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Software tools of the Computis European project to process mass spectrometry images

Robbe, Marie-France and Both, Jean-Pierre and Prideaux, Brendan and Klinkert, Ivo and Picauld, Vincent and Schramm, Thorsten and Hester, Alfons and Guevara, Victor and Stoeckli, Markus and Roempp, Andreas and Heeren, Ron and Spengler, Bernhard and Haan, Serge (2014) Software tools of the Computis European project to process mass spectrometry images. European Journal of Mass Spectrometry, 20 (5). pp. 351-360. ISSN 1356-1049

Abstract

Among the needs usually expressed by teams using mass spectrometry imaging, often arise user-friendly software able to quickly manage huge data volume and to provide efficient assistance for the interpretation of data. To answer this need, the Computis European project developed several complementary software tools to process mass spectrometry imaging data.
Data Cube Explorer provides a simple spatial and spectral exploration for MALDI-ToF and ToF-SIMS data. SpectViewer offers visualization functions, assistance to the interpretation of data, classification functionalities, peak list extraction to interrogate biological database, image overlay and can process data issued from MALDI-ToF, ToF-SIMS and DESI equipments. EasyReg2D is able to register two images, in ASCII format, issued from different technologies.
The collaboration between teams being hampered by the multiplicity of equipments and data formats, the project also developed a common data format (imzML) to facilitate the exchange of experimental data and their interpretation by the different software tools. The BioMap platform for visualization and exploration of MALDI-ToF and DESI images was adapted to parse imzML files, enabling its access to all project partners and more globally to a larger community of users.
Considering the huge advantages brought by the imzML standard format, a specific editor (vBrowser) for imzML files and converters from proprietary formats to imzML were developed to enable the use of imzML format by a broad scientific community. This initiative is paving the way towards the development of a large panel of software tools able to process mass spectrometry imaging datasets in the future.

Item Type: Article
Keywords: technolog; mass spectrometry; imaging; software
Date Deposited: 02 May 2016 23:45
Last Modified: 02 May 2016 23:45
URI: https://oak.novartis.com/id/eprint/23800

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