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The OptIPuter microscopy demonstrator project has been designed to enable concurrent and remote usage of world-class electron microscopes located in Oxford and San Diego. The project has constructed a network consisting of microscopes and computational and data resources that are all connected by a dedicated network infrastructure using the UK Lightpath and US Starlight systems. Key science drivers include examples from both materials and biological science. The resulting system is now a permanent link between the Oxford and San Diego microscopy centres. This will form the basis of further projects between the sites and expansion of the types of systems that can be remotely controlled, including optical, as well as electron, microscopy. Other improvements will include the updating of the Microsoft cluster software to the high performance computing (HPC) server 2008, which includes the HPC basic profile implementation that will enable the development of interoperable clients.

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. Datasets and reconstructions obtained by the latter techniques generate multiple three-dimensional (3D) reconstructions, that need to be combined together to provide all the multiscale information. In this work, we show how to implement montages within TxBR, a tomographic reconstruction software package. This work involves some new application of mathematical concepts related to volume preserving transformations and issues of gauge ambiguity, which are essential problems arising from the nature of the observation in an electron microscope. The purpose of TxBR is to handle those issues as generally as possible in order to correct for most distortions in the 3D reconstructions and allow for a seamless recombination of ET montages.

Electron tomography is a powerful tool for deriving three-dimensional (3D) structural information about biological systems within the spatial scale spanning 1 nm3 and 10 µm3. With this technique, it is possible to derive detailed models of subcellular components such as organelles and synaptic complexes and to resolve the 3D distribution of their protein constituents in situ. While there continues to be progress towards the integration of high-performance computing technologies with traditional electron tomography processes, there is a significant need for more transparent integration with applications and to minimize the administrative overhead and complexity (resource administration, authentication, scheduling, data delivery) passed on to the noncomputer scientist end user. Here we present the "Telescience Portal" (https://gridport.npaci.edu/Telescience) as an example of a fully integrated, web-based solution for performing end-to-end electron tomography. More than just a collection of individual applications, the Portal provides a transparent workflow, where simple intuitive interfaces for grid-enabled parallel computation, resource scheduling, remote instrumentation, advanced image processing and visualization, access to distributed/federated databases, and network-enabled data management and archival are tightly coupled within a secure environment which promotes increased collaboration between researchers. This tightly integrated Telescience system is a test-bed application for using grid resources to accelerate the throughput of data acquisition and processing, increase access to scarce and/or expensive instrumentation, and improve the accuracy of derived data products.

Scientific imaging instruments are used in a variety of disciplines to gather vital data for research and study. Specifically, in the biomedical field various types of biological imaging instruments, such as electron microscopes and light microscopes, are used everyday to acquire 2D and 3D datasets for further understanding of biological structures. Remote operation or "teleoperation" of instruments has become a popular solution for research scientists to acquire and share data across research domains separated by geographical barriers. A generalized software architecture solution is presented in this paper to use emerging software technologies to develop a reusable framework to easily integrate instruments for remote-operation in a safe and secure fashion. Web services have emerged as a popular technology to provide software applications with a framework to achieve interoperability and integration with other applications. This generalized software architecture was developed to take advantage of Web service middleware technology and to provide a solution for easily plugging in scientific imaging instruments for teleoperation. The architecture has also incorporated grid technology to achieve a more scalable and robust solution for handling the enormous data sets produced from these instruments. Finally a set of client libraries is presented to demonstrate a useful API for developers to quickly develop a graphical user interface to communicate and acquire data from these instruments

The Cybermedia Center (CMC), Osaka University, is a research institution that offers knowledge and technology resources obtained from advanced researches in the areas of large-scale computation, information and communication, multimedia content and education. Currently, CMC is involved in Japanese national Grid projects such as JGN II (Japan Gigabit Network), NAREGI and BioGrid. Not limited to Japan, CMC also actively takes part in international activities such as PRAGMA. In these projects and international collaborations, CMC has developed a Grid system that allows scientists to perform their analysis by remote-controlling the world's largest ultra-high voltage electron microscope located in Osaka University. In another undertaking, CMC has assumed a leadership role in BioGrid by sharing its experiences and knowledge on the system development for the area of biology. In this paper, we will give an overview of the BioGrid project and introduce the progress of the Telescience unit, which collaborates with the Telescience Project led by the National Center for Microscopy and Imaging Research (NCMIR). Furthermore, CMC collaborates with seven Computing Centers in Japan, NAREGI and National Institute of Informatics to deploy PKI base authentication infrastructure. The current status of this project and future collaboration with Grid Projects will be delineated in this paper.

Extended abstract of a paper presented at Microscopy and Microanalysis 2011 in Nashville, Tennessee, USA, August 7–August 11, 2011.

The application of electron tomography to cell biology has led to important insights into the 3D fine structure of subcellular processes and organelles. Tomography has been particularly useful for studying relatively large, multi-component structures such as the Golgi apparatus, mitochondria and synaptic complexes. When combined with very powerful high voltage electron microscopes, tomography has also provided high resolution quantitative views of extended structures such as neuronal dendrites in very thick sections (4 μm) at electron microscopic resolution. The utility of tomography is twofold: first, it provides 3D examination of subcellular structure without the need for serial section analysis; second, because the computed slices through the tomographic volumes can be much thinner than is possible to produce by physical sectioning, it reveals structural detail in the range of 5-30 nm that tends to be obscured in conventional thin sections. Tomographic analysis has forced re-assessment of long-standing views of organelles such as mitochondria and the Golgi apparatus and as the technique advances, additional insights are likely forthcoming.Electron tomography is an expensive technique, both in terms of the instruments used and the computational resources required. The three major high voltage electron microscope resources in the United States, San Diego, Boulder and Albany, all are actively engaged in tomographic research and offer this important technology to the scientific community at large.