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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