Presentation

Shanoir (Sharing NeurOImaging Resources) is an open source neuroinformatics platform designed to share, archive, search and visualize neuroimaging data. It provides a user-friendly secure web access and offers an intuitive workflow to facilitate the collecting and retrieving of neuroimaging data from multiple sources and a wizard to make the completion of metadata easy. Shanoir comes along many features such as anonymization of data, support for multi-centres clinical studies on subjects or group of subjects.

Shanoir offers an ontology-based data organization (OntoNeuroLOG). Among other things, this facilitates the reuse of data and metadata, the integration of processed data and provides traceability trough an evolutionary approach.

Shanoir allows researchers, clinicians, phD students and engineers to undertake quality research projects with an emphasis on remote collaboration. As a secure J2EE web application, it therefore allows you to safely storing and archiving, with no more requirements than a computer with an internet connection!

Furthermore, Shanoir is not only a web application: it is also a complete neuroinformatics platform in which you can easily integrate your existing processing tools or develop your own ones: see ShanoirTk.

Shanoir is a project carried out by the VisAGeS Team, based at IRISA (INRIA Rennes - Bretagne Atlantique Research Centre). This software is released under QPL 1.0 license.

Workflow

Features

Architecture

  • Collect neuroimaging data from several sources:
    • Dicom CD/DVD
    • Nifti
    • Analyze
    • PACS
    • Dicom SCP
  • Provide tools for transfering
  • Extensible and customizable informatics platform
  • Manage processed and raw data
  • Flexible neuroimaging data sharing
  • Data anonymization and patient privacy
  • Secure transfer of neuroimaging data
  • Online visualization of stored data
  • Data backup
  • Secure web access with user-friendly interface
  • Search data and metadata
  • Easy download of stored data
  • Filter query results
  • Ensure data integrity
  • Generate clinical study PDF reports
  • Ontology based data organization (OntoNeurolog)
  • User access control
  • Support for subjects, healthy volunteers and group of subjects
  • Support sharing neuroimaging for multi-center clinical studies
  • Easy reuse of the datasets

Coming soon

  • Quality checks (QC):
    • QC Examination protocol
    • QC Acquisition protocol
    • QC Image quality
    • Automatic, semi-automatic and manual
  • Provide tools for:
    • Quick retrieval of all data and metadata for a specific subject
    • Searching
    • Uploading
  • Workflow monitoring
  • Enhance management of processing pipelines
  • Administrative documents management and centralization

Toolbox

Shanoir comes with a set of tools combined in a toolbox named ShanoirTk. Shanoir is an open source neuroinformatics platform and allow you to freely make your own tools for your specific needs.

Frequently Asked Questions

In this section, you will find some elements of answers to your questions.

Why would I share my neuroimaging data ?

According to Whyte, A. (2008), "Neuroimaging Data Landscapes: Annex to SCARP Case Study No. 1", Digital Curation Centre, Retrieved 11/11/2009, from http://www.dcc.ac.uk/scarp, there are many advantages in sharing your neuroimaging data:

  • Comparison of findings across laboratories, and better assessment of reliability and reproducibility
  • Encouraging meta-analyses that explore phenomena not apparent in individual datasets
  • Access to existing data for investigators without neuroimaging facilities
  • More efficient use of neuroimaging data since this is relatively expensive to collect.

What about the image processing tools integration ?

One objective of research in neuroimaging is the construction of anatomical and functional cerebral maps under normal and pathological conditions.
Recent improvements in image processing techniques, such as segmentation, registration, delineation of the cortical ribbon, modeling of anatomical structures and multi-modality fusion, make possible this ambitious goal in neuroimaging.
Thus, most research teams in neuroinformatics produce processing tools and neuroimaging analysis software.

What are the others applications for neuroimaging data sharing ?

BAXSQL: BAXSQL is a data management tool developed to support the management of functional magnetic resonance imaging (fMRI) data sets in the Medical Grid Project (MGP) testbed (http://www.medgrid.org/).
Human Imaging Database: The Human Imaging Database (HID) is an extensible database management system developed to handle the increasingly large and diverse datasets collected as part of the MBIRN and FBIRN collaboratories and throughout clinical imaging communities at large.
LONI Image Data Archive: The LONI Image Data Archive (IDA) is a user-friendly environment for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data.
Extensible Neuroimaging Archiving Toolkit (XNAT): An Informatics Platform for Managing, Exploring, and Sharing Neuroimaging Data.
SINAPSE: SINAPSE is a consortium of six Scottish universities; Aberdeen, Dundee, Edinburgh, Glasgow, St. Andrews, and Stirling. It has been established with funding from the Scottish Funding Council, the Chief Scientific Office and the Universities. The aim of this world-class consortium is to create a strong dynamic network for a shared environment for strategic research development in brain imaging.

They use Shanoir


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