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How to convert data to imzML?

  • Thermo: converter for LTQ- and Orbitrap-based instruments is available for download here and an imzML export function is implemented in the new version of ImageQuest (version 1.1) by Thermo Fisher Scientific
  • 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
  • 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.

  • DataCubeExplorer by FOM-AMOLF, Amsterdam
  • BioMap by Markus Stöckli (currently works for 'CONTINUOUS' only)
  • MSiReader: open source software developed by North Carolina State University
  • omniSpect by Georgia Institute of Technology (updated weblink!)
  • Spectviewer: beta version is available for academic labs. Please contact
  • Quantinetix: commercial software by Imabiotech
  • MALDIVision: commercial software by PREMIER Biosoft
  • Cardinal: Statistical analysis package by Purdue University and Northeastern University (currently works for 'CONTINUOUS' only)
  • Public data repository PRIDE by the European Bioinformatics Institute, instructions on how to upload imzML data can be found here
  • open-source parser of imzML in Python by EMBL

Currently under development

  • 'msiQuant' by Per Andren / Patrik Källback (University of Upsalla, Sweden) is currently being updated to support imzML
  • 'SpectralAnalysis' by Josephine Bunch / Alan Race (NPL, UK)
  • 'TizViz': beta version is available. Please contact
  • '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 the 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