PyXNAT: XNAT in Python

• Main Authors: Yannick eSchwartz, Alexis eBarbot, Benjamin eThyreau, Vincent eFrouin, Gael eVaroquaux, Aditya eSiram, Daniel eMarcus, Jean-Baptiste ePoline
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2012-05-01
• Series: Frontiers in Neuroinformatics
• Subjects: Neuroimaging; database; neuroinformatics; XNAT; python
• Online Access: http://journal.frontiersin.org/Journal/10.3389/fninf.2012.00012/full

As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using high-level languages to automate data management and processing tasks. For this, a structured and programatic access to the data store is necessary. Web services are a first step toward this goal. They however lack in functionality and ease of use because they provide only low level interfaces to databases. We introduce here {PyXNAT}, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems. The choice of Python enables {PyXNAT} to expose the XNAT Web Services and unify their features with a higher level and more expressive language. {PyXNAT} provides XNAT users direct access to all the scientific packages in Python. Finally {PyXNAT} aims to be efficient and easy to use, both as a backend library to build XNAT clients and as an alternative frontend from the command line.