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    EPiK-a Workflow for Electron Tomography in Kepler.
    Procedia Comput Sci 2014 ;20:2295-2305
    National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA, USA.
    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.

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    Workflows for microarray data processing in the Kepler environment.
    BMC Bioinformatics 2012 May 17;13:102. Epub 2012 May 17.
    Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.
    Background: Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. Read More
    TxBR montage reconstruction for large field electron tomography.
    J Struct Biol 2012 Oct 27;180(1):154-64. Epub 2012 Jun 27.
    National Center For Microscopy and Imaging Research, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA.
    Electron tomography (ET) has been proven an essential technique for imaging the structure of cells beyond the range of the light microscope down to the molecular level. Large-field high-resolution views of biological specimens span more than four orders of magnitude in spatial scale, and, as a consequence, are rather difficult to generate directly. Various techniques have been developed towards generating those views, from increasing the sensor array size to implementing serial sectioning and montaging. Read More
    Fast auto-acquisition tomography tilt series by using HD video camera in ultra-high voltage electron microscope.
    Microscopy (Oxf) 2014 Nov;63 Suppl 1:i25
    Advanced Microscope Systems Design Dept., Hitachi High-Technologies Corporation, 882, Ichige, Hitachinaka, Ibaraki, Japan.
    The ultra-high voltage electron microscope (UHVEM) H-3000 with the world highest acceleration voltage of 3 MV can observe remarkable three dimensional microstructures of microns-thick samples[1]. Acquiring a tilt series of electron tomography is laborious work and thus an automatic technique is highly desired. We proposed the Auto-Focus system using image Sharpness (AFS)[2,3] for UHVEM tomography tilt series acquisition. Read More
    Three-dimensional transmission electron microscopy and its application to mitosis research.
    Methods Cell Biol 1999 ;61:81-111
    Division of Molecular Medicine, Wadsworth Center, New York State Department of Health, Albany 12201-0509, USA.
    Transmission electron microscopy produces images that are projections of the original object, with the consequence that features from different depths of the specimen overlap and give a confusing image. This problem is overcome by reconstructing the object in 3D from a series of 2D views using either serial thin section reconstruction or electron tomography. In the serial section approach, the series of 2D views is generated from images of successive serial sections cut thin enough to be effectively 2D slices of the specimen. Read More