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

Options

• PCA: principal component analysis
• k-means: spatially-aware k-means clustering (adopted from Alexandrov and Kobarg)
• spatial shrunken centroids: Allows the number of segments to decrease according to the data. This allows selection of the number of clusters (more details in Bemis et al.)

Output

• Pdf with the heatmaps and plots for the segmentation
• Tabular file with information on m/z and pixels: loadings/scores (PCA), toplabels/clusters (k-means), toplabels/classes (spatial shrunken centroids)
• Optional .RData file which contains the segmentation results and can be used for further exploration in R using the Cardinal package
• Optional: svg file with the first segmentation image