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Managing your microscopy big image data: Challenges, strategies, solutions

This webinar is brought to you by the Science/AAAS Custom Publishing Office

Managing your microscopy big image data: Challenges, strategies, solutions

Recorded 18 November 2015



Acquiring images using modern techniques such as light sheet fluorescence, confocal, or electron microscopy creates a significant data stream. Add modalities like multichannel, 3-D, and time-lapse, and managing the data sets generated soon becomes a serious issue. Researchers therefore need more efficient solutions for data storage and processing in terms of both computer hardware and software. In addition, changing workflows to incorporate these massive data requirements means substantial adaptation of training schemes and education. In this webinar, the panelists will discuss how these challenges can be addressed on both a conceptual level and in day-to-day research in the lab. They will outline systematic approaches to illustrate how microscope users can get greater benefit and more consistent results from big image data experiments, and will present examples of successful workflows. The webinar will be of interest to scientists in any research area using microscopy or analyzing big image data to gain information from multidimensional experiments. These areas include developmental research, neurobiology and cell biology, high-content screening, medical imaging, and materials science, among others.

During this webinar, the panelists will answer the live audience’s questions and discuss:

  • Image data heterogeneity and how to maintain compatibility between microscopy modalities (metadata, file formats, and open data interfaces)
  • Image processing based on computer clusters and worldwide networks
  • Strategies for automated data handling, processing, and storage workflows in a microscopy facility environment (for example, for automated whole slide imaging).

The webinar will last approximately 60 minutes.

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Speaker bios

Jason Swedlow, Ph.D.

University of Dundee
Dundee, Scotland

Dr. Swedlow received his Ph.D. in biophysics from the University of California, San Francisco (UCSF) after completing a B.A. in chemistry at Brandeis University in Massachusetts. He joined the Wellcome Trust Biocentre at the University of Dundee in the United Kingdom following postdoctoral training at UCSF and Harvard Medical School in the United States. Dr. Swedlow is currently a professor of quantitative cell biology at the University of Dundee. His research interests are the mechanisms and regulation of chromosome segregation during mitotic cell division, and the development of software tools for accessing, processing, sharing, and publishing large scientific image datasets. Dr. Swedlow is a co-founder of the Open Microscopy Environment (OME), an international consortium that develops and releases open source software for biological imaging. He also co-founded Glencoe Software, Inc., which commercializes and customizes OME technology for use in biopharma and data publishing, and BioImagingUK, a consortium of U.K. imaging scientists who develop, use, or administer imaging solutions for life sciences research. In 2011, Dr. Swedlow was named Social and Overall Innovator of the Year by the BBSRC and in 2012 became a Fellow of the Royal Society of Edinburgh.

Laurent Gelman, Ph.D.

Friedrich Miescher Institute
Basel, Switzerland

Dr. Gelman received his engineering undergraduate degree from the Institut National Agronomique in Paris, France, and a Master’s degree in immunology from the Pasteur Institute, also in Paris. After a Ph.D. under Johan Auwerx at the Institut Pasteur de Lille, he undertook his postdoctoral training with Pierre Chambon at the Institut de Génétique et de Biologie Moléculaire et Cellulaire in Strasbourg, France. He then moved to the University of Lausanne as a lecturer before joining the light microscopy facility at the Friedrich Miescher Institute (FMI) in Basel in 2006, leading the group from 2009 onwards. Since 2011 he has been co-head, together with Dr. Christel Genoud, of the Facility for Advanced Imaging and Microscopy at the FMI. One mission of the Facility is to establish user-friendly workflows ranging from sample preparation to image acquisition, image processing, and long-term data storage, especially for imaging modalities generating very big datasets or files, such as slide-scanning, high-content screening, and 3-D scanning electron microscopy.

Sean Sanders, Ph.D.

Washington, DC

Dr. Sanders did his undergraduate training at the University of Cape Town, South Africa, and his Ph.D. at the University of Cambridge, UK, supported by the Wellcome Trust. Following postdoctoral training at the National Institutes of Health and Georgetown University, Dr. Sanders joined TranXenoGen, a startup biotechnology company in Massachusetts working on avian transgenics. Pursuing his parallel passion for writing and editing, Dr. Sanders joined BioTechniques as an editor, before joining Science/AAAS in 2006. Currently, Dr. Sanders is the Director and Senior Editor for Custom Publishing for the journal Science and Program Director for Outreach.

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