A Python project for processing mass spectrometry imaging data (imzml) acquired from Bruker or Waters instruments.
Please cite: doi: https://doi.org/10.64898/2025.12.25.694368 A computational workflow for microscopy-guided ion identification in clinical mass spectrometry imaging datasets Ana-Maria Năstase, Ping K. Yip, Christopher E.G. Uff, Irma O’Meara, Hervé Barjat
The central class imat (which stands for image matrix) stores information about a mass spectrometry imaging dataset including its image size and mass channel intensities. This is the backbone of the rest of the modules of this Python project.
The rest of the modules inlcude:
- process_imat.py - Marshmallow class - which converts imzml files to imat object.
- synth_msi.py - SynthMSI class - generates synthetic MSI dataset when given 2 binary masks.
Instructions to be added soon. This project is set to be packaged soon.
Shield:
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License.
