XNAT Tools Home
XNAT Plugins
XNAT Plugins can be downloaded at www.xnat.org/download
See Deploying Plugins in XNAT for general setup instructions. Note that plugins often have version dependencies with XNAT, and/or with each other.
Container Service Plugin
Authors: XNAT Team / CIRC - John Flavin, Matt Kelsey, Kate Alpert
The Container Service plugin enables you to load Docker Images into a processing environment connected to your XNAT and run containerized processes from mounted XNAT archive data. These containers can be run from the XNAT UI, singly or in bulk.
Documentation: Container Service
Source Code: https://bitbucket.org/xnatdev/container-service
Batch Launch Plugin
Authors: XNAT Team - Kate Alpert
The Batch Launch Plugin is meant to be used in concert with the Container Service plugin to enable batch launching of computational processes.
Documentation: Batch Launch Plugin
Source Code: https://bitbucket.org/xnatx/xnatx-batch-launch-plugin
XNAT-OHIF Viewer Plugin
Authors: Institute of Cancer Research, London - James Darcy, Mo Al Sad, Simon Doran
The XNAT-OHIF Viewer plugin takes the hugely powerful Javascript-based Cornerstone DICOM viewer and adds significant XNAT-specific functionality, allowing you to open and view sessions, add annotations and draw segmentations or ROIs, and save data back to your XNAT project.
Documentation: XNAT OHIF Viewer
Source Code: https://bitbucket.org/icrimaginginformatics/ohif-viewer-xnat-plugin
XNAT JupyterHub Integration
Authors: CIRC - Andy Lassiter
The XNAT / JupyterHub integration allows users to launch Jupyter Notebooks with mounted XNAT project data as a prebuilt data exploration playground.
Documentation: XNAT Jupyter Integration
Source Code: https://github.com/NrgXnat/xnat-docker-compose/tree/features/jupyterhub
XNAT Project Sync (Xsync) Plugin
Authors: XNAT Team / CIRC - Mohana Ramaratnam, Mike Hodge, Michael Hileman
The Xsync plugin enables automatic synchronization of data from a project in one XNAT system to a project in a second XNAT system. Xsync can be configured to select which data is delivered, whether data needs to be de-identified in transit, and whether it should be delivered on a pre-set schedule.
Source Code: https://bitbucket.org/xnatdev/xsync
DICOM Query/Retrieve (DQR) Plugin
Authors: XNAT Team - Will Horton, Rick Herrick
The DICOM Query/Retrieve plugin is a powerful tool for connecting XNAT with a PACS and finding, requesting, or sending data between the two systems. It also includes highly customizable remapping and relabeling functions.
Source Code: https://bitbucket.org/xnatdev/dicom-query-retrieve
XNAT LDAP Authentication Plugin
Author: XNAT Team - Rick Herrick
The LDAP Authentication plugin allows you to configure and use an external LDAP server registry for authentication into an XNAT system.
Source Code: https://bitbucket.org/xnatdev/xnat-desktop-client
XNAT OpenID Authentication Plugin
Author: XNAT Team - Mohana Ramaratnam
The OpenID Authentication plugin allows you to configure and use an external OpenID server registry for authentication into an XNAT system.
Source Code: https://bitbucket.org/xnatx/openid-auth-plugin
Rad Read Plugin
Author: CIRC - Mike McKay
The Rad Read plugin adds the radiology read data type to XNAT, and provides a convenient form for quickly making rad read annotations. The functionality of the edit form was developed in concert with Joshua Shimony and Tammie Benzinger, radiologists and study PIs at Washington University School of Medicine.
Source Code / Documentation: https://bitbucket.org/nrg_customizations/nrg_plugin_radread
External Apps & Command Line Tools
Most external apps, except where noted, can be downloaded at www.xnat.org/download
These apps are all meant to run on your local development environment. Most are available for Mac OS, Windows and Linux.
XNAT Desktop Client (DXM)
Author: XNAT Team / UAR - Rick Herrick, Darko Ljubic, Marko Obradovic
The XNAT Desktop Transfer Manager (DXM) is a lightweight desktop-installed client that manages uploads and downloads of XNAT image session data. Recent features add support for bulk uploads and pixel anonymization.
Type: Desktop Application (Linux / Windows / Mac)
Source Code: https://bitbucket.org/xnatdev/xnat-desktop-client
DicomEdit
Author: XNAT Team - Dave Maffitt, Kevin Archie
DicomEdit is a small language for specifying modifications to DICOM metadata. It is used by both DicomBrowser and XNAT for scripted metadata modification. There are two versions of DicomEdit. The most up-to-date version of the language is 6.x, which supports editing DICOM sequences, private vendor tags, and many other new features.
Type: Language
Download / Source Code: https://bitbucket.org/xnatdcm/dicom-edit6
Face_Masking
Author: Misha Milchenko (WUSTL), Mohana Ramaratnam (Flywheel)
The Face Masking package implements anatomical surface modification algorithm customized to de-identify the facial pixel data of MR head images in a way that minimizes the impact on the resulting image analysis of the brain.
Type: Container / Pipeline / Processing algorithm
Download / Source Code: https://download.nrg.wustl.edu/pub/FaceMasking/
Docker Image: https://hub.docker.com/r/mohanar/facemasking
Container JSON: https://bitbucket.org/radiologics/radiologics_containers
XNAT Populate
Author: XNAT Team - Charlie Moore
XNAT Populate is a project which uploads image session data to an XNAT instance based on configuration YAML files. This utility comes with a wide variety of predefined datasets containing multiple modalities, multiple data formats, and other conditions that make it possible to test a wide variety of image handling scenarios.
Type: groovy command line script
Download / Source Code: https://bitbucket.org/xnatdev/xnat_populate
XNAT REST Tests
Author: XNAT Team - Charlie Moore, Rick Herrick, Kate Alpert, Tim Olsen
The XNAT REST tests provide a standard set automated tests to validate XNAT functionality on a test server.
Type: groovy (internal libraries), Java (test implementation)
Source Code: https://bitbucket.org/xnatdev/xnat_rest_tests
NRG_Selenium
Author: XNAT Team - Charlie Moore
NRG_Selenium is a Java framework built on Selenium designed to power automated testing on XNAT-based systems. Current mature projects using the framework include a base XNAT test suite, and CNDA Pipeline tests, Test systems in various states from early planning to containing a few base tests include TIP Pipeline tests, Visits & Protocols tests, and CNDA-specific webapp tests.
Type: Java (Maven based) Library
Download: Grab the latest dependency below with maven:
<dependency>
<groupId>org.nrg</groupId>
<artifactId>selenium</artifactId>
<version>4.0-SNAPSHOT</version>
</dependency>Source Code: https://bitbucket.org/xnatdev/nrg_selenium
PyXNAT
Author: IMAGEN - David Just
pyxnat is a Python library to communicate with XNAT which is an extensible database system for imaging and related data. pyxnat uses the RESTful Web Services provided by XNAT and aims to ease communications with an XNAT server to plug-in external tools or python scripts by exposing a simple and consistent API.
Type: Python Library / Command Line
Source Code / Documentation: https://github.com/pyxnat/pyxnat
XTOLM
Author: CIRC - Misha Milchenko
XTOLM is a local bash XNAT-aware console. This page documents a use case for computing whole brain volume using the Brain Extraction Tool for all MPRAGE scans in an MRI project in XNAT and saving statistics in a spreadsheet.
Type: Bash
Download / Source Code: https://github.com/NrgXnat/xnat_bash_utils
Legacy XNAT Applications and Tools
These open-source applications no longer receive updates, and may be limited in functionality, but may still be useful to the XNAT community.
Arc-Sync
Author: NRG - Kevin Archie
Arc-sync is a Python script that uses the XNAT REST API to make a local copy of session data in a named project. It works with Python 2.x (preferably 2.7) but not Python 3.x.
Download / Source Code: https://github.com/karchie/arc-sync
DicomBrowser
Author: NRG - Kevin Archie, Rick Herrick
DicomBrowser is an application for inspecting and modifying DICOM metadata in many files at once. A single imaging session can produce thousands of DICOM files; DicomBrowser allows users to view and edit a whole session—or even multiple sessions—at once. Users can save the original or modified files to disk, or send them across a network to a DICOM C-STORE service class provider, such as a PACS or an XNAT.
Type: Desktop Application. (Linux / Windows / Mac)
Download: https://www.xnat.org/download/dicombrowser/
Source Code: https://bitbucket.org/xnatdcm/dicombrowser
JAAT
Author: CIRC - Jenny Gurney, James Ransford, Matt House
JAAT enables researchers using XNAT to request bulk moves of DICOM data between XNAT repositories, or from PACS to XNAT, in an efficient, customized, and HIPAA compliant way.
Type: Perl Application
Source Code: https://bitbucket.org/nrg/jaat
XNAT Client Tools
Author: NRG - Tim Olsen
Very early iterations of command line tools that were developed against initial XNAT REST APIs to store and retrieve data from XNAT archives, including ArcGet, ArcRead, ArcSim and StoreXML.
Type: Bash / Command Line
XNAT-DICOM Gateway
Author: NRG - Misha Milchenko
Use XNAT Gateway to query XNAT for DICOM images from a DICOM viewing workstation. You can install the Gateway locally and connect to it as to any other DICOM server. DICOM requests are translated into XNAT requests, and the result is returned over DICOM networking protocol.
Type: Desktop application (Linux / Windows / Mac)
Download/Source Code: https://github.com/mmilch01/gatewaye
XNAT ML Plugins
Author: XNAT Team / CIRC – Rick Herrick, Matt Kelsey, Will Horton
The XNAT ML suite of plugins enables the collection of project data into training datasets, then allows you to upload and configure a model to train on that data. This set of plugins was based on the constructs of the NVIDIA Clara 2.0 set of models and training, which is now deprecated.
Legacy Image Viewer
Author: CIRC
The legacy XIMGView Image Viewer is built in HTML5 and shipped as the default viewer in XNAT for versions 1.6.4 – 1.7.6. This viewer has been largely supplanted by the XNAT-OHIF Viewer Plugin. However, it offers support for viewing NIFTI images and can be installed side-by-side with the XNAT OHIF Viewer.
Source Code / Documentation: https://bitbucket.org/xnatdev/xnat-image-viewer-plugin
XNAT Upload Assistant
Author: NRG - Rick Herrick
The XNAT Upload Assistant is a stand-alone desktop application that replaces the deprecated browser-based XNAT Image Upload Applet.
Type: Desktop application (Linux / Windows / Mac)
Download: https://www.xnat.org/download/upload-assistant/
XNAT Data Client (XDC)
Author: XNAT Team - Rick Herrick
The XNAT Data Client supports data transfer operations to and from the XNAT server. This version of the XDC tool has been broken out on its own so that it can be placed anywhere on the user’s system path.
Type: Command Line
Download / Source Code: https://bitbucket.org/xnatdev/data-client
XNAT Desktop
Author: NRG - Misha Milchenko
XNAT Desktop (XND for short) application is a graphical user interface purposed for organizing local files of arbitrary content, storing text metadata with managed files, distributed sharing of structured research data and measurements among desktop users, file repository servers and XNAT Enterprise archives.
Type: Desktop application (Linux, Windows, Mac)
Download / Source Code: https://github.com/mmilch01/xnd