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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 performance and stability in SCiLS Lab 2018b

For our products SCiLS Lab and SCiLS Lab MVS versions 2018b, a service release is available for download. It comes with an improved performance and stability as well as a more error-tolerant imzML import.

Additional information on all improvements can be found here: release notes.

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

Open Webinar: Data Analysis with SCiLS Lab

SCiLS Lab is the leading software for analysis of MS imaging data. Learn to master our powerful analysis and visualization software in this webinar.

In this Webinar, we introduce SCiLS Lab’s general capabilities as well as what is new with this year’s release. From interactive visualization in a single data set to comparative analysis of multiple samples.

This event is directed to both new customers and customers already familiar with SCiLS Lab: Get to know the software and its most important workflows.

Date: 21 November 2017 / 17 CET / 11 EST / 8 PST
Speaker: Dr. Jan H. Kobarg, Product Manager SCiLS Lab


To register for the SCiLS Lab Software Webinar, follow this link to our sign-up form: Register

Public datasets added to SCiLS Cloud

The list of public datasets has grown at SCiLS Cloud <>: You can now browse two more datasets which were created with our vendor-neutral software SCiLS Lab MVS.

These datasets have been available via the GigaScience (Oetjen et al., 2015) and Pride (Römpp et al., 2015) data archives, now added to our cloud storage, they can be explored interactively with our web service.

Furthermore, we made a new feature available at SCiLS Cloud: It is now possible to publicly share image annotations and load these without the necessity to register in advance.

Image annotation is provided to SCiLS Lab users as a distributed workflow between registered users. This allows an expert to annotate histologically stained images in microscopy resolution in their browser.

If you are a SCiLS Lab user, you can claim your personal storage space and start uploading data to SCiLS Cloud. Go to to learn how to connect your SCiLS Lab with SCiLS Cloud.

New application note on high-speed MALDI-TOF/TOF imaging available

Bruker Daltonics published a new application note on High-speed MALDI-TOF/TOF imaging of mouse brain tissue performed on intact proteins and after on-tissue digestion showing recent research in MALDI mass spec imaging and using our Software SCiLS Lab.

Click to download the ebook High-speed MALDI-TOF/TOF imaging.

SCiLS software demo workshop at OurCon V

30 August 2017

The program for the OurCon V mass spectrometry imaging conference from 25 to 28 September 2017 in Doorn is online.

SCiLS will contribute to the conference with a software demo workshop on Monday, 25 September. Attendees of the workshop learn important workflows and see the newest features in SCiLS Lab and SCiLS Cloud.

The workshop is unfortunately already fully booked, but we invite you to visit our posters or come to our booth during the coffee breaks if you are interested in SCiLS Lab and SCiLS Cloud.

Improved 3D visualization in SCiLS Lab 2018b

29 August 2017

For our products SCiLS Lab and SCiLS Lab MVS, an upgrade to version 2018b is available for download. SCiLS Lab 2018b comes with several new features, improvements and fixes; in particular an improved and faster 3D visualization.

Figure: New 3D transparency visualization of two m/z values introduced with SCiLS Lab version 2018b. The dataset contains serial sections adding up to 14,000 spectra of a squid provided by Janek von Byern, University of Vienna. The sections have been MALDI-imaged by Janina Oetjen, University of Bremen.

Additional information on all features can be found here: release notes.

Your SCiLS Lab should detect the installer for this update automatically, you can also get the most recent version from our downloads section.

We are hiring

23 August 2017

We are currently looking for a software developer for our team located in Bremen, Germany.

We looking forward for receiving your application.

Service Release for SCiLS Lab Core / SCiLS Lab Pro is available

21 August 2017

For our products SCiLS Lab Core and SCiLS Lab Pro (Version 2018a), a service release is available which adds six new features and fixes the following bugs:

  • Feature: Hotspot removal is now executed automatically
  • Feature: The gel view uses maximal contrast within the zoomed range
  • Feature: All loaded m/z images can now be batch saved as jpg or png images
  • Feature: imzML data is imported with a horizontal flip to conform with other softwares
  • Feature: Improved search for true/false attributes in region tree
  • Feature: Plotter can now combine auto y scaling with compare mode
  • Bugfix: Fixed a bug where region attributes did not appear when using the labels report table
  • Bugfix: Classification models imported from other sl files now correct deviations in normalization target values
  • Bugfix: Fixed bug where the importer falsely reported insufficient disk space
  • Bugfix: Fixed off-by-one error for spectrum ids in CSV export
  • Bugfix: Peak picking would not run despite pressing ‚Yes‘ in warning dialog
  • Bugfix: Several minor visualization bugs in the plotter
  • Bugfix: Several minor bug fixes

Your SCiLS Lab should detect the installer for this patch automatically, you can also get the most recent version from our downloads section.

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.