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MSI mz images (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
Will appear in the pdf output, if nothing given it will take the dataset name
one column with m/z values, optional second column with names (m/z values can also be selected as name)
m/z range to add on either side of the given m/z to create a window in which the mean of all intensities will be computed
The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots
The 'gaussian' smoothing method smooths images with a simple gaussian kernel. The 'adaptive' method uses bilateral filtering to preserve edges
Opacity scaling factor (1 is linear)
Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. More information on Cardinal

This tool uses the Cardinal image function to plot the intensity distribution of m/z features 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
  • Tabular file with m/z values:

    • One column with numeric m/z values (without empty fields or letters), another column with names for the m/z (m/z column can also be used as name)

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

    • m/z features outside the m/z range of the input file are ignored

        m/z        name
      100.0      analyte1
      100.01     analyte2
      100.02     analyte3