Reference implementation for the SpatialMetabolomics processing pipeline
This is a reference implementation of our pipeline for annotating high-resolution imaging mass spectrometry data. It is scientific code for demonstration purposes only.
- 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
- 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
- Run it, see what happens, ask Andy questions