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 eitherreference
ornew
file_inputs
→data_file
must point to the input file- 'reference' pipeline accepts only the
*.hdf5
format - 'new' pipeline accepts both
*.imzML
and*.hdf5
- 'reference' pipeline accepts only the
- 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