SCiLS Lab - The statistical analysis software

SCiLS Lab: Colon CancerOne of the challenges in MALDI imaging is the huge amount of generated data. A typical 2D MALDI-ToF imaging dataset contains about 10.000 - 100.000 different m/z values and about 10.000 - 100.000 pixels.

SCiLS Lab is the advanced software for visualization, analysis and interpretation of MALDI imaging data. From analysis of large individual datasets to the comparative analysis of sample cohorts for biomarker discovery, SCiLS Lab turns data into knowledge.

SCiLS Lab versions

SCiLS Lab as statistical package for MALDI imaging comes in two commercially available versions.


SCiLS Lab is the software package for 2D MALDI-ToF and 2D MALDI-FTICR imaging. SCiLS Lab can be used for the analysis of one or more 2D MALDI imaging datasets simultaneously. Contact us.

SCiLS Lab 3D

SCiLS Lab 3D: brain data setSCiLS Lab 3D is the dedicated solutions for 3D-MALDI-ToF and 3D MALDI-FTICR imaging. SCiLS Lab 3D can be used for construction of 3D MALDI imaging data from consecutive 2D datasets, and visualization and analysis of 3D MALDI imaging data. For more information, please contact us.

Bruker’s MALDI Molecular Imager

SCiLS Lab is a part of Bruker’s MALDI Molecular Imager solution. SCiLS Lab seamlessly integrates with Bruker's flexImaging software. It reads annotated data from flexImaging and can export results back into flexImaging.

Software features

SCiLS Lab implements numerous features for mining MALDI imaging data, e.g., the hierarchical structuring of large data sets, methods for spectrum-wise processing, solutions for univariate analysis, and procedures for unsupervised and supervised multivariate analysis. The main software features are illustrated in our summarized list of features (pdf).

SCiLS Lab: kidney data setFor more detailed presentation of software features and analysis examples, see our applications notesFor information on typical use cases, we offer a “learning-by-doing” overview of SCiLS Lab here: Examples of Data Analysis Workflows in SCiLS Lab.

System requirements

For SCiLS Lab and SCiLS Lab 3D the following system requirements apply:

  • Intel® Core™ i7 processor (equivalent or better)
  • Microsoft® Windows 7® 64 Bit operating system
  • 32 GB of RAM
  • Full-HD display (1920 x 1080)
  • Graphics card equal to or better than Nvidia® GeForce® GT 630 or ATI Radeon™ HD 6750

The SSD should be used to host the SCiLS h5 files used by SCiLS Lab. For 3D applications, 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 SSD(s).

Product information

Please contact us for more details and pricing information:

Dr. Dennis Trede
email info@scils.de
phone +49 421 2208 245