Code to integrate MALDI-MSI and Imaging mass cytometry data obtained on a single section.
The here provided code is part of the combined MALDI-MSI IMC methodology proposed in:
"Integration of Mass Cytometry and Mass Spectrometry Imaging for Spatially Resolved Single Cell Metabolic Profiling" Joana B Nunes, Marieke E Ijsselsteijn, Tamim Abdelaal, Rick Ursem, Manon van der Ploeg, Martin Giera, Bart Everts, Ahmed Mahfouz, Bram Heijs, Noel FCC de Miranda
The methodology combines mass spectrometry imaging-based metabolomics and imaging mass cytometry-based immunophenotyping on the same single tissue section to reveal metabolic heterogeneity within tissues and its association with specific cell populations like cancer cells or immune cells.
Two scripts are used for the integration of MALDI-MSI images with Imaging mass cytometry images. The following input is required:
- MALDI MSI TIFF files for each identified metabolite
- IMC images & cell segmentation masks
The MALDI_MSI_IMC_coregistration.py code is used to coregister the data after which the MALDI_MSI_IMC_integration.py code can be applied to generate metabolite abundances per cell identified by IMC.
Example data to get started with integrating MALDI-MSI and IMC data is available via https://figshare.com/s/c58ddc70fa8dc0602842
When using the methodology and/or code for any publications, please cite:
"Integration of Mass Cytometry and Mass Spectrometry Imaging for Spatially Resolved Single Cell Metabolic Profiling" Joana B Nunes, Marieke E Ijsselsteijn, Tamim Abdelaal, Rick Ursem, Manon van der Ploeg, Martin Giera, Bart Everts, Ahmed Mahfouz, Bram Heijs, Noel FCC de Miranda