XNAT-PIC Edit me
Preclinical imaging centers deal with many challenges mostly related to the variety of imaging instrumentation yielding huge volumes of raw data. The current procedures to collect, share and reuse preclinical image data are insufficient, thus revealing an urgent need of standardization in terms of data storage and image processing. XNAT for Preclinical Imaging Centers (XNAT-PIC) has been developed to overcome this limitation by extending XNAT’s basic functionalities to meet the needs of preclinical imaging facilities.
What is XNAT-PIC?
XNAT for Preclinical Imaging Centers (XNAT-PIC) consists of a set of tools built in Python and MATLAB to store, process and share preclinical imaging studies built on top of the XNAT imaging informatics platform.
Who is XNAT-PIC intended for?
XNAT-PIC is inteded for scientists, researchers and data stewards working in the preclinical and biomedical imaging field to support image data management and processing.
Which task can be solved with XNAT-PIC?
XNAT-PIC is a set of tools to support preclinical imaging scientists in their data management and processing needs. The Extensible Neuroimaging Archive Toolkit XNAT is an imaging informatics platform developed by the Neuroinformatics Research Group at the Washington University for the management, storage and analysis of biomedical image data. XNAT is an open-source project that can support a wide range of imaging modalities thanks to its extensibility.
XNAT-PIC consists of:
MRI2DICOM processes Magnetic Resonance (MR) images and convert them from ParaVision® (Bruker, Inc. Billerica, MA) file format to DICOM standard
XNAT-PIC Uploader to import and store multimodal DICOM image datasets to XNAT
XNAT-PIC Pipelines for analysing single or multiple subjects within the same project in XNAT.
Where can you find training materials and events about XNAT-PIC?
“Demonstrator 5: XNAT-PIC: expanding XNAT for image archiving and processing to Preclinical Imaging Centers”. EOSC-Life website
“Towards sharing and reusing of preclinical image data”. Euro-Bioimaging website
“Data Management: Biological and Preclinical Imaging Perspective”. Euro-Bioimaging Virtual Pub, February 12th, 2021.
- “XNAT-PIC: expanding XNAT for image archiving and processing to Preclinical Imaging Centers”. Demonstrator 5 from Populating EOSC-Life: Success stories for the Demonstrators – Session 1 from January 13, 2021.
If you use XNAT-PIC please cite:
- S. Zullino, A. Paglialonga, W. Dastrù, D. L. Longo, S. Aime. XNAT-PIC: Extending XNAT to Preclinical Imaging Centers, 2021. Pre-print: https://arxiv.org/abs/2103.02044
Tools used within XNAT-PIC?
|Tool or resource||Description||Related pages||Registry|
|MRI2DICOM||a Magnetic Resonance Imaging (MRI) converter from ParaVision® (Bruker, Inc. Billerica, MA) file format to DICOM standard||Researcher Data steward research Processing|
|XNAT||Open source imaging informatics platform. It facilitates common management, productivity, and quality assurance tasks for imaging and associated data.||Researcher Data analysis TransMed Assembly|
|XNAT-PIC Pipelines||Analysing of single or multiple subjects within the same project in XNAT||Researcher Data steward research Data analysis|
|XNAT-PIC Uploader||Import tool for multimodal DICOM image datasets to XNAT||Researcher Data steward research Collecting|