A parser for the imzML format used in imaging mass spectrometry. See specification here. Designed for use with imzML version 1.1.0. Outputs data as python lists and dicts.
The parser is developed by Alexandrov Team at EMBL Heidelberg.
pyimzML is available on PyPI. pyimzML should be installed with pip using one of these three options:
$ pip install pyimzmlwill install pyimzML from PyPI (easiest).$ pip install git+git://github.com/alexandrovteam/pyimzML.gitwill install pyimzML from github.- Download the source tarball from PyPI and
$ pip install pyimzml-x-x-x.tar.gz
Dependency Notes
- pyimzML has an optional dependency to lxml. If lxml is not installed, pyimzML will instead use the built-in cElementTree or ElementTree package.
Testing
To test your installation of pyimzML, you can download sample data from imzml.org and run the tests.
The pyimzml/ontology directory includes data derived from the following ontologies:
- Units of measurement ontology by George Gkoutos CC-BY license
- Mass spectrometry ontology by Gerhard Mayer et al. CC-BY license
- Imaging MS controlled vocabulary
Documentation is available on ReadTheDocs