SCiLS GmbH

What SCiLS GmbH does

SCiLS GmbH is a Bremen, Germany-based software company that develops analysis software for mass spectrometry imaging (MSI) data, with a primary focus on MALDI Imaging workflows. Founded in 2012 and operating with 1-10 employees, the company is a wholly owned subsidiary of Bruker Daltonics and operates as a specialized software product line within Bruker's mass spectrometry portfolio. SCiLS is described in source materials as the industry's tool of choice for MALDI Imaging data analysis, supporting data from all major mass spectrometry vendors including Bruker's FLEX series, MRMS, and timsTOF fleX instruments with ion mobility data support.

The company's product suite centers on SCiLS Lab, a comprehensive MALDI Imaging data analysis and visualization platform featuring advanced processing, machine learning algorithms, spatial segmentation, comparative analysis, classification models, 3D volumetric visualization, and SpatialOMx workflows. Complementary offerings include SCiLS Scope, a free lightweight viewer for sharing data in the open OME-TIFF format, and the SCiLS Ion Image Mapper module for spatial multiomics data fusion. The platform integrates with QuPath digital pathology software, Bruker's MetaboScape molecular annotation tool, and supports the open imzML and OME-TIFF industry standards for vendor-agnostic data exchange. The 2025 release (SCiLS 2025) expanded multiomics analysis capabilities and workflow automation.

SCiLS generates revenue through software licensing, subscriptions, and maintenance agreements for SCiLS Lab, distributed exclusively through Bruker Daltonics' global enterprise sales and distribution network. Pricing is not publicly disclosed, with sales handled via expert consultation and contact forms. SCiLS Scope is offered as a free download to lower barriers to collaboration and drive adoption. The software serves three primary customer segments: pharmaceutical companies (drug and metabolite distribution analysis, pharmacokinetics, whole-body imaging), academic life science research institutions (biomarker discovery, spatial multiomics, large-cohort clinical studies), and clinical research organizations (translational pathology, digital pathology integration). Reference customers include MD Anderson Cancer Center, Medical University of South Carolina, Technical University of Munich, and Proteopath GmbH.

Name

SCiLS GmbH

Legal name

SCiLS GmbH

Website

https://scils.de

Company type

Private

Founded year

2012

Operating status

Operating

Headcount range

1–10 employees

Short description

SCiLS GmbH develops MALDI Imaging data analysis software (SCiLS Lab and SCiLS Scope), distributed exclusively through Bruker's global sales network. It serves pharmaceutical, academic, and clinical research organizations with vendor-agnostic MSI analytics and spatial multiomics tools.

Ownership category

akta.pro rank

Product category

Mass Spectrometry Imaging Software

NAICS

Computer Systems Design and Related Services (54151)

SIC

Services-Computer Processing & Data Preparation (7374)

akta.pro industry

PRIMARYHLAGAJAD

Bioinformatics & Multi-omics Analysis Software

Healthcare & Life Sciences/Life Science Tools & Services (CRO/CDMO/Lab Services)/Life Science Software & Informatics (LIMS/ELN/Bioinformatics)

SECONDARYHLAGAJAC

Scientific Data Management & Data Platforms (SDMS/Data Lakehouse for R&D)

Healthcare & Life Sciences/Life Science Tools & Services (CRO/CDMO/Lab Services)/Life Science Software & Informatics (LIMS/ELN/Bioinformatics)

Keywords

• Mass spectrometry imaging
• MALDI imaging software
• Spatial multiomics analysis
• Biomarker discovery software
• MSI data visualization

Headquarters

HQ city

Bremen

HQ country

Germany

HQ region

Europe

Markets served

GTM type

B2B

Offering type

Software

Cost components

Technology or R&D, Personnel, Marketing or Sales, Operations

Revenue model

1. Software Licenses and Subscriptions: SCiLS Lab and SCiLS Scope are sold as commercial software products through Bruker. SCiLS Lab requires purchase/download registration, while SCiLS Scope offers free download. Revenue is generated through software licensing, subscriptions, and maintenance agreements.

Pricing tiers

Go-to-market motion1 record

Distribution channels2 records

Marketing channels4 records

Core offering

SCiLS GmbH develops specialized software tools for the analysis and visualization of mass spectrometry imaging (MSI) data, particularly MALDI Imaging datasets. Its flagship product SCiLS Lab provides advanced processing, machine learning algorithms, spatial segmentation, and comparative analysis capabilities, complemented by SCiLS Scope for data sharing and viewing and the SCiLS Ion Image Mapper for spatial multiomics data fusion. The software supports data from all major mass spectrometry vendors including Bruker's FLEX series, MRMS, and timsTOF fleX instruments.

Product overview

SCiLS offers a comprehensive software suite for mass spectrometry imaging data analysis, consisting of SCiLS Lab as the primary analytical platform and SCiLS Scope as a lightweight viewer for data sharing. The portfolio includes the SCiLS Ion Image Mapper for spatial multiomics data fusion and the SCiLS API for workflow automation. These products work together to provide end-to-end MALDI Imaging solutions, from automated data acquisition through SCiLS autopilot, to advanced statistical analysis and visualization, with export capabilities to industry-standard formats like OME-TIFF and imzML.

Differentiator

Problem solved

Functional benefit

Brands

• SCiLS Lab: Industry-leading software for MALDI Imaging data analysis, featuring powerful visualization, advanced data processing, machine learning algorithms, spatial segmentation, and support for SpatialOMx workflows.
• SCiLS Scope
• SCiLS Ion Image Mapper

Products and services

• SCiLS Lab Industry-leading software for the analysis and visualization of MALDI Imaging data, offering powerful visualization, advanced supervised and unsupervised machine learning, statistical analysis, comparative analysis, spatial segmentation, classification models, and volumetric 3D visualization. Used by pharmaceutical companies, academic researchers, and clinical research organizations for drug development, biomarker discovery, and translational pathology.
• SCiLS Scope

Quantifiable outcome

• Automatic quantification of ion discrimination between biological states with one click
• +1 more outcomes

Named customers4 records

Segments3 records

Ideal customer profiles3 records

Technology focussed Yes

API detail

Has API

Yes

API docs

API detail

Core technology

AI maturity

App detail

Integration3 records

AI capability5 records

Feature7 records

Partnerships

Three partnerships are on record, tiered core.

• QuPathcoreTechnology or IntegrationQuPath is an open source digital pathology software integrated with SCiLS Lab. The integration allows researchers to combine histomorphological insights from pathologists with spatially resolved molecular data from MALDI Imaging, enhancing both interpretation and discovery in translational pathology research.
• MetaboScape®coreTechnology or IntegrationMetaboScape® is Bruker's molecular annotation software integrated into SCiLS Lab for confident compound identification. The integration powers molecular annotation features within the MALDI Imaging analysis workflow.
• timsTOF fleXcoreTechnology or IntegrationSCiLS Lab displays mass-mobility ion images for timsTOF fleX ion mobility data, enabling CCS-enabled data interpretation and integration with iprm-PASEF workflow for high confidence molecular identification.

Scale indicators1 record

Recent moves6 records

Expansion highlights6 records

Emerging players

• Benchling: Cloud life sciences R&D platform expanding into multi-omics and analytical data workflows; competes for the same biotech informatics buyer and represents a modern SaaS alternative to SCiLS's desktop-based offering.
• OpenMSI / Cardinal (open source): Academic and community-driven open-source MSI analysis tools that compete with SCiLS Lab on core segmentation and statistical workflows, primarily for cost-sensitive academic users.

Direct peers

• Dotmatics: Scientific R&D informatics platform (including Luma and Genespring) used by pharma for multi-omics and image-based data analysis, providing an enterprise alternative to SCiLS Lab.
• Genedata: Enterprise biopharma informatics platform that, like SCiLS, serves large pharma R&D with specialized analysis software for omics and screening data, competing for similar informatics budget pools.
• Mestrelab Research: Vendor of analytical chemistry and MS data software (Mnova) used in pharma and academic labs; competes with SCiLS for analytical chemistry informatics budgets and offers similar vendor-agnostic data handling.
• ACD/Labs (Advanced Chemistry Development): Provides MS and analytical data software (Spectrus, MS Workbook) used by pharma for metabolite identification and structure elucidation, overlapping with SCiLS's metabolite and pharmaceutical distribution use cases.

Others

• QuPath: Open-source digital pathology platform that integrates with SCiLS Lab; functions as an adjacent ecosystem partner rather than a competitor, but increasingly expands into molecular image analysis that overlaps with SCiLS workflows.

Broad incumbents

• Shimadzu: Scientific instrument maker with MS imaging offerings (ImagingMS Solution) that overlap with SCiLS in tissue MALDI imaging workflows, competing across pharma and academic accounts.
• Thermo Fisher Scientific: Major MS imaging instrument and software vendor (ImageQuest, TissueView) that competes with SCiLS Lab in MALDI/DESI imaging analysis, but as part of a much broader life sciences instrumentation portfolio.
• Waters Corporation: Mass spectrometry and informatics vendor (MassLynx, HDI Imaging Software) serving overlapping pharma and academic customers with MS imaging capabilities, though Waters's software is more tightly coupled to its own instruments.

Market position

Strengths5 records

Weaknesses5 records

Competitive moat5 records

Key risks5 records

Key highlights6 records

Customer concentration

• LinkedInlinkedin.com/company/scils-gmbh

Revenue estimate

Valuation estimate

Number of profiles

Profiles1 record

Funding overview

Funding rounds

Investors

Funding detail is available on the Subscription and Enterprise plan.Contact sales →

M&A

Investments

M&A and investment is available on the Subscription and Enterprise plan.Contact sales →

Frequently asked questions about SCiLS GmbH