A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions

Electron tomography is an imaging technique that allows for the elucidation of three-dimensional structural information of biological specimens in a very general context, including cellular in situ observations. The approach starts by collecting a set of images at different projection directions by tilting the specimen stage inside the microscope. Therefore, a crucial preliminary step is to precisely define the acquisition geometry by aligning all the tilt images to a common reference. Errors introduced in this step will lead to the appearance of artifacts in the tomographic reconstruction, rendering them unsuitable for the sample study. Focusing on fiducial-based acquisition strategies, this work proposes a deep-learning algorithm to detect misalignment artifacts in tomographic reconstructions by analyzing the characteristics of these fiducial markers in the tomogram. In addition, we propose an algorithm designed to detect fiducial markers in the tomogram with which to feed the classification algorithm in case the alignment algorithm does not provide the location of the markers. This open-source software is available as part of the Xmipp software package inside of the Scipion framework, and also through the command-line in the standalone version of Xmipp.

Image processing tools for the validation of CryoEM maps

The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded.

ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation

Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline.

The Scipion framework, originally developed for SPA (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project.

The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.

On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy

Single-particle analysis (SPA) by cryo-electron microscopy comprises the estimation of many parameters along its image-processing pipeline. Overfitting observed in SPA is normally due to misestimated parameters, and the only way to identify these is by comparing the estimates of multiple algorithms or, at least, multiple executions of the same algorithm.

Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands of macromolecules that are assumed to be structurally identical are combined into a single 3D map representing the Coulomb potential of the macromolecule under study. This article discusses possible caveats along the image-processing path and how to avoid them to obtain a reliable 3D structure. Some of these problems are very well known in the community. These may be referred to as sample-related (such as specimen denaturation at interfaces or non-uniform projection geometry leading to underrepresented projection directions). The rest are related to the algorithms used. While some have been discussed in depth in the literature, such as the use of an incorrect initial volume, others have received much less attention. However, they are fundamental in any data-analysis approach. Chiefly among them, instabilities in estimating many of the key parameters that are required for a correct 3D reconstruction that occur all along the processing workflow are referred to, which may significantly affect the reliability of the whole process. In the field, the term overfitting has been coined to refer to some particular kinds of artifacts. It is argued that overfitting is a statistical bias in key parameter-estimation steps in the 3D reconstruction process, including intrinsic algorithmic bias. It is also shown that common tools (Fourier shell correlation) and strategies (gold standard) that are normally used to detect or prevent overfitting do not fully protect against it. Alternatively, it is proposed that detecting the bias that leads to overfitting is much easier when addressed at the level of parameter estimation, rather than detecting it once the particle images have been combined into a 3D map. Comparing the results from multiple algorithms (or at least, independent executions of the same algorithm) can detect parameter bias. These multiple executions could then be averaged to give a lower variance estimate of the underlying parameters.

Algorithmic robustness to preferred orientations in single particle analysis by CryoEM

The presence of preferred orientations in single particle analysis (SPA) by cryo-Electron Microscopy (cryoEM) is currently one of the hurdles preventing many structural analyses from yielding high-resolution structures. Although the existence of preferred orientations is mostly related to the grid preparation, in this technical note, we show that some image processing algorithms used for angular assignment and three-dimensional (3D) reconstruction are more robust than others to these detrimental conditions. We exemplify this argument with three different data sets in which the presence of preferred orientations hindered achieving a 3D reconstruction without artifacts or, even worse, a 3D reconstruction could never be achieved.

Local resolution estimates of cryoEM reconstructions

The field of cryoEM has quickly advanced in last years with the new biochemical, technological, methodological and computational developments. It has allowed significant progresses in Structural Biology, typically reaching quasi-atomic resolutions in the reconstructed maps. However, this rapid advance has also generated new questions relevant to resolution estimates. The global resolution metrics and their criteria have been deeply discussed in the last decade, but despite that, it remains as an important issue in the field. Recently, the introduction of local resolution measurements has changed how cryoEM reconstructions are interpreted, providing information about the existence of heterogeneity, flexibility, and angular assignment errors, and using it as a tool to aid in modeling. In this review we revisit the concept of local resolution and the different algorithms in the current state of the art. However, the concept of local resolution is not uniquely defined, and each implementation measures different features. This may lead to inappropriate interpretation of local resolution maps. Hence, a set of good practices is provided in this review to avoid misleading and over-interpretation of the reconstructions.

Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening

The analysis of structure factors in 3D cryo-EM Coulomb potential maps and their "enhancement" at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accomplish this enhancement is by means of the so-called B-factor correction, which applies a global filter to boost high frequencies with some dampening considerations related to noise amplification. The results are maps with a better visual aspect and a quasiflat spectrum at medium and high frequencies. This practice is so widespread that most map depositions in the Electron Microscopy Data Base (EMDB) only contain sharpened maps. Here, the use in cryoEM of global B-factor corrections is theoretically and experimentally analyzed. Results clearly illustrate that protein spectra present a falloff. Thus, spectral quasi-flattening may produce protein spectra with distortions when compared with experimental ones, this fact, combined with the practice of reporting only sharpened maps, generates a sub-optimal situation in terms of data preservation, reuse and reproducibility. Now that the field is more advanced, we put forward two suggestions: (1) to use methods which keep more faithfully the original experimental signal properties of macromolecules when "enhancing" the map, and (2) to further stress the need to deposit the original experimental maps without any postprocessing or sharpening, not only the enhanced maps. In the absence of access to these original maps data is lost, preventing their future analysis with new methods.

Measurement of local resolution in electron tomography

Resolution (global and local) is one of the most reported metrics of quality measurement in Single Particle Analysis (SPA). However, in electron tomography, the situation is different and its computation is not straightforward. Typically, resolution estimation is global and, therefore, reduces the assessment of a whole tomogram to a single number. However, it is known that tomogram quality is spatially variant. Still, up to our knowledge, a method to estimate local quality metrics in tomography is lacking. This work introduces MonoTomo, a method developed to estimate locally in a tomogram the highest reliable frequency component, expressed as a form of local resolution. The fundamentals lie in a local analysis of the density map via monogenic signals, which, in analogy to MonoRes, allows for local estimations. Results with experimental data show that the local resolution range that MonoTomo casts agrees with reported resolution values for experimental data sets, with the advantage of providing a local estimation. A range of applications of MonoTomo are suggested for further exploration.

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data set.

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.

Using Scipion for stream image processing at Cryo-EM facilities

Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world.

Blind estimation of DED camera gain in Electron Microscopy

The introduction of Direct Electron Detector (DED) videos in the Electron Microscope field has boosted Single Particle Analysis to a point in which it is currently considered to be a key technique in Structural Biology. In this article we introduce an approach to estimate the DED camera gain at each pixel from the movies themselves. This gain is needed to have the set of recorded frames into a coherent gray level range, homogeneous over the whole image. The algorithm does not need any other input than the DED movie itself, being capable of providing an estimate of the camera gain image, helping to identify dead pixels and cases of incorrectly calibrated cameras. We propose the algorithm to be used either to validate the experimentally acquired gain image (for instance, to follow its possible change over time) or to verify that there is no residual gain image after experimentally correcting for the camera gain. We show results for a number of DED camera models currently in use (DE, Falcon II, Falcon 3, and K2).

Membranes based on polymer miscibility for selective transport and separation of metallic ions

Polymer inclusion membranes (PIM) used for selective transport and separation of metallic ions have emerged in recent times. Their expansion depends on the method of preparation and their suitable structure and physico-chemical characteristics. In this paper, a novel category of membranes for ions separation is reported. The membranes were synthesized by thermally induced phase separation using a mixture of polyvinylidene fluoride (PVDF) and cellulose triacetate (CTA) plasticized by tris(2-ethylhexyl) phosphate (TEHP) and with di-(2-ethylhexyl) phosphoric acid (D2EHPA) incorporated into the polymer as carrier to increase specific interactions between polymers. PIM membrane exhibited a hydrophobic (∼100°) and thermally stable up to ∼200°C porous homogenous structure. The transport of Ni(II), Zn(II) and Pb(II) from aqueous solutions was studied by competitive transport across polymer inclusion membranes (PIM). Competitive transport of ions in solution across PIM provide the selectivity order: Ni²⁺ (45%)>Pb²⁺ (35%)>Zn²⁺ (5%). A long-term transport experiment was carried out to study the durability of the system.

Effect of coating on the environmental applications of zero valent iron nanoparticles: the lindane case

Commercial stabilized slurry of zero-valent iron nanoparticles (nZVI) as well as laboratory-synthesized polymer-stabilized NZVI nanoparticles were used for lindane (γ-hexachlorocyclohexane) degradation studies in aqueous solution. In the present study, polymer-stabilized iron nanoparticles were stabilized using polyethylene glycol (PEG, Mn ~400 and ~950-1050) and polytetrahydrofuran (PTHF, Mn ~650). To study the effectiveness of the different nanoparticles, a quantitative monitorization of lindane degradation by using solid-phase extraction (SPE) and a qualitative measurement of generated volatile by-products by headspace-solid phase microextraction (HS-SPME) followed by GC/MS were carried out. The obtained data were compared and contrasted with the results obtained in previous work. Results showed that the nanoparticles studied in this work possess superior dechlorination performance compared with previous observations. The freshly prepared Fe(0)-PEG400, Fe(0)-PEG1050 and Fe(0)-PTHF exhibited high reactivity during the dechlorination process of lindane in a very short time. The results obtained with the synthesized nanoparticles were similar to those obtained with commercial nanoparticles. However, in all cases reactivity decreased at reaction's late stage. Degradation of lindane by the studied nanoparticles removed 99.9% of the lindane initial concentration after 72h, except for Fe(0)-PTHF nanoparticles, for which the reaction stopped after 5min. In all cases, the reaction followed a second order kinetics. Finally, comparing the results from this study with our previous work, where different nature polymers were considered (Fe(0)-CMC, Fe(0)-PAA and Fe(0)-PAP), more gradual degradation profile of lindane was observed for Fe(0)-PAA and Fe(0)-CMC. It should be noted that in the present case, the reaction of lindane was speeded up with commercial and Fe(0)-PEG nanoparticles. Nevertheless, in the later case, the composition of by-products was affected by the presence of partially degraded intermediates. Taking into account the current technologies, the high removal rates obtained and the acceptable degradation times required, the proposed technology is suitable for its aimed purpose.

Local analysis of strains and rotations for macromolecular electron microscopy maps

Macromolecular complexes perform their physiological functions by local rearrangements of their constituents and biochemically interacting with their reaction partners. These rearrangements may involve local rotations and the induction of local strains causing different mechanical efforts and stretches at the different areas of the protein. The analysis of these local deformations may reveal important insight into the way proteins perform their tasks. In this paper we introduce a method to perform this kind of local analysis using Electron Microscopy volumes in a fully objective and automatic manner. For doing so, we exploit the continuous nature of the result of an elastic image registration using B-splines as its basis functions. We show that the results obtained by the new automatic method are consistent with previous observations on these macromolecules.

Three-dimensional orientation of poly(l-lactide) crystals under uniaxial drawing

Three-dimensional strain-induced crystallization upon poly (l-lactide) stretching revealed by X-ray diffraction texture analysis via pole figure measurements.

Towards the development of eco-friendly disposable polymers: ZnO-initiated thermal and hydrolytic degradation in poly(l-lactide)/ZnO nanocomposites

Schematic representation showing catalytic reaction in poly(l-lactide)/ZnO nanocomposites.

Development of magnetoelectric CoFe2O4 /poly(vinylidene fluoride) microspheres

Magnetoelectric microspheres based on piezoelectric poly(vinylidene fluoride) (PVDF) and magnetostrictive CoFe₂O₄ (CFO), a novel morphology for polymer-based ME materials, have been developed by an electrospray process.

Relevance study of bare and coated zero valent iron nanoparticles for lindane degradation from its by-product monitorization

Zero-valent iron nanoparticles (NZVI) as well as polymer-stabilized nanoparticles were synthesized and used for lindane (γ-hexachlorocyclohexane) degradation in aqueous solution. To study the effectiveness of the different coated nanoparticles, simple and rapid analytical methods have been developed to measure and to detect lindane and its by-products. For the monitorization of lindane degradation solid-phase extraction (SPE) was used, while volatile by-products formation measurement was carried out by headspace-solid phase microextraction (HS-SPME) followed by GC/MS. The SPE-GC/MS method provides low detection limits (0.2 μg L(-1)), high recovery (above 95%) and it is a valuable tool for kinetic studies of the degradation process for each polymer used, while HS-SPME-GC/MS has proved to be an effective tool for the extraction and evaluation of volatile degradation by-products.

Reutilization of thermostable polyester wastes by means of agglomeration with phenolic resins

We report on the possibility of obtaining organic polymeric matrixes allowing the development of new high performance fire-resistant products by recycling downsized thermostable waste materials. Phenolic resins have been used as binders for recycled waste. Furthermore, considering that reinforced plastic triturations have superior properties (chemical, mechanical, water resistance, etc.) to wood agglomerates, significant advantages over conventional materials are anticipated. In summary, we propose a viable solution to some of the known problems caused by the consumption of wood and to the needs of strengthened plastic processing engineering. Using resins as a binder, several fire-resistant prototypes were prepared from polyester waste, and their mechanical properties, thermal stability, and fire-resistant properties were analyzed.