Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. More information on Cardinal

This tool combines several mass spectrometry imaging data files.

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

• Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before the tools analysis starts.

  • Optional file with pixel coordinates and annotation:

    • Tabular file: One column with x values, one column with y values and one column with annotations

    • The file is allowed to have any column names as header (in this case set "Tabular file contains a header line" to yes)

    • Pixel with coordinates outside the coordinates of the input file are ignored

      x_coord     y_coord    annotation
        1            1        healthy
        2            1        healthy
        3            1        disease
        ...
        ...
      

• For xy shifts with tabular file: Tabular file with x and y coordinates shift and file name

  • Each input file is renamed and shifted in x and y direction according to this tabular file. In the example the files have about the same pixel dimensions which is smaller than 510x260.

  • The file can have any column names as header (in this case set "Tabular file contains a header line" to "Yes") or no header at all (set "Tabular file contains a header line" to "No").

    x_shift     y_shift    file name
       0            0       file1
      510           0       file2
       0           260      file3
      510          260      file4
      ...
      ...
    

Options

• "automatic combination": files are automatically arranged in a grid, subfiles are named according to the input file name
• "xy shifts": each file can be moved in x and y direction according to the users need (define one tabular file in the order in which the files are loaded in the history (bottom to top) and define for each file the x and y coordinates shifts in separate columns and the file name in a third column as shown above). The xy shift option combines all datasets and removes all duplicated pixels (same x and y coordinates).
• "Set all file coordinates to 1/1 as origin" can be choosen to override current pixel coordinates of the input file and set their minimal x and minimal y values to 1. Then the shifts from the xy shift tabular files are used to move the pixels of each dataset.
• In case the input files have not exactly the same m/z values set "Do the files have different m/z axis?" to "Yes". Then functionalities of the "MALDIquant" package are used to combine the datasets.

Tips

• The combine tool puts all samples into a common x-y-grid, therefore pixel coordinates will change. In case the pixels are already annotated, the annotations should be provided as tabular files and the tool will return an annotation file with the new pixel coordinates. This annotation file can then be used together with the combined MSI data for tools in which the annotation is required (e.g. 'MSI classification') or useful (e.g. 'MSI spectra plots').

Output

• MSI data as imzML file (in continuous format when m/z axis were the same; in processed format when m/z axis were different)
• Pdf with pixel positions and annotations of the combined files
• Tabular file with pixel annotations (x,y,column with input file names and annotation columns)