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CANDLE Presentation

CANDLE presentation for March 2 2018 ITCR PI Meeting

Eric A. Stahlberg, Ph.D. 

Strategic and Data Science Initiatives Director

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Mervi Heiskanen onto ITCR Presentation

Software Carpentry Presentation

Presentation to the ITCR TOW February 8, 2018 by Jonah Duckles, Software Carpentry, Executive Director.

 

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Mervi Heiskanen onto ITCR Presentation

Posters

List of posters

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Mervi Heiskanen onto ITCR 2017 Annual PI Meeting

LesionTracker: Open-source extensible web viewer for oncology research and clinical trials

LesionTracker is an ITCR U24 funded project to create an open-source extensible imaging platform for measuring and longitudinally tracking lesions for oncology clinical trials and research.  The viewer runs in modern HTML5 compliant web-browsers.  We are working with several other ITCR project to integrate our viewer platform with other projects.  All source code as well as demos are available through the github site accessible through the Open Health Imaging Foundation (OHIF) website at www.ohif.org (OHIF is a non-profit 501c(3) foundation that supports open-source medical imaging techologies).

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Gordon Harris onto ITCR Training Assets

GenePattern Notebook

The GenePattern Notebook environment gives GenePattern users the ability to interleave text, graphics and code with their GenePattern analyses to create "notebooks" that can be edited, shared and published. GenePattern Notebooks are built on the Jupyter Notebook system and extend it, allow researchers to embed the hundreds of analysis and machine learning methods in GenePattern within a notebook, without the need to write code.

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Mervi Heiskanen onto ITCR Training Assets

NDEx - Video Demo - June 2016

This video demo was prduced for the Annual ITCR PI Meeting hosted by The Broad Institute in June 2016 and consists of 3 parts:

  • Part 1 describes several UI improvements for network search, including examples of advanced search features.
  • Part 2 introduces the new network visualizer that has been deployed to the NDEx Public server at the beginning of July 2016.
  • Finally, in part 3, we demonstrate a network round-trip between NDEx and Cytoscape that shows how layout and graphic style information are faithfully preserved.

For more information, please visit the NDEx Website and follow us on Twitter and LinkedIn

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Rudolf T Pillich onto ITCR Training Assets

Tools to Analyze Morphology and Spatially Mapped Molecular Data

Motivation: Predict treatment outcome, select, monitor treatments; Reduce inter-observer variability in diagnosis; Computer assisted exploration of new classification schemes; Multi-scale cancer simulations

 

Analysis pipelines for multi-scale, integrative image analysis. Cell, Nuclear Segmentation & Deep Learning
Database infrastructure to manage and query images and Pathomics features.  MongoDB based FeatureDB
HPC software that targets clusters, cloud computing, and leadership scale systems. HPC Region Template infrastructure targeting NSF XSEDE and Titan
Interactive visualization tools to link Pathomics feature and image data; integrate Pathomics image and “omic” data.  caMicroscope, Feature Explorer and 3D Slicer Pathology
Dissemination:  HPC, Containers, Cancer Imaging Archive (TCIA), Linked Image/NLP analytics

 

 

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Joel Haskin Saltz onto ITCR 2016 Annual PI Meeting

QIICR: Quantitative Imaging Informatics for Cancer Research

Overview demonstration for the NCI ITCR QIICR project, http://qiicr.org presented on June 13, 2016 at the annual ITCR face-to-face meeting.

 

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Mervi Heiskanen onto ITCR Training Assets

UCSC Xena Basic Tutorial

UCSC Xena is a tool that allows researchers and bioinformaticians to easily and securely view both their own cancer genomics data and data from large consortiums, such as TCGA, TARGET and GTEx. This video shows how to use Xena.

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Mary Goldman onto ITCR Training Assets

Posters

Posters

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Mervi Heiskanen onto ITCR 2016 Annual PI Meeting

Posters

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Mervi Heiskanen onto ITCR 2016 Annual PI Meeting

Meeting Notes

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Mervi Heiskanen onto ITCR 2016 Annual PI Meeting