This repository contains a Python library for processing imaging mass spectrometry data.
See the documentation on readthedocs
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Dependancies:
- numpy
- scipy
- pyMS
- pyimzML
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install this branch with pip
sudo pip install pyImagingMSpec
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
- Data should be in .imzml format
If you're having difficulty running the pipeline get in touch with http://www.embl.de/research/units/scb/alexandrov/