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Large Scale Data Management, Computation, and Analysis for Quantitative Imaging Research

Ashish Sharma, Ph.D.

Department of Biomedical Informatics, Emory University

Fred Prior, Ph.D.

Department of Biomedical Informatics,Univ. of Arkansas for Medical Sciences

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High Quality Data

The Role of Data Curation

Data Dump orInformation Resource

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Challenges to Advances in Quantitative Imaging

“Data! Data! Data!” he cried impatiently. “I

can’t make bricks without clay.”

— Sherlock Holmes

• Large, well-curated, repositories• High Quality Data• Radiology, Pathology, RT• Clinical, Genomic• Derived Feature Sets• Security and Access Control• Flexible Access

• Co-Located Computation• Reproducible pipelines

• Systematic, Reproducible tools for imaging phenotype/biomarker exploration

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Resources Provided by the UAMS + Emory QIN

Features

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Built on The Cancer Imaging Archive

TCIA encourages and supports cancer-related open science communities by hosting and managing the data archive,, and relevant resources to facilitate collaborative research.

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RT Collections and Curation Process Partial collections:

• RTOG 0522• NRG-1106 (private)• NRG-1308 (Private)

TCGA-HNSC

Additional collections in process or planned

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Automated RT, Image Set CurationIndividual Bulk Correction

Reduce the time needed to

correct data inconsistencies

Curation Time: Days few minutes(15 Collections 120K images)

Extend POSDA to all curation related checks and activities

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Digital Pathology

caMicroscope

• Visualization of Pathology Images and Features

• Data Management

• Native Support for Scanner Format (Scanner caMic)

• Dynamic Services (launch analysis from browser)

• Scientific Mashups (DataScope and DataCafe)

Supported by NCIP/CTIIP Project; ITCR U24

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Pragmatic Randomized Trial of Proton versus Photon Therapy for Locally Advanced Breast Cancer

• Treatment plans for Photon (left) and Proton (right) Adjuvant therapy for Lung cancer

• Dose Value Histogram Demonstrates that with IMRT, 50% of the heart receives ~ 36 Gy, while proton delivers < 3Gy.

Dose Value Histogram

Intensity Modulated

Radiation Therapy

Proton Therapy

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Data Access

REST APIs to access TCIA Data

APIs to access protected data (coming soon)

Mashups from fusion of diverse datasets to support

• Data exploration

• Hypothesis formulation

• Discovery of latent relationships and patterns

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Reproducible Science

Incentives for data sharing

TCIA assigns DOIs for individual collections as well as data subsets that were used in publications

One click access to data via DOI

Use this DOI to get a Nature Scientific Data publication

Will be developing mechanisms to track usage

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Co-Located Data Analysis

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Radiomics Portal

(Galaxy + Lessons from Connectome Workbench)

Fast access to co-located data

Imaging, RT, RadiomicFeatures (TCIA)

Clinical and other structured (i2b2/Eureka!)

Lung Segmentation Pilot

Tool Dissemination

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Lung Analysis Pipeline

1. Segment lung field from CT

2. Use three parallel

segmentation algorithms to

identify all closed structures

3. Voting algorithm produces final

segmented regions

4. Feature Extraction (shape,

texture, margin,...)

5. Feature Classification

(optional)

6. Image-based phenotype

Top, Green Expert Manual Segmentation

Bottom, Blue Automated Segmentation

The results of three independent automatic

segmentation algorithms are combined using a

voting mechanism to arrive at final automatic

segmentation.

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Biomarker Exploration Pipeline

• Data Loading: Radiomics data is integrated into Eureka! Custom sources can be incorporated via REST APIs

• Construct Radiomic Phenotypes: Using the Eureka GUI, users can explore their radiomics data and construct radiomicphenotypes, that incorporate clinical, imaging and computed features. These phenotypes are captured as graphs and stored in a graph database (Neo4J)

i2b2

TCIA

MongoDB & Others…

RadiomicPhenotypes

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Eureka! Clinical Analytics

• Open source (Apache 2 license) RESTful clinical phenotyping systemClinical phenotyping: computing temporal patterns from EHR data reflecting disease, therapeutic response and prognosis

• Supports loading data and computed phenotypes from data warehouses and flat files into i2b2, Neo4j and flat files

• One REST service + web interface controlling many ETL processes setup with configurable metadata stored in an extended i2b2 metadata schema

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Use Cases• Construct phenotypes by

fusing clinical and derived feature data

• Compute phenotypes on available data

• Ongoing pilot with NLST data

• LungRADS

• Study changes to LungRADSscreening recommendations by incorporating demographics

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Summary

• TCIA is a stable yet continually evolving and expanding information resource for QIN and other Cancer Imaging initiatives

• Radiomic & Radiogenomic analyses require information fusion and HPC pipelines to deal with large subject populations and advanced computationally intensive algorithms

• We are exploring the potential of OODA graph statistics for multi-parametric biomarker discovery and validation.

• NCI QIN: Resources for development

and validation of Radiomic Analyses &

Adaptive Therapy — PI: Prior, Sharma

(UAMS, Emory)

• NCIP/Leidos caMicroscope — A Digital

Pathology Integrative Query System;

PI: Sharma

• PCORI, Pragmatic Randomized Trial of

Proton versus Photon Therapy for

Locally Advanced Breast Cancer to

compare the effectiveness of photon vs.

proton Radiotherapy. (PI: Bekelman)

• Leidos Biomedical Research, Contract

16X011 for NCI, Maintenance and

Extension of The Cancer Imaging

Archive (TCIA), (PI: Prior)