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23.03.2016 I Workshop on Imaging Mass Spectrometry with SCiLS Lab software training from 29-31

WIMS 2016: 1st Workshop on Imaging Mass Spectrometry with SCiLS Lab software training in Saint-Malo from 29-31 March 2016.

Only a few days left until the 1st Workshop on Imaging Mass Spectrometry in Saint-Malo starts. The Workshop focuses on practical courses and hands-on trainings directed to experts and beginners in the field of Imaging Mass Spectrometry. Users and interested persons of SCiLS Lab have the chance to participate in an interactive software training organized by SCiLS.

Participation in the software training requires registration for the workshop which is possible in a few days via
the workshop website:

08.03.2016 I Registration still open for the interactive software training after the Bruker User Meeting
01.03.2016 I SCiLS presented recent results on automated tumor typing of tissue sections
22.02.2016 I Service release for our MALDI imaging software SCiLS Lab 2015b available for download
16.02.2016 I SCiLS participates at MSACL 2016 US in Palm Springs, CA
11.02.2016 I Register for the interactive software training subsequent to the Bruker User Meeting in Kassel
08.02.2016 I Project meeting of the EU Horizon 2020 project METASPA CE at ICL in London
05.02.2016 I Service release for our MALDI imaging software SCiLS Lab 2015b available for download
20.01.2016 I These researchers recently used SCiLS Lab to publish scientific results in journals
20.01.2016 I OurCon IV announced: Application and Development of mass spectrometry imaging
Improved integration with the METASPACE online annotation platform

25 July 2017

For our product SCiLS Lab 2018a, a service release is available which improved the integration with the METASPACE online platform for automatic annotation. Our service release comes with the following improvements:

  • Now the data export is scheduled as a background task without locking the user interface. This also enables to batch export data.
  • The performance of the METASPACE export is significantly increased and is about 4 times faster than in previous versions.
  • When exporting data to imzML files we prevent gaps and blank lines in the image representation of the METASPACE engine.

If you have installed SCiLS Lab then the software will automatically check for updates and point out the new available service release. If you want to update manually, please go to downloads and select SCiLS Lab 2018a release.

For more info on METASPACE please also visit the website of the European project METASPACE.

The new SCiLS Cloud and SCiLS Lab software solutions, now with MultiVendor Support (MVS)

5 June 2017

SCiLS Lab is your tool of choice for deriving new insights from mass spectrometry imaging data. The most recent version SCiLS Lab 2018a is now available for download. It features statistical analysis and visualization of mass spectrometry imaging data such as:

  • Instant visualization of ion images, spectra, and numerous statistical visualization options
  • Region attributes to manage meta-information like clinical annotations or experiment settings
  • Comparative analysis for uncovering discriminative m/z-markers
  • Co-localization analysis for discovering correlated m/z-values
  • Spatial segmentation for automatic annotation of prominent features
  • Component analysis for extraction of underlying trends
  • Classification model calculation based on training data and classification of new samples
  • Construction, visualization and analysis of 3D models from consecutive measurements

With SCiLS Lab you can compose, compare and analyse multiple data sets of virtually unlimited size. SCiLS Lab is able to process the following data:

  • Native support for all major Bruker mass spectrometer
  • Vendor-neutral imzML format

SCiLS Lab is closely connected to SCiLS Cloud which offers additional workflows:

  • Secure access with a standard web browser
  • Upload and share data, results and insights
  • Allow partners or team members to annotate histologically stained images

You can download the update here: SCiLS Lab 2018a.

If you have any problems with SCiLS Lab or questions on data analysis please don’t hesitate to contact our software support team at

New publication about organization and localization of small molecules within microbial assemblages

17 January 2017

SCiLS contributed to the following publication about organization and localization of small molecules within microbial assemblages and has been named Editor’s Pick:

Garg, N.; Zeng, Y.; Edlund, A.; Melnik, A. V.; Sanchez, L. M.; Mohimani, H.; Gurevich, A.; Miao, V.; Schiffler, S.; Lim, Y. W.; Luzzatto-Knaan, T.; Cai, S.; Rohwer, F.; Pevzner, P. A.; Cichewicz, R. H.; Alexandrov, T. & Dorrestein, P. C. (2016): “Spatial molecular architecture of the microbial community of a peltigera lichen”, mSystems, American Society for Microbiology, 1, e00139-16.

Microbes are commonly studied as individual species, but they exist as mixed assemblages in nature. At present, we know very little about the spatial organization of the molecules, including natural products that are produced within these microbial networks. Lichens represent a particularly specialized type of symbiotic microbial assemblage in which the component microorganisms exist together. These composite microbial assemblages are typically comprised of several types of microorganisms representing phylogenetically diverse life forms, including fungi, photosymbionts, bacteria, and other microbes. Here, we employed matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry to characterize the distributions of small molecules within a Peltigera lichen. In order to probe how small molecules are organized and localized within the microbial consortium, analytes were annotated and assigned to their respective producer microorganisms using mass spectrometry-based molecular networking and metagenome sequencing. The spatial analysis of the molecules not only reveals an ordered layering of molecules within the lichen but also supports the compartmentalization of unique functions attributed to various layers. These functions include chemical defense (e.g., antibiotics), light-harvesting functions associated with the cyanobacterial outer layer (e.g., chlorophyll), energy transfer (e.g., sugars) surrounding the sun-exposed cyanobacterial layer, and carbohydrates that may serve a structural or storage function and are observed with higher intensities in the non-sun-exposed areas (e.g., complex carbohydrates).

For more information, visit the journal’s website or contact the authors of the paper.

SCiLS is now a part of Bruker’s journey

4 January 2017

We are pleased to announce that SCiLS now is a part of Bruker’s journey.

We are looking forward to continuing the work within this new framework together with you and as a part of Bruker’s global infrastructure making mass spec-based imaging more accessible.

For the complete press release please visit: Bruker News.