Software tools – MS Imaging

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 by Thermo Fisher Scientific
Waters: imzML files can be generated using an export filter in Waters’ High Definition Imaging (HDI) software
Bruker: flexImaging by Bruker and SCiLS Lab by SCiLS provide 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)
Guide for conversion of high mass resolution data to imzML by METASPACE

imzML validator open source software developed by University of Bayreuth (latest version can be downloaded here)

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

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