A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography.

The "missing wedge" of a single tilt in electron tomography introduces severe artifacts into the reconstructed results. To reduce the "missing wedge" effect, a widely used method is "multiple-tilt reconstruction," which collects projections using multiple axes. However, as the number of tilt series increases, the computing and memory costs also rise. The degree of parallelism is limited by the sample thickness, and a large memory requirement cannot be met by most multicore computers. In our study, we present a new fully distributed multiple-tilt simultaneous iterative reconstruction technique (DM-SIRT). To improve the parallelism of the reconstruction process and reduce the memory requirements of each process, we formulate the multiple-tilt reconstruction as a consensus optimization problem and design a DM-SIRT algorithm. Experiments show that in addition to slightly better resolution, DM-SIRT can obtain a 13.9 × accelerated ratio compared with the full multiple-tilt reconstruction version. It also has a 97% decrease in memory overhead and is 16 times more scalable than the full reconstruction version.

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.

EPiK-a Workflow for Electron Tomography in Kepler.

Scientific workflows integrate data and computing interfaces as configurable, semi-automatic graphs to solve a scientific problem. Kepler is such a software system for designing, executing, reusing, evolving, archiving and sharing scientific workflows. Electron tomography (ET) enables high-resolution views of complex cellular structures, such as cytoskeletons, organelles, viruses and chromosomes. Imaging investigations produce large datasets. For instance, in Electron Tomography, the size of a 16 fold image tilt series is about 65 Gigabytes with each projection image including 4096 by 4096 pixels. When we use serial sections or montage technique for large field ET, the dataset will be even larger. For higher resolution images with multiple tilt series, the data size may be in terabyte range. Demands of mass data processing and complex algorithms require the integration of diverse codes into flexible software structures. This paper describes a workflow for Electron Tomography Programs in Kepler (EPiK). This EPiK workflow embeds the tracking process of IMOD, and realizes the main algorithms including filtered backprojection (FBP) from TxBR and iterative reconstruction methods. We have tested the three dimensional (3D) reconstruction process using EPiK on ET data. EPiK can be a potential toolkit for biology researchers with the advantage of logical viewing, easy handling, convenient sharing and future extensibility.