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How to convert data to imzML?

  • Thermo: converter for LTQ- and Orbitrap-based instruments is available for download
  • Waters: imzML files can be generated using an export filter in Waters' High Definition Imaging (HDI) software
  • Bruker: the new version of flexImaging (version 4.1) by Bruker provides an imzML export function
  • ABI/Shimadzu: 'Analyze' format can be converteed by 'toimzml' module. Please contact Jean-Pierre Both
  • mzML: imzMLConverter (converts mzML to imzML)
  • mspire - a gem for programming language ruby: the mspire executable has a subcommand to_imzml. (commandline interface with rich options) 

Software tools

imzML is already implemented in several MS imaging applications.

Currently under development

  • msiQuant by Per Andren / Patrik Källback is currently being updated to support imzML
  • TizViz: beta version is available. Please contact Christian Fuchsberger
  • 'LabMSI' is under development by Katsutoshi Takahashi, AIST, Japan
  • mMass by Martin Strohalm
  • "Indigo Platform" including DESI imaging by Prosolia (Randy Jullian)
  • Internal data handling for MS imaging at Novartis (Stöckli lab)


    Application examples

    Examples for teh use and implementation of imzML can be found in the MS image gallery.


    More detailed information on MS imaging software tools which were developed by COMPUTIS partners is presented below and in the submenu of this section.

    • Browsing through selected ion images
    • Coregistration of images
    • Extensive analysis tools
    • Free to download!

    Mirion (Justus Liebig University)

    • Mass spectra directly accessible through image
    • Overlay of different masses
    • Overlay of optical and MS image
    • Compatible with high mass accuracy images