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Table 1 Available software for the processing and visualization of laser ablation inductively coupled plasma mass spectrometry imaging (LA-ICP-MSI)

From: Software solutions for evaluation and visualization of laser ablation inductively coupled plasma mass spectrometry imaging (LA-ICP-MSI) data: a short overview

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 https://ms-imaging.org/wp/createtargetanalyzethis/ [64, 91]
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 http://cardinalmsi.org/ [67, 92]
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 https://ms.biomed.cas.cz/cyclobranch/docs/html/index.html [71, 72, 93]
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 https://amolf.nl/download/datacubeexplorer [62, 63]
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 http://www.waters.com/waters/en_US/High-Definition-Imaging-%28HDI%29-Software/nav.htm?cid=134833914&&locale=us_EN [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 https://github.com/AlanRace/jimzMLParser [95, 96]
LA-iMageS Visualization of LA-ICP-MSI data ELAN XL Mac OS, Linux, Windows Java 2017-01-01 GPL Yes Yes http://www.la-images.net/ [3, 40]
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/ https://github.com/sgibb/MALDIquantForeign/ [12, 13]
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 http://www.chemmind.com/en/support_download.html [66, 67]
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 https://github.com/hallz/massPix [69, 97]
MayaVi Visualization of scientific data with Python Python compatible formats Mac OS, Linux, Windows Python 2005-09-13 BSD Yes Yes http://mayavi.sourceforge.net/install.html [46, 98]
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 https://bitbucket.org/lababi/rmsigui [68, 99, 100]
MSIdV Visualization of MSI data imzML Windows Python V 1.1 2016-04-13 NLD Yes Yes https://sourceforge.net/projects/msidv/ [70, 101]
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 https://ms-imaging.org/wp/paquan/ [66, 102]
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) [47, 49, 50]
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 https://openmsi.nersc.gov/openmsi/client/ [103, 104]
OmniSpect Visualization and analysis of MSI data Analyze 7.5, imzML, mzXML, netCDF Mac OS, Linux, Windows MATLAB 2013-02-26 NLD Yes Yes https://cs.appstate.edu/~rmp/omnispect.zip [60, 105]
OpenMIMS ImageJ plugin for analyzing NanoSIMS 50 and 50L data, DFI Cameca SIMS Mac OS, Linux, Windows Java 2018-04-05 NLD Yes Yes https://github.com/BWHCNI/OpenMIMS [65, 106]
Origin and OriginPro Scientific data analysis and graphing Connectors to C, Python, R, MATLAB, LabView, EXCEL Windows Proprietary 2018-01-10 OriginLab No No https://www.originlab.com/index.aspx?go=Products/Origin [84, 107]
PMOD Biomedical imaging and quantification, DFI Clinical and (pre)clinical systems Mac OS, Linux, Windows Java NA PMOD Technologies LLC No No https://www.pmod.com/web/ [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 https://scils.de/download/ [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 https://github.com/AlanRace/SpectralAnalysis [58, 110]
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/ [61, 111]
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]
  1. Apache-2.0—Apache License 2.0 (https://www.apache.org/licenses/), Artistic-2.0—Artistic License 2.0 (https://opensource.org/licenses/Artistic-2.0), AUT—Authors that have established this software need to be contacted to obtain respective software and further information, BSD—BSD License (https://opensource.org/licenses/bsd-license.html), DFI—designed for special instrumentation, GPL—GNU General Public License (https://www.gnu.org/licenses/gpl.html), MSI—Mass Spectrometry Imaging, NA—No information accessible, NERSC—National Energy Research Scientific Computing Center (USA), NLD—No license defined, REG—requires registration, license agreement or personal data, SMAK—SMAK License (https://www.sams-xrays.com/license)
  2. aIn case of missing versions/release dates, the date of a relevant publication is listed
  3. bWebpages were last accessed February 6, 2019