Marker-free image registration of electron tomography tilt-series

<p>Abstract</p> <p>Background</p> <p>Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3D reconstruction. Current alignment techniques usually employ gold particles or image derived markers to correctly align the images. When these markers are not present, correlation between adjacent views is used to align them. However, sequential pairwise correlation is prone to bias and the resulting alignment is not always optimal.</p> <p>Results</p> <p>In this paper we introduce an algorithm to find regions of the tilt series which can be tracked within a subseries of the tilt series. These regions act as landmarks allowing the determination of the alignment parameters. We show our results with synthetic data as well as experimental cryo electron tomography.</p> <p>Conclusion</p> <p>Our algorithm is able to correctly align a single-tilt tomographic series without the help of fiducial markers thanks to the detection of thousands of small image patches that can be tracked over a short number of images in the series.</p

3D reconstruction of biological structures: automated procedures for alignment and reconstruction of multiple tilt series in electron tomography

Transmission electron microscopy allows the collection of multiple views of specimens and their computerized three-dimensional reconstruction and analysis with electron tomography. Here we describe development of methods for automated multi-tilt data acquisition, tilt-series processing, and alignment which allow assembly of electron tomographic data from a greater number of tilt series, yielding enhanced data quality and increasing contrast associated with weakly stained structures. This scheme facilitates visualization of nanometer scale details of fine structure in volumes taken from plastic-embedded samples of biological specimens in all dimensions. As heavy metal-contrasted plastic-embedded samples are less sensitive to the overall dose rather than the electron dose rate, an optimal resampling of the reconstruction space can be achieved by accumulating lower dose electron micrographs of the same area over a wider range of specimen orientations. The computerized multiple tilt series collection scheme is implemented together with automated advanced procedures making collection, image alignment, and processing of multi-tilt tomography data a seamless process. We demonstrate high-quality reconstructions from samples of well-described biological structures. These include the giant Mimivirus and clathrin-coated vesicles, imaged in situ in their normal intracellular contexts. Examples are provided from samples of cultured cells prepared by high-pressure freezing and freeze-substitution as well as by chemical fixation before epoxy resin embedding

Approche problème inverse pour l’alignement de séries en tomographie électronique

International audienceIn the refining industry, morphological measurements of particles have become an essential part in the characterization catalyst supports. Through these parameters, one can infer the specific physicochemical properties of the studied materials. One of the main acquisition techniques is electron tomography (or nanotomography). 3D volumes are reconstructed from sets of projections from different angles made by a Transmission Electron Microscope (TEM). This technique provides a real three-dimensional information at the nanometric scale. A major issue in this method is the misalignment of the projections that contributes to the reconstruction. The current alignment techniques usually employ fiducial markers such as gold particles for a correct alignment of the images. When the use of markers is not possible, the correlation between adjacent projections is used to align them. However, this method sometimes fails. In this paper, we propose a new method based on the inverse problem approach where a certain criterion is minimized using a variant of the Nelder and Mead simplex algorithm. The proposed approach is composed of two steps. The first step consists of an initial alignment process, which relies on the minimization of a cost function based on robust statistics measuring the similarity of a projection to its previous projections in the series. It reduces strong shifts resulting from the acquisition between successive projections. In the second step, the pre-registered projections are used to initialize an iterative alignment-refinement process which alternates between (i) volume reconstructions and (ii) registrations of measured projections onto simulated projections computed from the volume reconstructed in (i). At the end of this process, we have a correct reconstruction of the volume, the projections being correctly aligned. Our method is tested on simulated data and shown to estimate accurately the translation, rotation and scale of arbitrary transforms. We have successfully tested our method with real projections of different catalyst supports.Dans le domaine du raffinage, les mesures morphologiques de particules sont devenues indispensables pour caractériser les supports de catalyseurs. A travers ces paramètres, on peut remonter aux spécificités physico-chimiques des matériaux étudiés. Une des techniques d’acquisition utilisées est la tomographie électronique (ou nanotomographie). Des volumes 3D sont reconstruits à partir de séries de projections sous différents angles obtenues par Microscopie Électronique en Transmission (MET). Cette technique permet d’obtenir une réelle information tridimensionnelle à l’échelle du nanomètre. Un problème majeur dans ce contexte est le mauvais alignement des projections qui contribuent à la reconstruction. Les techniques d’alignement actuelles emploient habituellement des marqueurs de réference tels que des nanoparticules d’or pour un alignement correct des images. Lorsque l’utilisation de marqueurs n’est pas possible, l’alignement de projections adjacentes est obtenu par corrélation entre ces projections. Cependant, cette méthode échoue parfois. Dans cet article, nous proposons une nouvelle méthode basée sur une approche de type problème inverse où un certain critère est minimisé en utilisant une variante de l’algorithme de Nelder et Mead, qui exploite le concept de simplexe. Elle est composéé de deux étapes. La première étape consiste en un processus d’alignement initial s’appuyant sur la minimisation d’une fonction de coût basée sur des statistiques robustes, mesurant la similarité entre une projection et les projections précédentes de la série. Elle vise à réduire les forts déplacements, résultant de l’acquisition entre les projections successives. Dans la seconde étape, les projections pré-recalées sont employées pour initialiser un processus itératif et alterné d’alignement et reconstruction, minimisant alternativement une fonction de coût basée sur la reconstruction du volume et une fonction basée sur l’alignement d’une projection avec sa version simulée obtenue à partir du volume reconstruit. A la fin de ce processus, nous obtenons une reconstruction correcte du volume, les projections étant correctement alignées. Notre méthode a été testée sur des données simulées et prouve qu’elle récupère d’une manière précise les changements dans les paramètres de translation, rotation et mise à l’échelle. Nous avons testé avec succès notre méthode pour les projections réelles de différents supports de catalyseur

TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy

<p>Abstract</p> <p>Background</p> <p>Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomography fills the gap between high resolution structural methods (X-ray diffraction or nuclear magnetic resonance) and optical microscopy. We developed new software for transmission electron tomography, TomoJ. TomoJ is a plug-in for the now standard image analysis and processing software for optical microscopy, ImageJ.</p> <p>Results</p> <p>TomoJ provides a user-friendly interface for alignment, reconstruction, and combination of multiple tomographic volumes and includes the most recent algorithms for volume reconstructions used in three-dimensional electron microscopy (the algebraic reconstruction technique and simultaneous iterative reconstruction technique) as well as the commonly used approach of weighted back-projection.</p> <p>Conclusion</p> <p>The software presented in this work is specifically designed for electron tomography. It has been written in Java as a plug-in for ImageJ and is distributed as freeware.</p

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

Microscopic imaging and technolog