Preclinical Imaging XNAT-enabled Informatics

PIXI logo

Preclinical researchers use the PIXI platform to manage workflows, harmonize imaging databases, and enable deployment of analytic and computational pipelines in preclinical imaging.

What is PIXI?

Preclinical imaging is becoming increasingly important to cancer research and other disease research, with the development and adoption of Patient-Derived Xenographs (PDXs) and Genetically Engineered Mouse Models (GEMMs) into research workflows. With this importance comes a renewed emphasis on reproducible research.

However, reproducibility is difficult to achieve with the proliferation of imaging platforms, differences in imaging formats and protocols, differences in animal models, and variability in analytic pipelines. At the core of this problem of reproducibility is the lack of a common computing platform built on standards and best practices.

Enter the Preclinical Imaging XNAT-enabled Informatics (PIXI) platform. PIXI is based on XNAT, the most widely-adopted open-source imaging research software platform in the world.

The development of PIXI is supported by the Information Technology for Cancer Research (ITCR) program of the National Cancer Institute (NCI) grant #U24CA253531 (MPIs: Kooresh I. Shoghi, PhD, Daniel S. Marcus, PhD).

Preclinical Image Data Management

PIXI is a free and open-source plugin for XNAT which provides robust support for storing, organizing and managing DICOM image data including PET, CT, MRI, SPECT, and more.

Data Organization and Metadata

PIXI extends XNAT's data organization and metadata capabilities to support preclinical research workflows with new data types and metadata fields for small animal subjects and experiments (including drug therapies, caliper measurements, and more).

Search and Reporting

PIXI supports searching and reporting of preclinical data and metadata in addition to the standard XNAT search and reporting features.

Batch Data Entry
Batch Data Entry

Batch data entry forms with Excel-like functionality have been developed for efficient and streamlined data entry in PIXI.

Hotel Image Splitter
Hotel Image Splitting

Integrated containerized workflow for splitting hotel image data into individual subjects.


Use the XNAT-OHIF Viewer to view and annotate your preclinical imaging data.

New updates to OHIF to support preclinical 4D PET/CT workflows.

Container Service

Use XNAT's Container Service to run processing pipelines in Docker containers on your preclinical data.


Integrated Jupyter Notebook environment for interactive data analysis and visualization.


Integrated web-based MATLAB environment for interactive data analysis and visualization. (Requires MATLAB license)

Diagram showing how a PIXI server interfaces with data collection, imaging research, computation, and a network of federated data stores


PIXI is now available for download as a free and open-source XNAT plugin. For detailed instructions on how to use PIXI and its features, please refer to the documentation.

You will first need to have an XNAT instance to install PIXI on. If your don't already have one, you can download XNAT and find documentation on how to use it on the XNAT wiki.

If you have any questions about PIXI, please feel free to contact us.


PIXI is available for demonstration at xnat.pixi.org. Please register for an account, and we will enable your access as soon as possible.

For detailed instructions on how to use PIXI and its features, please refer to the documentation.

Video Tutorials

Watch the Introduction to PIXI video series on YouTube. You can also check out the XNAT Academy and XNAT-OHIF Viewer videos for more general information on using XNAT and the XNAT-OHIF Viewer.

Outreach and Events

  • Co-clinical Imaging Research Resource Program (CIRP) Annual Meeting May 3 - 4, 2023 Virtual
  • Preclinical Imaging Consortium May 10 - 12, 2023 Michigan State University East Lansing, MI
  • SNMMI Annual Meeting June 24 - 27, 2023 Chicago, IL Booth #8051
  • World Molecular Imaging Congress (WMIC) Sept 5 - 9, 2023 Prague, Czech Republic Booth #1
  • NCI Informatics Technology for Cancer Research (ITCR) Annual Meeting Sept 11 - 13, 2023 University of Chicago Chicago, IL
  • PIXI: A resource for managing and analyzing preclinical image datasets Organized by the Image Data Science (IDS) Interest Group of the World Molecular Imaging Society (WMIS) Feb 27, 2024 12:00PM EST Live Webinar
  • Co-clinical Imaging Research Resource Program (CIRP) Annual Meeting May 20 - 21, 2024 Hybrid

Contact Us

Have questions about PIXI? Want to be added to the mailing list? Interested in becoming an early adopter? Please fill out the form below, and we will get back to you as soon as possible. Fields marked with a (*) are required.

We ask early adopters to fill out all fields in this form.