SCiLS™ Software Solutions

Analysis and visualization of MALDI Imaging data has never been easier.

Powerful visualization and reporting

• Explore every feature in every spectrum 
  
• Study molecular images directly in histopathological context
• Compelling statistical charts and reports
• Volumetric visualization of 3D MS imaging studies (optional)
  

Advanced data processing and analysis

• Advanced supervised and unsupervised machine learning algorithms
• Comparative analysis to uncover discriminative and correlated features
• Spatial segmentation and component analysis for untargeted clustering
• Metadata annotations for efficient region characterization and grouping
• Classification models for categorization of unlabeled samples
• Analyte quantitation based on dilution series
  

Workflow and extensibility

• Comprehensive tools for targeted and untargeted SpatialOMx^®
• Integration with histological annotations from digital pathology
• Extensive application programming interface (API) for automated reporting and advanced workflow integration
• Export MS imaging data to the open industry standard imzML
• Import MS imaging datasets from imzML or from various third party vendors’ imaging data formats (optional)
• Integrated molecular annotation powered by MetaboScape^® (optional)
• Integrated iprm-PASEF workflow to identify ion images with confidence
• Explore spatial multiomics data using the SCiLS™ Ion Image Mapper

System requirements​
The following system requirements are recommended:

• Intel Core i7 processor or Intel Xeon processor (or equivalent) with at least 4 cores
• Microsoft Windows 11 64-bit operating system
• 64 GB of RAM (128 GB recommended for large datasets)
• 1 TB disk space (SSD recommended, see below)
• Full HD display (1920 x 1080) or larger
• Graphics adapter supporting OpenGL 3.2, at least 4 GB GPU memory recommended

For best performance, a solid state drive (SSD) should be used to host the SCiLS™ Lab data files.

SCiLS™ Scope lowers the barriers for sharing and viewing MALDI Imaging and MALDI HiPLEX-IHC data. With an easy-to-use, lightweight interface and data in the open OME-TIFF format, it is ideal for sharing data between collaborators who want to focus on examining ion images. Review and analyse ion images intuitively by adjusting their brightness and contrast, overlaying individual channels, and measure distances between biologically relevant structures. 

The software fits seamlessly into the SCiLS™ autopilot workflow, which automates data acquisition, importing data into SCiLS™ Lab and exporting predefined target ion images into the OME-TIFF format. A ready-to-go solution for MALDI Imaging and MALDI HiPLEX-IHC.

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 (optional). For timsTOF fleX ion mobility data, SCiLS™ Lab displays mass-mobility ion images allowing CCS-enabled data interpretation.
 
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 discovery, and translational pathology research to complement immunohistochemistry.
 
SCiLS™ Lab supports intuitive workflows for MALDI Imaging quantitation of target molecules directly from tissue. It can interpret MALDI MS/MS Imaging data generated using iprm-PASEF^® and integrates with MetaboScape^® for the molecular annotation of compounds with confidence. The SCiLS™ Ion Image Mapper allows easy integration of MALDI Imaging-based spatial multiomics data. For integration with histology SCiLS™ Lab provides an interface to the powerful open source software QuPath, widely used in digital pathology.

Large sample cohorts in clinical research studies
In clinical biomarker studies for the discovery of discriminating ions, large sample cohorts and huge amounts of data need to be analyzed. SCiLS™ Lab makes it easy to link sample metainformation to MALDI MSI data, saving time and avoiding errors. Histological annotations from digital pathology are integrated using an interface to the powerful and widely used open source application QuPath.

Automatic elucidation of spectral features discriminating pathophysiological alterations are easily performed. With just one click, SCiLS™ Lab automatically quantifies how well ions discriminate between 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!

Whole body imaging
The visualization of drug and metabolite distributions within whole-body tissue sections remains a challenging methodology with respect to sample processing, acquisition, and computational data analysis.  

SCiLS™ Lab offers tools for the entire MALDI MSI data analysis workflow. Multiple data sets composed of millions of spectra can be processed using one software, from the registration of multiple individual data sets over spectral preprocessing to comprehensive statistical analysis.