CIM-XNAT
Welcome to the CIM-XNAT information website!
Small animal imaging facilities are highly specialized centers that provide the research community access to cutting-edge imaging technologies. These centers have therefore to deal with the complexity and the variety of preclinical image datasets in terms of archiving and retrieving image datasets as well as for the management and processing. Whereas at clinical level XNAT , an open-source imaging informatics software platform dedicated for importing, archiving, processing and securely distributing imaging and related study data is available and widely exploited, to date, no custom or standard solutions are available to preclinical imaging centers to fulfill these tasks. Therefore, we have overcome these limitations by developing dedicated tools for XNAT to facilitate image storage, annotation, and processing at preclinical level. A XNAT instance for archiving and processing preclinical medical images is available at EUBI-XNAT .
XNAT-PIC
XNAT for Preclinical Imaging Centers (XNAT-PIC) is a free and open-source Windows desktop application (GNU General Public License – GPL, v3), which offers several tools to expand the XNAT core functionalities to support the preclinical imaging community and to promote open science practices. The adoption of these tools will improve the findability, the access, the interoperability, and reusability (FAIR) of preclinical image datasets.
Which features does XNAT-PIC offer?
Uploader
to easily import DICOM image datasets into the XNAT platform. It supports upload of whole projects, or of sessions, subjects and experiments (scans).
Grouping Annotation Interface
to efficiently cope with different experimental protocols by labelling subjects with dedicated Custom Variables to manage several types of cohorts (e.g. treated/untreated, timepoints, doses, etc..).
MRI2DICOM Converter
to convert Bruker raw data to DICOM standard, including DICOM tags for new MRI modalities, such as Chemical Exchange Saturation Transfer (CEST).Let’s Start! Download and start using XNAT-PIC!
Versions
XNAT-PIC v2.0
Stand-alone SW
XNAT-PIC is available for download and immediately usable without requiring additional setup.
User-friendly interface
We have designed an interface that is easy to navigate and understand, which facilitates user interaction with the system.
Secure Access
Credentials to connect to an XNAT instance to load images dataset from the desktop client are protected by cryptographic algorithm.
Additional Files
Ability to upload non-DICOM files such as parametric maps, results, etc. to the XNAT platform.
Improved Speed
The addition of multicore processing has enhanced the conversion speed of raw MRI file formats to the DICOM.
More objects
The user can convert, upload, or create an entire project, single subject, or experiment (scans) on XNAT.
Interface for grouping annotation
Interface designed with features and functions that allow users to easily group and categorize information regarding preclinical images.XNAT-PIC v1.0
Functionality of XNAT-PIC:- Convert experiments (pool of scans) from BRUKER format to standard DICOM.
- Upload experiments to XNAT platform.
- The custom variables are edited based on the folder structure.
Contact information
XNAT administrator:Kranthi Thej Kandula
Research
Fellow at University of Turin
mail:
kranthithej.kandula@unito.it
XNAT-PIC developer: Francesco Gammaraccio
Research
Fellow at University of Turin
mail:
francesco.gammaraccio@unito.it
Acknowledgements
European Union’s Horizon 2020 research and innovation programme under grant agreements #824087 (EOSC-LIFE project), #965345 (HealthyCloud project), #101058427 (EOSC4Cancer project) and # 1011100633 (EUCAIM project).
Group Leaders:
