~ 1/800.

Rapid Live Bacteria Counter Using Cassette-Type Flow Cytometry

We developed the rapid live bacteria counter (RLBC) with the disposable cassette to count live bacteria rapidly, simply and accurately for the food security. The RLBC has the following features: (1) The RLBC performs automatically following processes in the cassette: removing residues, staining live and dead bacteria and counting live bacteria by flow cytometry techniques. (2) This uses the multi staining to distinguish easily the fluorescence of live bacteria from the different fluorescence of foreign substances. (3)For accurate counting and the cassette breakage prevention , the micro flow-cell for the flow cytometry satisfies following conditions that the coincidence loss of live bacteria is below 0.05 and the pressure drop is below 1×105 Pa. The live bacteria count obtained with the RLBC and the classical cultural method for the test samples are highly correlated (R2 (E-Coli) = 0.97, R2 (Spinach) = 0.96, R2 (Carrot) = 0.91, R2 (Red cabbage) = 0.90).

Primary standard for the number concentration of liquid-borne particles in the 10 to 20 µm diameter range

The national primary standard for the number concentration of liquid-borne particles in the 10 to 20 µm diameter range has been developed at the National Institute of Advanced Industrial Science and Technology (AIST), Japan. The standard consists of a total number counting type flow cytometer (T-FCM) and an electronic balance. The T-FCM is a commercial flow cytometer modified so that the total number of particles in an aqueous suspension sampled in a test tube can be counted, and the electronic balance is used to determine the mass of the suspension. This standard is intended to be used for calibrating commercial standard suspensions of monodisperse polystyrene latex (PSL) particles. The measurand in the calibration is the mass-based number concentration (the particle number in a unit mass of a suspension), and the calibration capability covers the concentration range from 5 × 102 to 2 × 106 particles g−1. When the concentration of the suspension is higher than 2 × 103 particles g−1, the suspension is first diluted to about 1 × 103 particles g−1 to suppress the coincidence loss in particle counting by the T-FCM. The validity of the calibration with the T-FCM was examined by comparison with an independent method in which a scanning electron microscope (SEM) was used to determine the number concentration of particles deposited on a silicon wafer. For a suspension of 10 µm PSL particles with a concentration of approximately 1 × 106 particles g−1, the concentration values determined by the T-FCM and SEM methods were 1.042 × 106 and 1.035 × 106 particles g−1, respectively: The difference was less than 0.7%. The relative expanded uncertainty of the measurement by the T-FCM method with the coverage factor k = 2 was 4.4%.

Further calibration of the Swift ultraviolet/optical telescope

The Ultraviolet/Optical Telescope (UVOT) is one of three instruments onboard the Swift observatory. The photometric calibration has been published, and this paper follows up with details on other aspects of the calibration including a measurement of the point spread function with an assessment of the orbital variation and the effect on photometry. A correction for large scale variations in sensitivity over the field of view is described, as well as a model of the coincidence loss which is used to assess the coincidence correction in extended regions. We have provided a correction for the detector distortion and measured the resulting internal astrometric accuracy of the UVOT, also giving the absolute accuracy with respect to the International Celestial Reference System. We have compiled statistics on the background count rates, and discuss the sources of the background, including instrumental scattered light. In each case we describe any impact on UVOT measurements, whether any correction is applied in the standard pipeline data processing or whether further steps are recommended.

Photometric calibration of the Swift ultraviolet/optical telescope

We present the photometric calibration of the Swift UltraViolet/Optical Telescope (UVOT) which includes: optimum photometric and background apertures, effective area curves, colour transformations, conversion factors for count rates to flux, and the photometric zero points (which are accurate to better than 4 per cent) for each of the seven UVOT broadband filters. The calibration was performed with observations of standard stars and standard star fields that represent a wide range of spectral star types. The calibration results include the position dependent uniformity, and instrument response over the 1600-8000A operational range. Because the UVOT is a photon counting instrument, we also discuss the effect of coincidence loss on the calibration results. We provide practical guidelines for using the calibration in UVOT data analysis. The results presented here supersede previous calibration results.

Non-destructive actinide assay of neutron sources

Transuranic neutron sources were assayed using γ-spectrometry and neutron counting, with respect to revealing illicit trafficking of radioactive and nuclear materials. Source type and constituents were identified by γ-spectrometry. For determining the source strength of 244Cm, 252Cf, AmBe, AmLi and 238PuBe sources, a passive neutron coincidence collar was used with 3He counters in two moderator configurations. The electronics consist of independent channels of pulse amplifiers and discriminators as well as a shift register for coincidence counting. From the neutron output of the sources measured by gross neutron counting, the actinide content (or activity) can be assessed by adopting specific spontaneous fission and (α,n) reaction yields of individual isotopes from the literature. Various types of the sources can be characterized by the ratio of the real coincidence counts to total (singles) counts, R/T. This quantity is a specific constant for different types of spontaneously fissioning sources, not depending on their strength, while exhibits a power function increasing with the strength of (α,n) sources. An individual source of the latter type can additionally be characterized by the ratio of R/T to the product of detection efficiency and a factor taking into account coincidence loss, irrespective of the instrumental details (detector type and size, moderator thickness, etc.).

Xd_red-1.0: synchrotron and in-house X-ray diffraction data reduction and analysis program

The data-treatment modules available in the package provide: pro®le integration algorithms, incident-beam monitor scaling, corrections for coincidence loss, attenuators, Laue and polarization effects (different monochromator setups/incident-beam polarization states), correction for absorption, through a modi®ed version of ABSOR (Templeton & Templeton, 1973), and a polynomial scaling, from statistical analysis of reference re ection intensities. Geometrically dependent corrections are handled via program instructions during execution. In addition to established pro®le integration algorithms (Celtin & Abrahams, 1963; Lehmann & Larsen, 1974), a new method is released with xd_red. `Student-t' signi®cance tests are employed when increasing the lowand high-angle background areas until a hypothesis of the kind `no change in the background moving toward the peak maxima' is rejected. Without the need for any peak shape analysis, the method has proven robust and reliable in work with the large variation in pro®le shapes that can be encountered for different samples at a synchrotron. For all corrections applied, propagating errors are calculated and added to the counting statistical errors through a second-order Taylor expansion. Detailed information on the impact of the speci®c corrections on the total error is presented graphically and numerically. xd_red may either output all integrated and corrected observations, or can be used to merge a full set or speci®ed groups of equivalent data. The merging procedure is equipped with numerical and graphical tools to identify outliers. xd_red has several tools for a directional data analysis, carried out by a combination of a simple but robust pro®le analysis, and a directional statistical analysis on the merging residuals (Parkin, 2000).

Multilayer anode with crossed serpentine delay lines for high spatial resolution readout of microchannel plate detectors

We have designed, built, and tested the first successful imaging microchannel plate (MCP) detector that uses two crossed, printed circuit, serpentine delay lines, one stacked above the other in a three-dimensional architecture. Laser ablation machining is used to cut slots that allow delay lines in two layers parallel to the MCP to sample and read out x and y image positions. Previous readouts that use delay line timing to read out both dimensions of an image employ a wire-wound anode. The goal of this readout is to provide as many picture elements (pixels) as possible in two dimensions, with high temporal resolution, high throughput, high dynamic range, and good spatial linearity. This detector achieves this goal with off-the-shelf electronics and is robust for space flight. The full width half maximum (FWHM) spatial resolution is 32 μm at the center of the detector and is typically &amp;lt;35 μm throughout the detector. The rms linearity is 40 μm in each readout dimension, after applying only radial corrections for fringe field effects near the perimeter, and &amp;lt;20 μm after applying additional simple (one-dimensional) corrections. Throughput for 10% coincidence loss is limited by the measured baseline settling time to 4×105 s−1, but the current electronics limit is 1.1×105 s−1. The walk characteristics of the detector are described. We discuss fabrication techniques, application to space-based astronomy use, and design modifications to improve performance.

Optical emission spectrum of the NO 2+ dication

We recorded and rotationally analyzed a new emission band at 2563 Å obtained from a low-pressure, hot cathode and magnetically confined electric discharge through pure NO vapor. The available experimental data from photoion-fluorescence photon coincidence and translational energy loss spectroscopy, in conjunction with ab initio calculation, allowed assignment of the new band to the B 2Σ +- X 2Σ + (0, 0) transition of the NO 2+ ion.