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XNAT eXtenible aNatomy Archiving Toolkit

XNAT eXtenible aNatomy Archiving Toolkit. Steve Pieper, PhD Isomics, Inc. Slides Courtesy Dan Marcus, Washington U., St Louis Randy Buckner, Harvard U. Topics. NIH Data Sharing Policy. http://grants.nih.gov/grants/policy/data%5Fsharing/. Additional Goals for Data Sharing Tools.

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XNAT eXtenible aNatomy Archiving Toolkit

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  1. XNATeXtenible aNatomy Archiving Toolkit Steve Pieper, PhD Isomics, Inc. Slides Courtesy Dan Marcus, Washington U., St Louis Randy Buckner, Harvard U.

  2. Topics

  3. NIH Data Sharing Policy • http://grants.nih.gov/grants/policy/data%5Fsharing/

  4. Additional Goals for Data Sharing Tools • Tools should be painless and even helpful • Ideally you should want to use the tools independent of the Data Sharing requirements • Tools should be compatible with existing methodologies • DICOM transfers • easy upload/download of data for processing • database schema adaptable to application use cases • Tools should not require excessive system or database administrator time committment • Tools must be robust and efficient

  5. Building informatics tools for brain imaging research Randy Buckner Dan Marcus May 10, 2006

  6. Data Capture DATA INPUTS NEUROIMAGING GENETICS OTHER SOURCES

  7. Data Capture DATA INPUTS NEUROIMAGING GENETICS BAD DATA OTHER SOURCES Integrity: Do I have the data? Quality Control: Are the data any good?

  8. Local Use DATA INPUTS NEUROIMAGING GENETICS BAD DATA OTHER SOURCES Application: Can I do things with the data? Automation: Can I do these things automatically?

  9. Collaboration DATA INPUTS NEUROIMAGING GENETICS BAD DATA OTHER SOURCES Access: Are colleagues getting the data they need? Security: Are colleagues getting data they shouldn’t?

  10. Public access DATA INPUTS NEUROIMAGING GENETICS BAD DATA OTHER SOURCES Privacy: Am I respecting the rights of the study participants? Convenience: How usable are the data?

  11. CAPTURE QUARANTINE LOCAL USE COLLABORATION PUBLIC ACCESS NEUROIMAGING GENETICS OTHER SOURCES The XNAT workflow • Quality control • Data archiving • Data access • Security • Visualization • Automation • Integration • Data sharing

  12. What is XNAT? The Extensible Neuroimaging (anatomy) Archive Toolkit (XNAT) is… • A workflow • A data archive • Web-based productivity tools New: XNAT is now part of the NA-MIC Kit • WashU is funded by NA-MIC to improve ease-of-installation and interoperability with other tools

  13. More about XNAT • Open Source • BSD-style license based on Slicer License • DICOM Server • Push images directly to XNAT • Can Attach Arbitrary Files to a Subject or Project • Web Interface, Java API, and Command Line Access Utilities • Leverages standard web database tools • Java, Apache, Tomcat, Postgres • Active Developer and User Community • Core developer group under Dan Marcus at Washington University Saint Louis • Further development and application under Randy Buckner at Harvard • Supported by BIRN, NA-MIC, and other projects

  14. Jakarta Turbine Actions Screens Display The XNAT Architecture Client applications XNAT API XML Schemas Form handler Search engine List generator Report generator Database generator XNAT engine XFT Relational database Data files Data store

  15. XNAT Generator Welcome to XNAT Database Schema Data Documents Java Classes HTML Pages CRATE TABLE table ( name, VARCHAR(50), idMethod, VARCHAR(50), DEFAULT 'null‘, type, VARCHAR(50), ID INT UNSIGNED, NOT NULL AUTO_INCREMENT, PRIMARY KEY (ID) ); … CREATE TABLE table_column ( name VARCHAR(50) javaName VARCHAR(50) primaryKey VARCHAR(50) XML Schema public class Experiment extends org.cnl.cnda.om.BaseExperiment implements Persistent { public static final long MILLIS_IN_DAY = 86400000; public static long getDays(Calendar c1, Calendar c2) { long time1 = c1.getTime().getTime(); <?xml version="1.0" encoding="UTF-8"?> <xs:schema xmlns:xnat="xnat.xsd" xmlns:xs="http://www.w3.org/2001/XMLSchema" elementFormDefault="qualified" attributeFormDefault="unqualified"> <xs:element name="Database"> <xs:annotation> <xs:appinfo> <xnat:dbinfo database.name="CNDA" database="MYSQL"/> </xs:appinfo> </xs:annotation> </xs:element> <xs:element name="wm_mod_scheltens"> <xs:complexType> <xs:sequence> <xs:element ref="experiment"/> <xs:element name="session_id" type="xs:string"/> <xs:element name="assessment"> … <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 3.2//EN"> $page.setTitle("CNDA -- Integrating the Neurouniverse") $page.setLinkColor($ui.alink) $page.setVlinkColor($ui.vlink) <html> <body> <table border="0"> <tr> <td bgcolor="#336600"> … <?xml version="1.0" encoding="UTF-8"?> <session id="050202_vc1000"> <subject map_num="0001" lab_id="0001"> <age>78</age> <gender>male</gender> <handedness>right</handedness> <cohort>ADRC</cohort> </subject> <session_info> <acq_date>5/1/2002</acq_date> <pi>Randy Buckner</pi> <operator>Dan

  16. Database XNAT integrates storage, web, and exchange formats XML Web pages

  17. CAPTURE QUARANTINE LOCAL USE COLLABORATION PUBLIC ACCESS NEUROIMAGING GENETICS OTHER SOURCES The XNAT workflow in practice

  18. mBDR, Central, MyXNAT • Morphometry BIRN Data Repository • Currated, User Support to Coordinate Submissions • XNAT Central • Anyone Can Create a Project and Upload • Your Local Database • Run your own instance inside your firewall

  19. XNAT in practice: local use Study Relationship between white matter lesions and cognition in nondemented aging and in early-stage Alzheimer’s Disease Investigators Jeff Burns and colleagues at Washington University’s ADRC XNAT’s role Data integration, automated image processing, image visualization, data entry, quality control, data access

  20. XNAT in practice: local use • Data capture (& quality control

  21. XNAT in practice: local use • Data capture (& quality control) • Auto. Image processing (& more QC)

  22. XNAT in practice: local use • Data capture (& quality control) • Auto. Image processing (& more QC) • Online data analysis & entry (& more QC)

  23. XNAT in practice: local use • Data capture (& quality control) • Auto. Image processing (& more QC) • Online data analysis & entry (& more QC) • Exploration, download

  24. XNAT in practice: local use • Data capture (& quality control) • Auto. Image processing (& more QC) • Online data analysis & entry (& more QC) • Exploration, download • Offline analysis & publication

  25. XNAT in practice: collaboration Study SASHA (Semi-automated shape analysis): quantitative analysis of shape and size of cortical and subcortical brain regions in non-AD and AD adults. Investigators BIRN investigators at Washington University (Randy Buckner), MGH (Bruce Fischl), BWH (Steve Pieper), and Johns Hopkins (Mike Miller) XNAT’s role Data integration, distribution, image visualization

  26. XNAT in practice: collaboration • Freesurfer • 3D Slicer • LDDMM • Teragrid • SRB • XNAT Segment & visualization Grid proc. & storage Image acquisition Shape analysis

  27. XNAT in practice: public access Study OASIS: A Cross-sectional sample of MR images and related data from 400 individuals across the lifespan, including 200 younger, 100 older non-demented, and 100 early stage AD Investigators Dan Marcus, Randy Buckner, Tracy Wang, Jamie Parker, Washington University’s ADRC XNAT’s role Data integration, automated image processing, user interface, image visualization, distribution

  28. Open Access Structural Imaging Series • 400 subjects • 100 < 65 years old • 100 > 65 years old • 100 DAT • 3 or 4 T1-weighted MPRAGE images for each subject • 20 reliability scans

  29. XNAT-based OASIS website

  30. CAPTURE QUARANTINE LOCAL USE COLLABORATION PUBLIC ACCESS NEUROIMAGING GENETICS OTHER SOURCES A review of where we’re at

  31. Subcortical Segmentation Elderly Control Alzheimer’s Individual mBIRN: Data Sharing Applied toMorphometry and Disease

  32. mBIRN Goals • Support Multi-Site Multi-Vendor Structural Neuroimaging Research • Provide End-to-End Suite of Tools and Techniques • Sensitive Detection • Large N for Statistical Power • Support Scientific Interpretation 1 Year Volumetric Change red/yellow 5-20% increase blue 5-10% decrease BIRN-ADNI Collaboration

  33. mBIRN Integration distortion correction tools acquisition protocols local databases PubMed (.xcat) BIRN (.xar) Visualization & Interpretation IBVD . . . workflows analysis tools population statistics BrainInfo

  34. mBIRN Informatics • BIRN Data Repository (BDR) • eXtensible Neuroimaging Archive Tool (XNAT) http://www.xnat.org • XML-Based Clinical Experiment Data Exchange Schema (XCEDE) http://www.xcede.org • Stores Images, Demographics, Clinical Data, Analysis Results • 3D Slicer Interoperability (currently read-only, read/write prototype exists)

  35. Query Atlas Module • BIRN Scientific Interpretation Tool • Compatible with fMRI and Morphometry Datasets in BIRN-Standard Formats • Provides a Link Between Images and Text Databases • Uses Anatomic Labeling + Ontologies • Links to Definitions, Publications, Quantifications • E.g. Wikipedia, PubMed, IBVD, BrainInfo

  36. Query Atlas Features • Input:.xcat or .qdec from .xar • Hardware Accelerated Interactive 3D Annotation • Ontology Engine • FreeSurfer, UMLS, BIRNLex, NeuroNames, IBVD • Interactive Browser • Direct Browser Launch to Search Sites using Selected Terms

  37. QDEC • Query, Design, Estimate, Contrast of Population Statistics • XNAT to Select Subjects • FreeSurfer QDEC Runs on Server • .QDEC file in .XAR Web Download • Slicer3 Interactive Visualization • Integrated with Query Atlas

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