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Blog from June, 2016
Over the last couple of decades, “challenges” have been successfully employed to spur scientific research, “leverage ingenuity” and foster the translation of scientific advances into more widespread use. The topics for the challenges have covered a large spectrum of critical issues from self-driving cars and robots for “dangerous, degraded, human-engineered environments” to topics in energy, education and human health. “Challenges” have also becoming increasingly important in the medical imaging research community. Such challenges have been an integral part of prestigious conferences such as MICCAI (Medical Image Computing and Computer Assisted Intervention) and International Symposium on Biomedical Imaging (ISBI) and are being planned at a number of other venues. The underlying rationale for these challenges is driven by the realization that every year we see the publication of numerous algorithms published in the scientific literature, yet a very small fraction are translated into clinical use. Challenges can be an effective means to comprehensively assess the performance of algorithms by comparing them on common, sufficiently large and diverse datasets using realistic tasks and valid evaluation metrics. MedICI is an open-source project that is developing infrastructure and support to host medical imaging challenges across radiology, digital pathology, and genomics. We will describe the architecture of the system including the integration of CodaLab, caMicrosocope, and ePAD. We will walk through the process of hosting and participating in challenges from the perspective of the organizer and participant, describe past and on-going challenges and share successes as well as lessons learned.
SYNOPSIS:
Dr. Jayashree Kalpathy-Cramer is the co-director of the Quantitative Tumor Imaging at Martinos (QTIM) lab at the Athinoula A. Martinos Center for Biomedical Imaging at Massachusetts General Hospital and Assistant Professor of Radiology at Harvard Medical School. She has a Bachelor of Technology in Electrical Engineering (EE) from IIT Bombay, a Ph.D. in EE from Rensselaer Polytechnic Institute, and an M.S. in Biomedical Informatics from Oregon Health & Science University (OHSU). Her areas of research includes quantitative imaging in cancer, image analysis for retinal imaging, cloud computing and machine learning. She has organized challenges in the area of medical image retrieval and analysis for the last decade.
SUMMARY:
Topic: MedICI: A Platform for Medical Image Computing Challenges
Speaker: Jayashree Kalpathy-Cramer, Ph.D.
Date: Wednesday, July 6, 2016
Time: 11 AM – 12 PM ET
Room: 2W910-912
You are invited to listen to Dr. Kalpathy-Cramer's in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
Presentation: View Dr. Kalpathy-Cramer's presentation slides in PDF and PowerPoint below:
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series presents talks from innovators in the research and informatics communities. The biweekly presentations allow thought leaders to share their work and discuss trends across a diverse set of domains and interests. The goals of the Speaker Series are: to share leading edge research; to inform the community of new tools, trends, and ideas; to inspire innovation; and to provide a forum from which new collaborations can begin. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
caMicroscope and DataScope is one of the three Clinical and Translational Informatics Projects that were funded by NCI/NCIP. This project had two distinct, but integrated goals namely: a) caMicroscope — A digital pathology platform that supports visualization, annotation and analysis of digital pathology data; and b) DataScope — an interactive data integration, query and exploration system. In this talk I will be doing a deep dive into the capabilities of both these systems. caMicroscope provides the community with an open source solution that can visualize whole slide pathology images, create and display both human and machine generated annotations, and run analysis algorithms on the images. In this talk I will provide an overview of caMicroscope, summarize some of it’s deployments, and provide a roadmap for upcoming features. DataScope is part of the Integrative Query System and provides an interactive environment to integrate and explore disparate datasets. Providers can use DataScope to create rich exploration systems that end users can use to slice-dice the underlying datasets, in a highly declarative fashion, without any software development. The talk will touch upon some of its recent deployments and upcoming features.
SYNOPSIS:
BIO:
Ashish Sharma is an Assistant Professor at Emory University Department of Biomedical Informatics. Dr. Sharma’s research interests include data management and integration systems with a specific emphasis on biomedical imaging (Rad, Path and RT), as well as leveraging distributed and cloud computing systems for co-located, large scale data processing. He has also done extensive work in the area of scientific visualization and graph mining. His research involves close collaboration with researchers in both Radiomics/Radiogenomics and Pathomics. He (jointly with Fred Prior) leads a resource grant for the Quantitative Imaging Network, as well as various NCI grants and contracts in the area of middleware systems for image data management, sharing, and analysis. Dr. Sharma received his Ph.D. in 2005 in Computer Science from the University of Southern California.
SUMMARY:
Topic: caMicroscope and DataScope
Speaker: Ashish Sharma, Ph.D.
Date: Wednesday, June 22, 2016
Time: 11 AM – 12 PM ET
You are invited to listen to Dr. Sharma presentation in Room 2W910-912 in the NCI Shady Grove Building on Medical Center Drive or via WebEx.
About the NCI CBIIT Speaker Series:
The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) Speaker Series is a bi-weekly knowledge-sharing forum featuring both internal and external speakers on topics of interest to the biomedical informatics and research communities. For additional information, including past speaker series presentations, visit the CBIIT Speaker Series page.
Individuals with disabilities who need reasonable accommodation to participate in this program should contact the Office of Space and Facilities Management (OSFM) at 240-276-5900 or the Federal TTY Relay number 1-800-877-8339.
