Functional immunomics for mechanistic insights of therapeutic targets

Advanced Immunophenotyping & Single-Cell Technologies

The Immunomics module at CIPHE explores in depth the immune and stromal compartments with a strong focus on immune-oncology, autoimmunity, and inflammation. Our agile team of engineers, by harnessing a wide array of advanced single-cell technologies, designs complex and tailored functional analyses that unravel the complexity of immune responses in health and disease.

Head of Platform: Hervé Luche, PhD

Team & experts

+40

immunophenotyping panels developed since 2012

+ 30

markers per cell

+ 200

parameters

Multi-center

immunomics capacity

3Rs

compliance

Full integration

– bioinformatics

Advance your research

Partnering with CIPHE means working with a reliable and expert-driven team dedicated to advancing discovery in immunology.
Our strength lies in designing bespoke workflows—from experimental design and sample processing to instrumentation choice, panel development, and data integration—ensuring optimal strategies for each project.
Our engineers bring strong expertise in:
• Flow cytometry (spectral & mass)
• CITE-seq & scGenomics
• Large-scale multiparametric data analysis
Beyond immune system characterization, we specialize in immune–stromal interactions and functional assays, ensuring high-resolution, reproducible insights for every project.

40+ immunophenotyping panels developed since 2012 for mouse, rat, and human PBMCs, with optimized cell extraction protocols for a wide range of lymphoid and non-lymphoid tissues.
Proprietary panels deployable to partner sites, enabling multi-center immunomics studies with standardized workflows.
Expertise in technically demanding approaches, particularly quantitative cytometry across multiple immune lineages, providing detailed antigen density dynamics.
Massively Parallel Cytometry (MPC) pipeline: profiles up to 300 proteins across 16 cell populations in a single multiplexed suspension, delivering up to 43,200 independent measurements per experiment.
Aligned with 3Rs principles (Replace, Reduce, Refine), reflecting a commitment to responsible and efficient preclinical research.

Cutting-Edge Immunophenotyping & Massively Parallel Cytometry

Research and development is at the core of our platform. We continuously integrate new methodologies to expand the exploration of immune function:

Dedicated stromal pipelines across thymus, lung, pancreas, adrenal glands.
Multi-species immunometabolism panel to study metabolic regulation of immune responses.
Next-gen instrumentation for fragile/low-cellularity samples:
- EOS system (Levisort – LEVISORT 2025 funding)
- Pluto Alpha (Curiox).

Together, this suite of tools supports the creation of high-resolution cellular atlases and enables both local and systemic immune profiling.

Continuous R&D innovation

Our expertise is applied across a wide range of research areas:

Tumor immunology: immune cell infiltration & checkpoint analysis, metabolic profiling, biomarker discovery.
Single-cell functional analysis: high-content assays (32+ antibodies per cell), TH1/TH2/TH17/Treg characterization, cytokine networks, phospho-antigens.
In vitro & ex vivo functional assays: T, B, NK responses, proliferation, cytokine production, differentiation panels.
High-content immune phenotyping panels: 50+ subpopulations, covering blood and multiple organs (thymus, spleen, bone marrow, lung, intestine…).
Comprehensive immunity profiling workflow: from mouse cohorts to multiparametric data integration, supporting infection, inflammation, cancer, and vaccine studies.

Applications of our platform

CIPHE employs a robust bioinformatics pipeline for high-resolution integrative analysis of immune data:

Automated analysis of 200+ parameters per experiment.
Standardized datasets for longitudinal & comparative studies.
Integration of multi-modal data to deliver impactful biological insights.

Data integration & bioinformatics

Our work is performed under strict SOPs, ensuring reproducibility and quality.
CIPHE’s Immunomics platform is trusted by global research institutions and biotech companies, supporting both academic discovery and translational research.