The next version of Bruker’s flexImaging software will have an imzML export function. Since imzML can come in different flavors, we cannot ensure that third-party software can handle the files correctly. To allow compatibility tests, we have made two example files available under ftp://ftp.bdal.de/data/Support/TOF/compass-flex/flexImaging/imzML/
The MALDI-TOF example is stored in the “continuous” format with a common mass axis for all spectra. The FTMS example is stored in the “processed” format.
Please test the files with your software. Please report bugs, comments and suggestions to: maldi.sw.support@bdal.de
Please note: The coordinate system in flexImaging is based upon the optical image of the sample, if the optical image is much larger than the measured area then it is not uncommon to have a rather high number as lowest x- and y-coordinates in the dataset. This is reflected in the imzML file and could lead to a large empty space at the top and the left of the image, depending on the implementation of the visualization.
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