FASTDEF: Fast defocus and astigmatism estimation for high-throughput transmission electron microscopy

In this work we present a fast and automated algorithm for estimating the contrast transfer function (CTF) of a transmission electron microscope. The approach is very suitable for High Throughput work because: (a) it does not require any initial defocus estimation, (b) it is almost an order of magnitude faster than existing approaches, (c) it opens the way to well-defined extensions to the estimation of higher order aberrations, at the same time that provides defocus and astigmatism estimations comparable in accuracy to well established methods, such as Xmipp and CTFFIND3 approaches. The new algorithm is based on obtaining the wrapped modulating phase of the power spectra density pattern by the use of a quadrature filter. This phase is further unwrapped in order to obtain the continuous and smooth absolute phase map; then a Zernike polynomial fitting is performed and the defocus and astigmatism parameters are determined. While the method does not require an initial estimation of the defocus parameters or any non-linear optimization procedure, these approaches can be used if further refinement is desired. Results of the CTF estimation method are presented for standard negative stained images, cryo-electron microscopy images in the absence of carbon support, as well as micrographs with only ice. Additionally, we have also tested the proposed method with micrographs acquired from tilted and untilted samples, obtaining good results. The algorithm is freely available as a part of the Xmipp package [http://xmipp.cnb.csic.es].     

Leginon: an automated system for acquisition of images from vitreous ice specimens

We have developed a system to automatically acquire cryo-electron micrographs. The system is designed to emulate all of the decisions and actions of a highly trained microscopist in collecting data from a vitreous ice specimen. These include identifying suitable areas of vitreous ice at low magnification, determining the presence and location of specimen on the grid, automatically adjusting imaging parameters (focus, astigmatism) under low-dose conditions, and acquiring images at high magnification to either film or a digital camera. This system is responsible for every aspect of image acquisition and can run unattended, other than requiring periodic refilling of the cryogens, for over 24 h. The system has been tested out on a variety of specimens that represent typical challenges in the field of cryo-electron microscopy. The results show that the overall performance of the system is equivalent to that of an experienced microscopist.     

Automated acquisition of cryo-electron micrographs for single particle reconstruction on an FEI Tecnai electron microscope

AutoEM is a software package developed by Zhang et al. [J. Struct. Biol. 1356, 251] for semi-automated acquisition of cryo-electron micrographs from Tecnai series electron microscopes and is used frequently at the lowest level of automation. We report here on the new progress that we have made based on their preliminary work. A fourth low-dose state is created where the system can pre-select all the good holes in a grid square from a single CCD image taken at low magnification, making the system operative at much higher levels of automation. An additional control interface enables the operator to monitor the status of the program and the quality of the data, interact with the program, and direct the execution process according to intermediate results. When data acquisition is in progress, all useful information is automatically saved in certain text files which are easily accessible by a database. More detailed improvements and general advantages are illustrated and discussed. We have started to use the program to perform routine data collection. A number of applications show that the performance of the program is satisfactory and the quality of the micrographs and their power spectra acquired by the program is comparable to those manually collected under the same conditions.     

Images of purple membrane at 2.8 A resolution obtained by cryo-electron microscopy

Improvements in technique have produced electron micrographs of purple membrane that provide, after computer analysis, reproducibly measurable diffraction peaks extending to 2.8 A (1 A = 0.1 nm). The improvements include better specimen preparation, a more stable cryo-electron microscope with better alignment and the addition of an image-processing step, which gives weights to local areas of the image according to the local strength of the periodic component of the image. These improvements have enabled the calculation of a directly phased projection map at 2.8 A resolution.     

Automatic CTF correction for single particles based upon multivariate statistical analysis of individual power spectra

Three-dimensional electron cryomicroscopy of randomly oriented single particles is a method that is suitable for the determination of three-dimensional structures of macromolecular complexes at molecular resolution. However, the electron-microscopical projection images are modulated by a contrast transfer function (CTF) that prevents the calculation of three-dimensional reconstructions of biological complexes at high resolution from uncorrected images. We describe here an automated method for the accurate determination and correction of the CTF parameters defocus, twofold astigmatism and amplitude-contrast proportion from single-particle images. At the same time, the method allows the frequency-dependent signal decrease (B factor) and the non-convoluted background signal to be estimated. The method involves the classification of the power spectra of single-particle images into groups with similar CTF parameters; this is done by multivariate statistical analysis (MSA) and hierarchically ascending classification (HAC). Averaging over several power spectra generates class averages with enhanced signal-to-noise ratios. The correct CTF parameters can be deduced from these class averages by applying an iterative correlation procedure with theoretical CTF functions; they are then used to correct the raw images. Furthermore, the method enables the tilt axis of the sample holder to be determined and allows the elimination of individual poor-quality images that show high drift or charging effects.     

ASOCEM: Automatic Segmentation Of Contaminations in cryo-EM

Particle picking is currently a critical step in the cryo-electron microscopy single particle reconstruction pipeline. Contaminations in the acquired micrographs severely degrade the performance of particle pickers, resulting in many “non-particles” in the collected stack of particles. In this paper, we present ASOCEM (Automatic Segmentation Of Contaminations in cryo-EM), an automatic method to detect and segment contaminations, which requires as an input only the approximate particle size. In particular, it does not require any parameter tuning nor manual intervention. Our method is based on the observation that the statistical distribution of contaminated regions is different from that of the rest of the micrograph. This nonrestrictive assumption allows to automatically detect various types of contaminations, from the carbon edges of the supporting grid to high contrast blobs of different sizes. We demonstrate the efficiency of our algorithm using various experimental data sets containing various types of contaminations. ASOCEM is integrated as part of the KLT picker (Eldar et al., 2020) and is available at https://github.com/ShkolniskyLab/kltpicker2.     

Determination of astigmatism in TEM images

We have developed a new two-step algorithm to determine the astigmatism of images from transmission electron microscopes (TEMs). Instead of computing the radial average of the power spectrum, we divide the power spectrum of a TEM image 1 to m (typically 32) sectors. We use a technique based on perturbation analysis of the contrast transfer function (CTF) to assimilate sector averages of the power spectrum of an image, which are incoherent in the presence of astigmatism, to a coherent radial average corresponding to a nominal defocus value. This is based on the fact that small defocus change from a nominal value can be considered to be equivalent to a perturbation on the spatial frequency spectra. Thus, instead of measuring the angular defocus variations, we optimise the frequency change required to obtain a coherent radial average. Numerically, this is achieved by minimizing sigma(2)/sigma(1) of a matrix formed from the sector averages, where sigma(i) denotes the ith singular value of the matrix. After the minimisation procedure, the second singular value should be very small compared with the first singular value, indicating that the matrix is nearly rank unity. In the second step, the nominal defocus can be obtained from the coherent radial average using any good defocus estimation program, which assumes zero astigmatism. The defocus value at a sector can be obtained from this nominal defocus value and one of the parameters from the unconstrained optima. Our algorithm is tested on astigmatic images of carbon film, 2D crystals of bacteriorhodopsin and cryo-images of HIV cores.     

Zernike phase contrast cryo-electron tomography of whole mounted frozen cells

Cryo-electron tomography of frozen hydrated cells has provided cell biologists with an indispensable tool for delineating three-dimensional arrangements of cellular ultrastructure. To avoid the damage induced by electron irradiation, images of frozen hydrated biological specimens are generally acquired under low-dose conditions, resulting in weakly contrasted images that are difficult to interpret, and in which ultrastructural details remain ambiguous. Zernike phase contrast transmission electron microscopy can improve contrast, and can also fix a fatal problem related to the inherent low contrast of conventional electron microscopy, namely, image modulation due to the unavoidable setting of deep defocus. In this study, we applied cryo-electron tomography enhanced with a Zernike phase plate, which avoids image modulation by allowing in-focus setting. The Zernike phase contrast cryo-electron tomography has a potential to suppress grainy background generation. Due to the smoother background in comparison with defocus phase contrast cryo-electron tomography, Zernike phase contrast cryo-electron tomography could yield higher visibility for particulate or filamentous ultrastructure inside the cells, and allowed us to clearly recognize membrane protein structures.     

MtreeRing: An R package with graphical user interface for automatic measurement of tree ring widths using image processing techniques

Accurate measurements of ring-width series are essential for dendrochronological analyses. We present an R package MtreeRing for ring-width measurements on scanned digital images. A morphological alternate sequential filter is used for noise reduction in the original image. Ring boundaries are determined by the steepest negative slopes in the light reflectance of latewood-earlywood transitions. To automatically identify tree rings, the package provides three alternative methods (watershed-based segmentation, Canny edge detector, and a linear detection algorithm), each with advantages and disadvantages and suited to different wood anatomical features. The user can also manually mark tree rings on species with complex anatomical structures. The arcs of inner-rings and angles of successive inclined ring boundaries are used to correct ring-width series. Differences in ring-width measurements between MtreeRing and WinDENDRO in a given coniferous species (Larix gmelinii) were assessed, and no significant difference between programs was found. Furthermore, the package provides an R-based web application which was developed using the Shiny framework. This beginner-friendly application allows viewing and interacting with tree ring images. It requires no programming experience and can run on either a local computer or a remote server.     

Zero-loss energy filtering as improved imaging mode in cryoelectronmicroscopy of frozen-hydrated specimens

One of the remaining problems in attaining higher structural resolution with cryoelectronmicroscopy of frozen-hydrated specimens is the low contrast of micrographs taken close to the electron optical focus. By measuring electron energy loss spectra (EELS) of ice layers we show that a large fraction of incident electrons undergoes an inelastic electron-plasmon scattering process. Thus these electrons do not carry structural information of the protein but increase the background of the electron image and therefore reduce the contrast of the negative. Here we report the improvement in contrast gained by filtering out inelastically scattered electrons using an energy-filtered transmission electron microscope (EFTEM). This gain in contrast permits a dramatic decrease in defocusing values, resulting in improved structural resolution. In addition, the increased signal to noise ratio allows the recording of micrographs at a reduced electron dose. This should result in less damage to vitrified and unstained proteins and other beam-sensitive specimens.     

Preferred orientations of LDL in vitreous ice indicate a discoid shape of the lipoprotein particle

The structure of the human low-density lipoprotein (LDL) was analyzed in vitreous ice using cryo-electron microscopy (cryo-EM). In relatively thick cryo-EM preparations, random orientation of LDL particles produced various types of projections on the microscope screen, including circular projections with a high-density ring and rectangular projections with two high-density bands. However, in especially thin preparations, preferred, non-random orientations of the LDL particle produced only circular projections of the lipoprotein structure. In preparations with high LDL concentrations, ordered two-dimensional arrays, including hexagonal arrangements of circular projections and short stacks of rectangular projections, were observed. These observations are consistent with a discoid shape of the LDL particle, and suggest that surface tension forces may influence orientation of the LDL disc in thin aqueous films. Face-on orientation of LDL in especially thin cryo-EM preparations may explain earlier difficulties in identifying discoid features of the lipoprotein particle, and illustrates that some caution is warranted when attempts are made to reconstruct the three-dimensional structure of LDL from cryo-electron micrographs.     

EMAN: semiautomated software for high-resolution single-particle reconstructions

We present EMAN (Electron Micrograph ANalysis), a software package for performing semiautomated single-particle reconstructions from transmission electron micrographs. The goal of this project is to provide software capable of performing single-particle reconstructions beyond 10 A as such high-resolution data become available. A complete single-particle reconstruction algorithm is implemented. Options are available to generate an initial model for particles with no symmetry, a single axis of rotational symmetry, or icosahedral symmetry. Model refinement is an iterative process, which utilizes classification by model-based projection matching. CTF (contrast transfer function) parameters are determined using a new paradigm in which data from multiple micrographs are fit simultaneously. Amplitude and phase CTF correction is then performed automatically as part of the refinement loop. A graphical user interface is provided, so even those with little image processing experience will be able to begin performing reconstructions. Advanced users can directly use the lower level shell commands and even expand the package utilizing EMAN's extensive image-processing library. The package was written from scratch in C++ and is provided free of charge on our Web site. We present an overview of the package as well as several conformance tests with simulated data.     

Conformations of macromolecules and their complexes from heterogeneous datasets

We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both discrete and continuous macromolecular conformational spectra. These algorithms naturally incorporate conformational heterogeneity without resort to sorting and classification, or prior knowledge of the type of heterogeneity present. They are applicable to single-particle diffraction and image datasets produced by X-ray lasers and cryo-electron microscopy, respectively, and particularly suitable for systems not easily amenable to purification or crystallization.     

Accounting for phenology in the analysis of animal movement

The analysis of animal tracking data provides important scientific understanding and discovery in ecology. Observations of animal trajectories using telemetry devices provide researchers with information about the way animals interact with their environment and each other. For many species, specific geographical features in the landscape can have a strong effect on behavior. Such features may correspond to a single point (eg, dens or kill sites), or to higher dimensional subspaces (eg, rivers or lakes). Features may be relatively static in time (eg, coastlines or home‐range centers), or may be dynamic (eg, sea ice extent or areas of high‐quality forage for herbivores). We introduce a novel model for animal movement that incorporates active selection for dynamic features in a landscape. Our approach is motivated by the study of polar bear (Ursus maritimus) movement. During the sea ice melt season, polar bears spend much of their time on sea ice above shallow, biologically productive water where they hunt seals. The changing distribution and characteristics of sea ice throughout the year mean that the location of valuable habitat is constantly shifting. We develop a model for the movement of polar bears that accounts for the effect of this important landscape feature. We introduce a two‐stage procedure for approximate Bayesian inference that allows us to analyze over 300 000 observed locations of 186 polar bears from 2012 to 2016. We use our model to estimate a spatial boundary of interest to wildlife managers that separates two subpopulations of polar bears from the Beaufort and Chukchi seas.     

3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy

We use cryo-electron microscopy to compare 3D shapes of 158 bp long DNA minicircles that differ only in the sequence within an 18 bp block containing either a TATA box or a catabolite activator protein binding site. We present a sorting algorithm that correlates the reconstructed shapes and groups them into distinct categories. We conclude that the presence of the TATA box sequence, which is believed to be easily bent, does not significantly affect the observed shapes.     

On the structures of filamentous bacteriophage Ff (fd,f1, M13)

The filamentous bacteriophage (Inovirus) strain Ff (fd, f1, M13) is widely used in molecular biophysics as a simple model system. A low resolution molecular model of the fd protein coat has been reported, derived from iterative helical real space reconstruction of cryo-electron micrographs (cryoEM). This model is significantly different from the model previously derived from X-ray fibre diffraction and solid-state NMR. We show that the cryoEM model agrees neither with solid-state NMR data nor with X-ray fibre diffraction data of fd, and has some puzzling structural features, for instance nanometre holes through the protein coat. We refine the cryoEM model against the X-ray data, and find that the model after refinement closely approximates the model derived directly from X-ray fibre diffraction and solid-state NMR data. We suggest possible reasons for the differences between the models derived from cryoEM and X-ray diffraction.     

Direct Measurement of Water States in Cryopreserved Cells Reveals Tolerance toward Ice Crystallization

Complex living systems such as mammalian cells can be arrested in a solid phase by ultrarapid cooling. This allows for precise observation of cellular structures as well as cryopreservation of cells. The state of water, the main constituent of biological samples, is crucial for the success of cryogenic applications. Water exhibits many different solid states. If it is cooled extremely rapidly, liquid water turns into amorphous ice, also called vitreous water, a glassy and amorphous solid. For cryo-preservation, the vitrification of cells is believed to be mandatory for cell survival after freezing. Intracellular ice crystallization is assumed to be lethal, but experimental data on the state of water during cryopreservation are lacking. To better understand the water conditions in cells subjected to freezing protocols, we chose to directly analyze their subcellular water states by cryo-electron microscopy and tomography, cryoelectron diffraction, and x-ray diffraction both in the cryofixed state and after warming to different temperatures. By correlating the survival rates of cells with their respective water states during cryopreservation, we found that survival is less dependent on ice-crystal formation than expected. Using high-resolution cryo-imaging, we were able to directly show that cells tolerate crystallization of extra- and intracellular water. However, if warming is too slow, many small ice crystals will recrystallize into fewer but bigger crystals, which is lethal. The applied cryoprotective agents determine which crystal size is tolerable. This suggests that cryoprotectants can act by inhibiting crystallization or recrystallization, but they also increase the tolerance toward ice-crystal growth.     

Three-dimensional reconstruction of bovine brain V-ATPase by cryo-electron microscopy and single particle analysis

Bovine V-ATPase from brain clathrin-coated vesicles was investigated by cryo-electron microscopy and single particle analysis. Our studies revealed great flexibility of the central linker region connecting V₁ and V₀. As a consequence, the two sub-complexes were processed separately and the resulting volumes were merged computationally. We present the first three-dimensional (3D) map of a V-ATPase obtained from cryo-electron micrographs. The overall resolution was estimated 34 Å by Fourier shell correlation (0.5 cutoff). Our 3D reconstruction shows a large peripheral stalk and a smaller, isolated peripheral density, suggesting a second, less well-resolved peripheral connection. The 3D map reveals new features of the large peripheral stator and of the collar-like density attached to the membrane domain. Our analyses of the membrane domain indicate the presence of six proteolipid subunits. In addition, we could localize the V₀ subunit a flanking the large peripheral stalk.     

Accurate modeling of single-particle cryo-EM images quantitates the benefits expected from using Zernike phase contrast

The use of a Zernike-type phase plate in biologic cryo-electron microscopy allows the imaging, without using defocus, of what are predominantly phase objects. It is thought that such phase-plate implementations might result in higher quality images, free from the problems of CTF correction that occur when images must be recorded at extremely high values of defocus. In single-particle cryo-electron microscopy it is hoped that these improvements in image quality will facilitate work on structures that have proved difficult to study, either because of their relatively small size or because the structures are not completely homogeneous. There is still a need, however, to quantitate how much improvement can be gained by using a phase plate for single-particle cryo-electron microscopy. We present a method for quantitatively modeling the images recorded with 200keV electrons, for single particles embedded in vitreous ice. We then investigate what difference the use of a phase-plate device could have on the processing of single-particle data. We confirm that using a phase plate results in single-particle datasets in which smaller molecules can be detected, particles can be more accurately aligned and problems of heterogeneity can be more easily addressed.     

The future is cold: cryo-preparation methods for transmission electron microscopy of cells

Our knowledge of the organization of the cell is linked, to a great extent, to light and electron microscopy. Choosing either photons or electrons for imaging has many consequences on the image obtained, as well as on the experiment required in order to generate the image. One apparent effect on the experimental side is in the sample preparation, which can be quite elaborate for electron microscopy. In recent years, rapid freezing, cryo-preparation and cryo-electron microscopy have been more widely used because they introduce fewer artefacts during preparation when compared with chemical fixation and room temperature processing. In addition, cryo-electron microscopy allows the visualization of the hydrated specimens. In the present review, we give an introduction to the rapid freezing of biological samples and describe the preparation steps. We focus on bulk samples that are too big to be directly viewed under the electron microscope. Furthermore, we discuss the advantages and limitations of freeze substitution and cryo-electron microscopy of vitreous sections and compare their application to the study of bacteria and mammalian cells and to tomography.