Generation of integer and fractional vortex beams based on liquid crystal electronically reconfigurable spiral phase plates.

The manufacturing and characterization of a large-size 72-electrode liquid crystal-based reconfigurable spiral phase plate (SPP) is presented. The SPP is addressed by a custom-made driver with 72 independent channels, which allows for the generation of any arbitrary integer or fractional optical vortex beam with topological charges ranging from -24 to +24. The 25 mm diameter device is fabricated using direct laser writing, leading to a fill factor over 99%. The device performance and flexibility exceed previous transparent reconfigurable SPP in terms of size, tuning range, and fill factor. The device and the light path have been simulated using the angular spectrum propagation method, showing excellent correspondence.

Validation of electrodeposited 241Am alpha-particle sources for use in liquified gas detectors at cryogenic temperatures.

This paper describes a procedure for the validation of alpha-particle sources (exempt unsealed sources) to be used in experimental setups with liquefied gases at cryogenic temperatures (down to -196 °C) and high vacuum. These setups are of interest for the development and characterization of neutrino and dark matter detectors based on liquid argon, among others. Due to the high purity requirements, the sources have to withstand high vacuum and cryogenic temperatures for extended periods. The validation procedure has been applied to 241Am sources produced by electrodeposition.

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.

Identification of dyes and matrices for dye doped polymer waveguide emitters covering the visible spectrum.

Polymer based photonic devices offer the possibility cost effective roll-to-roll manufacture of photonic devices. The incorporation of luminescent dopants within a solid polymer waveguide allows for the generation of light within the device avoiding tedious mechanical light coupling. However, when a dopant is embedded in a solid matrix, depending on its concentration and the nature of materials involved, the emitted light may be quenched due to aggregation effects. In this work, thin films and ridge waveguides processed by UV-photolithography have been successfully obtained from a selection of standard photopolymerizable organic monomers, SU8, EpoCore and OrmoStamp doped with a selection of standard dyes like Rhodamine-B, Coumarin-540A and Pyrromethene-580. All structures were manufactured on glass substrates. An analysis of the solubility and optical properties including band gap energy, absorption coefficient ([Formula: see text]) and fluorescence of the doped photoresists at different concentrations has been performed. Photoresists doped with Rhodamine-B shows a higher energy of indirect allowed band gap transition (2.04-2.09 eV) compared to previously reported pure Rhodamine-B thin films (1.95-1.98 eV). Fabrication protocols of dye doped photoresists covering the entire visible spectrum is established.

The chaperonin CCT controls T cell receptor-driven 3D configuration of centrioles.

T lymphocyte activation requires the formation of immune synapses (IS) with antigen-presenting cells. The dynamics of membrane receptors, signaling scaffolds, microfilaments, and microtubules at the IS determine the potency of T cell activation and subsequent immune response. Here, we show that the cytosolic chaperonin CCT (chaperonin-containing TCP1) controls the changes in reciprocal orientation of the centrioles and polarization of the tubulin dynamics induced by T cell receptor in T lymphocytes forming an IS. CCT also controls the mitochondrial ultrastructure and the metabolic status of T cells, regulating the de novo synthesis of tubulin as well as posttranslational modifications (poly-glutamylation, acetylation, Δ1 and Δ2) of αß-tubulin heterodimers, fine-tuning tubulin dynamics. These changes ultimately determine the function and organization of the centrioles, as shown by three-dimensional reconstruction of resting and stimulated primary T cells using cryo-soft x-ray tomography. Through this mechanism, CCT governs T cell activation and polarity.

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.

Rapid detection of pathogens using lyotropic liquid crystals.

Lyotropic liquid crystals play an important role in many biological environments, such as micelles, liposomes, and phospholipid bilayers of cell membranes. In this work, we explore the performance of lyotropic liquid crystals as biosensors for macromolecules, proteins and whole microorganisms in hydrophilic media, i.e., the natural media where these specimens exist. The aim is to detect specific targets employing simple, unpowered sensors that can be used in the field, with minimum additional equipment. A number of different structures have been explored. The novelty in this work is the inclusion of a new optical effect, flow enhanced amplification, that allows for the semiquantitative detection of microscopic targets in lyotropic liquid crystal cells using the naked eye only.

Dynamic multilevel spiral phase plate generator.

The design and characterisation of a reconfigurable multi-level spiral phase plate is shown. The device is based on a pie-shape liquid-crystal structure with 24 slices driven by custom electronics that allow independent excitation control of each electrode. The electrooptical cell was manufactured using maskless laser ablation lithography and has shown an unprecedented high fill factor. The topological charge can be dynamically changed between 1, 2, 3, 4, 6, 8 and 12. The device has been calibrated and characterised at 632.8 nm but can be employed at any wavelength in the visible and near infrared spectrum, just modifying the driving parameters of the electrodes. The experimental results have been compared to predictions derived from simulations. An excellent correspondence between theoretical and experimental result has been found in all cases.

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).

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.

One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).

A review of resolution measures and related aspects in 3D Electron Microscopy.

Fourier Shell Correlation, Spectral Signal-to-Noise Ratio, Fourier Neighbour Correlation, and Differential Phase Residual are different measures that have been proposed over time to determine the spatial resolution achieved by a certain 3D reconstruction. Estimates of B-factors to describe the reduction in signal-to-noise ratio with increasing resolution is also a useful parameter. All these concepts are interrelated and different thresholds have been given for each one of them. However, the problem of resolution assessment in 3DEM is still far from settled and preferences are normally adopted in order to choose the "correct" threshold. In this paper we review the different concepts, their theoretical foundations and the derivation of their statistical distributions (the basis for establishing sensible thresholds). We provide theoretical justifications for some common practices in the field for which a formal justification was missing. We also analyze the relationship between SSNR and B-factors, the electron dose needed for achieving a given contrast and resolution, the number of images required, etc. Finally, we review the consequences for the number of particles needed to achieve a certain resolution and how to analyze the Signal-to-Noise Ratio for a sequence of imaging operations.

Nematic liquid crystal reorientation around multi-walled carbon nanotubes mapped via Raman microscopy.

We have studied the formation of topological defects in liquid crystal (LC) matrices induced by multiwalled carbon nanotubes (MWCNTs) and external electric fields. The defects are ascribable to a distortion of the LC molecular director in proximity of the MWCNT surface. The system is analyzed macroscopically using spectroscopic variable angle ellipsometry. Concurrently, confocal micro-Raman spectroscopy is used to study the system state at the microscale. This allows to acquire a three-dimensional, spatially-resolved map of the topological defect, determining scale length variations and orientation topography of the LC molecules around the MWCNT.

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. One of the central players in this wide-reaching change is the continuous development of image processing software. Here we present Scipion, a software framework for integrating several 3DEM software packages through a workflow-based approach. Scipion allows the execution of reusable, standardized, traceable and reproducible image-processing protocols. These protocols incorporate tools from different programs while providing full interoperability among them. Scipion is an open-source project that can be downloaded from http://scipion.cnb.csic.es.

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.

Particle alignment reliability in single particle electron cryomicroscopy: a general approach.

Electron Microscopy is reaching new capabilities thanks to the combined effect of new technologies and new image processing methods. However, the reconstruction process is still complex, requiring many steps and elaborated optimization procedures. Therefore, the possibility to reach a wrong structure exists, justifying the need of robust statistical tests. In this work, we present a conceptually simple alignment test, which does not require tilt-pair images, to evaluate the alignment consistency between a set of projection images with respect to a given 3D density map. We test the approach on a number of problems in 3DEM, especially the ranking and evaluation of initial 3D volumes and high resolution 3D maps, where we show its usefulness in providing an objective evaluation for maps that have recently been subject to a strong controversy in the field. Additionally, this alignment statistical test can be linked to the early stages of structure solving of new complexes, streamlining the whole process.

Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited.

Cryo-Electron Microscopy (cryo-EM) of macromolecular complexes is a fundamental structural biology technique which is expanding at a very fast pace. Key to its success in elucidating the three-dimensional structure of a macromolecular complex, especially of small and non-symmetric ones, is the ability to start from a low resolution map, which is subsequently refined with the actual images collected at the microscope. There are several methods to produce this first structure. Among them, Random Conical Tilt (RCT) plays a prominent role due to its unbiased nature (it can create an initial model based on experimental measurements). In this article, we revise the fundamental mathematical expressions supporting RCT, providing new expressions handling all key geometrical parameters without the need of intermediate operations, leading to improved automation and overall reliability, essential for the success of cryo-EM when analyzing new complexes. We show that the here proposed RCT workflow based on the new formulation performs very well in practical cases, requiring very few image pairs (as low as 13 image pairs in one of our examples) to obtain relevant 3D maps.

Tunable liquid crystal cylindrical micro-optical array for aberration compensation.

A tunable aberration compensation device for rectangular micro-optical systems is proposed and demonstrated. This device, which is based in nematic liquid crystal and a micro-electrode structure, forms gradients in the index of refraction as a function of voltage. We have developed a fringe skeletonizing application in order to extract the 3D wavefront from an interference pattern. This software tool obtains the optical aberrations using Chebyshev polynomials. By using phase shifted electrical signals the aberrations can be controlled independently. A complete independent control over the spherical and coma aberration has been demonstrated. Also, an independent control over the astigmatism aberration has been demonstrated in a broad range. This device has promising applications where aberration compensation is required. The independent compensation achieved for some coefficients, such as astigmatism for example, is more than 2.4 waves.

Three-dimensional reconstruction methods in Single Particle Analysis from transmission electron microscopy data.

The Transmission Electron Microscope provides two-dimensional (2D) images of the specimens under study. However, the architecture of these specimens is defined in a three-dimensional (3D) coordinate space, in volumetric terms, making the direct microscope output somehow "short" in terms of dimensionality. This situation has prompted the development of methods to quantitatively estimate 3D volumes from sets of 2D images, which are usually referred to as "three-dimensional reconstruction methods". These 3D reconstruction methods build on four considerations: (1) The relationship between the 2D images and the 3D volume must be of a particularly simple type, (2) many 2D images are needed to gain 3D volumetric information, (3) the 2D images and the 3D volume have to be in the same coordinate reference frame and (4), in practical terms, the reconstructed 3D volume will only be an approximation to the original 3D volume which gave raise to the 2D projections. In this work we will adopt a quite general view, trying to address a large community of interested readers, although some sections will be particularly devoted to the 3D analysis of isolated macromolecular complexes in the application area normally referred to as Single Particle Analysis (SPA).

A statistical approach to the initial volume problem in Single Particle Analysis by Electron Microscopy.

Cryo Electron Microscopy is a powerful Structural Biology technique, allowing the elucidation of the three-dimensional structure of biological macromolecules. In particular, the structural study of purified macromolecules -often referred as Single Particle Analysis(SPA)- is normally performed through an iterative process that needs a first estimation of the three-dimensional structure that is progressively refined using experimental data. It is well-known the local optimisation nature of this refinement, so that the initial choice of this first structure may substantially change the final result. Computational algorithms aiming to providing this first structure already exist. However, the question is far from settled and more robust algorithms are still needed so that the refinement process can be performed with sufficient guarantees. In this article we present a new algorithm that addresses the initial volume problem in SPA by setting it in a Weighted Least Squares framework and calculating the weights through a statistical approach based on the cumulative density function of different image similarity measures. We show that the new algorithm is significantly more robust than other state-of-the-art algorithms currently in use in the field. The algorithm is available as part of the software suite Xmipp (http://xmipp.cnb.csic.es) and Scipion (http://scipion.cnb.csic.es) under the name "Significant".