PyXNAT: XNAT in Python

Yannick Schwartz, Alexis Barbot, Benjamin Thyreau, Vincent Frouin, Gaël Varoquaux, Aditya Siram, Daniel S. Marcus, Jean Baptiste Poline

Research output: Contribution to journalArticle

24 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number12
JournalFrontiers in Neuroinformatics
Volume6
Issue numberMARCH
DOIs
Publication statusPublished - 2012 May 24

ASJC Scopus subject areas

  • Neuroscience (miscellaneous)
  • Biomedical Engineering
  • Computer Science Applications

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    Schwartz, Y., Barbot, A., Thyreau, B., Frouin, V., Varoquaux, G., Siram, A., Marcus, D. S., & Poline, J. B. (2012). PyXNAT: XNAT in Python. Frontiers in Neuroinformatics, 6(MARCH), [12]. https://doi.org/10.3389/fninf.2012.00012