Galaxy | Tool Preview

MSI segmentation (version
Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)
Choose Yes if peak detection has already been done.
Choose no if your input is an Analyze7.5 or continuous imzML file
Colours for the plots
Colours for the plots 0
Use same value to reproduce previous results
Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. More information on Cardinal

This tool provides three different Cardinal functions for unsupervised clustering/spatial segmentation of mass spectrometry imaging data.

Input data

  • MSI data: 3 types of input data can be used:

    • imzml file (upload imzml and ibd file via the "composite" function) Introduction to the imzml format
    • Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
    • Cardinal "MSImageSet" or "MSImagingExperiment" saved as .RData
    • NA intensities are not allowed
    • duplicated coordinates will be removed