The Digital Slide Archive
13 Jun 2017 | | Contributor(s):: David A Gutman, Lee Cooper
Presentation at the 2017 Informatics Technology for Cancer Research Annual Meeting Advanced development of an open-source platform for web-based integrative digital image analysis in cancer.
Activities to Promote Technology Research Collaborations (APTRC) PA-17-143 Pre-Application Webinar
24 Feb 2017 | | Contributor(s):: Juli Klemm, Tony Dickherber
Pre-application seminar held February 24, 2017 for FOA PA-17-143
Life after MOOCS: Online Science Education Needs a New Revolution
03 Feb 2017 | | Contributor(s):: Phillip Compeau
ITCR Monthly PI Meeting, February 3, 2017 Presentation by Phillip Compeau (Carnegie Mellon U.)
Extending 3D Slicer to support ground truth pathology tissue segmentation data for integrated pathology/radiology image analysis competitions.
06 Jan 2017 | | Contributor(s):: Joel Haskin Saltz, Andrey Fedorov, Jayashree Kalpathy-Cramer
ITCR PI Monthly Meeting January 6, 2017 Collaborative project goal: Improve support in 3D Slicer for pathology imaging, generate high quality, well curated “ground truth” annotations, integrate key aspects of the Stony Brook ITCR project (FeatureDB) into the MGH project and...
Providing National Cyberinfrastructure to Biologists, esp. Genomicists
02 Sep 2016 | | Contributor(s):: Tom Doek, Mervi Heiskanen
National Center for Genome Analysis Support (NCGAS) provides access to High Performance Computing resources for biologists. NCGAS also maintains a curated set of applications and Galaxy instances of their software, as well as provides bioinformatics expertise.
An Extensible and Scalable Knowledge System Architecture for Cancer Research
06 May 2016 | | Contributor(s):: Daniel Crichton
ITCR May 2016 PI meeting presentation on development of an advanced knowledge system to capture, share and support reproducible analysis from the biomarker data results.
08 Feb 2016 | | Contributor(s):: Michael Reich
GenomeSpace (http://www.genomespace.org) is a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes',...
Pathology Image Informatics Platform for visualization, analysis and management
07 Oct 2015 | | Contributor(s):: Metin Gurcan, Anant Madabhushi, Anne Martel
This multi-institutional proposal seeks to expand on an existing, freely available pathology image viewer (Sedeen Image Viewer) to create a pathology informatics platform (PIIP) for managing, annotating, sharing, and quantitatively analyzing digital Pathology Imaging (DPI) data. Sedeen has become...
Next-Generation Clustered Heat Maps (NG-CHM)
07 Oct 2015 | | Contributor(s):: Weinstein John, Bradley Broom
Clustered Heat Maps (CHMs) have been referred to as the ubiquitous visual icons of post-genomic biology -- the most frequent type of visualization for large molecular profiling databases. However, “traditional” CHMs are static images -- a serious limitation. Accordingly, we have now...
Open source diffusion MRI technology for brain cancer research
07 Oct 2015 | | Contributor(s):: Lauren O\'Donnell
Using measurements of water diffusion, dMRI can give unique insights into the microstructure and cellular orientation of tissues. There is a growing awareness in the neurosurgery community that diffusion models must move beyond the current clinical standard of the diffusion tensor for better...
ITCR Monthly Teleconference September 4, 2015
07 Oct 2015 | | Contributor(s):: Juli Klemm
Brain Cancer Imaging Analytics
02 Oct 2015 | | Contributor(s):: Christos Davatzikos
The transition of oncologic imaging from its “industrial era” to it is “information era” demands analytical methods that 1) extract information from this data that is clinically and biologically relevant; 2) integrate imaging, clinical, and genomic data via rigorous...
Tools for Creation of Integrated Data Repository for Cancer Research
16 Jun 2015 | | Contributor(s):: Guoqian Jiang
Admin Supplement Proposal Parent Projects: DeepPhe (PIs: Savova and Jacobson) caCDE-QA (PI: Jiang)
A Semantic Web-based Quality Assurance Tool for Cancer Study Common Data Elements
16 Jun 2015 | | Contributor(s):: Guoqian Jiang
A poster presentation from the caCDE-QA project (PI: Jiang)
Analysis, integration and visualization of DNA methylation sequencing data
07 Nov 2014 | | Contributor(s):: Maureen Sartor
Integrative epigenomic/genomic profiling and biomarker discovery of HPV+ and HPV- squamous cancers.
Summarization of Big Data
07 Nov 2014 | | Contributor(s):: Jeffrey A. Blimes
All about assay selection...
Biomedical Evidence Graph
03 Oct 2014 | | Contributor(s):: Josh Stuart
Tools to Analyze Morphology and Spatially Mapped Molecular Data
03 Oct 2014 | | Contributor(s):: Joel Saltz
Cloud Supercomputer Aided Diagnostic Imaging Decision Support System
18 Jun 2014 | | Contributor(s):: Hiro Yoshida
ITCR PI meeting presentation on project status.
Quantitative Image Informatics for Cancer Research (QIICR)
04 Apr 2014 | | Contributor(s):: Andrey Fedorov, Ron Kikinis