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SIMSdata

A Python reformatting and processing pipeline for ToF-SIMS imaging mass spectrometry data.

About

This package was developed by the Center for Nanophase Materials Sciences at Oak Ridge National Laboratory to facillitate restructuring of data acquired ION-TOF ToF-SIMS instrumentation. The workflow is designed to accept binary data files exported from IONTOF software, process the data files to identify mass spectral peaks, and output a 4-dimensional data hypercube as a HDF5 file for use in further analysis.

Getting Started

Dependencies

This package was built with the Anaconda distribution of Python 3.6. All required packages and modules are included with Anaconda.

The full list of required packages is:

  • Numpy
  • Scipy
  • scikit-learn
  • h5py
  • matplotlib

Installation

Download the module and save to a directory included in your machine's PYTHONPATH variable, or otherwise add the directory to the machine's PYTHONPATH. Alternatively, the path to the module can be specified at runtime using line 10 of workflow.py.

Usage

  • Open the file workflow.py in a text editor
  • Enter the directory which contains the SIMSdata module as "libdir" in line 10
  • Enter the number of CPU cores to use for processing as "cores" in line 22
  • Enter the directory which contains the data files to be processed as "path" in line 24
  • Enter the filename prefix (PREFIX ONLY) of the data files to be processed as "prefix" in line 25
  • In line 40, specify parameters for xy_bins, z_bins, counts_threshold, tof_resolution, and chunk_size for the SIMS data model.
  • Save and execute workflow.py. The output HDF5 file will be created in the directory entered as "path"