This repository is for developing and evaluating various implementations of single-node spatial metabolomics pipelines. As such, it's not at all production ready and can easily eat your cat^W^Wall available RAM.

Having said that, here's how to install and run the pipelines:

• Install the necessary Python modules: pip install -r requirements.txt
• (Optional, for faster measure_of_chaos) install OpenCV 3.0
• Copy the example.json template and edit it as necessary:
  • method can be either reference or new
  • file_inputs→data_file must point to the input file
    • 'reference' pipeline accepts only the *.hdf5 format
    • 'new' pipeline accepts both *.imzML and *.hdf5
• Run the pipeline: python2 pipelines.py your_config.json
• The following results are stored in file_inputs→results_folder:
  • a file with scores for all formulae;
  • a file with scores only for the formulae that pass the thresholds
  • images for each (formula, adduct) pair that passes the filter