Program | Main function | Data formats | Platform | Programming language | Version/release or publication datea | License | Open source | Free of cost | Project webpageb/ References |
---|---|---|---|---|---|---|---|---|---|
4000 Series Imaging | MSI data acquisition, DFI | 4000 Series instrumentation from Applied BMac OSystems | Windows | .NET | V 3 | Novartis and Applied Biosystems | No | REG | https://ms-imaging.org/wp/4000-series-imaging/ [73] |
BioMap | Visualization of biological imaging data, multiple data types (MSI, optical, CT etc.) are supported | Analyze 7.5, imzML | Mac OS, Linux, Windows | IDL™ | V 3.8.0.4, 2016-09-11 | Novartis | No | REG | https://ms-imaging.org/wp/biomap/ [22] |
CreateTarget/AnalyzeThis! | MSI data acquisition, DFI | Bruker | Windows | Visual Basic 6 | 2006-09-12 | University of Leuven (Belgium) | No | Yes | |
Cardinal | Preprocessing, statistics, spatial segmentation and visualization of MSI data | Analyze 7.5, imzML | Mac OS, Linux, Windows | R | 2018-12-18 | Artistic-2.0 | Yes | Yes | |
CycloBranch | Analysis of MSI data with special focus on dereplication of organic compounds | Bruker, Thermo, Waters, mzML, mzXML, imzML, mgf, txt | Mac OS, Linux, Windows | C++ | 2018-11-18 | GPL | Yes | Yes | |
DataCube Explorer | Visualization of large MSI data sets | Analyze 7.5, imzML, AMOLF | Windows | NET 4 | V 2.3.0.0, 2014-05-27 | AMOLF | No | REG | |
ELAI—Excel-based Laser-Ablation Imaging | Generation, analysis and visualization of LA-ICP-MSI data | Tabular | Windows | Microsoft Excel with Visual Basic for Applications (VBA) | 2016-02-05 | NLD | Yes | AUT | AUT [23] |
HDIP | Processing and visualization of LA-ICP-MSI data | HDF5, raw instrument data (not further specified) | Windows | Proprietary | 2018-07-03 | Teledyne | No | No | http://www.teledynecetac.com/products/laser-ablation/hdip-imaging-software [74] |
HDI—High Definition Imaging | Processing and visualization of multimodal Waters MSI data and statistics, DFI | Waters | Windows | Proprietary | V 1.4, 2016-06 | Waters | No | No | [94] |
IMAGEREVEAL | Statistical analyses, quantification, comparison with reference images, refinement | Analyze 7.5, imzML, kbd, IMDX | Windows | Proprietary | 2018-08-22 | Shimzadzu | No | No | https://www.shimadzu.com/an/lifescience/imaging/reveal.html [77] |
IMAGENA—Image Generation and Analysis | Creation and analysis of images from LA-ICP-MS data | Tabular | Mac OS, Linux, Windows | C++,Qt | 2011-10-01 | NLD | No | AUT | AUT [33] |
iQuant2 | Creation and analysis of images from LA-ICP-MS data | Tabular | Windows | Visual Basic 2008 Express Edition | 2018-02-23 | NLD | No | AUT | AUT [35] |
ImageQuest | Processing, manipulation and analysis of MSI data, DFI | Thermo | Windows | Proprietary | V 1.0.1, 2009-05 | Thermo Fisher Scientific | No | No | https://www.thermofisher.com/order/catalog/product/10137985 [76] |
imzML Converter | Creation of imzML files from raw data | mzML, tabular | Mac OS, Linux, Windows | Java | V 1.3.0, 2012-08-30 | NLD | No | REG | http://www.cs.bham.ac.uk/~ibs/imzMLConverter/ [95] |
ISIDAS—Interactive Spectral Imaging Data Analysis Software | Creation of MSI files | Tabular | Mac OS, Linux, Windows | Python | 2010-10-29 | NLD | No | AUT | AUT [37] |
jimzMLParser | Parsing imzML and mzML files in Java | imzML, mzML | Mac OS, Linux, Windows | Java library | 2018-12-18 | NLD | Yes | Yes | |
LA-iMageS | Visualization of LA-ICP-MSI data | ELAN XL | Mac OS, Linux, Windows | Java | 2017-01-01 | GPL | Yes | Yes | |
LabMSI | Analysis and visualization of MSI data | imzML | Mac OS, Linux, Windows | LabView | 2015-07-01 | NLD | No | AUT | AUT [41] |
MALDIquant, MALDIquantForeign | R library for import and processing of MS(I) data | Analyze 7.5, imzML, tabular | Mac OS, Linux, Windows | R package | 2018-11-26 | GPL | Yes | Yes | https://github.com/sgibb/MALDIquant/ |
MALDIVision | Processing, visualization and analysis of MSI data | Analyze 7.5, imzML | Mac OS, Windows | Proprietary | V 2.22 | Premier Biosoft | No | No | http://premierbiosoft.com/maldi-tissue-imaging/ [14] |
MassImager | Data mining/screening in MSI data (advanced statistics) and visualization | ANDI (CDF), ASCII (TXT), Matlab, mzXML | Windows | Proprietary | V 1.0 2018-02-05 | Chemmind Technologies | No | No | |
massPix | Analysis of MSI data in R, with special focus on lipids | imzML | Mac OS, Linux, Windows | R package | 2017-08-08 | NLD | Yes | Yes | |
MayaVi | Visualization of scientific data with Python | Python compatible formats | Mac OS, Linux, Windows | Python | 2005-09-13 | BSD | Yes | Yes | |
MMSIT | Control software for Voyager STR and sSTR instruments, DFI | Voyager | Windows | Proprietary | 2007-12-02 | Novartis | No | REG | https://ms-imaging.org/wp/mmsit/ [82] |
MSI.R/RmsiGUI | Visualization and plotting of MSI data, statistics and processing of large data sets on computer clusters | imzML | Mac OS, Linux, Windows | Java, R | 2018-12-19 | GPL | Yes | Yes | https://bitbucket.org/lababi/msi.r |
MSIdV | Visualization of MSI data | imzML | Windows | Python | V 1.1 2016-04-13 | NLD | Yes | Yes | |
msIQuant | Quantification and visualization of large MSI data sets | imzML | Windows | C++, .NET | V 2.0.2.14 2016-05-25 | Uppsala University | No | REG | |
MSiReader | Analysis of high-resolution MSI data | Analyze 7.5, imzML, mzXML, Tabular | Mac OS, Linux, Windows | MATLAB | V 1.0 2018-01 | BSD | Yes | Yes | http://www4.ncsu.edu/~dcmuddim/downloads.html (not working on Jan 8 2019) |
OpenMSI | Web platform for management and visualization of MSI data | Analyze 7.5, imzML, raw (various) | Web platform with API | Proprietary | 2013-10-02 | NERSC | No | REG | |
OmniSpect | Visualization and analysis of MSI data | Analyze 7.5, imzML, mzXML, netCDF | Mac OS, Linux, Windows | MATLAB | 2013-02-26 | NLD | Yes | Yes | |
OpenMIMS | ImageJ plugin for analyzing NanoSIMS 50 and 50L data, DFI | Cameca SIMS | Mac OS, Linux, Windows | Java | 2018-04-05 | NLD | Yes | Yes | |
Origin and OriginPro | Scientific data analysis and graphing | Connectors to C, Python, R, MATLAB, LabView, EXCEL | Windows | Proprietary | 2018-01-10 | OriginLab | No | No | |
PMOD | Biomedical imaging and quantification, DFI | Clinical and (pre)clinical systems | Mac OS, Linux, Windows | Java | NA | PMOD Technologies LLC | No | No | [86] |
pyimzML | Library for parsing MSI data with Python | imzML | Mac OS, Linux, Windows | Python library | 2018-09-20 | Apache-2.0 | Yes | Yes | https://github.com/alexandrovteam/pyimzML [108] |
Quantinetix | Quantification and visualization of MSI data | Bruker, Sciex, Thermo, Waters, imzML | Mac OS, Linux, Windows | Proprietary | NA | ImaBiotech | No | No | https://www.imabiotech.com/quantinetix-mass-spec-imabiotech/ [109] |
SCiLS Lab MVS | Visualization and analysis of MSI data | Bruker, imzML | Windows | Proprietary | V 7.01.10764 | SCiLS Lab | No | No | [90] |
SILLS—Signal Integration for Laboratory Laser Systems | Data reduction and quantification of LA-ICP-MSI data | ELAN XL | Windows | MATLAB, EXCEL | NA | ETH Zürich | No | REG | http://www.orefluids.ethz.ch/software/sills.html [54] |
SMAK—Sam’s Microprobe Analysis Kit | Analysis toolkit for imaging data; initially for x-ray microprobes | Tabular | Mac OS (wine), Windows | Python | V 1.50 2018-11-10 | SMAK | Yes | Yes | https://www.sams-xrays.com/smak [57] |
SpectralAnalysis | Analysis and visualization of MSI data, statistics | imzML | Mac OS, Linux, Windows | C, Java, MATLAB | 2018-10-30 | Apache-2.0 | Yes | Yes | |
SpectViewer | Visualization of MSI data, suitable for very large data files without binning | imzML | Linux, Windows | Proprietary | 2014-10-07 | NLD | No | AUT | https://ms-imaging.org/wp/imzml/software-tools/cea-spect-viewer/ |
TissueView | Visualization and manipulation of MSI data, export of images | Applied BMac OSystems | Windows | Proprietary | V 1.1, 2010-05-21 | ThermoFisher/Applied Biosystems/MDS Sciex, DFI | No | No | https://assets.thermofisher.com/TFS-Assets/LSG/Warranties/cms_052419.pdf [112] |