README

Reference implementation for the SpatialMetabolomics processing pipeline

What is this repository for?

This is a reference implementation of our pipeline for annotating high-resolution imaging mass spectrometry data. It is scientific code for demonstration purposes only.

How do I get set up?

• Requires pyIMS and pyMS
  • clone from https://github.com/andy-d-palmer/pyMS, https://github.com/andy-d-palmer/pyIMS
  • add the local directory to the python path os.path.append(my/local//directory/python_code)
• install pyimzml
  • pip install pyimzml
• other dependencies:
  • h5py
  • numpy
  • scipy
• Clone pySpatialMetabolomics
  • https://github.com/andy-d-palmer/pySpatialMetabolomics
  • add the local directory to the python path

Processing a dataset

• Data should be in .imzml format
• The pipeline currently only supports centroid data
  • using centroided data is highly recommended for run time and annotation performance

Contribution guidelines

• Run it, see what happens, ask Andy questions

Who do I talk to?

[email protected]