Software tools

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 SCIEX: ‘Analyze’ format can be converted by ‘toimzml’ module. Please contact Jean-Pierre Both
  • Shimadzu: imzML can be exported in Imaging MS Solution 1.1 by Shimadzu
  • mzML: imzMLConverter (converts mzML to imzML and can stitch multiple imzML files)
  • mspire – a gem for programming language ruby: the mspire executable has a subcommand to_imzml. (commandline interface)

Software tools

imzML is already implemented in several MS imaging applications:

  • MSiReader: open source software developed by North Carolina State University
  • SpectralAnalysis by University of Birmingham / NPL
  • DataCubeExplorer by FOM-AMOLF, Amsterdam
  • BioMap by Markus Stöckli (currently works for ‘CONTINUOUS’ only)
  • omniSpect by Georgia Institute of Technology (updated weblink!)
  • Spectviewer: beta version is available for academic labs. Please contact Jean-Pierre Both
  • Quantinetix: commercial software by Imabiotech
  • MALDIVision: commercial software by PREMIER Biosoft
  • Cardinal: Statistical analysis package by Purdue University and Northeastern University (now also supports ‘PROCESSED’ data)
  • MSI.R open source software developed by CINVESTAV Unidad Irapuato, Mexico
  • msiQuant by University of Uppsala now supports imzML
  • 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

  • ‘LabMSI’ is under development by Katsutoshi Takahashi, AIST, Japan
  • ‘TizViz’: beta version is available. Please contact Christian Fuchsberger
  • 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.

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