CONFERENCE SERIES: Informatics & IT
Recorded at: Bio-IT World Conference & Expo
Digital Course: Imaging Informatics: Data Management and Annotation for the Life Sciences
About this Product:
The richness of information in images has made it one of the most popular readouts for high throughput screening in recent years. This increasing amount of images requires the development of tools to better manage, annotate and automatically interpret them. However, neither the infrastructure nor software has been able to keep up with the fast growth of image data. This digital course offers you some solutions including data and file management, annotation, image and metadata integration, etc. The main focus of this course is to share available resources, experiences and promote discussion for current needs in the HCS community.
Some key topics include:
What are the current challenges in data and image file management, processing and organization?
What is the scale of current data and what is to come?
What are labs and companies doing with large scale image file and metadata storage and sharing?
What steps are being taken to organize and standardize this data? Is it being done well?
How can cross-platform images and data be transformed into knowledge? How can these different modalities be integrated?
How do you organize and annotate the data in such a way that it is poised for extraction by researchers for downstream processing?
Imaging as it relates to academia versus industry? Is there are difference? What are the considerations?
About this Product:
Over 125 Minutes
Site License: $1380
Agenda At A Glance
Beyond the Mouse Gene Expression—Creating a Pipeline for Neuroscience Resources
Chinh Dang, Ph.D., Senior Director of Technology, Allen Institute for Brain Science
The Allen Mouse Brain Atlas was completed in 2007. The project profiled more than 20,000 gene expression patterns in the mouse brain and generated 600 terabytes of data. Since then, more than 1 petabyte of data has been generated by the Developing Mouse Brain, the Mouse Spinal Cord and the first sets of data on the Human Brain and Developing Human Brain. I will highlight our approach for building the pipeline and handling of the images as well as how to integrate these resources into a common framework.
Biography: Chinh Dang received her BA in Biology at the University of Denver and MS in Information Systems at the University of Colorado. She has spent more than 15 years in the life sciences industry creating bioinformatics software and data management systems. At the Allen Institute for Brain Science, Chinh leads the Technology team in developing the high-throughput data pipeline and web presentation of the Allen Brain Atlas resources.
Image Informatics for Multidimensional Light Microscopy
Kevin Eliceiri, Ph.D., Director, Laboratory for Optical and Computational Instrumentation, College of Engineering, University of Wisconsin-Madison
We are developing a complete, open source system for handling biomedical images, including image acquisition, data storage, metadata (experimental data associated with an image), visualization, analysis, annotation, and database interconnectivity. The software makes extensive use of several open source systems for handling images: the Open Microscopy Environment (OME; image database), FARSIGHT (image visualization), Cell Profiler (image analysis) and ImageJ (image processing). We have also developed an open file format called OME-TIFF: fully compatible multi-page TIFF with rich metadata embedded in OME-XML format, the OME standard and Bio-Formats, a Java library for reading and writing dozens of common microscopy file formats, including processing and conversion of metadata into OME-TIFF format. We are working to integrate these packages and others into a cohesive whole to provide microscopists with a complete toolset for overcoming the challenges of working with digital multidimensional images.
Biography: Kevin Eliceiri received his undergraduate and graduate training in Microbiology and Biotechnology at the University of Wisconsin in Madison. He worked in Professor John White's laboratory developing imaging approaches for the model nematode C. elegans. He received further post-graduate training at the National Integrated Microscopy Resource (Madison, Wisconsin) in the area of computer science and microscopy. Since 2000 he has been at the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin at Madison. He is currently director of the LOCI and a Principal Investigator in the Laboratory of Molecular Biology at the University of Wisconsin in Madison Graduate School. His current research focuses on the development of novel optical imaging methods for investigating cell signaling and cancer progression, and the development of software for multidimensional image analysis.
Adaptation Biological Image Analysis Methods for an Open Server/Client Software: OMERO-PSLID Project
Baek Hwan (BK) Cho, Ph.D., Postdoctoral Fellow, Murphy Lab, Lane Center for Computational Biology, Carnegie Mellon University
It is now possible to analyze protein location patterns in biological microscope images by automatic methods using computer vision and machine learning techniques. However, for practical users of those analysis methods, it is necessary to make them easy to use. After reviewing our image analysis webapp (PSLID) and an open server/client software for visualization, management and analysis of biological microscope images (OMERO), I will talk about a project that plumbs PSLID into OMERO in order to let people use our anaylsis methods easily.
Biography: Dr. Baek Hwan Cho received his Ph.D. from Dept. of Biomedical Engineering at Hanyang University, Seoul, Korea. He is currently working as a postdoctoral research fellow for Prof. Robert Murphy at the Lane Center for Computational Biology, Carnegie Mellon University. His research interests include automatic protein localization from fluorescent microscopy images, understanding T cell activation using the protein localization methods, and publicizing those methods with open source software.
Developing a Repository for Microscopy Data for Researchers and the Public - The Cell: An Image Library
David Orloff, MBA, Manager, Image Library, ASCB - American Society for Cell Biology
The challenges of creating a public repository of images encompass, political, legal, and technological arenas. There is also the challenge of making the resource a valuable tool for both qualitative and quantitative analysis. I will discuss these challenges, as well as, the use of multiple ontologies for annotation and what to do when there is no appropriate ontology.
Biography: David Orloff received his BS in Biochemistry at the University of Maryland. From there he went to work on one of the early generation protein sequence databases, the Protein Information Resource. He then received his MBA in the Management of Science, Technology, and Innovation at the George Washington University. He is now Manager of the The Cell: An Image Library™ at ASCB, an NIGMS funded project for the development of an image repository for researchers.
Using Informatics Methods to Visualize and Explore the Spatiotemporal Gene Expression Landscape of the Murine Brain
Lydia Ng, Ph.D., Director of Atlas Development, Allen Institute for Brain Science
Studying gene expression provides a powerful means of understanding structure-function relationships in the nervous system. The availability of large-scale gene expression image data such as the Allen Mouse Brain and Developing Mouse Brain Atlases enables new possibilities for computer aided understanding of brain organization. I will present an overview of the automated informatics data processing pipeline that has been developed to enable the navigation and analysis of these large image datasets.
Biography: Lydia Ng joined the Allen Institute in 2004 and currently leads the atlas development team responsible for the design and implementation of the Institute’s web applications as well as visualization and data mining tools. Her research background includes image processing and analysis, image registration, data analysis and mining. She received a B.E. in electrical engineer and a B.Sc. in computer science from the University of New South Wales (Sydney, Australia) and a Ph.D. in electronics at Macquarie University (Sydney, Australia).
This digital course provides special footage of all Bio-IT Keynote Sessions. The Tuesday and Wednesday Keynote presentations offered vivid examples of the current and future impact of technology in data for research and drug discovery opportunities. Also included as part of the Wednesday Keynote material is The Benjamin Franklin Award presentation. The Benjamin Franklin Award is given to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences. The Thursday Keynote panel featured a series of succinct, forward looking presentations. Special guest speakers shared their unique perspective on the future challenges facing the research, pharma, and medical communities.
Making the World’s Knowledge Computable
Stephen Wolfram, Ph.D., CEO, Wolfram Research; Creator of Wolfram\Alpha
Interacting with Complex Information Landscapes: Integration and Next Generation User Interfaces
Bryn Roberts, Ph.D., Global Head, Informatics, Pharma Research and Early Development, F. Hoffmann-La Roche
Benjamin Franklin Award & Presentation
Jonathan Eisen, Ph.D., Professor, Genome Center, University of California, Davis
Keynote Panel Chairperson
Kevin Davies, Editor-in-Chief, Bio-IT World
Pharma Futurology: 2016 and Beyond
Yury Rozenman, Global Head of Marketing, Pharmaceutical and Life Sciences Sector, BT Global Sciences
Global Risk Informatics: The Application of High Performance Computing to Public Health
Debra Goldfarb, Senior Director, Strategy, Microsoft
Ecosystem-Driven Approaches for 21st Century Biomedicine
Ken Buetow, Ph.D., Associate Director for Bioinformatics and Information Technology, National Cancer Institute
Integration of Real Time Discovery and Clinical Care
Ben Heywood, Co-founder and Chairman, PatientsLikeMe
The Goody-Gaga Effect: Health Communication at the Nexus of Social Media and Popular Culture
Mark Boguski, M.D., Ph.D., Founder, Resounding Health Incorporated
Gaming in the Workplace
Martin D. Leach, Ph.D., Executive Director, MRL IT for Discovery & Pre-Clinical Sciences, Merck & Co.
About the Conference:
Bio-IT World Conference & Expo
Enabling Technology. Leveraging Data. Transforming Medicine.
Since its debut in 2002, the annual Bio-IT World Conference & Expo (www.bio-itworldexpo.com) has established itself as a premier event showcasing the myriad applications of IT and informatics to biomedical research and the drug discovery enterprise. The Conference attracts a highly influential audience consisting of senior level scientists, IT professionals and Executives from organizations across the life sciences industry including Pharmaceutical, Biotechnology, Health Systems, Academia, Government and National Laboratories. In 2011, over 2,000 delegates gathered from 29 countries to share information and discuss enabling technologies that are driving the drug discovery process and transforming medicine. The event features concurrent tracks with 160+ technology and scientific presentations.