Welcome to Shanoir, your medical imaging research platform!

Shanoir: your FAIR self-service platform for medical imaging research

Available under https://shanoir.irisa.fr and https://shanoir-ofsep.irisa.fr

What is Shanoir?

Shanoir (SHAring iN vivO Imaging Resources) is a web platform (open-source) for clinical and preclinical research, designed to import, share, archive, search and visualize all kind of medical imaging data (BIDS, MR, CT, PT, EEG, Bruker). Its origin goes back to neuroimaging, but its usage is now open for all kind of organs. It provides a user-friendly, secure web access and offers an intuitive workflow to facilitate the collecting and retrieving of imaging data from multiple sources and a wizzard to make the completion of metadata easy. Shanoir comes along with many features such as pseudonymization of data for all imports, automatic NIfTI conversion, support for multi-centres clinical studies and many more, please see below.

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 secured Jakarta EE web application, it therefore allows you 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 platform in which you can easily integrate your existing processing tools or develop your own workflow using either the REST-interface, DICOMWeb-interface, ShanoirUploader or existing Python scripts for search and download.

Shanoir is a project initiated by the Empenn Team, based at IRISA (INRIA Rennes – Bretagne Atlantique Research Centre). This software is released under GPL v3.0 license.

Consortium Shanoir

The evolution of the open-source software Shanoir is voted by the Consortium Shanoir (operated by Inria).
More here…

More information on GitHub:


What is new in Shanoir?


As we store medical data we take security very seriously, that is why we worked a lot on this side for Shanoir:

  • Keycloak (http://www.keycloak.org)
    Instead of again and again redeveloping and securing our home-made user management we use a standardized and tested Open Source Identity and Access Management tool and its protocols
  • OpenID Connect as authentication protocol
  • Full control for principal investigators: who can access? to what data? with which rights?
  • A new DICOM pseudonymization module configurable and based on the 2010 DICOM Supplement 142
  • Data encryption on production servers
  • Security audits on production servers
  • Conformity to new European rules, starting from 25.05.2018
    • General Data Protection Regulation, GDPR (in French: règlement général sur la protection des données (RGPD))

To comply with new technological standards and a better user experience Shanoir is a 100% Single-Page-Application:

  • Angular 12 as front-end technology (https://angular.io)
  • To support as many browsers as possible, even mobile browsers, we choose to implement Shanoir on using Angular 12 as base framework for the front-end
  • New designed user interface that simplifies the usage of Shanoir
  • Integrated browser viewer for DICOM with OHIF-Viewer and NIfTI images with Papaya
Import formats
DICOMweb support
New DICOM and NIfTI viewer + medInria
  • Shanoir integrates by default the OHIF-Viewer (https://ohif.org)
  • Shanoir makes use of the Papaya JavaScript WebViewer to display
    DICOM and NIfTI files in a web browser (http://ric.uthscsa.edu/mango/papaya.html)
  • medInria (https://med.inria.fr), a desktop application to view and process images,
    remains the viewer for data within Shanoir and remains its connection to access to Shanoir
Pipelines and processing – directly connected
  • On using the interface CARMIN, Shanoir, connects to processing platforms,
    especially VIP (https://www.creatis.insa-lyon.fr/vip/) and Boutiques (https://boutiques.github.io)
    to access to a large scope of pipelines
  • Individual pipeline integrations are possible
  • The pipelines execute in a dedicated cluster environment
  • The processing results are integrated back into Shanoir
BIDS-native, brain imaging data structure
  • Shanoir today uses a proprietary file data structure to store its data
  • Shanoir uses BIDS to structure its internal data
  • This will help to easily import and exports BIDS-validated and standardized data
    on using Shanoir.
Old features, well liked, but refreshed
  • Ontology based data organization (OntoNeurolog) for multi-center clinical and preclinical studies
  • Automatic conversion of DICOM files to NIfTI files
  • Harmonization of DICOM meta-data during import
  • Clinical scores management
  • Command line access to Shanoir on using Python scripts
New search and mass data download
  • A simplified search field, that searches in all data has been added based on Apache Solr technology
  • On using this search simplified mass data downloads on using a “shopping cart” will be possible
  • All DICOM meta-data will be indexed and searchable
Microservices architecture: ready for population imaging

Before Shanoir was a monolithic application deployed on one single server instance on using old Java Enterprise architecture, now this has changed:

  • The entire Shanoir application consists of multiple independent microservices, where each of them has its autonomous functionality
  • This makes it a lot easier for developers to know where to work on
  • This has lead to a very modular architecture that has nearly no limits in scaling up to whatever data volume may be achieved
Cloud-native: Containerization/Docker

Each microservice of Shanoir runs in its own Docker container, that makes Shanoir deployable and better runable on new cloud infrastructures, that scale up to no limits if required.

REST services and swagger
  • REST is the new technology to contact the API-Gateway of Shanoir
  • All microservices provide swagger interface definitions to even generate clients to call Shanoir in whatever client implementation language desired
Human and small animal data and images in one server
  • Easily a plugin for preclinical data can be integrated into Shanoir
  • This leads to one Shanoir server available in the browser, that manages in the same application clinical (human) and preclincial (animal) meta-data and images

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