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MSI mz images (version 2.10.0.0)

MSI data:

Input file as imzML (composite upload), Analyze7.5 (composite upload) or Cardinal MSImageSet saved as RData (regular upload)

Centroided input:

Choose Yes if peak detection has already been done.

Processed imzML file:

Choose no if your input is an Analyze7.5 or continuous imzML file

Title:

Will appear in the pdf output, if nothing given it will take the dataset name

m/z of interest (e.g. internal Calibrants):

one column with m/z values, optional second column with names (m/z values can also be selected as name)

Column with m/z values:

Column with name of m/z values:

Tabular file contains a header line:

plusminus m/:

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

Contrast enhancement:

The 'histogram' equalization method flatterns the distribution of intensities. The hotspot 'suppression' method uses thresholding to reduce the intensities of hotspots

Image smoothing:

The 'gaussian' smoothing method smooths images with a simple gaussian kernel. The 'adaptive' method uses bilateral filtering to preserve edges

Colorscale:

Image Background:

Alpha power:

Opacity scaling factor (1 is linear)

Display colorkey in plot:

Linear normalization of image:

Export first valid m/z from tabular file as SVG:

Overlay image:

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
 ...
 ...

Tips

In case tabular file cannot be selected in drop-down menu: Datatype in Galaxy must be tabular otherwise file will not appear in selection window (if Galaxy auto-detection was wrong, datatype can be changed by pressing the pen button (edit attributes))
The contrast enhance and image smoothing functions require a certain number (about 2%) of m/z features with intensities > 0 across all spectra

Output

Single Pdf with the heatmap images
optional: svg file with the heatmap of the first valid m/z in the tabular file