How to convert data to imzML?
How do I check my imzML is correct?
- imzML validator open source software developed by University of Bayreuth (latest version can be downloaded here)
imzML is already implemented in many free software tools…
- 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
- 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
- massPix by MRC Human Nutrition Research and University of Cambridge, UK.
- CycloBranch now supports imzML.
- MSIdV by Kyushu University.
- LabMSI by Katsutoshi Takahashi, AIST, Japan
…and commercial tools
- Public data repository PRIDE by the European Bioinformatics Institute, instructions on how to upload imzML data can be found here
- METASPACE web-based ‘Molecular Annotation Engine’ by METASPACE Consortium
Software tools currently under development
- ‘TizViz’: beta version is available. Please contact Christian Fuchsberger
- ‘Indigo Platform’ including DESI imaging by Prosolia (Randy Jullian)
- MSImageViewer: Internal data handling for MS imaging at Novartis (Stöckli lab)