SCiLS Lab is your tool of choice for deriving new insights from mass spectrometry imaging data. The most recent version SCiLS Lab 2019a 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

This version of SCiLS Lab also provides improved integration with the online METASPACE annotation platform:

  • Schedule data export as a background task from SCiLS Lab
  • Increased performance of accessing data will write files faster
  • Eliminated the case where coordinates could overlap in imzML files

You can download the update here: SCiLS Lab 2019a.

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