README Documentation Status

This repository contains a Python library for processing imaging mass spectrometry data.

See the documentation on readthedocs

Installation

  • Dependancies:
    • numpy
    • scipy
    • pyMS
    • pyimzML
  • install this branch with pip
sudo pip install pyImagingMSpec

Package Contents

This library is currently includes

  • data container class for a imaging mass spectrum
  • tools for normalising imaging mass spectrometry data
  • data container class for ion images
  • tools for processing ion images
  • some preliminary implementations of data converation utilities

Processing a dataset

  • Data should be in .imzml format

Who do I talk to?

If you’re having difficulty running the pipeline get in touch with http://www.embl.de/research/units/scb/alexandrov/

License

This project is licensed under Apache 2.0 license.