SCiLS Lab

SCiLS Lab is a software platform developed by Bruker for the analysis and visualization of mass spectrometry imaging (MSI) data. It supports data from all major mass spectrometry vendors, including Bruker's FLEX series and MRMS instruments, as well as datasets in the open imzML format. The software is used across academic research and industry for applications in pharmaceutical drug development, tissue-resolved biomarker discovery, and translational pathology research as a complement to immunohistochemistry.

SCiLS Lab is designed to handle large and complex MALDI Imaging datasets, enabling comparative analysis of multiple samples in both 2D and 3D. It supports label-free imaging across multiple molecular classes, from proteins to small molecules, and provides tools for spatial multiomics data fusion and analysis. A companion application, SCiLS Scope, provides a lightweight interface for sharing and viewing MALDI Imaging and MALDI HiPLEX-IHC data with collaborators.

Visualization and Reporting

• Interactive exploration of every spectral feature across datasets
• Molecular images displayed directly in histopathological context
• Statistical charts and exportable reports
• Volumetric visualization of 3D MS imaging studies (optional)
• Side-by-side loading and arrangement of multiple datasets
• Visualization of compositions of datasets of virtually unlimited size
• Generation and visualization of 3D models from consecutive 2D MALDI Imaging datasets

Data Processing and Analysis

• Supervised and unsupervised machine learning algorithms
• Comparative analysis to identify discriminative and correlated spectral features
• Spatial segmentation and component analysis for untargeted clustering
• Metadata annotations for region characterization and sample grouping
• Classification models for categorization of unlabeled samples
• Analyte quantitation based on dilution series, including direct quantitation from tissue
• Automatic quantification of how well ions discriminate between biological states
• Built-in multivariate statistics module for unsupervised spatial segmentation
• Export of biomarker candidate lists for subsequent analysis

Workflow and Integration Capabilities

• Tools for targeted and untargeted SpatialOMx workflows
• Integration with histological annotations from digital pathology via an interface to QuPath
• Extensive API for automated reporting and advanced workflow integration
• Export of MS imaging data to the open imzML industry standard
• Import of MS imaging datasets from imzML or third-party vendor formats (optional)
• Integrated molecular annotation powered by MetaboScape (optional)
• Integrated iprm-PASEF workflow for high-confidence ion image identification using MALDI MS/MS Imaging on the timsTOF fleX
• SCiLS Ion Image Mapper for fusion and joint analysis of spatial multiomics datasets from a single tissue section
• Display of mass-mobility ion images for timsTOF fleX ion mobility data, enabling CCS-enabled data interpretation
• Automated imaging run setup via SCiLS autopilot, including data import and OME-TIFF export

Clinical and Large Cohort Research Support

• Linking of sample metainformation to MALDI MSI data for large clinical study cohorts
• Automatic elucidation of spectral features discriminating pathophysiological alterations
• Processing of multiple datasets composed of millions of spectra within a single software environment
• Whole-body tissue section imaging support, covering sample registration, spectral preprocessing, and statistical analysis

SCiLS Scope

• Lightweight, easy-to-use interface for sharing and viewing MALDI Imaging and MALDI HiPLEX-IHC data
• Uses the open OME-TIFF format for straightforward data sharing between collaborators
• Supports adjustment of brightness and contrast, overlaying of individual ion image channels, and distance measurement between biological structures
• Integrates with the SCiLS autopilot workflow for automated data acquisition and export
• Available as a free download

System Requirements

• Intel Core i7 (5th generation or later) or Intel Xeon (v3 or later) processor with at least 4 cores
• Microsoft Windows 10 or 11 (64-bit only, minimum version 1607)
• 64 GB RAM (128 GB recommended for large datasets)
• 1 TB disk space (SSD recommended for best performance)
• Full-HD display (1920 x 1080) or larger
• Graphics adapter supporting OpenGL 4.0 with at least 4 GB GPU memory recommended

SCiLS Lab licenses are available through the Bruker Store, including a free trial license option. The software automatically checks for and notifies users of available updates. Supporting resources include tutorial videos, example datasets, a published bibliography, and training materials through the Bruker Customer Training Academy.