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March, 2011

Microsoft Research Connections Blog

The Microsoft Research Connections blog shares stories of collaborations with computer scientists at academic and scientific institutions to advance technical innovations in computing, as well as related events, scholarships, and fellowships.

March, 2011

  • Microsoft Research Connections Blog

    InnerEye: Visual Recognition in the Hospital

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    The neurosurgeon hovers over the patient, preparing to excise a life-threatening brain tumor. In this delicate operation, there is no margin for error: the tumor needs to be cut out with minimal damage to the surrounding healthy tissue. By using simple hand gestures, the surgeon signals a computer to display high-resolution scans of the patient’s brain, showing the physician where to place her scalpel, detailing the boundaries between diseased and healthy tissue. No longer must the neurosurgeon stop to refer to the patient’s image data during the operation, removing her gloves and potentially compromising the sterile surgical field. The upshot for the patient: reduced time under anesthesia and a lower risk of introduced infection.

    Interactive Segmentation of CT and MR Scans

    Science fiction? Far from it. This scenario and others like it are on the verge of realization thanks to ground-breaking InnerEye project being conducted by Microsoft Research and a host of collaborators, including Johns Hopkins Medical Institute, The University of Oxford, Cornell Medical School, Massachusetts General Hospital, the University of Washington, Kings College London, and Cambridge University Hospitals

    The analysis of medical images is essential in modern medicine. As images have achieved higher and higher resolutions, the increasing amount of patient data has presented new challenges and opportunities, from diagnosis to therapy. The InnerEye research shows how a single, underlying image-recognition algorithm can enable a multitude of clinical applications, such as semantic image navigation, multimodal image registration, quality control, content-based image search, and natural user interfaces for surgery.

    InnerEye takes advantage of advances in computer-human interactions that have put computers on a path to work for us and collaborate with us. The development of a natural user interface (NUI) enables computers to adapt to you and be more integrated into your environment via speech, touch, and gesture. As NUI systems become more powerful and are imbued with more situational awareness, they can provide beneficial, real-time interactions that will be seamless and naturally suited to your context—in short, systems will understand where you are and what you’re doing.

    At this year’s TechFest—the annual event that showcases the latest work from Microsoft Research’s labs around the world—InnerEye is one of several projects that show where Microsoft is headed with NUI technologies, and how “futuristic” computing experiences are quickly becoming a reality. Building on the success of Kinect—a prime example of NUI technology reaching consumer scale—Microsoft Research continues to explore technologies that will enable the coming shift in how humans will communicate with machines, and vice versa. The possibilities are seemingly endless in how we approach the integration of computing into our lives and can enable a new era of creativity, social interaction, and technological scenarios.

    Antonio Criminisi, Researcher, Microsoft Research and Kristin Tolle, Director, Natural User Interface Team, Microsoft Research Connections division of Microsoft Research

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    Free MBF Workshop at RENCI in North Carolina

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    Microsoft Biology FoundationWe recently posted a preview of the Microsoft Biology Foundation (MBF) for development evaluation purposes. Now, we're following up with a special, free, two-day MBF workshop from April 19 to 20, 2011, at the Renaissance Computing Institute in Chapel Hill, North Carolina, hosted by the Microsoft Biology Initiative. The workshop includes a quick introduction to Microsoft Visual Studio 2010, the Microsoft .NET Framework, C#, and the MBF Object Model. Plus, our hands-on lab will give you the opportunity to write a sample application that employs the file parsers, algorithms, and web connectors in MBF. For complete details about the event, or to register, please see the MBF Workshop website.

    We will also cover some MBF training modules throughout the day, including:

    • Module 1: Introduction to Visual Studio 2010 and C#. This comprehensive introduction to the Microsoft Visual Studio programming environment and Microsoft .NET will teach you how to create a project, get started with C#, and perform runtime debugging. Also, you will get hands-on lab experience by building applications in Visual Studio 2010.
    • Module 2: Introduction to the Microsoft Biology Foundation. This overview will introduce you to MBF basics through discussions of its scenarios and architectures and includes a starter project. The starter project is a hands-on lab that will help you get the experience you need to work with sequences, parsers, formatters, and the transcription algorithm that is supplied in MBF.
    • Module 3: Working with Sequences. In this module, you'll learn more about the Sequence data type in MBF, including how to load sequences into memory and save them, the different sequence types that are available, how to use sequence metadata, and how data virtualization support enables support for large data sets in a hands-on lab setting.
    • Module 4: Parsers and Formatters. In Parsers and Formatters, you'll explore MBF's built-in sequence parsers, formatters, alphabets, and encoders. This module will also introduce the method of expanding MBF with custom alphabets, parsers, and formatters. The hands-on lab will walk you through the steps that are required to build a simple custom parser and formatter for a fabricated biology data format.
    • Module 5: Algorithms. In this module, you will examine the algorithms that are defined in MBF for sequence alignment, multi-sequence alignment, sequence fragment assembly, transcription, translation, and pattern matching against sequences. You'll also learn how to create custom algorithms. The hands-on lab will walk you through the steps that are required to build an application to run algorithms against sequences loaded with MBF and will teach you how to perform sequence alignment, assembly, and transformations.
    • Module 6: Web Services. This module will introduce Microsoft .NET web services, the web service architecture in MBF, the built-in web service support in MBF for BLAST (Basic Local Alignment Search Tool), and ClustalW. You will also learn how to call these services asynchronously and build custom service wrappers. In the hands-on lab, you'll build an application that executes the BLAST algorithm by using web services against handlers for BLAST, pass sequences and sequence fragments to BLAST, change the BLAST parameters, and display the results from a BLAST run.

    We hope you will join us for this free two-day event. Whether your goal is to get trained on MBF or simply to evaluate MBF and its Microsoft .NET model, you can expect to get a tremendous return on your time investment.

    We look forward to meeting you on April 19 in Chapel Hill.

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     Swatee Surve, Research Program Manager, Health and Wellbeing, Microsoft Research Connections

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    Brazilian Research Celebrated

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    On March 17, Microsoft Research Connections and the São Paulo Research Foundation (better known by its Portuguese acronym: FAPESP) held a workshop to mark the ongoing collaborative efforts of the Microsoft Research-FAPESP Institute. The theme of the workshop—revisiting the past and planning for the future—provided the scientific community with a historical perspective on the Institute's completed projects, its ongoing initiatives, and the prospects for future investments.

    Harold Javid, Director of Microsoft Research Connections, Carlos Henrique de Brito Cruz, Scientific Director of FAPESP and Michel Levy, President of Microsoft Brazil during the meeting MSR-FAPESP Institute Workshop: revisiting the past and planning the future.

    Harold Javid, Director of Microsoft Research Connections, Carlos Henrique de Brito Cruz, Scientific Director of FAPESP and Michel Levy, President of Microsoft Brazil during the meeting MSR-FAPESP Institute Workshop: revisiting the past and planning the future. 

    The presentation of newly funded research projects broke with tradition this year: previously restricted to researchers and teams who are directly involved with the selected projects, the event was opened to all professionals and researchers interested in learning more about the opportunities created by the program. By so doing, the Institute reached out to researchers and scientists from other areas of knowledge, while simultaneously stressing the role of information technology in accelerating scientific research on priority themes.

    The event was attended by Carlos Henrique de Brito Cruz, scientific director of FAPESP, and Michel Levy, president of Microsoft Brazil. Leonardo de Moura, a senior researcher at Microsoft Research in the United States who specializes in theorems and the optimization and verification of software, presented the first lecture, "Symbolic Reasoning @ Microsoft: Tackling Impossible Tasks." Harold Javid, the director of Microsoft Research Connections (a division of Microsoft Research) explored the theme of e-science, addressing such fertile areas for collaboration as medical imaging research, a new approach to creating digital narratives, and compelling possibilities for sharing "big time" views of history.

    Announced at the workshop were the four projects that were selected in the latest call for proposals. The researchers who were responsible for the approved proposals then made brief presentations of their studies.

    • Eleanor Patricia Cerdeira Morellato, Bioscience Institute of Universidade Estadual Paulista (Unesp), presented the e-Phenology project, which implements new technologies to monitor ecology and climate change in the tropics. This multidisciplinary project combines research in computer science and phenology, a branch of ecology that studies the development cycle of living organisms and its relation to such environmental conditions as temperature, light, and humidity.
    • Junia Coutinho Anacleto, Center of Exact Sciences and Technologies at Universidade Federal de São Carlos (UFSCar), presented a project that will use natural user interface (NUI) technology to help patients develop their social skills. Developed in partnership with the Center for Intensive Attention to Health (CAIS) and Clemente Ferreira, a hospital that serves people with neurological and psychiatric disorders, the project also seeks to improve the interaction between health professionals.
    • Ronaldo Fumio Hashimoto, Institute of Mathematics and Statistics at the University of São Paulo (USP), presented a project that will use math and computational modeling to examine the biological processes that underlie molecular organization and the regulatory relationships of molecules and genes. The research will use new computational and statistical techniques to understand how biological processes occur and how to prevent those that cause disease from taking place.
    • Regina Célia de Matos Pires, Instituto Agronômico (IAC), presented a project that will use environmental monitoring and genetic modeling to calculate the potential of sugarcane cultivars based on the availability of groundwater. This research is important in light of forecasts that predict expanded cultivation of sugarcane in arid regions of Brazil. Pires intends to use sensors that monitor the interactions of climate, soil, and water with the development of plants, in order to understand the dynamics that are involved in the transfer of water among the soil, plant, and atmosphere, and to illuminate its interactions in the production system.

    All of these endeavors align perfectly with the mission of the Microsoft Research-FAPESP Institute for IT Research, which is to support bold, innovative projects that apply technology to enable or accelerate research that will help humanity.

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    —Juliana Salles, Senior Program Manager, Microsoft Research Connections

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