Software tools

How to convert data to imzML?

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
  • SCiLS Lab commercial software by SCiLS
  • 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
  • METASPACE web-based ‘Molecular Annotation Engine’ by METASPACE Consortium
  • 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)