MS Software

SCiLS™ Lab

The world-leading software for analysis of mass spectrometry imaging data from all major mass spectrometry vendors, including Bruker’s FLEX series and MRMS

Turn data into knowledge

Analysis and visualization in one software


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MS Software

SCiLS™ Lab

Easy to use
Supports all major Bruker instruments and data from other major mass spectrometry vendors.
2D and 3D visualization allows a multitude of applications in pharmaceutical, medical, and industrial research.
Advanced processing and analysis with next generation machine learning algorithms.
Integral part of the MALDI Molecular Drug Imager, the rapifleX MALDI Tissuetyper, and the spatialOMx workflows from timsTOF flex.



Software for MS imaging data analysis

Statistical analysis of MALDI Imaging data has never been easier with the software from Bruker.

Essential visualization and processing

  • Instant visualization of ion images and spectra
  • Numerous visualization options
  • Easy-to-use computational tools

Advanced processing and analysis
  • Advanced machine learning algorithms for data sets of virtually unlimited size
  • 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
  • Multiple annotations for characterizing regions in clinical and pre-clinical studies
  • Classification models for categorization of unlabeled samples
  • Perform absolute quantitation for MS imaging data​
  • Support tissue-based SpatialOMx workflows and visualizing the distribution of detected compounds in the tissues

Also available
  • Construction, visualization, and analysis of three-dimensional models
SCiLS™ Lab is the industry’s tool of choice for deriving new insights from mass spectrometry imaging data. Used across science and industry, the software sets new standards in analysis and visualization, simplifying everyday work and boosting research output.

System requirements​
The following system requirements apply:

  • Intel Core i7 processor or Intel Xeon processor (equivalent or better)
  • Microsoft Windows 7 64 Bit or Microsoft Windows 10 64 Bit operating system
  • 32 GB of RAM
  • SATA III solid-state drive (SSD)
  • Full-HD display (1920 x 1080)
  • Graphics card supporting OpenGL 3.2
The SSD should be used to host the SCiLS™ Lab files. The best way to improve the recommended system is to add more RAM and a RAID0 configuration of SATA III SSDs. The data which shall be imported or processed should then be stored on the SSDs.




World-leading software for analysis of mass spectrometry imaging

SCiLS™ Lab integrates data from all major mass spectrometry vendors, including Bruker’s FLEX series and MRMS, as well as datasets provided in the open imzML format.

Comparative analysis of multiple samples can be visualized in both 2D and 3D, enabling a multitude of applications in pharmaceutical drug development, tissue-resolved biomarker research, and translational pathology research to complement immunohistochemistry.

SCiLS™ Lab’s workflows for MSI quantitation enables easy quantification of target molecules directly from tissue. SCiLS™ Lab integrates with the SpatialOMx workflow from MetaboScape® and visualizes the annotated MALDI molecular tissue images of detected features (metabolites, lipids, glycans).

For timsTOF fleX ion mobility data, SCiLS™ Lab can display the mobility images allowing CCS-aware data interpretation.



Label-free molecular imaging mass spectrometry ranging from proteins to small molecules

SCiLS™ Lab can be used for the analysis of one or more MALDI Imaging datasets. Multiple data sets can be loaded and spatially aligned in a tiled manner. Compositions of data sets of virtually unlimited size can be visualized and statistically analysed for detailed interpretation. Also, SCiLS™ Lab can be used for construction of 3D MALDI Imaging data from consecutive 2D datasets, and visualization and analysis of 3D MALDI Imaging data.

Distribution of three distinct m/z values in a 3D reconstruction of 49 sagittal mouse brain sections containing a non-metastasizing cerebellar tumor with SCiLS™ Lab.
Statistical analysis with SCiLS™ Lab: Automatically group samples according to meta-data provided with experiments – perform classification and prediction with machine learning methods for tissue typing or biomarker discovery. ​

Large cohort of samples from clinical pathology
In pioneering biomarker studies, the discovery of discriminating ions was either done manually or performed using custom-written software scripts. Because the number of samples – and therefore the amount of data – to be analysed in biomarker studies is huge, manual data analysis is both time-consuming and error-prone.

Automatic elucidation of spectral features discriminating pathophysiological alterations can now easily be performed in SCiLS™ Lab. With just one click, SCiLS™ Lab automatically quantifies how well all ions discriminate different biological states. The resulting list of novel biomarker candidates can be easily exported for subsequent analysis.

Discover the powerful data mining capabilities that are now just a single click away with SCiLS™ Lab.

Whole body imaging
For the pioneering work carried out in 2006, whole body MALDI Imaging challenged methodology and also the computational aspects. To visualize drug and metabolite distributions within whole-body tissue sections, several manual data processing steps were performed using a variety of commercial, academic, and custom software.

All processing of data sets composed of millions of spectra can now be performed using one software. From the registration of multiple individual data sets into one analysis file to preprocessing spectra to comprehensive statistical analysis, SCiLS™ Lab offers the entire data analysis workflow.

Label-free targeted imaging and distribution mapping for drug discovery and DMPK/PD: Low operational cost and high specificity – differentiate drug and metabolite distributions, quantify target compounds, and integrate with histology.



"With SCiLS Lab our team saved endless hours of manual comparisons. This unique feature was eagerly anticipated by us."

Rita Casadonte, PhD, Proteopath GmbH

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