README #

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/