SCiLS Lab

SCiLS Lab by Bruker is an analysis and visualization software designed specifically for mass spectrometry imaging (MSI) data. According to the vendor, this user-friendly software is aimed at small to large companies in various industries, including pharmaceutical research, medical research, industrial research, clinical biomarker studies, and digital pathology. With its intuitive workflows, extensive features, and integration capabilities, SCiLS Lab is positioned as a valuable tool for professionals in these fields.

Key Features

Easy to use: According to the vendor, SCiLS Lab supports all major mass spectrometry vendors and offers intuitive workflows for MSI quantitation directly from tissue. It also integrates with histological annotations from digital pathology and provides an extensive application programming interface (API) for automated reporting and advanced workflow integration.

Visualization: The software enables instant and intuitive visualization of ion images and mass spectra, as claimed by the vendor. It offers flexible rendering options for visualizing spatial compound distributions and distribution patterns. Additionally, it provides statistical charts and reports, and optionally allows volumetric visualization of 3D MS imaging studies.

Analysis: According to the vendor, SCiLS Lab employs advanced machine learning algorithms for data sets of virtually unlimited size. It facilitates comparative analysis to uncover discriminative and correlated spectral features. The software supports unsupervised spatial segmentation and component analysis for untargeted clustering and data mining. It also enables metadata annotations for characterizing regions in clinical and pre-clinical studies, provides classification models for categorization of unlabeled samples, and allows analyte quantitation based on dilution series.

Integrated: SCiLS Lab serves as an integral part of various workflows, including the MALDI Molecular Drug Imager, the rapifleX MALDI Tissuetyper, and the SpatialOMx workflows from timsTOF fleX, according to the vendor. It integrates with histological annotations from digital pathology and supports the export of MS imaging data to the open industry standard imzML. Additionally, it offers the option to import MS imaging datasets from imzML or from various third-party vendors' imaging data formats.

Label-free MS imaging for all classes of molecules: According to the vendor, this feature enables the analysis of multiple MALDI Imaging datasets, allowing them to be loaded and arranged side by side. It facilitates the visualization and statistical analysis of compositions of data sets of virtually unlimited size. SCiLS Lab also provides tools for generating and visualizing 3D models from consecutive 2D MALDI imaging datasets.

Large sample cohorts in clinical research studies: The software simplifies the analysis of large sample cohorts and huge amounts of data in clinical biomarker studies, according to the vendor. It links sample metainformation to MALDI MSI data, saving time and avoiding errors. SCiLS Lab integrates histological annotations from digital pathology using an interface to the powerful open-source application QuPath. It also facilitates the automatic elucidation of spectral features discriminating pathophysiological alterations and quantifies how well ions discriminate between different biological states. Additionally, it enables easy export of lists of novel biomarker candidates for subsequent analysis.

Whole body imaging: SCiLS Lab offers tools for the entire MALDI MSI data analysis workflow, as stated by the vendor. It enables the processing of multiple data sets composed of millions of spectra using one software. The software facilitates spectral preprocessing and comprehensive statistical analysis. It also supports label-free targeted imaging and distribution mapping for drug discovery and DMPK/PD.