A toolkit for the characterization of CCD cameras for transmission electron microscopy

Quantifying noise limitations of neural network segmentations in high-resolution transmission electron microscopy

Motivated by the need for low electron dose transmission electron microscopy imaging, we report the optimal frame dose (i.e.e-/Å2) range for object detection and segmentation tasks with neural networks. The MSD-net architecture shows promising abilities over the industry standard U-net architecture in generalising to frame doses below the range included in the training set, for both simulated and experimental images. It also presents a heightened ability to learn from lower dose images. The MSD-net displays mild visibility of a Au nanoparticle at 20-30 e-/Å2, and converges at 200 e-/Å2 where a full segmentation of the nanoparticle is achieved. Between 30 and 200 e-/Å2 object detection applications are still possible. This work also highlights the importance of modelling the modulation transfer function when training with simulated images for applications on images acquired with scintillator based detectors such as the Gatan Oneview camera. A parametric form of the modulation transfer function is applied with varying ranges of parameters, and the effects on low electron dose segmentation is presented.

Raimond B. G. Ravelli (25 March 1968-30 June 2023)

Raimond B. G. Ravelli is remembered.

Validation of the Mental Illness Sexual Stigma Questionnaire (MISS-Q) in a sample of Brazilian adults in psychiatric care

OBJECTIVE

We evaluated the psychometric properties of a new instrument "Mental Illness Sexual Stigma Questionnaire" (MISS-Q).

METHODS

We interviewed 641 sexually active adults (ages 18-80) attending public outpatient psychiatric clinics in Rio de Janeiro about their stigma experiences.

RESULTS

Nine factors were extracted through exploratory factor analysis (EFA) and labeled: 'individual discrimination by others'; 'staff willingness to talk about sexuality'; 'staff and family prohibitions'; 'sexual devaluation of self'; 'perceived attractiveness'; 'mental illness concealment'; 'perceived sexual role competence'; 'withdrawal'; and 'locus of social-sexual control'. 'Withdrawal' and 'locus of social-sexual control' showed poor psychometric properties and were excluded from further analysis. The remaining seven factors had high factorial loadings (.39 to .86), varying from sufficient to optimal reliability (Ordinal α ranged from .57 to .88), and good convergent and discriminant validity.

CONCLUSIONS

The resulting MISS-Q is the first instrument assessing mental illness sexual stigma with demonstrated psychometric properties. It may prove useful in reducing stigma, protecting sexual health, and promoting recovery.

Conceptualizing the Dynamics between Bicultural Identification and Personal Social Networks

An adequate understanding of the acculturation processes affecting immigrants and their descendants involves ascertaining the dynamic interplay between the way these individuals manage their multiple (and sometimes conflictual) cultural value systems and identifications and possible changes in their social networks. To fill this gap, the present research examines how key acculturation variables (e.g., strength of ethnic/host cultural identifications, bicultural identity integration or BII) relate to the composition and structure of bicultural individuals' personal social networks. In Study 1, we relied on a generationally and culturally diverse community sample of 123 Latinos residing in the US. Participants nominated eight individuals (i.e., alters) from their habitual social networks and across two relational domains: friendships and colleagues. Results indicated that the interconnection of same ethnicity alters across different relationship domains is linked to cultural identifications, while the amount of coethnic and host individuals in the network is not. In particular, higher interconnection between Latino friends and colleagues was linked to lower levels of U.S.

IDENTIFICATION

Conversely, the interconnection of non-Latino friends and colleagues was associated with lower levels of Latino identification. This pattern of results suggests that the relational context for each type of cultural identification works in a subtractive and inverse manner. Further, time spent in the US was linked to both Latino and U.S. cultural identifications, but this relationship was moderated by the level of BII. Specifically, the association between time in the US and strength of both cultural identities was stronger for individuals reporting low levels of BII. Taking the findings from Study 1 as departure point, Study 2 used an agent-based model data simulation approach to explore the dynamic ways in which the content and the structure of an immigrant's social network might matter over time in predicting three possible identity patterns: coexisting cultural identifications, conflicting cultural identifications, and a mixture of the two. These simulations allowed us to detect network constellations, which lead to identification or disidentification with both cultures. We showed that distinct patterns of social relations do not lead to identity outcomes in a deterministic fashion, but that often many different outcomes are probable.

A posteriori correction of camera characteristics from large image data sets

Large datasets are emerging in many fields of image processing including: electron microscopy, light microscopy, medical X-ray imaging, astronomy, etc. Novel computer-controlled instrumentation facilitates the collection of very large datasets containing thousands of individual digital images. In single-particle cryogenic electron microscopy (“cryo-EM”), for example, large datasets are required for achieving quasi-atomic resolution structures of biological complexes. Based on the collected data alone, large datasets allow us to precisely determine the statistical properties of the imaging sensor on a pixel-by-pixel basis, independent of any “a priori” normalization routinely applied to the raw image data during collection (“flat field correction”). Our straightforward “a posteriori” correction yields clean linear images as can be verified by Fourier Ring Correlation (FRC), illustrating the statistical independence of the corrected images over all spatial frequencies. The image sensor characteristics can also be measured continuously and used for correcting upcoming images.

Quantifying resolution limiting factors in subtomogram averaged cryo-electron tomography using simulations

Cryo-electron tomography (CET) is the only available technique capable of characterizing the structure of biological macromolecules in conditions close to the native state. With the advent of subtomogram averaging, as a post-processing step to CET, resolutions in the (sub-) nanometer range have become within reach. In addition to advances in instrumentation and experiments, the reconstruction scheme has improved by inclusion of more accurate contrast transfer function (CTF) correction methods, better defocus estimation, and better alignments of the tilt-series and subtomograms. To quantify the importance of each contribution, we have split the full process from data collection to reconstruction into different steps. For the purpose of evaluation we have acquired tilt-series of ribosomes in such a way that we could precisely determine the defocus of each macromolecule. Then, we simulated tilt-series using the InSilicoTEM package and applied tomogram reconstruction and subtomogram averaging. Through large scale simulations under different conditions and parameter settings we find that tilt-series alignment is the resolution limiting factor for our experimental data. Using simulations, we find that when this alignment inaccuracy is alleviated, tilted CTF correction improves the final resolution, or equivalently, the same resolution can be achieved using less particles. Furthermore, we predict from which resolution onwards better CTF correction and defocus estimation methods are required. We obtain a final average using 3198 ribosomes with a resolution of 2.2nm on the experimental data. Our simulations suggest that with the same number of particles a resolution of 1.2nm could be achieved by improving the tilt-series alignment.

Determination of localized visibility in off-axis electron holography

Off-axis electron holography is a wavefront-split interference method for the transmission electron microscope that allows the phase shift and amplitude of the electron wavefront to be separated and quantitatively measured. An additional, third component of the holographic signal is the coherence of the electron wavefront. Historically, wavefront coherence has been evaluated by measurement of the holographic fringe visibility (or contrast) based on the minimum and maximum intensity values. We present a method based on statistical moments is presented that allows allow the visibility to be measured in a deterministic and reproducible fashion suitable for quantitative analysis. We also present an algorithm, based on the Fourier-ratio method, which allows the visibility to be resolved in two-dimensions, which we term the local visibility. The local visibility may be used to evaluate the loss of coherence due to electron scattering within a specimen, or as an aid in image analysis and segmentation. The relationship between amplitude and visibility may be used to evaluate the composition and mass thickness of a specimen by means of a 2-D histogram. Results for a selection of elements (C, Al, Si, Ti, Cr, Cu, Ge, and Au) are provided. All presented visibility metrics are biased at low-dose conditions by the presence of shot-noise, for which we provide methods for empirical normalization to achieve linear response.

Image formation modeling in cryo-electron microscopy

Accurate modeling of image formation in cryo-electron microscopy is an important requirement for quantitative image interpretation and optimization of the data acquisition strategy. Here we present a forward model that accounts for the specimen's scattering properties, microscope optics, and detector response. The specimen interaction potential is calculated with the isolated atom superposition approximation (IASA) and extended with the influences of solvent's dielectric and ionic properties as well as the molecular electrostatic distribution. We account for an effective charge redistribution via the Poisson-Boltzmann approach and find that the IASA-based potential forms the dominant part of the interaction potential, as the contribution of the redistribution is less than 10%. The electron wave is propagated through the specimen by a multislice approach and the influence of the optics is included via the contrast transfer function. We incorporate the detective quantum efficiency of the camera due to the difference between signal and noise transfer characteristics, instead of using only the modulation transfer function. The full model was validated against experimental images of 20S proteasome, hemoglobin, and GroEL. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.

Characterization of detector modulation-transfer function with noise, edge, and holographic methods

We developed a new method for characterization of detector performance used in the transmission electron microscope (TEM) based on the measured contrast of holographic fringes. The new method changes spatial frequency of the measured holographic fringes, generated by an electrostatic biprism and Schottky or cold field-emission gun, to sample the modulation-transfer function (MTF) of the detector. The MTF of a Gatan Ultrascan™ 1000 charged-coupled detector (CCD) is evaluated using the new method and the results are compared to the established noise and slanted-edge method results. Requirements for accuracy of the edge and noise MTF methods are discussed. We consider issues surrounding incomplete read-out and how it affects the gain reference normalization of the detector. We evaluate how the MTF affects optimization of experimental parameters in the TEM.

Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images

The typical dose used to record cryo-electron microscopy images from vitrified biological specimens is so high that radiation-induced structural alterations are bound to occur during data acquisition. Integration of all scattered electrons into one image can lead to significant blurring, particularly if the data are collected from an unsupported thin layer of ice suspended over the holes of a support film. Here, the dose has been fractioned and exposure series have been acquired in order to study beam-induced specimen movements under low dose conditions, prior to bubbling. Gold particles were added to the protein sample as fiducial markers. These were automatically localized and tracked throughout the exposure series and showed correlated motions within small patches, with larger amplitudes of motion vectors at the start of a series compared with the end of each series. A non-rigid scheme was used to register all images within each exposure series, using natural neighbor interpolation with the gold particles as anchor points. The procedure increases the contrast and resolution of the examined macromolecules.

Cellular nanoimaging by cryo electron tomography

Cryo electron tomography is a technique that allows visualization of biological specimens in three dimensions with nanometer resolution. For cryo immobilized life sciences samples it can reveal cellular morphology, the shape of membranous structures, and depict internal macromolecular arrangements and large proteins. Cryo electron tomography is a unique technique in structural biology research because it is the only tool that enables direct visualization of the cellular space at molecular resolution. Here we present the methods that we apply in our lab to perform cellular cryo electron tomography, which require expertise on cell biology for cell growth, physics for electron microscopy, and image processing for reconstruction and 3D visualization. We define the instrumentation, materials, and protocols for cryo electron tomography of whole cells, including cell growth, specimen vitrification, microscope alignments, data acquisition, tomographic image reconstruction, and 3D visualization techniques.

Characterization of an x-ray phase contrast imaging system based on the miniature synchrotron MIRRORCLE-6X

PURPOSE

The implementation of in-line x-ray phase contrast imaging (PCI) for soft-tissue patient imaging is hampered by the lack of a bright and spatially coherent x-ray source that fits into the hospital environment. This article provides a quantitative characterization of the phase-contrast enhancement of a PCI system based on the miniature synchrotron technology MIRRORCLE-6X.

METHODS

The phase-contrast effect was measured using an edge response of a plexiglass plate as a function of the incident angle of radiation. We have developed a comprehensive x-ray propagation model based on the system's components, properties, and geometry in order to interpret the measurement data. Monte-Carlo simulations are used to estimate the system's spectral properties and resolution.

RESULTS

The measured ratio of the detected phase-contrast to the absorption contrast is currently in the range 100% to 200%. Experiments show that with the current implementation of the MIRRORCLE-6X, a target smaller than 30-40 μm does not lead to a larger phase-contrast. The reason for this is that the fraction of x-rays produced by the material (carbon filament and glue) that is used for mounting the target in the electron beam is more than 25% of the total amount of x-rays produced. This increases the apparent source size. The measured phase-contrast is at maximum two times larger than the absorption contrast with the current set-up.

CONCLUSIONS

Calculations based on our model of the present imaging system predict that the phase-contrast can be up to an order of magnitude larger than the absorption contrast in case the materials used for mounting the target in the electron beam do not (or hardly) produce x-rays. The methods described in this paper provide vital feedback for guiding future modifications to the design of the x-ray target of MIRRORCLE-type system and configuration of the in-line PCI systems in general.

Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate

Radiation damage is an important resolution limiting factor both in macromolecular X-ray crystallography and cryo-electron microscopy. Systematic studies in macromolecular X-ray crystallography greatly benefited from the use of dose, expressed as energy deposited per mass unit, which is derived from parameters including incident flux, beam energy, beam size, sample composition and sample size. In here, the use of dose is reintroduced for electron microscopy, accounting for the electron energy, incident flux and measured sample thickness and composition. Knowledge of the amount of energy deposited allowed us to compare doses with experimental limits in macromolecular X-ray crystallography, to obtain an upper estimate of radical concentrations that build up in the vitreous sample, and to translate heat-transfer simulations carried out for macromolecular X-ray crystallography to cryo-electron microscopy. Stroboscopic exposure series of 50-250 images were collected for different incident flux densities and integration times from Lumbricus terrestris extracellular hemoglobin. The images within each series were computationally aligned and analyzed with similarity metrics such as Fourier ring correlation, Fourier ring phase residual and figure of merit. Prior to gas bubble formation, the images become linearly brighter with dose, at a rate of approximately 0.1% per 10 MGy. The gradual decomposition of a vitrified hemoglobin sample could be visualized at a series of doses up to 5500 MGy, by which dose the sample was sublimed. Comparison of equal-dose series collected with different incident flux densities showed a dose-rate effect favoring lower flux densities. Heat simulations predict that sample heating will only become an issue for very large dose rates (50 e(-)Å(-2) s(-1) or higher) combined with poor thermal contact between the grid and cryo-holder. Secondary radiolytic effects are likely to play a role in dose-rate effects. Stroboscopic data collection combined with an improved understanding of the effects of dose and dose rate will aid single-particle cryo-electron microscopists to have better control of the outcome of their experiments.

A fast algorithm for computing and correcting the CTF for tilted, thick specimens in TEM

Today, the resolution in phase-contrast cryo-electron tomography is for a significant part limited by the contrast transfer function (CTF) of the microscope. The CTF is a function of defocus and thus varies spatially as a result of the tilting of the specimen and the finite specimen thickness. Models that include spatial dependencies have not been adopted in daily practice because of their high computational complexity. Here we present an algorithm which reduces the processing time for computing the 'tilted' CTF by more than a factor 100. Our implementation of the full 3D CTF has a processing time on the order of a Radon transform of a full tilt-series. We derive and validate an expression for the damping envelope function describing the loss of resolution due to specimen thickness. Using simulations we quantify the effects of specimen thickness on the accuracy of various forward models. We study the influence of spatially varying CTF correction and subsequent tomographic reconstruction by simulation and present a new approach for space-variant phase-flipping. We show that our CTF correction strategies are successful in increasing the resolution after tomographic reconstruction.