eXtensible Neuroimaging Archive Toolkit (XNAT) Washington University Neuroinformatics Group

What is XNAT?  An environment for developing experimental data archives (data store & archiving tools).  Data store: relational database for non-image data specified directory structure for image data.  Archiving tools: Web application for uploading, entering, searching, visualizing, and otherwise exploring data. Command-line tools for batch handling data.

Why do we need XNAT (or something like it)? Raw images Metadata Assessments Demographic s Processed images Derived data Derived data

Why do we need XNAT (or something like it)? Integrated Data Store Secure User Interface Assessments SubjectMR Session RawProcessed Derived DemographicsMetadata

What is XML Schema?  XML Schema is a language for describing the structure and contents of an XML document. Bird XMLXML Schema

XML Schema is the lingua franca for data exchange  Data exchange requires standard open data formats.  XML Schema is the language in which these open formats are defined.  Many fields (e.g. genetics, medicine) have already implemented XML Schema-based standards.  So an application that automatically archives, searches, and displays XML Schema-based data would be really useful…

Data Documents Welcome to XNAT XNAT Generator … … XML Schema 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 ( nameVARCHAR(50) javaNameVARCHAR(50) primaryKeyVARCHAR(50) 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 ( nameVARCHAR(50) javaNameVARCHAR(50) primaryKeyVARCHAR(50) public class Experiment extends org.cnl.cnda.om.BaseExperiment implements Persistent { public static final long MILLIS_IN_DAY = ; public static long getDays(Calendar c1, Calendar c2) { long time1 = c1.getTime().getTime(); public class Experiment extends org.cnl.cnda.om.BaseExperiment implements Persistent { public static final long MILLIS_IN_DAY = ; public static long getDays(Calendar c1, Calendar c2) { long time1 = c1.getTime().getTime(); $page.setTitle("CNDA -- Integrating the Neurouniverse") $page.setLinkColor($ui.alink) $page.setVlinkColor($ui.vlink) … $page.setTitle("CNDA -- Integrating the Neurouniverse") $page.setLinkColor($ui.alink) $page.setVlinkColor($ui.vlink) … Database Schema 78 male right ADRC 5/1/2002 Randy Buckner Dan 78 male right ADRC 5/1/2002 Randy Buckner Dan Java ClassesHTML Pages

This XML schema structure…

…becomes this database table

More complicated elements…

…yield more complicated tables

XNAT is a three-tiered architecture Raw Image Data Processed Images XML Data Files Data Tables Management Tables SQL Database Flat file system Data Store XNAT Engine XNAT Schema Web server User Interface Command line Web browser

The web application emphasizes usability and quality control  Clean user interface  Search and download, no statistics.  Quality control

Security is pretty important too  Password protected login and session timeout.  Secondary password and IP-address restriction on most sensitive data.  User access privileges set by data type and meta data values (e.g. “Dan can view but not edit R Buckner’s fMRI data.”)  Signed approval on new user accounts and changes to existing accounts.  Logins, queries, and downloads written to daily log files.

XNAT is completely open source  All of XNAT’s dependencies are open source.  Turbine (Apache Jakarta) provides “a servlet based framework that allows [developers] to quickly build web applications.”  ImageJ (NIH) provides the foundation for the image viewer.  MySQL and PostgreSQL databases are supported.

XNAT improvements are on the way  Data quarantine  Data history  Direct XML  Database exchange  Improved image viewer with subcortical segmentation and fMRI plugins.  Improved mechanisms for controlling display of data.  Improved mechanisms for validating user input from web forms.